From fc709fec546519803aec2e5b2547ad2c4974bd3d Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Tue, 24 Oct 2023 10:16:36 -0400 Subject: [PATCH 01/60] chore(hardware): bump python-can for new OE The new OE needs a new version of python-can because the old wasn't compatible with python 3.10. This updates it. --- hardware/Pipfile | 2 +- hardware/Pipfile.lock | 308 ++++++++++++------ .../drivers/can_bus/driver.py | 20 -- hardware/setup.py | 2 +- .../drivers/can_bus/test_driver.py | 10 +- 5 files changed, 216 insertions(+), 126 deletions(-) diff --git a/hardware/Pipfile b/hardware/Pipfile index ef1497cee78..71e61a4ca78 100644 --- a/hardware/Pipfile +++ b/hardware/Pipfile @@ -4,7 +4,7 @@ verify_ssl = true name = "pypi" [packages] -python-can = "==3.3.4" +python-can = "==4.2.2" pyserial = "==3.5" typing-extensions = ">=4.0.0,<5" numpy = "==1.21.2" diff --git a/hardware/Pipfile.lock b/hardware/Pipfile.lock index 29a90038227..5b490b78cd9 100644 --- a/hardware/Pipfile.lock +++ b/hardware/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "e648179e894ecd8eab6eaf4d0a75f1bde4c9aa087ab04e79d8058210f4318c8b" + "sha256": "43ea4ee6292ac8f3b6dc212797e25858e1c153870894cef383ad5c67a499e6e1" }, "pipfile-spec": 6, "requires": { @@ -16,13 +16,74 @@ ] }, "default": { - "aenum": { + 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"version": "==3.3.4" + "version": "==4.2.2" }, "typing-extensions": { "hashes": [ - "sha256:88a4153d8505aabbb4e13aacb7c486c2b4a33ca3b3f807914a9b4c844c471c26", - "sha256:d91d5919357fe7f681a9f2b5b4cb2a5f1ef0a1e9f59c4d8ff0d3491e05c0ffd5" + "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36", + "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2" ], "index": "pypi", - "version": "==4.6.3" + "version": "==4.7.1" }, "wrapt": { "hashes": [ @@ -233,11 +303,11 @@ }, "click": { "hashes": [ - "sha256:7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e", - "sha256:bb4d8133cb15a609f44e8213d9b391b0809795062913b383c62be0ee95b1db48" + "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28", + "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de" ], "markers": "python_version >= '3.7'", - "version": "==8.1.3" + "version": "==8.1.7" }, "coverage": { "hashes": [ @@ -386,77 +456,113 @@ }, "kiwisolver": { 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"sha256:d8af70af76652554bd134c22b3e8a1cc46ed7d91edcdd721ef1a0c51a84a5293" + "sha256:1d6ed233af05e679efb96b1851550ea95bbb64b7c490b0f5aa52996c11e92a20", + "sha256:e0d8d0ac2f12da61956eb2306b69f9469b42f4deb0f3cb6ed47b9cce9996ced3" ], "markers": "python_version >= '3.7'", - "version": "==0.11.1" + "version": "==0.11.2" }, "pillow": { "hashes": [ @@ -680,11 +786,11 @@ }, "platformdirs": { "hashes": [ - "sha256:b0cabcb11063d21a0b261d557acb0a9d2126350e63b70cdf7db6347baea456dc", - "sha256:ca9ed98ce73076ba72e092b23d3c93ea6c4e186b3f1c3dad6edd98ff6ffcca2e" + "sha256:cf8ee52a3afdb965072dcc652433e0c7e3e40cf5ea1477cd4b3b1d2eb75495b3", + "sha256:e9d171d00af68be50e9202731309c4e658fd8bc76f55c11c7dd760d023bda68e" ], "markers": "python_version >= '3.7'", - "version": "==3.8.0" + "version": "==3.11.0" }, "pluggy": { "hashes": [ @@ -756,11 +862,11 @@ }, "pyparsing": { "hashes": [ - "sha256:d554a96d1a7d3ddaf7183104485bc19fd80543ad6ac5bdb6426719d766fb06c1", - 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"sha256:d91d5919357fe7f681a9f2b5b4cb2a5f1ef0a1e9f59c4d8ff0d3491e05c0ffd5" + "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36", + "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2" ], "index": "pypi", - "version": "==4.6.3" + "version": "==4.7.1" }, "zipp": { "hashes": [ diff --git a/hardware/opentrons_hardware/drivers/can_bus/driver.py b/hardware/opentrons_hardware/drivers/can_bus/driver.py index 083f4ec5a2d..07e78891de9 100644 --- a/hardware/opentrons_hardware/drivers/can_bus/driver.py +++ b/hardware/opentrons_hardware/drivers/can_bus/driver.py @@ -2,7 +2,6 @@ from __future__ import annotations import logging import asyncio -import platform from typing import Optional, Union, Dict, Any import concurrent.futures @@ -17,25 +16,6 @@ log = logging.getLogger(__name__) -if platform.system() == "Darwin": - # TODO (amit, 2021-09-29): remove hacks to support `pcan` when we don't - # need it anymore. - # Super bad monkey patch to deal with MAC issue: - # https://github.com/hardbyte/python-can/issues/1117 - from can.interfaces.pcan import basic - - basic.TPCANMsgMac = basic.TPCANMsg - basic.TPCANMsgFDMac = basic.TPCANMsgFD - basic.TPCANTimestampMac = basic.TPCANTimestamp - - from can.interfaces.pcan import pcan - - pcan.TPCANMsgMac = pcan.TPCANMsg - pcan.TPCANMsgFDMac = pcan.TPCANMsgFD - pcan.TPCANTimestampMac = pcan.TPCANTimestamp - # end super bad monkey patch - - class CanDriver(AbstractCanDriver): """The can driver.""" diff --git a/hardware/setup.py b/hardware/setup.py index c874cd55618..9ae440551f4 100644 --- a/hardware/setup.py +++ b/hardware/setup.py @@ -47,7 +47,7 @@ def get_version() -> str: DESCRIPTION = "Hardware control for Opentrons Robots." PACKAGES = find_packages(where=".", exclude=["tests.*", "tests"]) INSTALL_REQUIRES = [ - "pyserial==3.5", + "pyserial==4.2.2", f"opentrons_shared_data=={VERSION}", ] diff --git a/hardware/tests/opentrons_hardware/drivers/can_bus/test_driver.py b/hardware/tests/opentrons_hardware/drivers/can_bus/test_driver.py index 2956d8dd360..4a5f2b7e75d 100644 --- a/hardware/tests/opentrons_hardware/drivers/can_bus/test_driver.py +++ b/hardware/tests/opentrons_hardware/drivers/can_bus/test_driver.py @@ -1,5 +1,5 @@ """Can Driver tests.""" -from typing import AsyncGenerator +from typing import AsyncGenerator, Iterator, cast import pytest from can import Bus, Message @@ -16,7 +16,7 @@ def bus_channel() -> str: @pytest.mark.slow @pytest.fixture -def can_bus(bus_channel: str) -> Bus: +def can_bus(bus_channel: str) -> Iterator[Bus]: """A virtual can bus fixture.""" bus = Bus(bus_channel, interface="virtual") yield bus @@ -38,7 +38,11 @@ async def test_send(subject: CanDriver, can_bus: Bus) -> None: ) await subject.send(message) - recv = can_bus.recv() + # recv() returns an Optional where None indicates a timeout, but + # if you pass timeout=None (or don't specify, that's the default) + # then the bus will wait indefinitely so this isn't actually a + # possibility + recv = cast(Message, can_bus.recv()) assert recv.data == bytearray([1, 2, 3, 4]) assert recv.arbitration_id == 0x1FFFFFFF From f85279d5f0893fbf2b7a4583f5a30c2571ebbec6 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Fri, 27 Oct 2023 19:51:29 +0000 Subject: [PATCH 02/60] fix(shared-data): properly exclude tests in sdist We excluded the top level tests but apparently also need to do that for the subdirectories. --- shared-data/python/setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/shared-data/python/setup.py b/shared-data/python/setup.py index ab592c2e944..b5bd6eb8a1a 100644 --- a/shared-data/python/setup.py +++ b/shared-data/python/setup.py @@ -142,7 +142,7 @@ def get_version(): "Does not need to be installed manually; only a dependency of the " "opentrons package" ) -PACKAGES = find_packages(where=".", exclude=["tests"]) +PACKAGES = find_packages(where=".", exclude=["tests", "tests.*"]) INSTALL_REQUIRES = [ "jsonschema==3.0.2", "typing-extensions>=4.0.0,<5", From 2617343a6cdbe4c2634b9a142c27c3c79b13d57c Mon Sep 17 00:00:00 2001 From: caila-marashaj Date: Fri, 27 Oct 2023 16:58:52 -0400 Subject: [PATCH 03/60] bump pytest in server utils --- server-utils/Pipfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/server-utils/Pipfile b/server-utils/Pipfile index fce71d9e3c3..68ceeebf0e7 100755 --- a/server-utils/Pipfile +++ b/server-utils/Pipfile @@ -12,7 +12,7 @@ server-utils = { editable = true, path = "." } # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 atomicwrites = { version = "==1.4.0", sys_platform = "== 'win32'" } colorama = { version = "==0.4.4", sys_platform = "== 'win32'" } -pytest = "~=6.1" +pytest = "~=7.1" pytest-asyncio = "~=0.18" pytest-cov = "==2.10.1" pytest-lazy-fixture = "==0.6.3" From ae72dfa1d30668bf7091c5b3558058c083d891c9 Mon Sep 17 00:00:00 2001 From: caila-marashaj Date: Fri, 27 Oct 2023 17:14:56 -0400 Subject: [PATCH 04/60] bump pytest-asyncio --- api/Pipfile | 2 +- server-utils/Pipfile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/api/Pipfile b/api/Pipfile index ac63c870096..45cb9aef979 100755 --- a/api/Pipfile +++ b/api/Pipfile @@ -13,7 +13,7 @@ coverage = "==5.1" mypy = "==0.910" numpydoc = "==0.9.1" pytest = "==7.0.1" -pytest-asyncio = "~=0.18" +pytest-asyncio = "~=0.16" pytest-cov = "==2.10.1" pytest-lazy-fixture = "==0.6.3" pytest-xdist = "~=2.2.1" diff --git a/server-utils/Pipfile b/server-utils/Pipfile index 68ceeebf0e7..b29d72ae0f7 100755 --- a/server-utils/Pipfile +++ b/server-utils/Pipfile @@ -13,7 +13,7 @@ server-utils = { editable = true, path = "." } atomicwrites = { version = "==1.4.0", sys_platform = "== 'win32'" } colorama = { version = "==0.4.4", sys_platform = "== 'win32'" } pytest = "~=7.1" -pytest-asyncio = "~=0.18" +pytest-asyncio = "~=0.16" pytest-cov = "==2.10.1" pytest-lazy-fixture = "==0.6.3" pytest-xdist = "~=2.2.1" From 5b12e03b4c52e1902728cb60e6a6e5ccc558132e Mon Sep 17 00:00:00 2001 From: caila-marashaj Date: Tue, 31 Oct 2023 14:19:51 -0400 Subject: [PATCH 05/60] rest of updates from api Pipfile --- api/Pipfile | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/api/Pipfile b/api/Pipfile index 45cb9aef979..304daf41ae2 100755 --- a/api/Pipfile +++ b/api/Pipfile @@ -16,15 +16,15 @@ pytest = "==7.0.1" pytest-asyncio = "~=0.16" pytest-cov = "==2.10.1" pytest-lazy-fixture = "==0.6.3" -pytest-xdist = "~=2.2.1" -sphinx = "==5.0.1" -twine = "==4.0.2" -wheel = "==0.30.0" -typeguard = "==2.12.1" +pytest-xdist = "~=2.5.0" +sphinx = "==4.4.0" +twine = "==4.0.0" +wheel = "==0.37.0" +typeguard = "==2.13.1" sphinx-substitution-extensions = "==2020.9.30.0" sphinxext-opengraph = "==0.8.1" sphinx-tabs = ">=3.4.1,<4" -mock = "~=4.0.2" +mock = "~=4.0.3" flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" From d52da42eaeaca0025d81a9b08f44db90ef9f17da Mon Sep 17 00:00:00 2001 From: caila-marashaj Date: Tue, 31 Oct 2023 14:42:09 -0400 Subject: [PATCH 06/60] hardware Pipfile update --- hardware/Pipfile | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/hardware/Pipfile b/hardware/Pipfile index 71e61a4ca78..9e4d818e1d6 100644 --- a/hardware/Pipfile +++ b/hardware/Pipfile @@ -7,25 +7,25 @@ name = "pypi" python-can = "==4.2.2" pyserial = "==3.5" typing-extensions = ">=4.0.0,<5" -numpy = "==1.21.2" +numpy = "==1.22.3" pydantic = "==1.8.2" [dev-packages] -pytest = "==7.0.1" +pytest = "==7.1.1" pytest-lazy-fixture = "==0.6.3" pytest-cov = "==2.10.1" -mypy = "==0.910" +mypy = "==0.942" black = "==22.3.0" flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" flake8-noqa = "~=1.2.1" -mock = "~=4.0.2" +mock = "~=4.0.3" types-mock = "==4.0.1" -hypothesis = "~=6.36.1" -pytest-asyncio = "~=0.18" +hypothesis = "~=6.39.5" +pytest-asyncio = "~=0.16" matplotlib = "*" opentrons-shared-data = { editable = true, path = "../shared-data/python" } [requires] -python_version = "3.7" +python_version = "3.10" From 9ce515d904a9bdfde3aefe68bee1b21bd6362091 Mon Sep 17 00:00:00 2001 From: caila-marashaj Date: Tue, 31 Oct 2023 15:17:33 -0400 Subject: [PATCH 07/60] shared-data/python updates --- shared-data/python/Pipfile | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/shared-data/python/Pipfile b/shared-data/python/Pipfile index 07b539b1774..220882fc360 100644 --- a/shared-data/python/Pipfile +++ b/shared-data/python/Pipfile @@ -4,16 +4,16 @@ verify_ssl = true name = "pypi" [dev-packages] -mypy = "==0.800" +mypy = "==0.942" flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" flake8-noqa = "~=1.2.1" -twine = "==2.0.0" -wheel = "==0.30.0" -pytest = "==7.0.1" +twine = "==4.0.0" +wheel = "==0.37.1" +pytest = "==7.1.1" pytest-cov = "==2.10.1" -pytest-xdist = "~=2.2.1 " +pytest-xdist = "~=2.5.0 " typeguard = "~=2.13" # specify typing-extensions explicitly to force lockfile inclusion on Python >= 3.8 typing-extensions = ">=4.0.0,<5" From 7abc8c445e751c23eff191a32116b379d87680ba Mon Sep 17 00:00:00 2001 From: caila-marashaj Date: Tue, 31 Oct 2023 15:42:09 -0400 Subject: [PATCH 08/60] server-utils changes --- server-utils/Pipfile | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/server-utils/Pipfile b/server-utils/Pipfile index b29d72ae0f7..884c71d694f 100755 --- a/server-utils/Pipfile +++ b/server-utils/Pipfile @@ -4,7 +4,7 @@ verify_ssl = true name = "pypi" [requires] -python_version = "3.7" +python_version = "3.10" [dev-packages] server-utils = { editable = true, path = "." } @@ -16,10 +16,10 @@ pytest = "~=7.1" pytest-asyncio = "~=0.16" pytest-cov = "==2.10.1" pytest-lazy-fixture = "==0.6.3" -pytest-xdist = "~=2.2.1" -requests = "==2.26.0" -mock = "~=4.0.2" -mypy = "==0.910" +pytest-xdist = "~=2.5.0" +requests = "==2.27.1" +mock = "~=4.0.3" +mypy = "==0.942" flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" @@ -33,15 +33,16 @@ sqlalchemy2-stubs = "==0.0.2a21" python-box = "==5.4.1" [packages] -anyio = "==3.3.0" +anyio = "==3.6.1" fastapi = "==0.68.1" python-dotenv = "==0.19.0" +pick 21ebf0bd5c feat(app): update deck config in device details for run status (#13866) python-multipart = "==0.0.5" pydantic = "==1.8.2" typing-extensions = ">=4.0.0,<5" uvicorn = "==0.14.0" wsproto = "==1.0.0" systemd-python = { version = "==234", sys_platform = "== 'linux'" } -idna = "==3.2" -sqlalchemy = "==1.4.32" +idna = "==3.3" +sqlalchemy = "==1.4.35" aiosqlite = "==0.17.0" From d0873c1c25b70a4bc44ef262dca9d152651deb7b Mon Sep 17 00:00:00 2001 From: caila-marashaj Date: Tue, 31 Oct 2023 15:49:29 -0400 Subject: [PATCH 09/60] g code testing updates --- g-code-testing/Pipfile | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/g-code-testing/Pipfile b/g-code-testing/Pipfile index 1a23292c6f5..c57185ddf48 100644 --- a/g-code-testing/Pipfile +++ b/g-code-testing/Pipfile @@ -11,7 +11,7 @@ server-utils = { editable = true, path = "./../server-utils" } opentrons-shared-data = { editable = true, path = "../shared-data/python" } opentrons_hardware = { editable = true, path = "../hardware" } g-code-testing = { editable = true, path = "." } -anyio = "==3.3.0" +anyio = "==3.6.1" pydantic = "==1.8.2" # opentrons dependency on linux, spec'd here to force lockfile inclusion # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 @@ -19,18 +19,18 @@ systemd-python = { version = "==234", sys_platform = "== 'linux'" } [dev-packages] diff-match-patch = "==20200713" -pytest = "~=6.1" -pytest-aiohttp = "==0.3.0" +pytest = "~=7.1" +pytest-aiohttp = "==3.8.1" pytest-cov = "==2.10.1" -pytest-xdist = "~=2.2.1 " -mock = "~=4.0.2" -mypy = "==0.812.0" +pytest-xdist = "~=2.5.0" +mock = "~=4.0.3" +mypy = "==0.942.0" flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" flake8-noqa = "~=1.2.1" -black = "==22.3.0" +black = "==22.0" decoy = "~=1.10.0" [requires] -python_version = "3.7" +python_version = "3.10" From 4bac0daf0a14d2975585635b46fd1fbd4d1f5200 Mon Sep 17 00:00:00 2001 From: caila-marashaj Date: Wed, 1 Nov 2023 18:49:48 -0400 Subject: [PATCH 10/60] update server and Pipfile updates --- robot-server/Pipfile | 22 +++++++++++----------- update-server/Pipfile | 10 +++++----- 2 files changed, 16 insertions(+), 16 deletions(-) diff --git a/robot-server/Pipfile b/robot-server/Pipfile index fdc7b17a261..c0f99823e46 100755 --- a/robot-server/Pipfile +++ b/robot-server/Pipfile @@ -4,7 +4,7 @@ verify_ssl = true name = "pypi" [requires] -python_version = "3.7" +python_version = "3.10" [dev-packages] robot-server = { editable = true, path = "." } @@ -12,16 +12,16 @@ robot-server = { editable = true, path = "." } # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 atomicwrites = { version = "==1.4.0", sys_platform = "== 'win32'" } colorama = { version = "==0.4.4", sys_platform = "== 'win32'" } -pytest = "~=6.1" -pytest-asyncio = "~=0.18" +pytest = "~=7.1" +pytest-asyncio = "~=0.16" pytest-cov = "==2.10.1" pytest-lazy-fixture = "==0.6.3" -pytest-xdist = "~=2.2.1" -requests = "==2.26.0" +pytest-xdist = "~=2.5.0" +requests = "==2.27.1" tavern = "~=1.6" -graphviz = "==0.17" -mock = "~=4.0.2" -mypy = "==0.910" +graphviz = "==0.19" +mock = "~=4.0.3" +mypy = "==0.942" flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" @@ -38,7 +38,7 @@ python-box = "==5.4.1" opentrons = { editable = true, path = "../api" } opentrons-shared-data = { editable = true, path = "../shared-data/python" } notify-server = { editable = true, path = "../notify-server" } -anyio = "==3.3.0" +anyio = "==3.6.1" fastapi = "==0.68.1" python-dotenv = "==0.19.0" python-multipart = "==0.0.5" @@ -47,8 +47,8 @@ typing-extensions = ">=4.0.0,<5" uvicorn = "==0.14.0" wsproto = "==1.0.0" systemd-python = { version = "==234", sys_platform = "== 'linux'" } -idna = "==3.2" -click = "==8.0.1" +idna = "==3.3" +click = "==8.1.2" # TODO(mc, 2022-04-04): this dep is newer than the OT-2 for dev environment reasons # remove this TODO when Opentrons/buildroot has updated to newer numpy # https://github.com/Opentrons/buildroot/pull/148 diff --git a/update-server/Pipfile b/update-server/Pipfile index 50ff797de6c..440ef091a31 100644 --- a/update-server/Pipfile +++ b/update-server/Pipfile @@ -4,7 +4,7 @@ verify_ssl = true name = "pypi" [packages] -aiohttp = "==3.4.4" +aiohttp = "==3.8.1" typing-extensions = "==3.10.0.0" [dev-packages] @@ -13,19 +13,19 @@ flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" flake8-noqa = "~=1.1.0" -pytest = "==6.1.0" +pytest = "==7.1.1" pytest-watch = "~=4.2.0" pytest-cov = "==2.10.1" pytest-aiohttp = "==0.3.0" -coverage = "==5.1" +coverage = "==6.3.2 # atomicwrites and colorama are pytest dependencies on windows, # spec'd here to force lockfile inclusion # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 atomicwrites = {version="==1.4.0", sys_platform="== 'win32'"} colorama = {version="==0.4.4", sys_platform="== 'win32'"} -mypy = "==0.940" +mypy = "==0.942" black = "==22.3.0" decoy = "~=1.10" [requires] -python_version = "3.7" +python_version = "3.10" From 7bdb66bf3c1eb8d16a8181a227dc461777b1238e Mon Sep 17 00:00:00 2001 From: caila-marashaj Date: Thu, 2 Nov 2023 11:01:13 -0400 Subject: [PATCH 11/60] sysytem server & top level Pipfile updates --- system-server/Pipfile | 18 +++++++++--------- usb-bridge/Pipfile | 16 ++++++++-------- 2 files changed, 17 insertions(+), 17 deletions(-) diff --git a/system-server/Pipfile b/system-server/Pipfile index 8ee68d02103..9e97c88916d 100644 --- a/system-server/Pipfile +++ b/system-server/Pipfile @@ -6,13 +6,13 @@ name = "pypi" [packages] fastapi = "==0.68.1" uvicorn = "==0.14.0" -anyio = "==3.3.0" +anyio = "==3.6.1" typing-extensions = ">=4.0.0,<5" pyjwt = "==2.6.0" python-dotenv = "==0.19.0" python-multipart = "==0.0.5" pydantic = "==1.8.2" -sqlalchemy = "==1.4.32" +sqlalchemy = "==1.4.35" systemd-python = { version = "==234", sys_platform = "== 'linux'" } importlib-metadata = ">=4.13.0,<5" server-utils = {editable = true, path = "./../server-utils"} @@ -23,26 +23,26 @@ flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" flake8-noqa = "~=1.2.1" -pytest = "~=6.1" +pytest = "~=7.1" pytest-asyncio = "==0.18" pytest-cov = "==2.10.1" pytest-lazy-fixture = "==0.6.3" -pytest-xdist = "~=2.2.1" +pytest-xdist = "~=2.5.0" tavern = "~=1.6" -coverage = "==5.1" +coverage = "==6.3" # atomicwrites and colorama are pytest dependencies on windows, # spec'd here to force lockfile inclusion # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 atomicwrites = { version = "==1.4.0", sys_platform = "== 'win32'" } colorama = { version = "==0.4.4", sys_platform = "== 'win32'" } sqlalchemy2-stubs = "==0.0.2a21" -mypy = "==0.910" +mypy = "==0.942" black = "==22.3.0" decoy = "~=1.10" -mock = "~=4.0.2" +mock = "~=4.0.3" types-mock = "==4.0.1" types-requests = "==2.25.6" -requests = "==2.26.0" +requests = "==2.27.1" [requires] -python_version = "3.7" +python_version = "3.10" diff --git a/usb-bridge/Pipfile b/usb-bridge/Pipfile index 23b79bb6716..b98cf65ebac 100644 --- a/usb-bridge/Pipfile +++ b/usb-bridge/Pipfile @@ -6,7 +6,7 @@ name = "pypi" [packages] typing-extensions = "==3.10.0.0" pyserial = "==3.5" -pyudev = "==0.24.0" +pyudev = "==0.23.2" [dev-packages] ot3usb = {path = ".", editable = true} @@ -14,24 +14,24 @@ flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" flake8-noqa = "~=1.1.0" -pytest = "==7.0.1" -pytest-asyncio = "~=0.18" +pytest = "==7.1.1" +pytest-asyncio = "~=0.16" pytest-lazy-fixture = "==0.6.3" pytest-watch = "~=4.2.0" pytest-cov = "==2.10.1" pytest-aiohttp = "==0.3.0" -pytest-xdist = "~=2.2.1" -coverage = "==5.1" +pytest-xdist = "~=2.5.0" +coverage = "==6.2" # atomicwrites and colorama are pytest dependencies on windows, # spec'd here to force lockfile inclusion # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 atomicwrites = {version="==1.4.0", sys_platform="== 'win32'"} colorama = {version="==0.4.4", sys_platform="== 'win32'"} -mypy = "==0.940" +mypy = "==0.942" black = "==22.3.0" decoy = "~=1.10" -mock = "~=4.0.2" +mock = "~=4.0.3" types-mock = "==4.0.1" [requires] -python_version = "3.7" +python_version = "3.10" From 55a69ae2e05c95f07658343190751a9fc2db1711 Mon Sep 17 00:00:00 2001 From: caila-marashaj Date: Thu, 2 Nov 2023 11:05:08 -0400 Subject: [PATCH 12/60] {hardware testing update --- hardware-testing/Pipfile | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/hardware-testing/Pipfile b/hardware-testing/Pipfile index 8f5fc8c5cd6..1da0ae2f6c3 100644 --- a/hardware-testing/Pipfile +++ b/hardware-testing/Pipfile @@ -12,17 +12,17 @@ pyserial = "==3.5" [dev-packages] atomicwrites = "==1.4.1" -colorama = "==0.4.5" -pytest = "==6.1.0" +colorama = "==0.4.4" +pytest = "==7.1.1" pytest-cov = "==2.10.1" -mypy = "==0.910" +mypy = "==0.942" black = "==22.3.0" flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" flake8-noqa = "~=1.2.1" -requests = "==2.26.0" +requests = "==2.27.1" types-requests = "==2.25.6" [requires] -python_version = "3.7" +python_version = "3.10" From 9863b6fe7fe390c7d150d1bcc9ccaacb5ebb641d Mon Sep 17 00:00:00 2001 From: caila-marashaj Date: Thu, 2 Nov 2023 11:23:21 -0400 Subject: [PATCH 13/60] app testing updates --- app-testing/Pipfile | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/app-testing/Pipfile b/app-testing/Pipfile index 12dfe7880a0..64274bc892a 100644 --- a/app-testing/Pipfile +++ b/app-testing/Pipfile @@ -4,21 +4,21 @@ url = "https://pypi.org/simple" verify_ssl = true [packages] -pytest = "==7.2.0" +pytest = "==7.1.1" black = "==22.12.0" selenium = "==4.7.2" -importlib-metadata = "==5.0.0" -requests = "==2.28.1" +importlib-metadata = "==4.11.3" +requests = "==2.27.1" python-dotenv = "==0.21.0" -pytest-xdist = "==3.0.2" -mypy = "==0.991" +pytest-xdist = "==2.5.0" +mypy = "==0.942" types-requests = "==2.28.11.5" rich = "==13.0.0" -atomicwrites = "==1.4.1" +atomicwrites = "==1.4.0" pyreadline3 = "==3.4.1" pydantic = "==1.10.4" pygithub = "==1.57" ruff = "==0.0.236" [requires] -python_version = "3.11" +python_version = "3.10" From 36dfd4e1d75793c2a53bc730a6445ae4ee7adc9f Mon Sep 17 00:00:00 2001 From: caila-marashaj Date: Thu, 2 Nov 2023 11:26:21 -0400 Subject: [PATCH 14/60] notify server updates --- notify-server/Pipfile | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/notify-server/Pipfile b/notify-server/Pipfile index f3b463c939d..9cd06b04505 100644 --- a/notify-server/Pipfile +++ b/notify-server/Pipfile @@ -4,7 +4,7 @@ url = "https://pypi.org/simple/" verify_ssl = true [requires] -python_version = "3.7" +python_version = "3.10" [packages] opentrons = { editable = true, path = "../api" } @@ -19,12 +19,12 @@ notify-server = { editable = true, path = "." } flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" -mock = "~=4.0.2" -mypy = "==0.800" -pytest = "==6.1.0" +mock = "~=4.0.3" +mypy = "==0.942" +pytest = "==7.1.1" pytest-cov = "==2.10.1" -pytest-asyncio = "==0.15.1" -pytest-xdist = "~=2.2.1" +pytest-asyncio = "==0.16.0" +pytest-xdist = "~=2.5.0" # pytest dependencies on windows, spec'd here to force lockfile inclusion # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 atomicwrites = { version = "==1.4.0", sys_platform = "== 'win32'" } From 85b9bc54efaa827b928834bc93acae0bac7a6a32 Mon Sep 17 00:00:00 2001 From: caila-marashaj Date: Thu, 2 Nov 2023 13:50:46 -0400 Subject: [PATCH 15/60] fixed quote in update server Pipfile --- update-server/Pipfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/update-server/Pipfile b/update-server/Pipfile index 440ef091a31..563b4f3a0fc 100644 --- a/update-server/Pipfile +++ b/update-server/Pipfile @@ -17,7 +17,7 @@ pytest = "==7.1.1" pytest-watch = "~=4.2.0" pytest-cov = "==2.10.1" pytest-aiohttp = "==0.3.0" -coverage = "==6.3.2 +coverage = "==6.3.2" # atomicwrites and colorama are pytest dependencies on windows, # spec'd here to force lockfile inclusion # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 From 38fd3ae175deb7386996c10cf7d471b620db5997 Mon Sep 17 00:00:00 2001 From: caila-marashaj Date: Thu, 2 Nov 2023 13:57:22 -0400 Subject: [PATCH 16/60] take out pasted commit msg --- server-utils/Pipfile | 1 - 1 file changed, 1 deletion(-) diff --git a/server-utils/Pipfile b/server-utils/Pipfile index 884c71d694f..fca1db021fc 100755 --- a/server-utils/Pipfile +++ b/server-utils/Pipfile @@ -36,7 +36,6 @@ python-box = "==5.4.1" anyio = "==3.6.1" fastapi = "==0.68.1" python-dotenv = "==0.19.0" -pick 21ebf0bd5c feat(app): update deck config in device details for run status (#13866) python-multipart = "==0.0.5" pydantic = "==1.8.2" typing-extensions = ">=4.0.0,<5" From 476ca7d28c4bf58aabf85f059e4ca51a305dbdde Mon Sep 17 00:00:00 2001 From: Ryan Howard Date: Tue, 28 Nov 2023 16:56:09 -0500 Subject: [PATCH 17/60] handle breaking changes from 3.7 to 3.10 (#14050) --- api/src/opentrons/drivers/smoothie_drivers/driver_3_0.py | 4 ++-- scripts/push.mk | 2 +- scripts/python.mk | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/api/src/opentrons/drivers/smoothie_drivers/driver_3_0.py b/api/src/opentrons/drivers/smoothie_drivers/driver_3_0.py index 41bd554682c..956bc59c192 100755 --- a/api/src/opentrons/drivers/smoothie_drivers/driver_3_0.py +++ b/api/src/opentrons/drivers/smoothie_drivers/driver_3_0.py @@ -1896,8 +1896,8 @@ async def update_firmware( # noqa: C901 "stdout": asyncio.subprocess.PIPE, "stderr": asyncio.subprocess.PIPE, } - if loop: - kwargs["loop"] = loop + #if loop: + # kwargs["loop"] = loop log.info(update_cmd) before = time() proc = await asyncio.create_subprocess_shell(update_cmd, **kwargs) diff --git a/scripts/push.mk b/scripts/push.mk index 4f114daa64e..a6d191a229a 100644 --- a/scripts/push.mk +++ b/scripts/push.mk @@ -39,7 +39,7 @@ scp $(call id-file-arg,$(2)) $(scp-legacy-option-flag) $(3) "$(4)" root@$(1):/da ssh $(call id-file-arg,$(2)) $(3) root@$(1) \ "function cleanup () { rm -f /data/$(notdir $(4)) && mount -o remount,ro / ; } ;\ mount -o remount,rw / &&\ -cd /usr/lib/python3.7/site-packages &&\ +cd /usr/lib/python3.10/site-packages &&\ unzip -o /data/$(notdir $(4)) && cleanup || cleanup" endef diff --git a/scripts/python.mk b/scripts/python.mk index 9208271301b..bcc7c49a227 100644 --- a/scripts/python.mk +++ b/scripts/python.mk @@ -7,7 +7,7 @@ OT_PYTHON ?= python # Python version to use for a project's virtual environment. # Defaults to Python 3.7, which is the version that runs on the OT-2. # https://pipenv.pypa.io/en/latest/basics/#specifying-versions-of-python -OT_VIRTUALENV_VERSION ?= 3.7 +OT_VIRTUALENV_VERSION ?= 3.10 # Use legacy editable installs to avoid breaking mypy type-checking # when using newer versions of setuptools From c52e55966392ab8d3323242d7b81a025ada22dde Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Wed, 6 Dec 2023 13:09:25 -0500 Subject: [PATCH 18/60] update all the pipfiles --- api/Pipfile | 8 +- api/Pipfile.lock | 1181 ++++++++++++++------------ api/setup.py | 2 +- g-code-testing/Pipfile | 6 +- g-code-testing/Pipfile.lock | 1402 +++++++++++++++---------------- hardware/Pipfile.lock | 1056 +++++++++++------------ hardware/setup.py | 4 +- notify-server/Pipfile | 6 +- notify-server/Pipfile.lock | 685 ++++++--------- robot-server/Pipfile | 13 +- robot-server/Pipfile.lock | 1284 ++++++++++++---------------- robot-server/setup.py | 2 +- server-utils/Pipfile | 8 +- server-utils/Pipfile.lock | 677 +++++++-------- server-utils/setup.py | 2 +- shared-data/python/Pipfile | 4 +- shared-data/python/Pipfile.lock | 700 ++++++++------- system-server/Pipfile | 10 +- system-server/Pipfile.lock | 889 ++++++++++---------- update-server/Pipfile | 5 +- update-server/Pipfile.lock | 664 ++++++--------- usb-bridge/Pipfile | 4 +- usb-bridge/Pipfile.lock | 993 +++++++++++----------- 23 files changed, 4595 insertions(+), 5010 deletions(-) diff --git a/api/Pipfile b/api/Pipfile index 304daf41ae2..155192f2fcb 100755 --- a/api/Pipfile +++ b/api/Pipfile @@ -7,8 +7,8 @@ name = "pypi" # atomicwrites and colorama are pytest dependencies on windows, # spec'd here to force lockfile inclusion # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 -atomicwrites = { version = "==1.4.0", sys_platform = "== 'win32'" } -colorama = { version = "==0.4.4", sys_platform = "== 'win32'" } +atomicwrites = { version = "==1.4.0", markers="sys_platform=='win32'" } +colorama = { version = "==0.4.4", markers="sys_platform=='win32'" } coverage = "==5.1" mypy = "==0.910" numpydoc = "==0.9.1" @@ -23,7 +23,7 @@ wheel = "==0.37.0" typeguard = "==2.13.1" sphinx-substitution-extensions = "==2020.9.30.0" sphinxext-opengraph = "==0.8.1" -sphinx-tabs = ">=3.4.1,<4" +sphinx-tabs = ">=3.4.0,<4" mock = "~=4.0.3" flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" @@ -35,7 +35,7 @@ types-mock = "==4.0.1" types-setuptools = "==57.0.2" opentrons-shared-data = { editable = true, path = "../shared-data/python" } opentrons = { editable = true, path = "." } -opentrons-hardware = { editable = true, path = "./../hardware", extras= ["FLEX"] } +opentrons-hardware = { editable = true, path = "./../hardware", extras=["FLEX"] } # specify typing-extensions explicitly to force lockfile inclusion on Python >= 3.8 typing-extensions = ">=4.0.0,<5" pytest-profiling = "~=1.7.0" diff --git a/api/Pipfile.lock b/api/Pipfile.lock index 6a0090887a1..3d02c2fc8eb 100644 --- a/api/Pipfile.lock +++ b/api/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "e53961988b9cfe876088bf31ed01f5e145545b9b6d014eac255b723c262a245f" + "sha256": "8169f7821ebe1ec68b99ef25f55ea5c25afdcd02694c845510cd169e32fb3404" }, "pipfile-spec": 6, "requires": {}, @@ -15,14 +15,6 @@ }, "default": {}, "develop": { - "aenum": { - "hashes": [ - "sha256:27b1710b9d084de6e2e695dab78fe9f269de924b51ae2850170ee7e1ca6288a5", - "sha256:8cbd76cd18c4f870ff39b24284d3ea028fbe8731a58df3aa581e434c575b9559", - "sha256:e0dfaeea4c2bd362144b87377e2c61d91958c5ed0b4daf89cb6f45ae23af6288" - ], - "version": "==3.1.15" - }, "aionotify": { "hashes": [ "sha256:385e1becfaac2d9f4326673033d53912ef9565b6febdedbec593ee966df392c6", @@ -40,11 +32,11 @@ }, "anyio": { "hashes": [ - "sha256:929a6852074397afe1d989002aa96d457e3e1e5441357c60d03e7eea0e65e1b0", - "sha256:ae57a67583e5ff8b4af47666ff5651c3732d45fd26c929253748e796af860374" + "sha256:413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b", + "sha256:cb29b9c70620506a9a8f87a309591713446953302d7d995344d0d7c6c0c9a7be" ], "markers": "python_full_version >= '3.6.2'", - "version": "==3.3.0" + "version": "==3.6.1" }, "atomicwrites": { "hashes": [ @@ -64,11 +56,11 @@ }, "babel": { "hashes": [ - "sha256:04c3e2d28d2b7681644508f836be388ae49e0cfe91465095340395b60d00f210", - "sha256:fbfcae1575ff78e26c7449136f1abbefc3c13ce542eeb13d43d50d8b047216ec" + "sha256:33e0952d7dd6374af8dbf6768cc4ddf3ccfefc244f9986d4074704f2fbd18900", + "sha256:7077a4984b02b6727ac10f1f7294484f737443d7e2e66c5e4380e41a3ae0b4ed" ], "markers": "python_version >= '3.7'", - "version": "==2.13.0" + "version": "==2.13.1" }, "black": { "hashes": [ @@ -97,119 +89,112 @@ "sha256:fd57160949179ec517d32ac2ac898b5f20d68ed1a9c977346efbac9c2f1e779d" ], "index": "pypi", + "markers": "python_full_version >= '3.6.2'", "version": "==22.3.0" }, - "bleach": { - "hashes": [ - "sha256:1a1a85c1595e07d8db14c5f09f09e6433502c51c595970edc090551f0db99414", - "sha256:33c16e3353dbd13028ab4799a0f89a83f113405c766e9c122df8a06f5b85b3f4" - ], - "markers": "python_version >= '3.7'", - "version": "==6.0.0" - }, "certifi": { "hashes": [ - "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082", - "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9" + "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1", + "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474" ], "markers": "python_version >= '3.6'", - "version": "==2023.7.22" + "version": "==2023.11.17" }, "charset-normalizer": { "hashes": [ - "sha256:02673e456dc5ab13659f85196c534dc596d4ef260e4d86e856c3b2773ce09843", - "sha256:02af06682e3590ab952599fbadac535ede5d60d78848e555aa58d0c0abbde786", - "sha256:03680bb39035fbcffe828eae9c3f8afc0428c91d38e7d61aa992ef7a59fb120e", - "sha256:0570d21da019941634a531444364f2482e8db0b3425fcd5ac0c36565a64142c8", - "sha256:09c77f964f351a7369cc343911e0df63e762e42bac24cd7d18525961c81754f4", - 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'3.6'", + "version": "==1.16.0" }, "zipp": { "hashes": [ - "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b", - "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556" + "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31", + "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0" ], - "markers": "python_version < '3.10'", - "version": "==3.15.0" + "markers": "python_version >= '3.8'", + "version": "==3.17.0" } } } diff --git a/api/setup.py b/api/setup.py index 869305ca284..15b61b369a4 100755 --- a/api/setup.py +++ b/api/setup.py @@ -61,7 +61,7 @@ def get_version(): INSTALL_REQUIRES = [ f"opentrons-shared-data=={VERSION}", "aionotify==0.2.0", - "anyio==3.3.0", + "anyio==3.6.1", "jsonschema==3.0.2", "numpy>=1.15.1,<2", "pydantic==1.8.2", diff --git a/g-code-testing/Pipfile b/g-code-testing/Pipfile index c57185ddf48..0102b5cced5 100644 --- a/g-code-testing/Pipfile +++ b/g-code-testing/Pipfile @@ -15,12 +15,12 @@ anyio = "==3.6.1" pydantic = "==1.8.2" # opentrons dependency on linux, spec'd here to force lockfile inclusion # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 -systemd-python = { version = "==234", sys_platform = "== 'linux'" } +systemd-python = { version = "==234", markers="sys_platform=='linux'" } [dev-packages] diff-match-patch = "==20200713" pytest = "~=7.1" -pytest-aiohttp = "==3.8.1" +pytest-aiohttp = "==0.3.0" pytest-cov = "==2.10.1" pytest-xdist = "~=2.5.0" mock = "~=4.0.3" @@ -29,7 +29,7 @@ flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" flake8-noqa = "~=1.2.1" -black = "==22.0" +black = "==22.3.0" decoy = "~=1.10.0" [requires] diff --git a/g-code-testing/Pipfile.lock b/g-code-testing/Pipfile.lock index a335343967c..c94fbb8bf3e 100644 --- a/g-code-testing/Pipfile.lock +++ b/g-code-testing/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": "330370d3fa88efabdd5b0a94b42503ffdfd4cb6265bd50bc398dc4cfcc938939" + "sha256": "cd9a7f20e4b3472da3d0d473dce50c67d5f7952c1c6e67ff71538a7c54497b5c" }, "pipfile-spec": 6, "requires": { - "python_version": "3.7" + "python_version": "3.10" }, "sources": [ { @@ -16,14 +16,6 @@ ] }, "default": { - "aenum": { - "hashes": [ - "sha256:07ea89f43d78b3d5997b32b8d5b0ec3e5be17b3e05b7bac0154b8c484a4aeff5", - "sha256:859fe994719e6b5e39f15f73acd84e08b4e57dc642373b177a5fa6646798706a", - "sha256:8dbe15f446eb8264b788dfeca163fb0a043d408d212152397dc11377b851e4ae" - ], - "version": "==3.1.8" - }, "aionotify": { "hashes": [ "sha256:385e1becfaac2d9f4326673033d53912ef9565b6febdedbec593ee966df392c6", @@ -31,37 +23,46 @@ ], "version": "==0.2.0" }, + "aiosqlite": { + "hashes": [ + "sha256:6c49dc6d3405929b1d08eeccc72306d3677503cc5e5e43771efc1e00232e8231", + "sha256:f0e6acc24bc4864149267ac82fb46dfb3be4455f99fe21df82609cc6e6baee51" + ], + "markers": "python_version >= '3.6'", + "version": "==0.17.0" + }, "anyio": { 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], - "markers": "python_full_version < '3.8.0' and implementation_name == 'cpython' and python_full_version < '3.8.0' and python_full_version < '3.8.0'", - "version": "==1.4.3" - }, "types-mock": { "hashes": [ "sha256:1a470543be8de673e2ea14739622de3bfb8c9b10429f50338ba9ca1e868c15e9", @@ -1025,19 +1044,12 @@ }, "typing-extensions": { "hashes": [ - "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36", - "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2" + "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0", + "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef" ], "index": "pypi", - "version": "==4.7.1" - }, - "zipp": { - "hashes": [ - "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b", - "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556" - ], - "markers": "python_version >= '3.7'", - "version": "==3.15.0" + "markers": "python_version >= '3.8'", + "version": "==4.8.0" } } } diff --git a/hardware/setup.py b/hardware/setup.py index 9ae440551f4..1195e9ea727 100644 --- a/hardware/setup.py +++ b/hardware/setup.py @@ -47,12 +47,12 @@ def get_version() -> str: DESCRIPTION = "Hardware control for Opentrons Robots." PACKAGES = find_packages(where=".", exclude=["tests.*", "tests"]) INSTALL_REQUIRES = [ - "pyserial==4.2.2", + "pyserial==3.5", f"opentrons_shared_data=={VERSION}", ] EXTRAS = { - "FLEX": ["python-can==3.3.4"], + "FLEX": ["python-can==4.2.2"], } diff --git a/notify-server/Pipfile b/notify-server/Pipfile index 9cd06b04505..ad632ac242e 100644 --- a/notify-server/Pipfile +++ b/notify-server/Pipfile @@ -7,6 +7,7 @@ verify_ssl = true python_version = "3.10" [packages] +notify-server = { editable = true, path = "." } opentrons = { editable = true, path = "../api" } opentrons-shared-data = { editable = true, path = "../shared-data/python" } opentrons-hardware = { editable = true, path = "./../hardware" } @@ -15,7 +16,6 @@ pyzmq = "==19.*,>=19.0.2" typing-extensions = ">=4.0.0,<5" [dev-packages] -notify-server = { editable = true, path = "." } flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" @@ -27,6 +27,6 @@ pytest-asyncio = "==0.16.0" pytest-xdist = "~=2.5.0" # pytest dependencies on windows, spec'd here to force lockfile inclusion # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 -atomicwrites = { version = "==1.4.0", sys_platform = "== 'win32'" } -colorama = { version = "==0.4.4", sys_platform = "== 'win32'" } +atomicwrites = { version = "==1.4.0", markers="sys_platform =='win32'" } +colorama = { version = "==0.4.4", markers = "sys_platform=='win32'" } black = "==22.3.0" diff --git a/notify-server/Pipfile.lock b/notify-server/Pipfile.lock index 1b1d2ecf8a7..7e0b961473a 100644 --- a/notify-server/Pipfile.lock +++ b/notify-server/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": "ab0997d0755c728a39b26c02efbf824b231f237a6f9e008b6c5ac65a6ba8094f" + "sha256": "eb19ee7f1c562808d7f817593703637442707684a3115a774b1c4888bd421797" }, "pipfile-spec": 6, "requires": { - "python_version": "3.7" + "python_version": "3.10" }, "sources": [ { @@ -16,14 +16,6 @@ ] }, "default": { - "aenum": { - "hashes": [ - "sha256:07ea89f43d78b3d5997b32b8d5b0ec3e5be17b3e05b7bac0154b8c484a4aeff5", - "sha256:859fe994719e6b5e39f15f73acd84e08b4e57dc642373b177a5fa6646798706a", - "sha256:8dbe15f446eb8264b788dfeca163fb0a043d408d212152397dc11377b851e4ae" - ], - "version": "==3.1.8" - }, "aionotify": { "hashes": [ "sha256:385e1becfaac2d9f4326673033d53912ef9565b6febdedbec593ee966df392c6", @@ -33,27 +25,35 @@ }, "anyio": { "hashes": [ - "sha256:929a6852074397afe1d989002aa96d457e3e1e5441357c60d03e7eea0e65e1b0", - "sha256:ae57a67583e5ff8b4af47666ff5651c3732d45fd26c929253748e796af860374" + "sha256:413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b", + "sha256:cb29b9c70620506a9a8f87a309591713446953302d7d995344d0d7c6c0c9a7be" ], "markers": "python_full_version >= '3.6.2'", - "version": "==3.3.0" + "version": "==3.6.1" }, "attrs": { "hashes": [ - "sha256:2d27e3784d7a565d36ab851fe94887c5eccd6a463168875832a1be79c82828b4", - "sha256:626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd" + 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path = "." } # pytest dependencies on windows, spec'd here to force lockfile inclusion # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 -atomicwrites = { version = "==1.4.0", sys_platform = "== 'win32'" } -colorama = { version = "==0.4.4", sys_platform = "== 'win32'" } +atomicwrites = { version = "==1.4.0", markers="sys_platform=='win32'" } +colorama = { version = "==0.4.4", markers="sys_platform=='win32'" } pytest = "~=7.1" pytest-asyncio = "~=0.16" pytest-cov = "==2.10.1" @@ -38,6 +37,7 @@ python-box = "==5.4.1" opentrons = { editable = true, path = "../api" } opentrons-shared-data = { editable = true, path = "../shared-data/python" } notify-server = { editable = true, path = "../notify-server" } +robot-server = { editable = true, path = "." } anyio = "==3.6.1" fastapi = "==0.68.1" python-dotenv = "==0.19.0" @@ -46,13 +46,10 @@ pydantic = "==1.8.2" typing-extensions = ">=4.0.0,<5" uvicorn = "==0.14.0" wsproto = "==1.0.0" -systemd-python = { version = "==234", sys_platform = "== 'linux'" } +systemd-python = { version = "==234", markers="sys_platform == 'linux'" } idna = "==3.3" click = "==8.1.2" -# TODO(mc, 2022-04-04): this dep is newer than the OT-2 for dev environment reasons -# remove this TODO when Opentrons/buildroot has updated to newer numpy -# https://github.com/Opentrons/buildroot/pull/148 -numpy = "==1.21.2" +numpy = "==1.23.3" zipp = "==3.5.0" opentrons-hardware = { editable = true, path = "./../hardware" } sqlalchemy = "==1.4.32" diff --git a/robot-server/Pipfile.lock b/robot-server/Pipfile.lock index 7e977d6f731..97c6057d586 100644 --- a/robot-server/Pipfile.lock +++ b/robot-server/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": "dff9b5c0c0a442a884ac96695c64e24d61436e1b470c008871d531a9c01f2be9" + "sha256": "27598ca3470d9f807a7361b54990a6b3495a39d6488777ad1992bdc185024377" }, "pipfile-spec": 6, "requires": { - "python_version": "3.7" + "python_version": "3.10" }, "sources": [ { @@ -16,14 +16,6 @@ ] }, 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b/robot-server/setup.py index 18a5ddb34df..6510cfd7edd 100755 --- a/robot-server/setup.py +++ b/robot-server/setup.py @@ -56,7 +56,7 @@ def get_version(): f"opentrons-shared-data=={VERSION}", f"notify-server=={VERSION}", f"server-utils=={VERSION}", - "anyio==3.3.0", + "anyio==3.6.1", "fastapi==0.68.1", "python-dotenv==0.19.0", "python-multipart==0.0.5", diff --git a/server-utils/Pipfile b/server-utils/Pipfile index fca1db021fc..caf55306081 100755 --- a/server-utils/Pipfile +++ b/server-utils/Pipfile @@ -10,8 +10,8 @@ python_version = "3.10" server-utils = { editable = true, path = "." } # pytest dependencies on windows, spec'd here to force lockfile inclusion # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 -atomicwrites = { version = "==1.4.0", sys_platform = "== 'win32'" } -colorama = { version = "==0.4.4", sys_platform = "== 'win32'" } +atomicwrites = { version = "==1.4.0", markers="sys_platform=='win32'" } +colorama = { version = "==0.4.4", markers="sys_platform=='win32'" } pytest = "~=7.1" pytest-asyncio = "~=0.16" pytest-cov = "==2.10.1" @@ -41,7 +41,7 @@ pydantic = "==1.8.2" typing-extensions = ">=4.0.0,<5" uvicorn = "==0.14.0" wsproto = "==1.0.0" -systemd-python = { version = "==234", sys_platform = "== 'linux'" } +systemd-python = { version = "==234", markers="sys_platform=='linux'" } idna = "==3.3" -sqlalchemy = "==1.4.35" +sqlalchemy = "==1.4.32" aiosqlite = "==0.17.0" diff --git a/server-utils/Pipfile.lock b/server-utils/Pipfile.lock index 9c0ad3ac5ad..2d7a4146f6c 100644 --- a/server-utils/Pipfile.lock +++ b/server-utils/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": "6c0dfa476e6a1f837719069be4cce9505c07cab2aba9f226825e9a70da9b016b" + "sha256": "5c62484d3476443c39221fe8c12ae97d969adaa5ba5f139d3ce364524494d5b4" }, "pipfile-spec": 6, "requires": { - "python_version": "3.7" + "python_version": "3.10" }, "sources": [ { @@ -22,31 +22,33 @@ "sha256:f0e6acc24bc4864149267ac82fb46dfb3be4455f99fe21df82609cc6e6baee51" ], "index": "pypi", + "markers": "python_version >= '3.6'", "version": "==0.17.0" }, "anyio": { "hashes": [ - "sha256:929a6852074397afe1d989002aa96d457e3e1e5441357c60d03e7eea0e65e1b0", - "sha256:ae57a67583e5ff8b4af47666ff5651c3732d45fd26c929253748e796af860374" + "sha256:413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b", + "sha256:cb29b9c70620506a9a8f87a309591713446953302d7d995344d0d7c6c0c9a7be" ], "index": "pypi", - "version": "==3.3.0" + "markers": "python_full_version >= '3.6.2'", + "version": "==3.6.1" }, "asgiref": { "hashes": [ - "sha256:71e68008da809b957b7ee4b43dbccff33d1b23519fb8344e33f049897077afac", - "sha256:9567dfe7bd8d3c8c892227827c41cce860b368104c3431da67a0c5a65a949506" + "sha256:89b2ef2247e3b562a16eef663bc0e2e703ec6468e2fa8a5cd61cd449786d4f6e", + "sha256:9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed" ], "markers": "python_version >= '3.7'", - "version": "==3.6.0" + "version": "==3.7.2" }, "click": { "hashes": [ - "sha256:7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e", - "sha256:bb4d8133cb15a609f44e8213d9b391b0809795062913b383c62be0ee95b1db48" + "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28", + "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de" ], "markers": "python_version >= '3.7'", - "version": "==8.1.3" + "version": "==8.1.7" }, "fastapi": { "hashes": [ @@ -54,73 +56,71 @@ "sha256:94d2820906c36b9b8303796fb7271337ec89c74223229e3cfcf056b5a7d59e23" ], "index": "pypi", + "markers": "python_version >= '3.6'", "version": "==0.68.1" }, "greenlet": { "hashes": [ - "sha256:03a8f4f3430c3b3ff8d10a2a86028c660355ab637cee9333d63d66b56f09d52a", - "sha256:0bf60faf0bc2468089bdc5edd10555bab6e85152191df713e2ab1fcc86382b5a", - "sha256:18a7f18b82b52ee85322d7a7874e676f34ab319b9f8cce5de06067384aa8ff43", - "sha256:18e98fb3de7dba1c0a852731c3070cf022d14f0d68b4c87a19cc1016f3bb8b33", - 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"version": "==3.15.0" } } } diff --git a/server-utils/setup.py b/server-utils/setup.py index b049bc315a3..555d60932be 100755 --- a/server-utils/setup.py +++ b/server-utils/setup.py @@ -51,7 +51,7 @@ def get_version(): DESCRIPTION = "Common utilities for various Opentrons Python servers." PACKAGES = find_packages(where=".", exclude=["tests.*", "tests"]) INSTALL_REQUIRES = [ - "anyio==3.3.0", + "anyio==3.6.1", "fastapi==0.68.1", "python-dotenv==0.19.0", "python-multipart==0.0.5", diff --git a/shared-data/python/Pipfile b/shared-data/python/Pipfile index 220882fc360..ea1b637396c 100644 --- a/shared-data/python/Pipfile +++ b/shared-data/python/Pipfile @@ -19,8 +19,8 @@ typeguard = "~=2.13" typing-extensions = ">=4.0.0,<5" # pytest dependencies on windows, spec'd here to force lockfile inclusion # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 -atomicwrites = { version = "==1.4.0", sys_platform = "== 'win32'" } -colorama = { version = "==0.4.4", sys_platform = "== 'win32'" } +atomicwrites = { version = "==1.4.0", markers="sys_platform=='win32'" } +colorama = { version = "==0.4.4", markers="sys_platform=='win32'" } black = "==22.3.0" pytest-clarity = "~=1.0.0" diff --git a/shared-data/python/Pipfile.lock b/shared-data/python/Pipfile.lock index 0ed21f208a8..67379b9bf39 100644 --- a/shared-data/python/Pipfile.lock +++ b/shared-data/python/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "42d3f5bc6e1a22e3c568c41e9cf4a70127eece0a90b366542520cf2c6ab9bb75" + "sha256": "799ae57c11b367011184ba5242ccc99ae3a5c6624d5732aef9611d564b944af0" }, "pipfile-spec": 6, "requires": {}, @@ -16,11 +16,11 @@ "default": { "attrs": { "hashes": [ - "sha256:2d27e3784d7a565d36ab851fe94887c5eccd6a463168875832a1be79c82828b4", - "sha256:626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd" + "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04", + "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'", - "version": "==21.4.0" + "markers": "python_version >= '3.7'", + "version": "==23.1.0" }, "jsonschema": { "hashes": [ @@ -31,6 +31,7 @@ }, "opentrons-shared-data": { "editable": true, + "markers": "python_version >= '3.7'", "path": "." }, "pydantic": { @@ -63,30 +64,49 @@ }, "pyrsistent": { "hashes": [ - "sha256:0e3e1fcc45199df76053026a51cc59ab2ea3fc7c094c6627e93b7b44cdae2c8c", - "sha256:1b34eedd6812bf4d33814fca1b66005805d3640ce53140ab8bbb1e2651b0d9bc", - "sha256:4ed6784ceac462a7d6fcb7e9b663e93b9a6fb373b7f43594f9ff68875788e01e", - "sha256:5d45866ececf4a5fff8742c25722da6d4c9e180daa7b405dc0a2a2790d668c26", - "sha256:636ce2dc235046ccd3d8c56a7ad54e99d5c1cd0ef07d9ae847306c91d11b5fec", - "sha256:6455fc599df93d1f60e1c5c4fe471499f08d190d57eca040c0ea182301321286", - "sha256:6bc66318fb7ee012071b2792024564973ecc80e9522842eb4e17743604b5e045", - "sha256:7bfe2388663fd18bd8ce7db2c91c7400bf3e1a9e8bd7d63bf7e77d39051b85ec", - "sha256:7ec335fc998faa4febe75cc5268a9eac0478b3f681602c1f27befaf2a1abe1d8", - "sha256:914474c9f1d93080338ace89cb2acee74f4f666fb0424896fcfb8d86058bf17c", - "sha256:b568f35ad53a7b07ed9b1b2bae09eb15cdd671a5ba5d2c66caee40dbf91c68ca", - 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"markers": "python_version >= '3.7'", - "version": "==3.7.0" + "markers": "python_version >= '3.8'", + "version": "==3.17.0" } } } diff --git a/system-server/Pipfile b/system-server/Pipfile index 9e97c88916d..b90dd469298 100644 --- a/system-server/Pipfile +++ b/system-server/Pipfile @@ -12,13 +12,13 @@ pyjwt = "==2.6.0" python-dotenv = "==0.19.0" python-multipart = "==0.0.5" pydantic = "==1.8.2" -sqlalchemy = "==1.4.35" -systemd-python = { version = "==234", sys_platform = "== 'linux'" } +sqlalchemy = "==1.4.32" +systemd-python = { version = "==234", markers="sys_platform=='linux'" } importlib-metadata = ">=4.13.0,<5" server-utils = {editable = true, path = "./../server-utils"} +system_server = {path = ".", editable = true} [dev-packages] -system_server = {path = ".", editable = true} flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" @@ -33,8 +33,8 @@ coverage = "==6.3" # atomicwrites and colorama are pytest dependencies on windows, # spec'd here to force lockfile inclusion # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 -atomicwrites = { version = "==1.4.0", sys_platform = "== 'win32'" } -colorama = { version = "==0.4.4", sys_platform = "== 'win32'" } +atomicwrites = { version = "==1.4.0", markers="sys_platform=='win32'" } +colorama = { version = "==0.4.4", markers="sys_platform=='win32'" } sqlalchemy2-stubs = "==0.0.2a21" mypy = "==0.942" black = "==22.3.0" diff --git a/system-server/Pipfile.lock b/system-server/Pipfile.lock index 00a0d864ed3..7602be7cc64 100644 --- a/system-server/Pipfile.lock +++ b/system-server/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": "f8557d4a9b2a3206fb84ee900cd093611cb108d2b71b5602ad15cbe38b389540" + "sha256": "804cbca0f9a88f27e082425ba1c72e682ebb16e700baf2b311bae763ac2ed397" }, "pipfile-spec": 6, "requires": { - "python_version": "3.7" + "python_version": "3.10" }, "sources": [ { @@ -16,29 +16,38 @@ ] }, "default": { + "aiosqlite": { + "hashes": [ + 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563b4f3a0fc..9e955ac4e7d 100644 --- a/update-server/Pipfile +++ b/update-server/Pipfile @@ -4,7 +4,6 @@ verify_ssl = true name = "pypi" [packages] -aiohttp = "==3.8.1" typing-extensions = "==3.10.0.0" [dev-packages] @@ -21,8 +20,8 @@ coverage = "==6.3.2" # atomicwrites and colorama are pytest dependencies on windows, # spec'd here to force lockfile inclusion # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 -atomicwrites = {version="==1.4.0", sys_platform="== 'win32'"} -colorama = {version="==0.4.4", sys_platform="== 'win32'"} +atomicwrites = {version="==1.4.0", markers="sys_platform=='win32'"} +colorama = {version="==0.4.4", markers="sys_platform=='win32'"} mypy = "==0.942" black = "==22.3.0" decoy = "~=1.10" diff --git a/update-server/Pipfile.lock b/update-server/Pipfile.lock index cced41f3d19..fec15cc480d 100644 --- a/update-server/Pipfile.lock +++ b/update-server/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": 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@@ -25,8 +25,8 @@ coverage = "==6.2" # atomicwrites and colorama are pytest dependencies on windows, # spec'd here to force lockfile inclusion # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 -atomicwrites = {version="==1.4.0", sys_platform="== 'win32'"} -colorama = {version="==0.4.4", sys_platform="== 'win32'"} +atomicwrites = {version="==1.4.0", markers="sys_platform=='win32'"} +colorama = {version="==0.4.4", markers="sys_platform=='win32'"} mypy = "==0.942" black = "==22.3.0" decoy = "~=1.10" diff --git a/usb-bridge/Pipfile.lock b/usb-bridge/Pipfile.lock index 696341f437e..19c50bd893f 100644 --- a/usb-bridge/Pipfile.lock +++ b/usb-bridge/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": "5f8ac3a6a4adb5b7e0e6083b3b4498cb09e025459845b93ae748b4912a32f903" + "sha256": "568e6f27764e2c9c65b2deadc3ac1d8a72806ace02d5cfb8c7f1ec3b6dd50cdd" }, "pipfile-spec": 6, "requires": { - "python_version": "3.7" + "python_version": "3.10" }, "sources": [ { @@ -26,11 +26,19 @@ }, "pyudev": { "hashes": [ - "sha256:b2a3afe1c99ea751f8296652557eac559874da2a1b1ec0625178706ec5a345f3", - "sha256:d22451d9f10b4fef7737a0fa5c5664e7547cf9ae58a79084eb396e0ce9a0e406" + "sha256:32ae3585b320a51bc283e0a04000fd8a25599edb44541e2f5034f6afee5d15cc", + "sha256:50d94bef0669f9aabd323a2259be67e8d49b9ebab9eae27b2cf8262767f9a2ae" ], "index": "pypi", - "version": "==0.24.0" + "version": "==0.23.2" + }, + "six": { + "hashes": [ + "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926", + "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254" + ], + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'", + "version": "==1.16.0" }, "typing-extensions": { "hashes": [ @@ -45,120 +53,101 @@ "develop": { "aiohttp": { "hashes": [ - "sha256:02f9a2c72fc95d59b881cf38a4b2be9381b9527f9d328771e90f72ac76f31ad8", - "sha256:059a91e88f2c00fe40aed9031b3606c3f311414f86a90d696dd982e7aec48142", - 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"sha256:ee04010f26d5102399bd17f8df8bc38dc7ccd7701dc77f4a68c5b8d733406958", + "sha256:f3bc6af6e2b8f92eced34ef6a96ffb248e863af20ef4fde9448cc8c9b858b749", + "sha256:f7d6b36dd2e029b6bcb8a13cf19664c7b8e19ab3a58e0fefbb5b8461447ed5ec" ], "markers": "python_version >= '3.7'", - "version": "==3.8.1" + "version": "==1.9.4" } } } From a231b7cf74e499d6199b2be47da41282832f8dc3 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Wed, 6 Dec 2023 14:09:17 -0500 Subject: [PATCH 19/60] increment pipenv --- Makefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 1fb16b8ba87..ed86d48cca9 100755 --- a/Makefile +++ b/Makefile @@ -66,7 +66,7 @@ PYTHON_SETUP_TARGETS := $(addsuffix -py-setup, $(PYTHON_DIRS)) .PHONY: setup-py setup-py: - $(OT_PYTHON) -m pip install pipenv==2021.5.29 + $(OT_PYTHON) -m pip install pipenv==2023.11.15 $(MAKE) $(PYTHON_SETUP_TARGETS) @@ -266,4 +266,4 @@ test-js-internal: .PHONY: test-js-% test-js-%: - $(MAKE) test-js-internal tests="$(if $(tests),$(foreach test,$(tests),$*/$(test)),$*)" test_opts="$(test_opts)" cov_opts="$(cov_opts)" \ No newline at end of file + $(MAKE) test-js-internal tests="$(if $(tests),$(foreach test,$(tests),$*/$(test)),$*)" test_opts="$(test_opts)" cov_opts="$(cov_opts)" From 44fb1b84c7d565882905f3abd197dcd820e5d946 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Thu, 7 Dec 2023 11:00:24 -0500 Subject: [PATCH 20/60] increment mypy and thus pydantic mypy needs to be 0.981 to handle numpy pyis https://github.com/python/mypy/issues/13627 that means pydantic needs to be >1.9.0 to handle new internal apis --- api/Pipfile | 2 +- api/Pipfile.lock | 167 ++-- api/setup.py | 2 +- .../drivers/smoothie_drivers/driver_3_0.py | 2 +- g-code-testing/Pipfile | 4 +- g-code-testing/Pipfile.lock | 120 +-- hardware-testing/Pipfile | 2 +- hardware-testing/Pipfile.lock | 776 +++++++----------- hardware/Pipfile | 4 +- hardware/Pipfile.lock | 177 ++-- notify-server/Pipfile | 4 +- notify-server/Pipfile.lock | 120 +-- notify-server/setup.py | 2 +- robot-server/Pipfile | 4 +- robot-server/Pipfile.lock | 126 +-- robot-server/setup.py | 2 +- server-utils/Pipfile | 13 +- server-utils/Pipfile.lock | 394 ++------- server-utils/setup.py | 2 +- shared-data/python/Pipfile | 2 +- shared-data/python/Pipfile.lock | 150 ++-- shared-data/python/setup.py | 2 +- system-server/Pipfile | 7 +- system-server/Pipfile.lock | 136 +-- update-server/Pipfile | 2 +- update-server/Pipfile.lock | 55 +- usb-bridge/Pipfile | 2 +- usb-bridge/Pipfile.lock | 57 +- 28 files changed, 989 insertions(+), 1347 deletions(-) diff --git a/api/Pipfile b/api/Pipfile index 155192f2fcb..a2cf4813902 100755 --- a/api/Pipfile +++ b/api/Pipfile @@ -10,7 +10,7 @@ name = "pypi" atomicwrites = { version = "==1.4.0", markers="sys_platform=='win32'" } colorama = { version = "==0.4.4", markers="sys_platform=='win32'" } coverage = "==5.1" -mypy = "==0.910" +mypy = "==0.981" numpydoc = "==0.9.1" pytest = "==7.0.1" pytest-asyncio = "~=0.16" diff --git a/api/Pipfile.lock b/api/Pipfile.lock index 3d02c2fc8eb..2d9dc89bf38 100644 --- a/api/Pipfile.lock +++ b/api/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "8169f7821ebe1ec68b99ef25f55ea5c25afdcd02694c845510cd169e32fb3404" + "sha256": "4e0f3375a8c869d73bc486d144b4bfb9a158ffca346fb192d6cfde548f413f9f" }, "pipfile-spec": 6, "requires": {}, @@ -819,61 +819,63 @@ }, "mypy": { "hashes": [ - "sha256:088cd9c7904b4ad80bec811053272986611b84221835e079be5bcad029e79dd9", - "sha256:0aadfb2d3935988ec3815952e44058a3100499f5be5b28c34ac9d79f002a4a9a", - "sha256:119bed3832d961f3a880787bf621634ba042cb8dc850a7429f643508eeac97b9", - "sha256:1a85e280d4d217150ce8cb1a6dddffd14e753a4e0c3cf90baabb32cefa41b59e", - "sha256:3c4b8ca36877fc75339253721f69603a9c7fdb5d4d5a95a1a1b899d8b86a4de2", - "sha256:3e382b29f8e0ccf19a2df2b29a167591245df90c0b5a2542249873b5c1d78212", - "sha256:42c266ced41b65ed40a282c575705325fa7991af370036d3f134518336636f5b", - 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"sha256:bc2d086fb540d0fa52ce35afaded4ea526b8fc4d3339f783db55c95de40ef02e", + "sha256:d1e30ff2d8d58fb2a14961f7aac1bbb1c51f9bdd7da727be35c63826060b0bf3", + "sha256:f3b53ba93bb7725acab1e030bc2ecd012a817040fd7851b332f86e2f9bb98dc6" + ], + "version": "==0.2.15" }, "numpy": { "hashes": [ @@ -1058,31 +1060,44 @@ }, "pydantic": { "hashes": [ - "sha256:021ea0e4133e8c824775a0cfe098677acf6fa5a3cbf9206a376eed3fc09302cd", - "sha256:05ddfd37c1720c392f4e0d43c484217b7521558302e7069ce8d318438d297739", - "sha256:05ef5246a7ffd2ce12a619cbb29f3307b7c4509307b1b49f456657b43529dc6f", - "sha256:10e5622224245941efc193ad1d159887872776df7a8fd592ed746aa25d071840", - "sha256:18b5ea242dd3e62dbf89b2b0ec9ba6c7b5abaf6af85b95a97b00279f65845a23", - "sha256:234a6c19f1c14e25e362cb05c68afb7f183eb931dd3cd4605eafff055ebbf287", - "sha256:244ad78eeb388a43b0c927e74d3af78008e944074b7d0f4f696ddd5b2af43c62", - "sha256:26464e57ccaafe72b7ad156fdaa4e9b9ef051f69e175dbbb463283000c05ab7b", - 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"sha256:cdb4272678db803ddf94caa4f94f8672e9a46bae4a44f167095e4d06fec12979", + "sha256:d70916235d478404a3fa8c997b003b5f33aeac4686ac1baa767234a0f8ac2326", + "sha256:d8ce3fb0841763a89322ea0432f1f59a2d3feae07a63ea2c958b2315e1ae8adb", + "sha256:e0b214e57623a535936005797567231a12d0da0c29711eb3514bc2b3cd008d0f", + "sha256:e631c70c9280e3129f071635b81207cad85e6c08e253539467e4ead0e5b219aa", + "sha256:e78578f0c7481c850d1c969aca9a65405887003484d24f6110458fb02cca7747", + "sha256:f0ca86b525264daa5f6b192f216a0d1e860b7383e3da1c65a1908f9c02f42801", + "sha256:f1a68f4f65a9ee64b6ccccb5bf7e17db07caebd2730109cb8a95863cfa9c4e55", + "sha256:fafe841be1103f340a24977f61dee76172e4ae5f647ab9e7fd1e1fca51524f08", + "sha256:ff68fc85355532ea77559ede81f35fff79a6a5543477e168ab3a381887caea76" ], "markers": "python_full_version >= '3.6.1'", - "version": "==1.8.2" + "version": "==1.9.2" }, "pydocstyle": { "hashes": [ @@ -1235,7 +1250,7 @@ "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86", "sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==2.8.2" }, "readme-renderer": { @@ -1291,7 +1306,7 @@ "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926", "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==1.16.0" }, "sniffio": { @@ -1405,14 +1420,6 @@ "markers": "python_version >= '3.7'", "version": "==0.8.1" }, - "toml": { - "hashes": [ - "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b", - "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f" - ], - "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2'", - "version": "==0.10.2" - }, "tomli": { "hashes": [ "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc", diff --git a/api/setup.py b/api/setup.py index 15b61b369a4..9e251fc1f0d 100755 --- a/api/setup.py +++ b/api/setup.py @@ -64,7 +64,7 @@ def get_version(): "anyio==3.6.1", "jsonschema==3.0.2", "numpy>=1.15.1,<2", - "pydantic==1.8.2", + "pydantic==1.9.2", "pyserial==3.5", "typing-extensions>=4.0.0,<5", "click>=8.0.0,<9", diff --git a/api/src/opentrons/drivers/smoothie_drivers/driver_3_0.py b/api/src/opentrons/drivers/smoothie_drivers/driver_3_0.py index 956bc59c192..93a0816db8c 100755 --- a/api/src/opentrons/drivers/smoothie_drivers/driver_3_0.py +++ b/api/src/opentrons/drivers/smoothie_drivers/driver_3_0.py @@ -1896,7 +1896,7 @@ async def update_firmware( # noqa: C901 "stdout": asyncio.subprocess.PIPE, "stderr": asyncio.subprocess.PIPE, } - #if loop: + # if loop: # kwargs["loop"] = loop log.info(update_cmd) before = time() diff --git a/g-code-testing/Pipfile b/g-code-testing/Pipfile index 0102b5cced5..026ca783dd5 100644 --- a/g-code-testing/Pipfile +++ b/g-code-testing/Pipfile @@ -12,7 +12,7 @@ opentrons-shared-data = { editable = true, path = "../shared-data/python" } opentrons_hardware = { editable = true, path = "../hardware" } g-code-testing = { editable = true, path = "." } anyio = "==3.6.1" -pydantic = "==1.8.2" +pydantic = "==1.9.2" # opentrons dependency on linux, spec'd here to force lockfile inclusion # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 systemd-python = { version = "==234", markers="sys_platform=='linux'" } @@ -24,7 +24,7 @@ pytest-aiohttp = "==0.3.0" pytest-cov = "==2.10.1" pytest-xdist = "~=2.5.0" mock = "~=4.0.3" -mypy = "==0.942.0" +mypy = "==0.981" flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" diff --git a/g-code-testing/Pipfile.lock b/g-code-testing/Pipfile.lock index c94fbb8bf3e..805f05c5385 100644 --- a/g-code-testing/Pipfile.lock +++ b/g-code-testing/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "cd9a7f20e4b3472da3d0d473dce50c67d5f7952c1c6e67ff71538a7c54497b5c" + "sha256": "791f7b071facb00499fae66b09d598083b98076e85ec26f7c1484d1130e700f9" }, "pipfile-spec": 6, "requires": { @@ -136,7 +136,7 @@ "sha256:f89e21afe925fcfa655965ca8ea10f24773a1791400989ff32f467badfe4a064", "sha256:fa24255ae3c0ab67e613556375a4341af04a084bd58764731972bcbc8baeba36" ], - "markers": "python_version >= '3' and (platform_machine == 'aarch64' or (platform_machine == 'ppc64le' or (platform_machine == 'x86_64' or (platform_machine == 'amd64' or (platform_machine == 'AMD64' or (platform_machine == 'win32' or platform_machine == 'WIN32'))))))", + "markers": "python_version >= '3' and platform_machine == 'aarch64' or (platform_machine == 'ppc64le' or (platform_machine == 'x86_64' or (platform_machine == 'amd64' or (platform_machine == 'AMD64' or (platform_machine == 'win32' or platform_machine == 'WIN32')))))", "version": "==3.0.1" }, "h11": { @@ -223,32 +223,45 @@ }, "pydantic": { "hashes": [ - "sha256:021ea0e4133e8c824775a0cfe098677acf6fa5a3cbf9206a376eed3fc09302cd", - "sha256:05ddfd37c1720c392f4e0d43c484217b7521558302e7069ce8d318438d297739", - "sha256:05ef5246a7ffd2ce12a619cbb29f3307b7c4509307b1b49f456657b43529dc6f", - "sha256:10e5622224245941efc193ad1d159887872776df7a8fd592ed746aa25d071840", - "sha256:18b5ea242dd3e62dbf89b2b0ec9ba6c7b5abaf6af85b95a97b00279f65845a23", - "sha256:234a6c19f1c14e25e362cb05c68afb7f183eb931dd3cd4605eafff055ebbf287", - "sha256:244ad78eeb388a43b0c927e74d3af78008e944074b7d0f4f696ddd5b2af43c62", - "sha256:26464e57ccaafe72b7ad156fdaa4e9b9ef051f69e175dbbb463283000c05ab7b", - "sha256:41b542c0b3c42dc17da70554bc6f38cbc30d7066d2c2815a94499b5684582ecb", - "sha256:4a03cbbe743e9c7247ceae6f0d8898f7a64bb65800a45cbdc52d65e370570820", - "sha256:4be75bebf676a5f0f87937c6ddb061fa39cbea067240d98e298508c1bda6f3f3", - "sha256:54cd5121383f4a461ff7644c7ca20c0419d58052db70d8791eacbbe31528916b", - "sha256:589eb6cd6361e8ac341db97602eb7f354551482368a37f4fd086c0733548308e", - "sha256:8621559dcf5afacf0069ed194278f35c255dc1a1385c28b32dd6c110fd6531b3", - "sha256:8b223557f9510cf0bfd8b01316bf6dd281cf41826607eada99662f5e4963f316", - "sha256:99a9fc39470010c45c161a1dc584997f1feb13f689ecf645f59bb4ba623e586b", - "sha256:a7c6002203fe2c5a1b5cbb141bb85060cbff88c2d78eccbc72d97eb7022c43e4", - "sha256:a83db7205f60c6a86f2c44a61791d993dff4b73135df1973ecd9eed5ea0bda20", - "sha256:ac8eed4ca3bd3aadc58a13c2aa93cd8a884bcf21cb019f8cfecaae3b6ce3746e", - "sha256:e710876437bc07bd414ff453ac8ec63d219e7690128d925c6e82889d674bb505", - "sha256:ea5cb40a3b23b3265f6325727ddfc45141b08ed665458be8c6285e7b85bd73a1", - "sha256:fec866a0b59f372b7e776f2d7308511784dace622e0992a0b59ea3ccee0ae833" + "sha256:1061c6ee6204f4f5a27133126854948e3b3d51fcc16ead2e5d04378c199b2f44", + "sha256:19b5686387ea0d1ea52ecc4cffb71abb21702c5e5b2ac626fd4dbaa0834aa49d", + "sha256:2bd446bdb7755c3a94e56d7bdfd3ee92396070efa8ef3a34fab9579fe6aa1d84", + "sha256:328558c9f2eed77bd8fffad3cef39dbbe3edc7044517f4625a769d45d4cf7555", + "sha256:32e0b4fb13ad4db4058a7c3c80e2569adbd810c25e6ca3bbd8b2a9cc2cc871d7", + "sha256:3ee0d69b2a5b341fc7927e92cae7ddcfd95e624dfc4870b32a85568bd65e6131", + "sha256:4aafd4e55e8ad5bd1b19572ea2df546ccace7945853832bb99422a79c70ce9b8", + "sha256:4b3946f87e5cef3ba2e7bd3a4eb5a20385fe36521d6cc1ebf3c08a6697c6cfb3", + "sha256:4de71c718c9756d679420c69f216776c2e977459f77e8f679a4a961dc7304a56", + "sha256:5565a49effe38d51882cb7bac18bda013cdb34d80ac336428e8908f0b72499b0", + "sha256:5803ad846cdd1ed0d97eb00292b870c29c1f03732a010e66908ff48a762f20e4", + "sha256:5da164119602212a3fe7e3bc08911a89db4710ae51444b4224c2382fd09ad453", + "sha256:615661bfc37e82ac677543704437ff737418e4ea04bef9cf11c6d27346606044", + "sha256:78a4d6bdfd116a559aeec9a4cfe77dda62acc6233f8b56a716edad2651023e5e", + "sha256:7d0f183b305629765910eaad707800d2f47c6ac5bcfb8c6397abdc30b69eeb15", + "sha256:7ead3cd020d526f75b4188e0a8d71c0dbbe1b4b6b5dc0ea775a93aca16256aeb", + "sha256:84d76ecc908d917f4684b354a39fd885d69dd0491be175f3465fe4b59811c001", + "sha256:8cb0bc509bfb71305d7a59d00163d5f9fc4530f0881ea32c74ff4f74c85f3d3d", + "sha256:91089b2e281713f3893cd01d8e576771cd5bfdfbff5d0ed95969f47ef6d676c3", + "sha256:9c9e04a6cdb7a363d7cb3ccf0efea51e0abb48e180c0d31dca8d247967d85c6e", + "sha256:a8c5360a0297a713b4123608a7909e6869e1b56d0e96eb0d792c27585d40757f", + "sha256:afacf6d2a41ed91fc631bade88b1d319c51ab5418870802cedb590b709c5ae3c", + "sha256:b34ba24f3e2d0b39b43f0ca62008f7ba962cff51efa56e64ee25c4af6eed987b", + "sha256:bd67cb2c2d9602ad159389c29e4ca964b86fa2f35c2faef54c3eb28b4efd36c8", + "sha256:c0f5e142ef8217019e3eef6ae1b6b55f09a7a15972958d44fbd228214cede567", + "sha256:cdb4272678db803ddf94caa4f94f8672e9a46bae4a44f167095e4d06fec12979", + "sha256:d70916235d478404a3fa8c997b003b5f33aeac4686ac1baa767234a0f8ac2326", + "sha256:d8ce3fb0841763a89322ea0432f1f59a2d3feae07a63ea2c958b2315e1ae8adb", + "sha256:e0b214e57623a535936005797567231a12d0da0c29711eb3514bc2b3cd008d0f", + "sha256:e631c70c9280e3129f071635b81207cad85e6c08e253539467e4ead0e5b219aa", + "sha256:e78578f0c7481c850d1c969aca9a65405887003484d24f6110458fb02cca7747", + "sha256:f0ca86b525264daa5f6b192f216a0d1e860b7383e3da1c65a1908f9c02f42801", + "sha256:f1a68f4f65a9ee64b6ccccb5bf7e17db07caebd2730109cb8a95863cfa9c4e55", + "sha256:fafe841be1103f340a24977f61dee76172e4ae5f647ab9e7fd1e1fca51524f08", + "sha256:ff68fc85355532ea77559ede81f35fff79a6a5543477e168ab3a381887caea76" ], "index": "pypi", "markers": "python_full_version >= '3.6.1'", - "version": "==1.8.2" + "version": "==1.9.2" }, "pyrsistent": { "hashes": [ @@ -344,7 +357,7 @@ "sha256:f1a25a61495b6f7bb986accc5b597a3541d9bd3ef0016f50be16dbb32025b302", "sha256:fa411b1d8f371d3a49d31b0789eb6da2537dadbb2aef74a43aa99a78195c3f76" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==19.0.2" }, "robot-server": { @@ -368,7 +381,7 @@ "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926", "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==1.16.0" }, "sniffio": { @@ -912,33 +925,34 @@ }, "mypy": { "hashes": [ - "sha256:0e2dd88410937423fba18e57147dd07cd8381291b93d5b1984626f173a26543e", - "sha256:10daab80bc40f84e3f087d896cdb53dc811a9f04eae4b3f95779c26edee89d16", - "sha256:17e44649fec92e9f82102b48a3bf7b4a5510ad0cd22fa21a104826b5db4903e2", - "sha256:1a0459c333f00e6a11cbf6b468b870c2b99a906cb72d6eadf3d1d95d38c9352c", - "sha256:246e1aa127d5b78488a4a0594bd95f6d6fb9d63cf08a66dafbff8595d8891f67", - "sha256:2b184db8c618c43c3a31b32ff00cd28195d39e9c24e7c3b401f3db7f6e5767f5", - "sha256:2bc249409a7168d37c658e062e1ab5173300984a2dada2589638568ddc1db02b", - "sha256:3841b5433ff936bff2f4dc8d54cf2cdbfea5d8e88cedfac45c161368e5770ba6", - "sha256:4c3e497588afccfa4334a9986b56f703e75793133c4be3a02d06a3df16b67a58", - "sha256:5bf44840fb43ac4074636fd47ee476d73f0039f4f54e86d7265077dc199be24d", - "sha256:64235137edc16bee6f095aba73be5334677d6f6bdb7fa03cfab90164fa294a17", - "sha256:6776e5fa22381cc761df53e7496a805801c1a751b27b99a9ff2f0ca848c7eca0", - "sha256:6ce34a118d1a898f47def970a2042b8af6bdcc01546454726c7dd2171aa6dfca", - "sha256:6f6ad963172152e112b87cc7ec103ba0f2db2f1cd8997237827c052a3903eaa6", - "sha256:6f7106cbf9cc2f403693bf50ed7c9fa5bb3dfa9007b240db3c910929abe2a322", - "sha256:7742d2c4e46bb5017b51c810283a6a389296cda03df805a4f7869a6f41246534", - "sha256:9521c1265ccaaa1791d2c13582f06facf815f426cd8b07c3a485f486a8ffc1f3", - "sha256:a1b383fe99678d7402754fe90448d4037f9512ce70c21f8aee3b8bf48ffc51db", - "sha256:b840cfe89c4ab6386c40300689cd8645fc8d2d5f20101c7f8bd23d15fca14904", - "sha256:d8d3ba77e56b84cd47a8ee45b62c84b6d80d32383928fe2548c9a124ea0a725c", - "sha256:dcd955f36e0180258a96f880348fbca54ce092b40fbb4b37372ae3b25a0b0a46", - "sha256:e865fec858d75b78b4d63266c9aff770ecb6a39dfb6d6b56c47f7f8aba6baba8", - "sha256:edf7237137a1a9330046dbb14796963d734dd740a98d5e144a3eb1d267f5f9ee" + "sha256:06e1eac8d99bd404ed8dd34ca29673c4346e76dd8e612ea507763dccd7e13c7a", + "sha256:2ee3dbc53d4df7e6e3b1c68ac6a971d3a4fb2852bf10a05fda228721dd44fae1", + "sha256:4bc460e43b7785f78862dab78674e62ec3cd523485baecfdf81a555ed29ecfa0", + "sha256:64e1f6af81c003f85f0dfed52db632817dabb51b65c0318ffbf5ff51995bbb08", + "sha256:6e35d764784b42c3e256848fb8ed1d4292c9fc0098413adb28d84974c095b279", + "sha256:6ee196b1d10b8b215e835f438e06965d7a480f6fe016eddbc285f13955cca659", + "sha256:756fad8b263b3ba39e4e204ee53042671b660c36c9017412b43af210ddee7b08", + "sha256:77f8fcf7b4b3cc0c74fb33ae54a4cd00bb854d65645c48beccf65fa10b17882c", + "sha256:794f385653e2b749387a42afb1e14c2135e18daeb027e0d97162e4b7031210f8", + "sha256:8ad21d4c9d3673726cf986ea1d0c9fb66905258709550ddf7944c8f885f208be", + "sha256:8e8e49aa9cc23aa4c926dc200ce32959d3501c4905147a66ce032f05cb5ecb92", + "sha256:9f362470a3480165c4c6151786b5379351b790d56952005be18bdbdd4c7ce0ae", + "sha256:a16a0145d6d7d00fbede2da3a3096dcc9ecea091adfa8da48fa6a7b75d35562d", + "sha256:ad77c13037d3402fbeffda07d51e3f228ba078d1c7096a73759c9419ea031bf4", + "sha256:b6ede64e52257931315826fdbfc6ea878d89a965580d1a65638ef77cb551f56d", + "sha256:c9e0efb95ed6ca1654951bd5ec2f3fa91b295d78bf6527e026529d4aaa1e0c30", + "sha256:ce65f70b14a21fdac84c294cde75e6dbdabbcff22975335e20827b3b94bdbf49", + "sha256:d1debb09043e1f5ee845fa1e96d180e89115b30e47c5d3ce53bc967bab53f62d", + "sha256:e178eaffc3c5cd211a87965c8c0df6da91ed7d258b5fc72b8e047c3771317ddb", + "sha256:e1acf62a8c4f7c092462c738aa2c2489e275ed386320c10b2e9bff31f6f7e8d6", + "sha256:e53773073c864d5f5cec7f3fc72fbbcef65410cde8cc18d4f7242dea60dac52e", + "sha256:eb3978b191b9fa0488524bb4ffedf2c573340e8c2b4206fc191d44c7093abfb7", + "sha256:f64d2ce043a209a297df322eb4054dfbaa9de9e8738291706eaafda81ab2b362", + "sha256:fa38f82f53e1e7beb45557ff167c177802ba7b387ad017eab1663d567017c8ee" ], "index": "pypi", - "markers": "python_version >= '3.6'", - "version": "==0.942" + "markers": "python_version >= '3.7'", + "version": "==0.981" }, "mypy-extensions": { "hashes": [ @@ -1067,7 +1081,7 @@ "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc", "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f" ], - "markers": "python_version >= '3.7'", + "markers": "python_version < '3.11'", "version": "==2.0.1" }, "typing-extensions": { diff --git a/hardware-testing/Pipfile b/hardware-testing/Pipfile index 1da0ae2f6c3..96d2de6b9bd 100644 --- a/hardware-testing/Pipfile +++ b/hardware-testing/Pipfile @@ -15,7 +15,7 @@ atomicwrites = "==1.4.1" colorama = "==0.4.4" pytest = "==7.1.1" pytest-cov = "==2.10.1" -mypy = "==0.942" +mypy = "==0.981" black = "==22.3.0" flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" diff --git a/hardware-testing/Pipfile.lock b/hardware-testing/Pipfile.lock index 3ec46749af6..35bf79f025d 100644 --- a/hardware-testing/Pipfile.lock +++ b/hardware-testing/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": "317adb42f71108bc905d9220a1f3438732f3c42c2baadfbbd1d58ab499ef744d" + "sha256": "7ca3bff855c6090feac4bf3594ce0b9179f5c105622fb144eed7f35b35cb306d" }, "pipfile-spec": 6, "requires": { - "python_version": "3.7" + "python_version": "3.10" }, "sources": [ { @@ -16,14 +16,6 @@ ] }, "default": { - "aenum": { - "hashes": [ - "sha256:12ae89967f2e25c0ce28c293955d643f891603488bc3d9946158ba2b35203638", - "sha256:525b4870a27d0b471c265bda692bc657f1e0dd7597ad4186d072c59f9db666f6", - "sha256:aed2c273547ae72a0d5ee869719c02a643da16bf507c80958faadc7e038e3f73" - ], - "version": "==3.1.11" - }, "aionotify": { "hashes": [ "sha256:385e1becfaac2d9f4326673033d53912ef9565b6febdedbec593ee966df392c6", @@ -33,27 +25,27 @@ }, "anyio": { "hashes": [ - "sha256:929a6852074397afe1d989002aa96d457e3e1e5441357c60d03e7eea0e65e1b0", 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"sha256:e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6" + "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0", + "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef" ], - "markers": "python_version < '3.8' and python_version < '3.8'", - "version": "==4.3.0" + "markers": "python_version >= '3.8'", + "version": "==4.8.0" }, - "zipp": { + "urllib3": { "hashes": [ - "sha256:05b45f1ee8f807d0cc928485ca40a07cb491cf092ff587c0df9cb1fd154848d2", - "sha256:47c40d7fe183a6f21403a199b3e4192cca5774656965b0a4988ad2f8feb5f009" + "sha256:34b97092d7e0a3a8cf7cd10e386f401b3737364026c45e622aa02903dffe0f07", + "sha256:f8ecc1bba5667413457c529ab955bf8c67b45db799d159066261719e328580a0" ], - "markers": "python_version >= '3.7'", - "version": "==3.8.1" + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'", + "version": "==1.26.18" } } } diff --git a/hardware/Pipfile b/hardware/Pipfile index 9e4d818e1d6..0b302c13e6b 100644 --- a/hardware/Pipfile +++ b/hardware/Pipfile @@ -8,13 +8,13 @@ python-can = "==4.2.2" pyserial = "==3.5" typing-extensions = ">=4.0.0,<5" numpy = "==1.22.3" -pydantic = "==1.8.2" +pydantic = "==1.9.2" [dev-packages] pytest = "==7.1.1" pytest-lazy-fixture = "==0.6.3" pytest-cov = "==2.10.1" -mypy = "==0.942" +mypy = "==0.981" black = "==22.3.0" flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" diff --git a/hardware/Pipfile.lock b/hardware/Pipfile.lock index fbe3f84f3e0..a56c60f726d 100644 --- a/hardware/Pipfile.lock +++ b/hardware/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "01c645b089bc2fa82d85ecf7e12d80d2728fb6fbcf18f2eb8f0c9523fe78b671" + "sha256": "16eff2fac0ee431c4cd558ef6e2cc98fc2f2ec703e3e33bb639b948b8f5ccbfb" }, "pipfile-spec": 6, "requires": { @@ -115,32 +115,45 @@ }, "pydantic": { "hashes": [ - "sha256:021ea0e4133e8c824775a0cfe098677acf6fa5a3cbf9206a376eed3fc09302cd", - 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'3.11'", "version": "==2.0.1" }, "types-mock": { diff --git a/notify-server/Pipfile b/notify-server/Pipfile index ad632ac242e..24518fa3fc4 100644 --- a/notify-server/Pipfile +++ b/notify-server/Pipfile @@ -11,8 +11,6 @@ notify-server = { editable = true, path = "." } opentrons = { editable = true, path = "../api" } opentrons-shared-data = { editable = true, path = "../shared-data/python" } opentrons-hardware = { editable = true, path = "./../hardware" } -pydantic = "==1.8.2" -pyzmq = "==19.*,>=19.0.2" typing-extensions = ">=4.0.0,<5" [dev-packages] @@ -20,7 +18,7 @@ flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" mock = "~=4.0.3" -mypy = "==0.942" +mypy = "==0.981" pytest = "==7.1.1" pytest-cov = "==2.10.1" pytest-asyncio = "==0.16.0" diff --git a/notify-server/Pipfile.lock b/notify-server/Pipfile.lock index 7e0b961473a..fa41c21a2f5 100644 --- a/notify-server/Pipfile.lock +++ b/notify-server/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": 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"sha256:78a4d6bdfd116a559aeec9a4cfe77dda62acc6233f8b56a716edad2651023e5e", + "sha256:7d0f183b305629765910eaad707800d2f47c6ac5bcfb8c6397abdc30b69eeb15", + "sha256:7ead3cd020d526f75b4188e0a8d71c0dbbe1b4b6b5dc0ea775a93aca16256aeb", + "sha256:84d76ecc908d917f4684b354a39fd885d69dd0491be175f3465fe4b59811c001", + "sha256:8cb0bc509bfb71305d7a59d00163d5f9fc4530f0881ea32c74ff4f74c85f3d3d", + "sha256:91089b2e281713f3893cd01d8e576771cd5bfdfbff5d0ed95969f47ef6d676c3", + "sha256:9c9e04a6cdb7a363d7cb3ccf0efea51e0abb48e180c0d31dca8d247967d85c6e", + "sha256:a8c5360a0297a713b4123608a7909e6869e1b56d0e96eb0d792c27585d40757f", + "sha256:afacf6d2a41ed91fc631bade88b1d319c51ab5418870802cedb590b709c5ae3c", + "sha256:b34ba24f3e2d0b39b43f0ca62008f7ba962cff51efa56e64ee25c4af6eed987b", + "sha256:bd67cb2c2d9602ad159389c29e4ca964b86fa2f35c2faef54c3eb28b4efd36c8", + "sha256:c0f5e142ef8217019e3eef6ae1b6b55f09a7a15972958d44fbd228214cede567", + "sha256:cdb4272678db803ddf94caa4f94f8672e9a46bae4a44f167095e4d06fec12979", + "sha256:d70916235d478404a3fa8c997b003b5f33aeac4686ac1baa767234a0f8ac2326", + "sha256:d8ce3fb0841763a89322ea0432f1f59a2d3feae07a63ea2c958b2315e1ae8adb", + "sha256:e0b214e57623a535936005797567231a12d0da0c29711eb3514bc2b3cd008d0f", + "sha256:e631c70c9280e3129f071635b81207cad85e6c08e253539467e4ead0e5b219aa", + "sha256:e78578f0c7481c850d1c969aca9a65405887003484d24f6110458fb02cca7747", + "sha256:f0ca86b525264daa5f6b192f216a0d1e860b7383e3da1c65a1908f9c02f42801", + "sha256:f1a68f4f65a9ee64b6ccccb5bf7e17db07caebd2730109cb8a95863cfa9c4e55", + "sha256:fafe841be1103f340a24977f61dee76172e4ae5f647ab9e7fd1e1fca51524f08", + "sha256:ff68fc85355532ea77559ede81f35fff79a6a5543477e168ab3a381887caea76" ], - "index": "pypi", "markers": "python_full_version >= '3.6.1'", - "version": "==1.8.2" + "version": "==1.9.2" }, "pyrsistent": { "hashes": [ @@ -230,8 +242,7 @@ "sha256:f1a25a61495b6f7bb986accc5b597a3541d9bd3ef0016f50be16dbb32025b302", "sha256:fa411b1d8f371d3a49d31b0789eb6da2537dadbb2aef74a43aa99a78195c3f76" ], - "index": "pypi", - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==19.0.2" }, "setuptools": { @@ -247,7 +258,7 @@ "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926", "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==1.16.0" }, "sniffio": { @@ -449,33 +460,34 @@ }, "mypy": { "hashes": [ - "sha256:0e2dd88410937423fba18e57147dd07cd8381291b93d5b1984626f173a26543e", - "sha256:10daab80bc40f84e3f087d896cdb53dc811a9f04eae4b3f95779c26edee89d16", - "sha256:17e44649fec92e9f82102b48a3bf7b4a5510ad0cd22fa21a104826b5db4903e2", - "sha256:1a0459c333f00e6a11cbf6b468b870c2b99a906cb72d6eadf3d1d95d38c9352c", - "sha256:246e1aa127d5b78488a4a0594bd95f6d6fb9d63cf08a66dafbff8595d8891f67", - "sha256:2b184db8c618c43c3a31b32ff00cd28195d39e9c24e7c3b401f3db7f6e5767f5", - "sha256:2bc249409a7168d37c658e062e1ab5173300984a2dada2589638568ddc1db02b", - "sha256:3841b5433ff936bff2f4dc8d54cf2cdbfea5d8e88cedfac45c161368e5770ba6", - "sha256:4c3e497588afccfa4334a9986b56f703e75793133c4be3a02d06a3df16b67a58", - "sha256:5bf44840fb43ac4074636fd47ee476d73f0039f4f54e86d7265077dc199be24d", - "sha256:64235137edc16bee6f095aba73be5334677d6f6bdb7fa03cfab90164fa294a17", - "sha256:6776e5fa22381cc761df53e7496a805801c1a751b27b99a9ff2f0ca848c7eca0", - "sha256:6ce34a118d1a898f47def970a2042b8af6bdcc01546454726c7dd2171aa6dfca", - "sha256:6f6ad963172152e112b87cc7ec103ba0f2db2f1cd8997237827c052a3903eaa6", - "sha256:6f7106cbf9cc2f403693bf50ed7c9fa5bb3dfa9007b240db3c910929abe2a322", - "sha256:7742d2c4e46bb5017b51c810283a6a389296cda03df805a4f7869a6f41246534", - "sha256:9521c1265ccaaa1791d2c13582f06facf815f426cd8b07c3a485f486a8ffc1f3", - "sha256:a1b383fe99678d7402754fe90448d4037f9512ce70c21f8aee3b8bf48ffc51db", - "sha256:b840cfe89c4ab6386c40300689cd8645fc8d2d5f20101c7f8bd23d15fca14904", - "sha256:d8d3ba77e56b84cd47a8ee45b62c84b6d80d32383928fe2548c9a124ea0a725c", - "sha256:dcd955f36e0180258a96f880348fbca54ce092b40fbb4b37372ae3b25a0b0a46", - "sha256:e865fec858d75b78b4d63266c9aff770ecb6a39dfb6d6b56c47f7f8aba6baba8", - "sha256:edf7237137a1a9330046dbb14796963d734dd740a98d5e144a3eb1d267f5f9ee" + "sha256:06e1eac8d99bd404ed8dd34ca29673c4346e76dd8e612ea507763dccd7e13c7a", + "sha256:2ee3dbc53d4df7e6e3b1c68ac6a971d3a4fb2852bf10a05fda228721dd44fae1", + "sha256:4bc460e43b7785f78862dab78674e62ec3cd523485baecfdf81a555ed29ecfa0", + "sha256:64e1f6af81c003f85f0dfed52db632817dabb51b65c0318ffbf5ff51995bbb08", + "sha256:6e35d764784b42c3e256848fb8ed1d4292c9fc0098413adb28d84974c095b279", + "sha256:6ee196b1d10b8b215e835f438e06965d7a480f6fe016eddbc285f13955cca659", + "sha256:756fad8b263b3ba39e4e204ee53042671b660c36c9017412b43af210ddee7b08", + "sha256:77f8fcf7b4b3cc0c74fb33ae54a4cd00bb854d65645c48beccf65fa10b17882c", + "sha256:794f385653e2b749387a42afb1e14c2135e18daeb027e0d97162e4b7031210f8", + "sha256:8ad21d4c9d3673726cf986ea1d0c9fb66905258709550ddf7944c8f885f208be", + "sha256:8e8e49aa9cc23aa4c926dc200ce32959d3501c4905147a66ce032f05cb5ecb92", + "sha256:9f362470a3480165c4c6151786b5379351b790d56952005be18bdbdd4c7ce0ae", + "sha256:a16a0145d6d7d00fbede2da3a3096dcc9ecea091adfa8da48fa6a7b75d35562d", + "sha256:ad77c13037d3402fbeffda07d51e3f228ba078d1c7096a73759c9419ea031bf4", + "sha256:b6ede64e52257931315826fdbfc6ea878d89a965580d1a65638ef77cb551f56d", + "sha256:c9e0efb95ed6ca1654951bd5ec2f3fa91b295d78bf6527e026529d4aaa1e0c30", + "sha256:ce65f70b14a21fdac84c294cde75e6dbdabbcff22975335e20827b3b94bdbf49", + "sha256:d1debb09043e1f5ee845fa1e96d180e89115b30e47c5d3ce53bc967bab53f62d", + "sha256:e178eaffc3c5cd211a87965c8c0df6da91ed7d258b5fc72b8e047c3771317ddb", + "sha256:e1acf62a8c4f7c092462c738aa2c2489e275ed386320c10b2e9bff31f6f7e8d6", + "sha256:e53773073c864d5f5cec7f3fc72fbbcef65410cde8cc18d4f7242dea60dac52e", + "sha256:eb3978b191b9fa0488524bb4ffedf2c573340e8c2b4206fc191d44c7093abfb7", + "sha256:f64d2ce043a209a297df322eb4054dfbaa9de9e8738291706eaafda81ab2b362", + "sha256:fa38f82f53e1e7beb45557ff167c177802ba7b387ad017eab1663d567017c8ee" ], "index": "pypi", - "markers": "python_version >= '3.6'", - "version": "==0.942" + "markers": "python_version >= '3.7'", + "version": "==0.981" }, "mypy-extensions": { "hashes": [ @@ -605,7 +617,7 @@ "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc", "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f" ], - "markers": "python_version >= '3.7'", + "markers": "python_version < '3.11'", "version": "==2.0.1" }, "typing-extensions": { diff --git a/notify-server/setup.py b/notify-server/setup.py index ddeb93773a6..5cb1cb8e06e 100644 --- a/notify-server/setup.py +++ b/notify-server/setup.py @@ -50,7 +50,7 @@ def get_version(): f"opentrons=={VERSION}", f"opentrons-shared-data=={VERSION}", "pyzmq==19.0.2", - "pydantic==1.8.2", + "pydantic==1.9.2", ] diff --git a/robot-server/Pipfile b/robot-server/Pipfile index bf19a0840ea..0d2589c252e 100755 --- a/robot-server/Pipfile +++ b/robot-server/Pipfile @@ -20,7 +20,7 @@ requests = "==2.27.1" tavern = "~=1.6" graphviz = "==0.19" mock = "~=4.0.3" -mypy = "==0.942" +mypy = "==0.981" flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" @@ -42,7 +42,7 @@ anyio = "==3.6.1" fastapi = "==0.68.1" python-dotenv = "==0.19.0" python-multipart = "==0.0.5" -pydantic = "==1.8.2" +pydantic = "==1.9.2" typing-extensions = ">=4.0.0,<5" uvicorn = "==0.14.0" wsproto = "==1.0.0" diff --git a/robot-server/Pipfile.lock b/robot-server/Pipfile.lock index 97c6057d586..c5c54c750e9 100644 --- a/robot-server/Pipfile.lock +++ b/robot-server/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "27598ca3470d9f807a7361b54990a6b3495a39d6488777ad1992bdc185024377" + "sha256": "381b4b6885471b5eff4c6dbcb6612d4c363eaf208379a6d127c53630347ac0b2" }, "pipfile-spec": 6, "requires": { @@ -135,7 +135,7 @@ "sha256:f89e21afe925fcfa655965ca8ea10f24773a1791400989ff32f467badfe4a064", "sha256:fa24255ae3c0ab67e613556375a4341af04a084bd58764731972bcbc8baeba36" ], - "markers": "python_version >= '3' and (platform_machine == 'aarch64' or (platform_machine == 'ppc64le' or (platform_machine == 'x86_64' or (platform_machine == 'amd64' or (platform_machine == 'AMD64' or (platform_machine == 'win32' or platform_machine == 'WIN32'))))))", + "markers": "python_version >= '3' and platform_machine == 'aarch64' or (platform_machine == 'ppc64le' or (platform_machine == 'x86_64' or (platform_machine == 'amd64' or (platform_machine == 'AMD64' or (platform_machine == 'win32' or platform_machine == 'WIN32')))))", "version": "==3.0.1" }, "h11": { @@ -216,32 +216,45 @@ }, "pydantic": { "hashes": [ - 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"sha256:e78578f0c7481c850d1c969aca9a65405887003484d24f6110458fb02cca7747", + "sha256:f0ca86b525264daa5f6b192f216a0d1e860b7383e3da1c65a1908f9c02f42801", + "sha256:f1a68f4f65a9ee64b6ccccb5bf7e17db07caebd2730109cb8a95863cfa9c4e55", + "sha256:fafe841be1103f340a24977f61dee76172e4ae5f647ab9e7fd1e1fca51524f08", + "sha256:ff68fc85355532ea77559ede81f35fff79a6a5543477e168ab3a381887caea76" ], "index": "pypi", "markers": "python_full_version >= '3.6.1'", - "version": "==1.8.2" + "version": "==1.9.2" }, "pyrsistent": { "hashes": [ @@ -339,7 +352,7 @@ "sha256:f1a25a61495b6f7bb986accc5b597a3541d9bd3ef0016f50be16dbb32025b302", "sha256:fa411b1d8f371d3a49d31b0789eb6da2537dadbb2aef74a43aa99a78195c3f76" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==19.0.2" }, "robot-server": { @@ -363,7 +376,7 @@ "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926", "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==1.16.0" }, "sniffio": { @@ -736,7 +749,7 @@ "sha256:b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9", "sha256:cdf6525904cc597730141d61b36f2e4b8ecc257c420fa2f4549bac2c2d0cb72f" ], - "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2'", + "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==0.10.0" }, "jsonschema": { @@ -764,33 +777,34 @@ }, "mypy": { "hashes": [ - "sha256:0e2dd88410937423fba18e57147dd07cd8381291b93d5b1984626f173a26543e", - "sha256:10daab80bc40f84e3f087d896cdb53dc811a9f04eae4b3f95779c26edee89d16", - 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"sha256:e178eaffc3c5cd211a87965c8c0df6da91ed7d258b5fc72b8e047c3771317ddb", + "sha256:e1acf62a8c4f7c092462c738aa2c2489e275ed386320c10b2e9bff31f6f7e8d6", + "sha256:e53773073c864d5f5cec7f3fc72fbbcef65410cde8cc18d4f7242dea60dac52e", + "sha256:eb3978b191b9fa0488524bb4ffedf2c573340e8c2b4206fc191d44c7093abfb7", + "sha256:f64d2ce043a209a297df322eb4054dfbaa9de9e8738291706eaafda81ab2b362", + "sha256:fa38f82f53e1e7beb45557ff167c177802ba7b387ad017eab1663d567017c8ee" ], "index": "pypi", - "markers": "python_version >= '3.6'", - "version": "==0.942" + "markers": "python_version >= '3.7'", + "version": "==0.981" }, "mypy-extensions": { "hashes": [ @@ -997,7 +1011,7 @@ "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86", "sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==2.8.2" }, "pyyaml": { @@ -1136,7 +1150,7 @@ "sha256:f481f16baec5290e45aebdc2a5168ebc6d35189ae6fea7a58787613a25f6e875", "sha256:fff3573c2db359f091e1589c3d7c5fc2f86f5bdb6f24252c2d8e539d4e45f412" ], - "markers": "platform_python_implementation == 'CPython' and python_version < '3.13'", + "markers": "python_version < '3.13' and platform_python_implementation == 'CPython'", "version": "==0.2.8" }, "setuptools": { @@ -1152,7 +1166,7 @@ "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926", "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==1.16.0" }, "sniffio": { diff --git a/robot-server/setup.py b/robot-server/setup.py index 6510cfd7edd..6cfdd9ad421 100755 --- a/robot-server/setup.py +++ b/robot-server/setup.py @@ -60,7 +60,7 @@ def get_version(): "fastapi==0.68.1", "python-dotenv==0.19.0", "python-multipart==0.0.5", - "pydantic==1.8.2", + "pydantic==1.9.2", "typing-extensions>=4.0.0,<5", "uvicorn==0.14.0", "wsproto==1.0.0", diff --git a/server-utils/Pipfile b/server-utils/Pipfile index caf55306081..ae589d277a7 100755 --- a/server-utils/Pipfile +++ b/server-utils/Pipfile @@ -19,7 +19,7 @@ pytest-lazy-fixture = "==0.6.3" pytest-xdist = "~=2.5.0" requests = "==2.27.1" mock = "~=4.0.3" -mypy = "==0.942" +mypy = "==0.981" flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" @@ -33,15 +33,4 @@ sqlalchemy2-stubs = "==0.0.2a21" python-box = "==5.4.1" [packages] -anyio = "==3.6.1" -fastapi = "==0.68.1" -python-dotenv = "==0.19.0" -python-multipart = "==0.0.5" -pydantic = "==1.8.2" -typing-extensions = ">=4.0.0,<5" -uvicorn = "==0.14.0" -wsproto = "==1.0.0" -systemd-python = { version = "==234", markers="sys_platform=='linux'" } idna = "==3.3" -sqlalchemy = "==1.4.32" -aiosqlite = "==0.17.0" diff --git a/server-utils/Pipfile.lock b/server-utils/Pipfile.lock index 2d7a4146f6c..7f8c62a76ed 100644 --- a/server-utils/Pipfile.lock +++ b/server-utils/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "5c62484d3476443c39221fe8c12ae97d969adaa5ba5f139d3ce364524494d5b4" + "sha256": "cc50e1adfd1023979f6306f3470f3e3f51cfc9b8defa50cac882385f9d05f71e" }, "pipfile-spec": 6, "requires": { @@ -16,120 +16,6 @@ ] }, "default": { - "aiosqlite": { - "hashes": [ - "sha256:6c49dc6d3405929b1d08eeccc72306d3677503cc5e5e43771efc1e00232e8231", - "sha256:f0e6acc24bc4864149267ac82fb46dfb3be4455f99fe21df82609cc6e6baee51" - ], - "index": "pypi", - "markers": "python_version >= '3.6'", - "version": "==0.17.0" - }, - "anyio": { - "hashes": [ - "sha256:413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b", - "sha256:cb29b9c70620506a9a8f87a309591713446953302d7d995344d0d7c6c0c9a7be" - ], - "index": "pypi", - "markers": "python_full_version >= '3.6.2'", - "version": "==3.6.1" - }, - "asgiref": { - "hashes": [ - "sha256:89b2ef2247e3b562a16eef663bc0e2e703ec6468e2fa8a5cd61cd449786d4f6e", - "sha256:9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed" - ], - "markers": "python_version >= '3.7'", - "version": "==3.7.2" - }, - "click": { - "hashes": [ - "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28", - "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de" - ], - "markers": "python_version >= '3.7'", - "version": "==8.1.7" - }, - "fastapi": { - "hashes": [ - "sha256:644bb815bae326575c4b2842469fb83053a4b974b82fa792ff9283d17fbbd99d", - "sha256:94d2820906c36b9b8303796fb7271337ec89c74223229e3cfcf056b5a7d59e23" - ], - "index": "pypi", - "markers": "python_version >= '3.6'", - "version": "==0.68.1" - }, - "greenlet": { - "hashes": [ - "sha256:0a02d259510b3630f330c86557331a3b0e0c79dac3d166e449a39363beaae174", - "sha256:0b6f9f8ca7093fd4433472fd99b5650f8a26dcd8ba410e14094c1e44cd3ceddd", - 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+ "sha256:91089b2e281713f3893cd01d8e576771cd5bfdfbff5d0ed95969f47ef6d676c3", + "sha256:9c9e04a6cdb7a363d7cb3ccf0efea51e0abb48e180c0d31dca8d247967d85c6e", + "sha256:a8c5360a0297a713b4123608a7909e6869e1b56d0e96eb0d792c27585d40757f", + "sha256:afacf6d2a41ed91fc631bade88b1d319c51ab5418870802cedb590b709c5ae3c", + "sha256:b34ba24f3e2d0b39b43f0ca62008f7ba962cff51efa56e64ee25c4af6eed987b", + "sha256:bd67cb2c2d9602ad159389c29e4ca964b86fa2f35c2faef54c3eb28b4efd36c8", + "sha256:c0f5e142ef8217019e3eef6ae1b6b55f09a7a15972958d44fbd228214cede567", + "sha256:cdb4272678db803ddf94caa4f94f8672e9a46bae4a44f167095e4d06fec12979", + "sha256:d70916235d478404a3fa8c997b003b5f33aeac4686ac1baa767234a0f8ac2326", + "sha256:d8ce3fb0841763a89322ea0432f1f59a2d3feae07a63ea2c958b2315e1ae8adb", + "sha256:e0b214e57623a535936005797567231a12d0da0c29711eb3514bc2b3cd008d0f", + "sha256:e631c70c9280e3129f071635b81207cad85e6c08e253539467e4ead0e5b219aa", + "sha256:e78578f0c7481c850d1c969aca9a65405887003484d24f6110458fb02cca7747", + "sha256:f0ca86b525264daa5f6b192f216a0d1e860b7383e3da1c65a1908f9c02f42801", + "sha256:f1a68f4f65a9ee64b6ccccb5bf7e17db07caebd2730109cb8a95863cfa9c4e55", + "sha256:fafe841be1103f340a24977f61dee76172e4ae5f647ab9e7fd1e1fca51524f08", + "sha256:ff68fc85355532ea77559ede81f35fff79a6a5543477e168ab3a381887caea76" ], - "index": "pypi", "markers": "python_full_version >= '3.6.1'", - "version": "==1.8.2" + "version": "==1.9.2" }, "pydocstyle": { "hashes": [ @@ -826,7 +578,6 @@ "sha256:aae25dc1ebe97c420f50b81fb0e5c949659af713f31fdb63c749ca68748f34b1", "sha256:f521bc2ac9a8e03c736f62911605c5d83970021e3fa95b37d769e2bbbe9b6172" ], - "index": "pypi", "markers": "python_version >= '3.5'", "version": "==0.19.0" }, @@ -834,7 +585,6 @@ "hashes": [ "sha256:f7bb5f611fc600d15fa47b3974c8aa16e93724513b49b5f95c81e6624c83fa43" ], - "index": "pypi", "version": "==0.0.5" }, "requests": { @@ -865,7 +615,7 @@ "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926", "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==1.16.0" }, "sniffio": { @@ -921,7 +671,6 @@ "sha256:f7e4a3c0c3c596296b37f8427c467c8e4336dc8d50f8ed38042e8ba79507b2c9", "sha256:fff677fa4522dafb5a5e2c0cf909790d5d367326321aeabc0dffc9047cb235bd" ], - "index": "pypi", "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'", "version": "==1.4.32" }, @@ -947,7 +696,7 @@ "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc", "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f" ], - "markers": "python_version >= '3.7'", + "markers": "python_version < '3.11'", "version": "==2.0.1" }, "types-mock": { @@ -971,7 +720,6 @@ "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0", "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef" ], - "index": "pypi", "markers": "python_version >= '3.8'", "version": "==4.8.0" }, @@ -988,7 +736,6 @@ "sha256:2a76bb359171a504b3d1c853409af3adbfa5cef374a4a59e5881945a97a93eae", "sha256:45ad7dfaaa7d55cab4cd1e85e03f27e9d60bc067ddc59db52a2b0aeca8870292" ], - "index": "pypi", "version": "==0.14.0" }, "wsproto": { @@ -996,7 +743,6 @@ "sha256:868776f8456997ad0d9720f7322b746bbe9193751b5b290b7f924659377c8c38", "sha256:d8345d1808dd599b5ffb352c25a367adb6157e664e140dbecba3f9bc007edb9f" ], - "index": "pypi", "markers": "python_full_version >= '3.6.1'", "version": "==1.0.0" } diff --git a/server-utils/setup.py b/server-utils/setup.py index 555d60932be..2728aa4c86a 100755 --- a/server-utils/setup.py +++ b/server-utils/setup.py @@ -55,7 +55,7 @@ def get_version(): "fastapi==0.68.1", "python-dotenv==0.19.0", "python-multipart==0.0.5", - "pydantic==1.8.2", + "pydantic==1.9.2", "typing-extensions>=4.0.0,<5", "uvicorn==0.14.0", "wsproto==1.0.0", diff --git a/shared-data/python/Pipfile b/shared-data/python/Pipfile index ea1b637396c..3bc47618711 100644 --- a/shared-data/python/Pipfile +++ b/shared-data/python/Pipfile @@ -4,7 +4,7 @@ verify_ssl = true name = "pypi" [dev-packages] -mypy = "==0.942" +mypy = "==0.981" flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" diff --git a/shared-data/python/Pipfile.lock b/shared-data/python/Pipfile.lock index 67379b9bf39..13cfff4c0b2 100644 --- a/shared-data/python/Pipfile.lock +++ b/shared-data/python/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "799ae57c11b367011184ba5242ccc99ae3a5c6624d5732aef9611d564b944af0" + "sha256": "2d611ea3d172368c7ba5a2fbab4f113b2eef82b00b4d3b17bbc0f853df627a60" }, "pipfile-spec": 6, "requires": {}, @@ -36,31 +36,44 @@ }, "pydantic": { "hashes": [ - "sha256:021ea0e4133e8c824775a0cfe098677acf6fa5a3cbf9206a376eed3fc09302cd", - "sha256:05ddfd37c1720c392f4e0d43c484217b7521558302e7069ce8d318438d297739", 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"sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f" ], - "markers": "python_version < '3.11'", + "markers": "python_version >= '3.7'", "version": "==2.0.1" }, "twine": { diff --git a/shared-data/python/setup.py b/shared-data/python/setup.py index b5bd6eb8a1a..4dbcb119f69 100644 --- a/shared-data/python/setup.py +++ b/shared-data/python/setup.py @@ -146,7 +146,7 @@ def get_version(): INSTALL_REQUIRES = [ "jsonschema==3.0.2", "typing-extensions>=4.0.0,<5", - "pydantic==1.8.2", + "pydantic==1.9.2", ] diff --git a/system-server/Pipfile b/system-server/Pipfile index b90dd469298..dc6c390d9f8 100644 --- a/system-server/Pipfile +++ b/system-server/Pipfile @@ -8,12 +8,9 @@ fastapi = "==0.68.1" uvicorn = "==0.14.0" anyio = "==3.6.1" typing-extensions = ">=4.0.0,<5" -pyjwt = "==2.6.0" python-dotenv = "==0.19.0" python-multipart = "==0.0.5" -pydantic = "==1.8.2" -sqlalchemy = "==1.4.32" -systemd-python = { version = "==234", markers="sys_platform=='linux'" } +pydantic = "==1.9.2" importlib-metadata = ">=4.13.0,<5" server-utils = {editable = true, path = "./../server-utils"} system_server = {path = ".", editable = true} @@ -36,7 +33,7 @@ coverage = "==6.3" atomicwrites = { version = "==1.4.0", markers="sys_platform=='win32'" } colorama = { version = "==0.4.4", markers="sys_platform=='win32'" } sqlalchemy2-stubs = "==0.0.2a21" -mypy = "==0.942" +mypy = "==0.981" black = "==22.3.0" decoy = "~=1.10" mock = "~=4.0.3" diff --git a/system-server/Pipfile.lock b/system-server/Pipfile.lock index 7602be7cc64..32424cb43b7 100644 --- a/system-server/Pipfile.lock +++ b/system-server/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "804cbca0f9a88f27e082425ba1c72e682ebb16e700baf2b311bae763ac2ed397" + "sha256": "4707d9057be5081ab3f2a89b0d9e69d5951ad7a5204388394af2fb4f7c01e873" }, "pipfile-spec": 6, "requires": { @@ -118,7 +118,7 @@ "sha256:f89e21afe925fcfa655965ca8ea10f24773a1791400989ff32f467badfe4a064", "sha256:fa24255ae3c0ab67e613556375a4341af04a084bd58764731972bcbc8baeba36" ], - "markers": "python_version >= '3' and (platform_machine == 'aarch64' or (platform_machine == 'ppc64le' or (platform_machine == 'x86_64' or (platform_machine == 'amd64' or (platform_machine == 'AMD64' or (platform_machine == 'win32' or platform_machine == 'WIN32'))))))", + "markers": "python_version >= '3' and platform_machine == 'aarch64' or (platform_machine == 'ppc64le' or (platform_machine == 'x86_64' or (platform_machine == 'amd64' or (platform_machine == 'AMD64' or (platform_machine == 'win32' or platform_machine == 'WIN32')))))", "version": "==3.0.1" }, "h11": { @@ -148,39 +148,51 @@ }, "pydantic": { "hashes": [ - "sha256:021ea0e4133e8c824775a0cfe098677acf6fa5a3cbf9206a376eed3fc09302cd", - "sha256:05ddfd37c1720c392f4e0d43c484217b7521558302e7069ce8d318438d297739", - "sha256:05ef5246a7ffd2ce12a619cbb29f3307b7c4509307b1b49f456657b43529dc6f", - 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"sha256:fafe841be1103f340a24977f61dee76172e4ae5f647ab9e7fd1e1fca51524f08", + "sha256:ff68fc85355532ea77559ede81f35fff79a6a5543477e168ab3a381887caea76" ], "index": "pypi", "markers": "python_full_version >= '3.6.1'", - "version": "==1.8.2" + "version": "==1.9.2" }, "pyjwt": { "hashes": [ "sha256:69285c7e31fc44f68a1feb309e948e0df53259d579295e6cfe2b1792329f05fd", "sha256:d83c3d892a77bbb74d3e1a2cfa90afaadb60945205d1095d9221f04466f64c14" ], - "index": "pypi", "markers": "python_version >= '3.7'", "version": "==2.6.0" }, @@ -209,7 +221,7 @@ "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926", "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==1.16.0" }, "sniffio": { @@ -258,7 +270,6 @@ "sha256:f7e4a3c0c3c596296b37f8427c467c8e4336dc8d50f8ed38042e8ba79507b2c9", "sha256:fff677fa4522dafb5a5e2c0cf909790d5d367326321aeabc0dffc9047cb235bd" ], - "index": "pypi", "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'", "version": "==1.4.32" }, @@ -274,13 +285,6 @@ "editable": true, "path": "." }, - "systemd-python": { - "hashes": [ - "sha256:fd0e44bf70eadae45aadc292cb0a7eb5b0b6372cd1b391228047d33895db83e7" - ], - "markers": "sys_platform == 'linux'", - "version": "==234" - }, "typing-extensions": { "hashes": [ "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0", @@ -529,7 +533,7 @@ "sha256:b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9", "sha256:cdf6525904cc597730141d61b36f2e4b8ecc257c420fa2f4549bac2c2d0cb72f" ], - "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2'", + "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==0.10.0" }, "jsonschema": { @@ -557,33 +561,34 @@ }, "mypy": { "hashes": [ - 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"sha256:64e1f6af81c003f85f0dfed52db632817dabb51b65c0318ffbf5ff51995bbb08", + "sha256:6e35d764784b42c3e256848fb8ed1d4292c9fc0098413adb28d84974c095b279", + "sha256:6ee196b1d10b8b215e835f438e06965d7a480f6fe016eddbc285f13955cca659", + "sha256:756fad8b263b3ba39e4e204ee53042671b660c36c9017412b43af210ddee7b08", + "sha256:77f8fcf7b4b3cc0c74fb33ae54a4cd00bb854d65645c48beccf65fa10b17882c", + "sha256:794f385653e2b749387a42afb1e14c2135e18daeb027e0d97162e4b7031210f8", + "sha256:8ad21d4c9d3673726cf986ea1d0c9fb66905258709550ddf7944c8f885f208be", + "sha256:8e8e49aa9cc23aa4c926dc200ce32959d3501c4905147a66ce032f05cb5ecb92", + "sha256:9f362470a3480165c4c6151786b5379351b790d56952005be18bdbdd4c7ce0ae", + "sha256:a16a0145d6d7d00fbede2da3a3096dcc9ecea091adfa8da48fa6a7b75d35562d", + "sha256:ad77c13037d3402fbeffda07d51e3f228ba078d1c7096a73759c9419ea031bf4", + "sha256:b6ede64e52257931315826fdbfc6ea878d89a965580d1a65638ef77cb551f56d", + "sha256:c9e0efb95ed6ca1654951bd5ec2f3fa91b295d78bf6527e026529d4aaa1e0c30", + "sha256:ce65f70b14a21fdac84c294cde75e6dbdabbcff22975335e20827b3b94bdbf49", + "sha256:d1debb09043e1f5ee845fa1e96d180e89115b30e47c5d3ce53bc967bab53f62d", + "sha256:e178eaffc3c5cd211a87965c8c0df6da91ed7d258b5fc72b8e047c3771317ddb", + "sha256:e1acf62a8c4f7c092462c738aa2c2489e275ed386320c10b2e9bff31f6f7e8d6", + "sha256:e53773073c864d5f5cec7f3fc72fbbcef65410cde8cc18d4f7242dea60dac52e", + "sha256:eb3978b191b9fa0488524bb4ffedf2c573340e8c2b4206fc191d44c7093abfb7", + "sha256:f64d2ce043a209a297df322eb4054dfbaa9de9e8738291706eaafda81ab2b362", + "sha256:fa38f82f53e1e7beb45557ff167c177802ba7b387ad017eab1663d567017c8ee" ], "index": "pypi", - "markers": "python_version >= '3.6'", - "version": "==0.942" + "markers": "python_version >= '3.7'", + "version": "==0.981" }, "mypy-extensions": { "hashes": [ @@ -676,7 +681,6 @@ "sha256:69285c7e31fc44f68a1feb309e948e0df53259d579295e6cfe2b1792329f05fd", "sha256:d83c3d892a77bbb74d3e1a2cfa90afaadb60945205d1095d9221f04466f64c14" ], - "index": "pypi", "markers": "python_version >= '3.7'", "version": "==2.6.0" }, @@ -790,7 +794,7 @@ "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86", "sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==2.8.2" }, "pyyaml": { @@ -919,7 +923,7 @@ "sha256:f481f16baec5290e45aebdc2a5168ebc6d35189ae6fea7a58787613a25f6e875", "sha256:fff3573c2db359f091e1589c3d7c5fc2f86f5bdb6f24252c2d8e539d4e45f412" ], - "markers": "platform_python_implementation == 'CPython' and python_version < '3.13'", + "markers": "python_version < '3.13' and platform_python_implementation == 'CPython'", "version": "==0.2.8" }, "setuptools": { @@ -935,7 +939,7 @@ "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926", "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==1.16.0" }, "snowballstemmer": { @@ -975,7 +979,7 @@ "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc", "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f" ], - "markers": "python_version >= '3.7'", + "markers": "python_version < '3.11'", "version": "==2.0.1" }, "types-mock": { diff --git a/update-server/Pipfile b/update-server/Pipfile index 9e955ac4e7d..ef6739e8470 100644 --- a/update-server/Pipfile +++ b/update-server/Pipfile @@ -22,7 +22,7 @@ coverage = "==6.3.2" # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 atomicwrites = {version="==1.4.0", markers="sys_platform=='win32'"} colorama = {version="==0.4.4", markers="sys_platform=='win32'"} -mypy = "==0.942" +mypy = "==0.981" black = "==22.3.0" decoy = "~=1.10" diff --git a/update-server/Pipfile.lock b/update-server/Pipfile.lock index fec15cc480d..0cb4b8be550 100644 --- a/update-server/Pipfile.lock +++ b/update-server/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "f56a5bc2f30ea22c36819295de1a9dbe4f98866ce33209086a9c1df00ff6f2c5" + "sha256": "d158da946a995c0d41a424446a0b3b48283aa63a235d89af99a355550113e8ba" }, "pipfile-spec": 6, "requires": { @@ -277,33 +277,34 @@ }, "mypy": { "hashes": [ - "sha256:0e2dd88410937423fba18e57147dd07cd8381291b93d5b1984626f173a26543e", - "sha256:10daab80bc40f84e3f087d896cdb53dc811a9f04eae4b3f95779c26edee89d16", - "sha256:17e44649fec92e9f82102b48a3bf7b4a5510ad0cd22fa21a104826b5db4903e2", - "sha256:1a0459c333f00e6a11cbf6b468b870c2b99a906cb72d6eadf3d1d95d38c9352c", - "sha256:246e1aa127d5b78488a4a0594bd95f6d6fb9d63cf08a66dafbff8595d8891f67", - "sha256:2b184db8c618c43c3a31b32ff00cd28195d39e9c24e7c3b401f3db7f6e5767f5", - "sha256:2bc249409a7168d37c658e062e1ab5173300984a2dada2589638568ddc1db02b", - "sha256:3841b5433ff936bff2f4dc8d54cf2cdbfea5d8e88cedfac45c161368e5770ba6", - "sha256:4c3e497588afccfa4334a9986b56f703e75793133c4be3a02d06a3df16b67a58", - "sha256:5bf44840fb43ac4074636fd47ee476d73f0039f4f54e86d7265077dc199be24d", - "sha256:64235137edc16bee6f095aba73be5334677d6f6bdb7fa03cfab90164fa294a17", - "sha256:6776e5fa22381cc761df53e7496a805801c1a751b27b99a9ff2f0ca848c7eca0", - "sha256:6ce34a118d1a898f47def970a2042b8af6bdcc01546454726c7dd2171aa6dfca", - "sha256:6f6ad963172152e112b87cc7ec103ba0f2db2f1cd8997237827c052a3903eaa6", - "sha256:6f7106cbf9cc2f403693bf50ed7c9fa5bb3dfa9007b240db3c910929abe2a322", - "sha256:7742d2c4e46bb5017b51c810283a6a389296cda03df805a4f7869a6f41246534", - "sha256:9521c1265ccaaa1791d2c13582f06facf815f426cd8b07c3a485f486a8ffc1f3", - "sha256:a1b383fe99678d7402754fe90448d4037f9512ce70c21f8aee3b8bf48ffc51db", - "sha256:b840cfe89c4ab6386c40300689cd8645fc8d2d5f20101c7f8bd23d15fca14904", - "sha256:d8d3ba77e56b84cd47a8ee45b62c84b6d80d32383928fe2548c9a124ea0a725c", - "sha256:dcd955f36e0180258a96f880348fbca54ce092b40fbb4b37372ae3b25a0b0a46", - "sha256:e865fec858d75b78b4d63266c9aff770ecb6a39dfb6d6b56c47f7f8aba6baba8", - "sha256:edf7237137a1a9330046dbb14796963d734dd740a98d5e144a3eb1d267f5f9ee" + "sha256:06e1eac8d99bd404ed8dd34ca29673c4346e76dd8e612ea507763dccd7e13c7a", + "sha256:2ee3dbc53d4df7e6e3b1c68ac6a971d3a4fb2852bf10a05fda228721dd44fae1", + "sha256:4bc460e43b7785f78862dab78674e62ec3cd523485baecfdf81a555ed29ecfa0", + "sha256:64e1f6af81c003f85f0dfed52db632817dabb51b65c0318ffbf5ff51995bbb08", + "sha256:6e35d764784b42c3e256848fb8ed1d4292c9fc0098413adb28d84974c095b279", + "sha256:6ee196b1d10b8b215e835f438e06965d7a480f6fe016eddbc285f13955cca659", + "sha256:756fad8b263b3ba39e4e204ee53042671b660c36c9017412b43af210ddee7b08", + "sha256:77f8fcf7b4b3cc0c74fb33ae54a4cd00bb854d65645c48beccf65fa10b17882c", + "sha256:794f385653e2b749387a42afb1e14c2135e18daeb027e0d97162e4b7031210f8", + "sha256:8ad21d4c9d3673726cf986ea1d0c9fb66905258709550ddf7944c8f885f208be", + "sha256:8e8e49aa9cc23aa4c926dc200ce32959d3501c4905147a66ce032f05cb5ecb92", + "sha256:9f362470a3480165c4c6151786b5379351b790d56952005be18bdbdd4c7ce0ae", + "sha256:a16a0145d6d7d00fbede2da3a3096dcc9ecea091adfa8da48fa6a7b75d35562d", + "sha256:ad77c13037d3402fbeffda07d51e3f228ba078d1c7096a73759c9419ea031bf4", + "sha256:b6ede64e52257931315826fdbfc6ea878d89a965580d1a65638ef77cb551f56d", + "sha256:c9e0efb95ed6ca1654951bd5ec2f3fa91b295d78bf6527e026529d4aaa1e0c30", + "sha256:ce65f70b14a21fdac84c294cde75e6dbdabbcff22975335e20827b3b94bdbf49", + "sha256:d1debb09043e1f5ee845fa1e96d180e89115b30e47c5d3ce53bc967bab53f62d", + "sha256:e178eaffc3c5cd211a87965c8c0df6da91ed7d258b5fc72b8e047c3771317ddb", + "sha256:e1acf62a8c4f7c092462c738aa2c2489e275ed386320c10b2e9bff31f6f7e8d6", + "sha256:e53773073c864d5f5cec7f3fc72fbbcef65410cde8cc18d4f7242dea60dac52e", + "sha256:eb3978b191b9fa0488524bb4ffedf2c573340e8c2b4206fc191d44c7093abfb7", + "sha256:f64d2ce043a209a297df322eb4054dfbaa9de9e8738291706eaafda81ab2b362", + "sha256:fa38f82f53e1e7beb45557ff167c177802ba7b387ad017eab1663d567017c8ee" ], "index": "pypi", - "markers": "python_version >= '3.6'", - "version": "==0.942" + "markers": "python_version >= '3.7'", + "version": "==0.981" }, "mypy-extensions": { "hashes": [ @@ -426,7 +427,7 @@ "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc", "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f" ], - "markers": "python_version >= '3.7'", + "markers": "python_version < '3.11'", "version": "==2.0.1" }, "typing-extensions": { diff --git a/usb-bridge/Pipfile b/usb-bridge/Pipfile index 969f7793f3d..992d36a32b6 100644 --- a/usb-bridge/Pipfile +++ b/usb-bridge/Pipfile @@ -27,7 +27,7 @@ coverage = "==6.2" # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 atomicwrites = {version="==1.4.0", markers="sys_platform=='win32'"} colorama = {version="==0.4.4", markers="sys_platform=='win32'"} -mypy = "==0.942" +mypy = "==0.981" black = "==22.3.0" decoy = "~=1.10" mock = "~=4.0.3" diff --git a/usb-bridge/Pipfile.lock b/usb-bridge/Pipfile.lock index 19c50bd893f..58e4e5df515 100644 --- a/usb-bridge/Pipfile.lock +++ b/usb-bridge/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "568e6f27764e2c9c65b2deadc3ac1d8a72806ace02d5cfb8c7f1ec3b6dd50cdd" + "sha256": "adbb22a527580a6b606220ad427fc699d6e46a1507ddfc0f325720c6ded1e2cb" }, "pipfile-spec": 6, "requires": { @@ -37,7 +37,7 @@ "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926", "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==1.16.0" }, "typing-extensions": { @@ -503,33 +503,34 @@ }, "mypy": { "hashes": [ - "sha256:0e2dd88410937423fba18e57147dd07cd8381291b93d5b1984626f173a26543e", - "sha256:10daab80bc40f84e3f087d896cdb53dc811a9f04eae4b3f95779c26edee89d16", - "sha256:17e44649fec92e9f82102b48a3bf7b4a5510ad0cd22fa21a104826b5db4903e2", - "sha256:1a0459c333f00e6a11cbf6b468b870c2b99a906cb72d6eadf3d1d95d38c9352c", - "sha256:246e1aa127d5b78488a4a0594bd95f6d6fb9d63cf08a66dafbff8595d8891f67", - "sha256:2b184db8c618c43c3a31b32ff00cd28195d39e9c24e7c3b401f3db7f6e5767f5", - "sha256:2bc249409a7168d37c658e062e1ab5173300984a2dada2589638568ddc1db02b", - "sha256:3841b5433ff936bff2f4dc8d54cf2cdbfea5d8e88cedfac45c161368e5770ba6", - "sha256:4c3e497588afccfa4334a9986b56f703e75793133c4be3a02d06a3df16b67a58", - "sha256:5bf44840fb43ac4074636fd47ee476d73f0039f4f54e86d7265077dc199be24d", - "sha256:64235137edc16bee6f095aba73be5334677d6f6bdb7fa03cfab90164fa294a17", - "sha256:6776e5fa22381cc761df53e7496a805801c1a751b27b99a9ff2f0ca848c7eca0", - "sha256:6ce34a118d1a898f47def970a2042b8af6bdcc01546454726c7dd2171aa6dfca", - "sha256:6f6ad963172152e112b87cc7ec103ba0f2db2f1cd8997237827c052a3903eaa6", - "sha256:6f7106cbf9cc2f403693bf50ed7c9fa5bb3dfa9007b240db3c910929abe2a322", - "sha256:7742d2c4e46bb5017b51c810283a6a389296cda03df805a4f7869a6f41246534", - "sha256:9521c1265ccaaa1791d2c13582f06facf815f426cd8b07c3a485f486a8ffc1f3", - "sha256:a1b383fe99678d7402754fe90448d4037f9512ce70c21f8aee3b8bf48ffc51db", - "sha256:b840cfe89c4ab6386c40300689cd8645fc8d2d5f20101c7f8bd23d15fca14904", - "sha256:d8d3ba77e56b84cd47a8ee45b62c84b6d80d32383928fe2548c9a124ea0a725c", - "sha256:dcd955f36e0180258a96f880348fbca54ce092b40fbb4b37372ae3b25a0b0a46", - "sha256:e865fec858d75b78b4d63266c9aff770ecb6a39dfb6d6b56c47f7f8aba6baba8", - "sha256:edf7237137a1a9330046dbb14796963d734dd740a98d5e144a3eb1d267f5f9ee" + "sha256:06e1eac8d99bd404ed8dd34ca29673c4346e76dd8e612ea507763dccd7e13c7a", + "sha256:2ee3dbc53d4df7e6e3b1c68ac6a971d3a4fb2852bf10a05fda228721dd44fae1", + "sha256:4bc460e43b7785f78862dab78674e62ec3cd523485baecfdf81a555ed29ecfa0", + "sha256:64e1f6af81c003f85f0dfed52db632817dabb51b65c0318ffbf5ff51995bbb08", + "sha256:6e35d764784b42c3e256848fb8ed1d4292c9fc0098413adb28d84974c095b279", + "sha256:6ee196b1d10b8b215e835f438e06965d7a480f6fe016eddbc285f13955cca659", + "sha256:756fad8b263b3ba39e4e204ee53042671b660c36c9017412b43af210ddee7b08", + "sha256:77f8fcf7b4b3cc0c74fb33ae54a4cd00bb854d65645c48beccf65fa10b17882c", + "sha256:794f385653e2b749387a42afb1e14c2135e18daeb027e0d97162e4b7031210f8", + "sha256:8ad21d4c9d3673726cf986ea1d0c9fb66905258709550ddf7944c8f885f208be", + "sha256:8e8e49aa9cc23aa4c926dc200ce32959d3501c4905147a66ce032f05cb5ecb92", + "sha256:9f362470a3480165c4c6151786b5379351b790d56952005be18bdbdd4c7ce0ae", + "sha256:a16a0145d6d7d00fbede2da3a3096dcc9ecea091adfa8da48fa6a7b75d35562d", + "sha256:ad77c13037d3402fbeffda07d51e3f228ba078d1c7096a73759c9419ea031bf4", + "sha256:b6ede64e52257931315826fdbfc6ea878d89a965580d1a65638ef77cb551f56d", + "sha256:c9e0efb95ed6ca1654951bd5ec2f3fa91b295d78bf6527e026529d4aaa1e0c30", + "sha256:ce65f70b14a21fdac84c294cde75e6dbdabbcff22975335e20827b3b94bdbf49", + "sha256:d1debb09043e1f5ee845fa1e96d180e89115b30e47c5d3ce53bc967bab53f62d", + "sha256:e178eaffc3c5cd211a87965c8c0df6da91ed7d258b5fc72b8e047c3771317ddb", + "sha256:e1acf62a8c4f7c092462c738aa2c2489e275ed386320c10b2e9bff31f6f7e8d6", + "sha256:e53773073c864d5f5cec7f3fc72fbbcef65410cde8cc18d4f7242dea60dac52e", + "sha256:eb3978b191b9fa0488524bb4ffedf2c573340e8c2b4206fc191d44c7093abfb7", + "sha256:f64d2ce043a209a297df322eb4054dfbaa9de9e8738291706eaafda81ab2b362", + "sha256:fa38f82f53e1e7beb45557ff167c177802ba7b387ad017eab1663d567017c8ee" ], "index": "pypi", - "markers": "python_version >= '3.6'", - "version": "==0.942" + "markers": "python_version >= '3.7'", + "version": "==0.981" }, "mypy-extensions": { "hashes": [ @@ -694,7 +695,7 @@ "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc", "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f" ], - "markers": "python_version >= '3.7'", + "markers": "python_version < '3.11'", "version": "==2.0.1" }, "types-mock": { From bc89b9ef4f43ef77f1f865cae470c9e734629424 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Thu, 7 Dec 2023 17:14:51 -0500 Subject: [PATCH 21/60] api typing fixups after updates --- api/src/opentrons/_version.py | 2 +- .../drivers/smoothie_drivers/driver_3_0.py | 4 +- .../opentrons/hardware_control/adapters.py | 5 +- api/src/opentrons/hardware_control/api.py | 4 +- .../backends/ot3controller.py | 4 +- .../hardware_control/backends/ot3simulator.py | 4 +- .../hardware_control/execution_manager.py | 8 ++- .../instruments/ot2/instrument_calibration.py | 21 +++--- .../instruments/ot3/instrument_calibration.py | 23 ++++--- .../hardware_control/ot3_calibration.py | 8 +-- .../hardware_control/robot_calibration.py | 4 +- .../core/legacy/module_geometry.py | 2 +- .../protocol_api/instrument_context.py | 66 +++++++++--------- api/src/opentrons/protocol_api/labware.py | 44 ++++++------ .../opentrons/protocol_api/module_contexts.py | 68 +++++++++---------- .../protocol_api/protocol_context.py | 20 +++--- .../protocol_engine/state/geometry.py | 2 +- .../protocol_engine/state/modules.py | 2 +- api/src/opentrons/simulate.py | 2 +- api/src/opentrons/system/wifi.py | 16 ++++- api/src/opentrons/types.py | 24 ++++--- api/src/opentrons/util/linal.py | 12 ++-- .../opentrons/config/test_defaults_ot2.py | 7 +- api/tests/opentrons/conftest.py | 4 +- .../test_instrument_calibration.py | 10 +-- .../core/simulator/conftest.py | 4 +- .../protocol_api_old/test_context.py | 4 +- api/tests/opentrons/system/test_wifi.py | 8 +-- api/tests/opentrons/util/test_linal.py | 4 +- 29 files changed, 204 insertions(+), 182 deletions(-) diff --git a/api/src/opentrons/_version.py b/api/src/opentrons/_version.py index 385f024a111..6b26eac4ce5 100644 --- a/api/src/opentrons/_version.py +++ b/api/src/opentrons/_version.py @@ -9,7 +9,7 @@ import importlib_metadata as metadata # type: ignore[no-redef] try: - version: str = metadata.version("opentrons") # type: ignore[attr-defined] + version: str = metadata.version("opentrons") except Exception as e: logging.warning( "Could not determine version for opentrons, may be dev install, using 0.0.0-dev" diff --git a/api/src/opentrons/drivers/smoothie_drivers/driver_3_0.py b/api/src/opentrons/drivers/smoothie_drivers/driver_3_0.py index 93a0816db8c..c9958691e16 100755 --- a/api/src/opentrons/drivers/smoothie_drivers/driver_3_0.py +++ b/api/src/opentrons/drivers/smoothie_drivers/driver_3_0.py @@ -1667,7 +1667,7 @@ async def unstick_axes( self.push_active_current() self.set_active_current( { - ax: self._config.high_current["default"][ax] # type: ignore[misc] + ax: self._config.high_current["default"][ax] # type: ignore[literal-required] for ax in axes } ) @@ -1848,7 +1848,7 @@ async def hard_halt(self) -> None: await asyncio.sleep(0.25) self.run_flag.set() - async def update_firmware( # noqa: C901 + async def update_firmware( self, filename: str, loop: Optional[asyncio.AbstractEventLoop] = None, diff --git a/api/src/opentrons/hardware_control/adapters.py b/api/src/opentrons/hardware_control/adapters.py index 330734fc6f0..4497da88bf8 100644 --- a/api/src/opentrons/hardware_control/adapters.py +++ b/api/src/opentrons/hardware_control/adapters.py @@ -2,13 +2,12 @@ """ import asyncio import functools -from typing import Generic, TypeVar, Callable, Any, cast +from typing import Generic, TypeVar, Callable, Any, cast, Awaitable from .protocols import AsyncioConfigurable WrappedObj = TypeVar("WrappedObj", bound=AsyncioConfigurable, covariant=True) WrappedReturn = TypeVar("WrappedReturn") -WrappedFunc = TypeVar("WrappedFunc", bound=Callable[..., WrappedReturn]) # TODO: BC 2020-02-25 instead of overwriting __get_attribute__ in this class @@ -54,7 +53,7 @@ def __repr__(self) -> str: @staticmethod def call_coroutine_sync( loop: asyncio.AbstractEventLoop, - to_call: WrappedFunc, + to_call: Callable[..., Awaitable[WrappedReturn]], *args: Any, **kwargs: Any, ) -> WrappedReturn: diff --git a/api/src/opentrons/hardware_control/api.py b/api/src/opentrons/hardware_control/api.py index 92971e43d27..11445f3a525 100644 --- a/api/src/opentrons/hardware_control/api.py +++ b/api/src/opentrons/hardware_control/api.py @@ -167,8 +167,8 @@ def _update_door_state(self, door_state: DoorState) -> None: def _reset_last_mount(self) -> None: self._last_moved_mount = None - @classmethod # noqa: C901 - async def build_hardware_controller( + @classmethod + async def build_hardware_controller( # noqa: C901 cls, config: Union[RobotConfig, OT3Config, None] = None, port: Optional[str] = None, diff --git a/api/src/opentrons/hardware_control/backends/ot3controller.py b/api/src/opentrons/hardware_control/backends/ot3controller.py index c212b81b6b4..8d96014483e 100644 --- a/api/src/opentrons/hardware_control/backends/ot3controller.py +++ b/api/src/opentrons/hardware_control/backends/ot3controller.py @@ -971,8 +971,8 @@ async def set_hold_current(self, axis_currents: OT3AxisMap[float]) -> None: @asynccontextmanager async def motor_current( self, - run_currents: OT3AxisMap[float] = {}, - hold_currents: OT3AxisMap[float] = {}, + run_currents: Optional[OT3AxisMap[float]] = None, + hold_currents: Optional[OT3AxisMap[float]] = None, ) -> AsyncIterator[None]: """Update and restore current.""" assert self._current_settings diff --git a/api/src/opentrons/hardware_control/backends/ot3simulator.py b/api/src/opentrons/hardware_control/backends/ot3simulator.py index db5f2cdc8bb..2cd8c1a37ec 100644 --- a/api/src/opentrons/hardware_control/backends/ot3simulator.py +++ b/api/src/opentrons/hardware_control/backends/ot3simulator.py @@ -543,8 +543,8 @@ async def set_active_current(self, axis_currents: OT3AxisMap[float]) -> None: @asynccontextmanager async def motor_current( self, - run_currents: OT3AxisMap[float] = {}, - hold_currents: OT3AxisMap[float] = {}, + run_currents: Optional[OT3AxisMap[float]] = None, + hold_currents: Optional[OT3AxisMap[float]] = None, ) -> AsyncIterator[None]: """Save the current.""" yield diff --git a/api/src/opentrons/hardware_control/execution_manager.py b/api/src/opentrons/hardware_control/execution_manager.py index 5ad0f45912c..de7725f819c 100644 --- a/api/src/opentrons/hardware_control/execution_manager.py +++ b/api/src/opentrons/hardware_control/execution_manager.py @@ -1,8 +1,9 @@ import asyncio import functools -from typing import Set, TypeVar, Type, cast, Callable, Any, Awaitable, overload +from typing import Set, TypeVar, Type, cast, Callable, Any, overload from .types import ExecutionState from opentrons_shared_data.errors.exceptions import ExecutionCancelledError +from collections.abc import Coroutine TaskContents = TypeVar("TaskContents") @@ -74,10 +75,11 @@ async def wait_for_is_running(self) -> None: DecoratedReturn = TypeVar("DecoratedReturn") DecoratedMethodReturningValue = TypeVar( - "DecoratedMethodReturningValue", bound=Callable[..., Awaitable[DecoratedReturn]] + "DecoratedMethodReturningValue", + bound=Callable[..., Coroutine[None, None, DecoratedReturn]], ) DecoratedMethodNoReturn = TypeVar( - "DecoratedMethodNoReturn", bound=Callable[..., Awaitable[None]] + "DecoratedMethodNoReturn", bound=Callable[..., Coroutine[None, None, None]] ) SubclassInstance = TypeVar("SubclassInstance", bound="ExecutionManagerProvider") diff --git a/api/src/opentrons/hardware_control/instruments/ot2/instrument_calibration.py b/api/src/opentrons/hardware_control/instruments/ot2/instrument_calibration.py index f296f390a38..29900d68a6d 100644 --- a/api/src/opentrons/hardware_control/instruments/ot2/instrument_calibration.py +++ b/api/src/opentrons/hardware_control/instruments/ot2/instrument_calibration.py @@ -17,6 +17,11 @@ LabwareDefinition as TypeDictLabwareDef, ) +# These type aliases aid typechecking in tests that work the same on this and +# the hardware_control.instruments.ot3 variant +SourceType = types.SourceType +CalibrationStatus = types.CalibrationStatus + @dataclass class PipetteOffsetByPipetteMount: @@ -25,8 +30,8 @@ class PipetteOffsetByPipetteMount: """ offset: Point - source: types.SourceType - status: types.CalibrationStatus + source: SourceType + status: CalibrationStatus tiprack: typing.Optional[str] = None uri: typing.Optional[str] = None last_modified: typing.Optional[datetime] = None @@ -44,15 +49,15 @@ class PipetteOffsetCalibration: tiprack: str uri: str last_modified: datetime - source: types.SourceType - status: types.CalibrationStatus + source: SourceType + status: CalibrationStatus @dataclass class TipLengthCalibration: tip_length: float - source: types.SourceType - status: types.CalibrationStatus + source: SourceType + status: CalibrationStatus pipette: str tiprack: str last_modified: datetime @@ -65,8 +70,8 @@ def load_pipette_offset( # load default if pipette offset data do not exist pip_cal_obj = PipetteOffsetByPipetteMount( offset=Point(*default_pipette_offset()), - source=types.SourceType.default, - status=types.CalibrationStatus(), + source=SourceType.default, + status=CalibrationStatus(), ) # TODO this can be removed once we switch to using # ot3 pipette types in the ot3 hardware controller. diff --git a/api/src/opentrons/hardware_control/instruments/ot3/instrument_calibration.py b/api/src/opentrons/hardware_control/instruments/ot3/instrument_calibration.py index d42ae38b779..7e7352170b9 100644 --- a/api/src/opentrons/hardware_control/instruments/ot3/instrument_calibration.py +++ b/api/src/opentrons/hardware_control/instruments/ot3/instrument_calibration.py @@ -23,6 +23,11 @@ PIPETTE_OFFSET_CONSISTENCY_LIMIT: Final = 1.5 +# These type aliases aid typechecking in tests that work the same on this and +# the hardware_control.instruments.ot2 variant +SourceType = cal_top_types.SourceType +CalibrationStatus = cal_top_types.CalibrationStatus + @dataclass class InconsistentPipetteOffsets: @@ -41,8 +46,8 @@ class PipetteOffsetByPipetteMount: """ offset: Point - source: cal_top_types.SourceType - status: cal_top_types.CalibrationStatus + source: SourceType + status: CalibrationStatus last_modified: typing.Optional[datetime] = None @@ -63,8 +68,8 @@ class GripperCalibrationOffset: """ offset: Point - source: cal_top_types.SourceType - status: cal_top_types.CalibrationStatus + source: SourceType + status: CalibrationStatus last_modified: typing.Optional[datetime] = None @@ -74,8 +79,8 @@ def load_pipette_offset( # load default if pipette offset data do not exist pip_cal_obj = PipetteOffsetByPipetteMount( offset=Point(*default_pipette_offset()), - source=cal_top_types.SourceType.default, - status=cal_top_types.CalibrationStatus(), + source=SourceType.default, + status=CalibrationStatus(), ) # TODO this can be removed once we switch to using # ot3 pipette types in the ot3 hardware controller. @@ -90,7 +95,7 @@ def load_pipette_offset( offset=pip_offset_data.offset, last_modified=pip_offset_data.lastModified, source=pip_offset_data.source, - status=cal_top_types.CalibrationStatus( + status=CalibrationStatus( markedAt=pip_offset_data.status.markedAt, markedBad=pip_offset_data.status.markedBad, source=pip_offset_data.status.source, @@ -118,8 +123,8 @@ def load_gripper_calibration_offset( # load default if gripper offset data do not exist grip_cal_obj = GripperCalibrationOffset( offset=Point(*default_gripper_calibration_offset()), - source=cal_top_types.SourceType.default, - status=cal_top_types.CalibrationStatus(), + source=SourceType.default, + status=CalibrationStatus(), ) if gripper_id and ff.enable_ot3_hardware_controller(): grip_offset_data = gripper_offset.get_gripper_calibration_offset(gripper_id) diff --git a/api/src/opentrons/hardware_control/ot3_calibration.py b/api/src/opentrons/hardware_control/ot3_calibration.py index 37a10522a93..6c63b3d68d9 100644 --- a/api/src/opentrons/hardware_control/ot3_calibration.py +++ b/api/src/opentrons/hardware_control/ot3_calibration.py @@ -42,8 +42,8 @@ ) from opentrons.config.robot_configs import ( default_ot3_deck_calibration, - defaults_ot3, ) +from opentrons.config import defaults_ot3 from .util import DeckTransformState if TYPE_CHECKING: @@ -477,7 +477,7 @@ def _edges_from_data( # an N-sample rolling average. by inverting the sign of half the kernel, which is # why we need it to be even, we do the same thing but while also taking a finite # difference. - average_difference_kernel = np.concatenate( # type: ignore + average_difference_kernel = np.concatenate( ( np.full(average_width_samples // 2, 1 / average_width_samples), np.full(average_width_samples // 2, -1 / average_width_samples), @@ -954,7 +954,7 @@ def apply_machine_transform( """ belt_attitude_arr = np.array(belt_attitude) machine_transform_arr = np.array(defaults_ot3.DEFAULT_MACHINE_TRANSFORM) - deck_attitude_arr = np.dot(belt_attitude_arr, machine_transform_arr) # type: ignore[no-untyped-call] + deck_attitude_arr = np.dot(belt_attitude_arr, machine_transform_arr) deck_attitude = deck_attitude_arr.round(4).tolist() return deck_attitude # type: ignore[no-any-return] @@ -993,7 +993,7 @@ def validate_attitude_deck_calibration( """ curr_cal = np.array(deck_cal.attitude) row, _ = curr_cal.shape - rank: int = np.linalg.matrix_rank(curr_cal) # type: ignore + rank: int = np.linalg.matrix_rank(curr_cal) if row != rank: # Check that the matrix is non-singular return DeckTransformState.SINGULARITY diff --git a/api/src/opentrons/hardware_control/robot_calibration.py b/api/src/opentrons/hardware_control/robot_calibration.py index 1c776bffbdc..0d0f00f2479 100644 --- a/api/src/opentrons/hardware_control/robot_calibration.py +++ b/api/src/opentrons/hardware_control/robot_calibration.py @@ -51,7 +51,7 @@ def validate_attitude_deck_calibration( """ curr_cal = np.array(deck_cal.attitude) row, _ = curr_cal.shape - rank: int = np.linalg.matrix_rank(curr_cal) # type: ignore + rank: int = np.linalg.matrix_rank(curr_cal) if row != rank: # Check that the matrix is non-singular return DeckTransformState.SINGULARITY @@ -71,7 +71,7 @@ def validate_gantry_calibration(gantry_cal: List[List[float]]) -> DeckTransformS curr_cal = np.array(gantry_cal) row, _ = curr_cal.shape - rank: int = np.linalg.matrix_rank(curr_cal) # type: ignore + rank: int = np.linalg.matrix_rank(curr_cal) id_matrix = linal.identity_deck_transform() diff --git a/api/src/opentrons/protocol_api/core/legacy/module_geometry.py b/api/src/opentrons/protocol_api/core/legacy/module_geometry.py index 234a36fdc9a..e5a1fc28f89 100644 --- a/api/src/opentrons/protocol_api/core/legacy/module_geometry.py +++ b/api/src/opentrons/protocol_api/core/legacy/module_geometry.py @@ -463,7 +463,7 @@ def create_geometry( # apply the slot transform if any xform = np.array(xform_ser) - xformed = np.dot(xform, pre_transform) # type: ignore[no-untyped-call] + xformed = np.dot(xform, pre_transform) module_type = ModuleType(definition["moduleType"]) if module_type == ModuleType.MAGNETIC or module_type == ModuleType.TEMPERATURE: diff --git a/api/src/opentrons/protocol_api/instrument_context.py b/api/src/opentrons/protocol_api/instrument_context.py index 0a1743e382f..d3cd6777fda 100644 --- a/api/src/opentrons/protocol_api/instrument_context.py +++ b/api/src/opentrons/protocol_api/instrument_context.py @@ -1,7 +1,7 @@ from __future__ import annotations import logging -from contextlib import nullcontext +from contextlib import ExitStack from typing import Any, List, Optional, Sequence, Union, cast, Dict from opentrons_shared_data.errors.exceptions import ( CommandPreconditionViolated, @@ -107,12 +107,12 @@ def __init__( ] = trash self.requested_as = requested_as - @property # type: ignore + @property @requires_version(2, 0) def api_version(self) -> APIVersion: return self._api_version - @property # type: ignore + @property @requires_version(2, 0) def starting_tip(self) -> Union[labware.Well, None]: """ @@ -140,7 +140,7 @@ def reset_tipracks(self) -> None: tiprack.reset() self.starting_tip = None - @property # type: ignore[misc] + @property @requires_version(2, 0) def default_speed(self) -> float: """The speed at which the robot's gantry moves in mm/s. @@ -748,8 +748,8 @@ def return_tip(self, home_after: Optional[bool] = None) -> InstrumentContext: return self - @requires_version(2, 0) # noqa: C901 - def pick_up_tip( + @requires_version(2, 0) + def pick_up_tip( # noqa: C901 self, location: Union[types.Location, labware.Well, labware.Labware, None] = None, presses: Optional[int] = None, @@ -1155,9 +1155,9 @@ def consolidate( return self.transfer(volume, source, dest, **kwargs) - @publisher.publish(command=cmds.transfer) # noqa: C901 + @publisher.publish(command=cmds.transfer) @requires_version(2, 0) - def transfer( + def transfer( # noqa: C901 self, volume: Union[float, Sequence[float]], source: AdvancedLiquidHandling, @@ -1416,7 +1416,6 @@ def move_to( :param publish: Whether to list this function call in the run preview. Default is ``True``. """ - publish_ctx = nullcontext() if isinstance(location, (TrashBin, WasteChute)): self._core.move_to( @@ -1429,12 +1428,15 @@ def move_to( # TODO handle publish return self - if publish: - publish_ctx = publisher.publish_context( - broker=self.broker, - command=cmds.move_to(instrument=self, location=location), - ) - with publish_ctx: + with ExitStack() as contexts: + if publish: + contexts.enter_context( + publisher.publish_context( + broker=self.broker, + command=cmds.move_to(instrument=self, location=location), + ) + ) + _, well = location.labware.get_parent_labware_and_well() self._core.move_to( @@ -1447,7 +1449,7 @@ def move_to( return self - @property # type: ignore + @property @requires_version(2, 0) def mount(self) -> str: """ @@ -1457,7 +1459,7 @@ def mount(self) -> str: """ return self._core.get_mount().name.lower() - @property # type: ignore + @property @requires_version(2, 0) def speed(self) -> "PlungerSpeeds": """The speeds (in mm/s) configured for the pipette plunger. @@ -1485,7 +1487,7 @@ def speed(self) -> "PlungerSpeeds": assert isinstance(self._core, LegacyInstrumentCore) return cast(LegacyInstrumentCore, self._core).get_speed() - @property # type: ignore + @property @requires_version(2, 0) def flow_rate(self) -> "FlowRates": """The speeds, in µL/s, configured for the pipette. @@ -1502,7 +1504,7 @@ def flow_rate(self) -> "FlowRates": """ return self._core.get_flow_rate() - @property # type: ignore + @property @requires_version(2, 0) def type(self) -> str: """``'single'`` if this is a 1-channel pipette, or ``'multi'`` otherwise. @@ -1515,7 +1517,7 @@ def type(self) -> str: else: return "multi" - @property # type: ignore + @property @requires_version(2, 0) def tip_racks(self) -> List[labware.Labware]: """ @@ -1530,7 +1532,7 @@ def tip_racks(self) -> List[labware.Labware]: def tip_racks(self, racks: List[labware.Labware]) -> None: self._tip_racks = racks - @property # type: ignore + @property @requires_version(2, 0) def trash_container(self) -> Union[labware.Labware, TrashBin, WasteChute]: """The trash container associated with this pipette. @@ -1565,7 +1567,7 @@ def trash_container( ) -> None: self._user_specified_trash = trash - @property # type: ignore + @property @requires_version(2, 0) def name(self) -> str: """ @@ -1573,7 +1575,7 @@ def name(self) -> str: """ return self._core.get_pipette_name() - @property # type: ignore + @property @requires_version(2, 0) def model(self) -> str: """ @@ -1581,7 +1583,7 @@ def model(self) -> str: """ return self._core.get_model() - @property # type: ignore + @property @requires_version(2, 0) def min_volume(self) -> float: """ @@ -1591,7 +1593,7 @@ def min_volume(self) -> float: """ return self._core.get_min_volume() - @property # type: ignore + @property @requires_version(2, 0) def max_volume(self) -> float: """ @@ -1604,7 +1606,7 @@ def max_volume(self) -> float: """ return self._core.get_max_volume() - @property # type: ignore + @property @requires_version(2, 0) def current_volume(self) -> float: """ @@ -1612,7 +1614,7 @@ def current_volume(self) -> float: """ return self._core.get_current_volume() - @property # type: ignore + @property @requires_version(2, 7) def has_tip(self) -> bool: """Whether this instrument has a tip attached or not. @@ -1631,7 +1633,7 @@ def _has_tip(self) -> bool: """ return self._core.has_tip() - @property # type: ignore + @property @requires_version(2, 0) def hw_pipette(self) -> PipetteDict: """View the information returned by the hardware API directly. @@ -1641,7 +1643,7 @@ def hw_pipette(self) -> PipetteDict: """ return self._core.get_hardware_state() - @property # type: ignore + @property @requires_version(2, 0) def channels(self) -> int: """The number of channels on the pipette. @@ -1652,7 +1654,7 @@ def channels(self) -> int: """ return self._core.get_channels() - @property # type: ignore + @property @requires_version(2, 16) def active_channels(self) -> int: """The number of channels the pipette will use to pick up tips. @@ -1662,7 +1664,7 @@ def active_channels(self) -> int: """ return self._core.get_active_channels() - @property # type: ignore + @property @requires_version(2, 2) def return_height(self) -> float: """The height to return a tip to its tip rack. @@ -1673,7 +1675,7 @@ def return_height(self) -> float: """ return self._core.get_return_height() - @property # type: ignore + @property @requires_version(2, 0) def well_bottom_clearance(self) -> "Clearances": """The distance above the bottom of a well to aspirate or dispense. diff --git a/api/src/opentrons/protocol_api/labware.py b/api/src/opentrons/protocol_api/labware.py index eb25661bbf6..d06e08d2f74 100644 --- a/api/src/opentrons/protocol_api/labware.py +++ b/api/src/opentrons/protocol_api/labware.py @@ -85,17 +85,17 @@ def __init__(self, parent: Labware, core: WellCore, api_version: APIVersion): self._core = core self._api_version = api_version - @property # type: ignore + @property @requires_version(2, 0) def api_version(self) -> APIVersion: return self._api_version - @property # type: ignore[misc] + @property @requires_version(2, 0) def parent(self) -> Labware: return self._parent - @property # type: ignore[misc] + @property @requires_version(2, 0) def has_tip(self) -> bool: """Whether this well contains a tip. Always ``False`` if the parent labware @@ -121,7 +121,7 @@ def geometry(self) -> WellGeometry: return self._core.geometry raise APIVersionError("Well.geometry has been deprecated.") - @property # type: ignore + @property @requires_version(2, 0) def diameter(self) -> Optional[float]: """ @@ -130,7 +130,7 @@ def diameter(self) -> Optional[float]: """ return self._core.diameter - @property # type: ignore + @property @requires_version(2, 9) def length(self) -> Optional[float]: """ @@ -139,7 +139,7 @@ def length(self) -> Optional[float]: """ return self._core.length - @property # type: ignore + @property @requires_version(2, 9) def width(self) -> Optional[float]: """ @@ -148,7 +148,7 @@ def width(self) -> Optional[float]: """ return self._core.width - @property # type: ignore + @property @requires_version(2, 9) def depth(self) -> float: """ @@ -161,7 +161,7 @@ def depth(self) -> float: def display_name(self) -> str: return self._core.get_display_name() - @property # type: ignore + @property @requires_version(2, 7) def well_name(self) -> str: return self._core.get_name() @@ -349,7 +349,7 @@ def separate_calibration(self) -> bool: ) return False - @property # type: ignore + @property @requires_version(2, 0) def api_version(self) -> APIVersion: return self._api_version @@ -357,7 +357,7 @@ def api_version(self) -> APIVersion: def __getitem__(self, key: str) -> Well: return self.wells_by_name()[key] - @property # type: ignore + @property @requires_version(2, 0) def uri(self) -> str: """A string fully identifying the labware. @@ -366,7 +366,7 @@ def uri(self) -> str: """ return self._core.get_uri() - @property # type: ignore[misc] + @property @requires_version(2, 0) def parent(self) -> Union[str, Labware, ModuleTypes, OffDeckType]: """The parent of this labware---where this labware is loaded. @@ -403,7 +403,7 @@ def parent(self) -> Union[str, Labware, ModuleTypes, OffDeckType]: return labware_location - @property # type: ignore[misc] + @property @requires_version(2, 0) def name(self) -> str: """Can either be the canonical name of the labware, which is used to @@ -425,19 +425,19 @@ def name(self, new_name: str) -> None: assert isinstance(self._core, LegacyLabwareCore) cast(LegacyLabwareCore, self._core).set_name(new_name) - @property # type: ignore[misc] + @property @requires_version(2, 0) def load_name(self) -> str: """The API load name of the labware definition.""" return self._core.load_name - @property # type: ignore[misc] + @property @requires_version(2, 0) def parameters(self) -> "LabwareParameters": """Internal properties of a labware including type and quirks.""" return self._core.get_parameters() - @property # type: ignore + @property @requires_version(2, 0) def quirks(self) -> List[str]: """Quirks specific to this labware.""" @@ -446,7 +446,7 @@ def quirks(self) -> List[str]: # TODO(mm, 2023-02-08): # Specify units and origin after we resolve RSS-110. # Remove warning once we resolve RSS-109 more broadly. - @property # type: ignore + @property @requires_version(2, 0) def magdeck_engage_height(self) -> Optional[float]: """Return the default magnet engage height that @@ -471,7 +471,7 @@ def magdeck_engage_height(self) -> Optional[float]: else: return p["magneticModuleEngageHeight"] - @property # type: ignore[misc] + @property @requires_version(2, 15) def child(self) -> Optional[Labware]: """The labware (if any) present on this labware.""" @@ -589,7 +589,7 @@ def set_offset(self, x: float, y: float, z: float) -> None: else: self._core.set_calibration(Point(x=x, y=y, z=z)) - @property # type: ignore + @property @requires_version(2, 0) def calibrated_offset(self) -> Point: return self._core.get_calibrated_offset() @@ -780,7 +780,7 @@ def columns_by_index(self) -> Dict[str, List[Well]]: _log.warning("columns_by_index is deprecated. Use columns_by_name instead.") return self.columns_by_name() - @property # type: ignore + @property @requires_version(2, 0) def highest_z(self) -> float: """ @@ -796,17 +796,17 @@ def _is_tiprack(self) -> bool: """as is_tiprack but not subject to version checking for speed""" return self._core.is_tip_rack() - @property # type: ignore[misc] + @property @requires_version(2, 0) def is_tiprack(self) -> bool: return self._is_tiprack - @property # type: ignore[misc] + @property @requires_version(2, 15) def is_adapter(self) -> bool: return self._core.is_adapter() - @property # type: ignore[misc] + @property @requires_version(2, 0) def tip_length(self) -> float: return self._core.get_tip_length() diff --git a/api/src/opentrons/protocol_api/module_contexts.py b/api/src/opentrons/protocol_api/module_contexts.py index 8605069ccc7..f525fe6b320 100644 --- a/api/src/opentrons/protocol_api/module_contexts.py +++ b/api/src/opentrons/protocol_api/module_contexts.py @@ -63,18 +63,18 @@ def __init__( self._core_map = core_map self._api_version = api_version - @property # type: ignore[misc] + @property @requires_version(2, 0) def api_version(self) -> APIVersion: return self._api_version - @property # type: ignore[misc] + @property @requires_version(2, 14) def model(self) -> ModuleModel: """Get the module's model identifier.""" return cast(ModuleModel, self._core.get_model().value) - @property # type: ignore[misc] + @property @requires_version(2, 14) def type(self) -> ModuleType: """Get the module's general type identifier.""" @@ -265,14 +265,14 @@ def load_adapter_from_definition(self, definition: LabwareDefinition) -> Labware version=load_params.version, ) - @property # type: ignore[misc] + @property @requires_version(2, 0) def labware(self) -> Optional[Labware]: """The labware (if any) present on this module.""" labware_core = self._protocol_core.get_labware_on_module(self._core) return self._core_map.get(labware_core) - @property # type: ignore[misc] + @property @requires_version(2, 14) def parent(self) -> str: """The name of the slot the module is on. @@ -282,7 +282,7 @@ def parent(self) -> str: """ return self._core.get_deck_slot_id() - @property # type: ignore[misc] + @property @requires_version(2, 0) def geometry(self) -> LegacyModuleGeometry: """The object representing the module as an item on the deck. @@ -319,7 +319,7 @@ class TemperatureModuleContext(ModuleContext): _core: TemperatureModuleCore - @property # type: ignore[misc] + @property @requires_version(2, 14) def serial_number(self) -> str: """Get the module's unique hardware serial number.""" @@ -361,7 +361,7 @@ def deactivate(self) -> None: """Stop heating or cooling, and turn off the fan.""" self._core.deactivate() - @property # type: ignore[misc] + @property @requires_version(2, 0) def temperature(self) -> float: """The current temperature of the Temperature Module's deck in °C. @@ -370,7 +370,7 @@ def temperature(self) -> float: """ return self._core.get_current_temperature() - @property # type: ignore[misc] + @property @requires_version(2, 0) def target(self) -> Optional[float]: """The target temperature of the Temperature Module's deck in °C. @@ -379,7 +379,7 @@ def target(self) -> Optional[float]: """ return self._core.get_target_temperature() - @property # type: ignore[misc] + @property @requires_version(2, 3) def status(self) -> str: """One of four possible temperature statuses: @@ -404,7 +404,7 @@ class MagneticModuleContext(ModuleContext): _core: MagneticModuleCore - @property # type: ignore[misc] + @property @requires_version(2, 14) def serial_number(self) -> str: """Get the module's unique hardware serial number.""" @@ -493,7 +493,7 @@ def disengage(self) -> None: """Lower the magnets back into the Magnetic Module.""" self._core.disengage() - @property # type: ignore + @property @requires_version(2, 0) def status(self) -> str: """The status of the module, either ``engaged`` or ``disengaged``.""" @@ -511,7 +511,7 @@ class ThermocyclerContext(ModuleContext): _core: ThermocyclerCore - @property # type: ignore[misc] + @property @requires_version(2, 14) def serial_number(self) -> str: """Get the module's unique hardware serial number.""" @@ -642,7 +642,7 @@ def deactivate(self) -> None: """Turn off both the well block temperature controller and the lid heater.""" self._core.deactivate() - @property # type: ignore[misc] + @property @requires_version(2, 0) def lid_position(self) -> Optional[str]: """One of these possible lid statuses: @@ -655,7 +655,7 @@ def lid_position(self) -> Optional[str]: status = self._core.get_lid_position() return status.value if status is not None else None - @property # type: ignore[misc] + @property @requires_version(2, 0) def block_temperature_status(self) -> str: """One of five possible temperature statuses: @@ -669,7 +669,7 @@ def block_temperature_status(self) -> str: """ return self._core.get_block_temperature_status().value - @property # type: ignore[misc] + @property @requires_version(2, 0) def lid_temperature_status(self) -> Optional[str]: """One of five possible temperature statuses: @@ -685,61 +685,61 @@ def lid_temperature_status(self) -> Optional[str]: status = self._core.get_lid_temperature_status() return status.value if status is not None else None - @property # type: ignore[misc] + @property @requires_version(2, 0) def block_temperature(self) -> Optional[float]: """The current temperature of the well block in °C.""" return self._core.get_block_temperature() - @property # type: ignore[misc] + @property @requires_version(2, 0) def block_target_temperature(self) -> Optional[float]: """The target temperature of the well block in °C.""" return self._core.get_block_target_temperature() - @property # type: ignore[misc] + @property @requires_version(2, 0) def lid_temperature(self) -> Optional[float]: """The current temperature of the lid in °C.""" return self._core.get_lid_temperature() - @property # type: ignore[misc] + @property @requires_version(2, 0) def lid_target_temperature(self) -> Optional[float]: """The target temperature of the lid in °C.""" return self._core.get_lid_target_temperature() - @property # type: ignore[misc] + @property @requires_version(2, 0) def ramp_rate(self) -> Optional[float]: """The current ramp rate in °C/s.""" return self._core.get_ramp_rate() - @property # type: ignore[misc] + @property @requires_version(2, 0) def hold_time(self) -> Optional[float]: """Remaining hold time in seconds.""" return self._core.get_hold_time() - @property # type: ignore[misc] + @property @requires_version(2, 0) def total_cycle_count(self) -> Optional[int]: """Number of repetitions for current set cycle""" return self._core.get_total_cycle_count() - @property # type: ignore[misc] + @property @requires_version(2, 0) def current_cycle_index(self) -> Optional[int]: """Index of the current set cycle repetition""" return self._core.get_current_cycle_index() - @property # type: ignore[misc] + @property @requires_version(2, 0) def total_step_count(self) -> Optional[int]: """Number of steps within the current cycle""" return self._core.get_total_step_count() - @property # type: ignore[misc] + @property @requires_version(2, 0) def current_step_index(self) -> Optional[int]: """Index of the current step within the current cycle""" @@ -757,13 +757,13 @@ class HeaterShakerContext(ModuleContext): _core: HeaterShakerCore - @property # type: ignore[misc] + @property @requires_version(2, 14) def serial_number(self) -> str: """Get the module's unique hardware serial number.""" return self._core.get_serial_number() - @property # type: ignore[misc] + @property @requires_version(2, 13) def target_temperature(self) -> Optional[float]: """The target temperature of the Heater-Shaker's plate in °C. @@ -772,7 +772,7 @@ def target_temperature(self) -> Optional[float]: """ return self._core.get_target_temperature() - @property # type: ignore[misc] + @property @requires_version(2, 13) def current_temperature(self) -> float: """The current temperature of the Heater-Shaker's plate in °C. @@ -781,19 +781,19 @@ def current_temperature(self) -> float: """ return self._core.get_current_temperature() - @property # type: ignore[misc] + @property @requires_version(2, 13) def current_speed(self) -> int: """The current speed of the Heater-Shaker's plate in rpm.""" return self._core.get_current_speed() - @property # type: ignore[misc] + @property @requires_version(2, 13) def target_speed(self) -> Optional[int]: """Target speed of the Heater-Shaker's plate in rpm.""" return self._core.get_target_speed() - @property # type: ignore[misc] + @property @requires_version(2, 13) def temperature_status(self) -> str: """One of five possible temperature statuses: @@ -808,7 +808,7 @@ def temperature_status(self) -> str: """ return self._core.get_temperature_status().value - @property # type: ignore[misc] + @property @requires_version(2, 13) def speed_status(self) -> str: """One of five possible shaking statuses: @@ -823,7 +823,7 @@ def speed_status(self) -> str: """ return self._core.get_speed_status().value - @property # type: ignore[misc] + @property @requires_version(2, 13) def labware_latch_status(self) -> str: """One of six possible latch statuses: diff --git a/api/src/opentrons/protocol_api/protocol_context.py b/api/src/opentrons/protocol_api/protocol_context.py index 02293be7298..4d520ea4f54 100644 --- a/api/src/opentrons/protocol_api/protocol_context.py +++ b/api/src/opentrons/protocol_api/protocol_context.py @@ -166,7 +166,7 @@ def __init__( self._unsubscribe_commands: Optional[Callable[[], None]] = None self.clear_commands() - @property # type: ignore + @property @requires_version(2, 0) def api_version(self) -> APIVersion: """Return the API version supported by this protocol context. @@ -188,7 +188,7 @@ def _hw_manager(self) -> HardwareManager: ) return HardwareManager(hardware=self._core.get_hardware()) - @property # type: ignore + @property @requires_version(2, 0) def bundled_data(self) -> Dict[str, bytes]: """Accessor for data files bundled with this protocol, if any. @@ -210,7 +210,7 @@ def __del__(self) -> None: if getattr(self, "_unsubscribe_commands", None): self._unsubscribe_commands() # type: ignore - @property # type: ignore + @property @requires_version(2, 0) def max_speeds(self) -> AxisMaxSpeeds: """Per-axis speed limits when moving this instrument. @@ -577,7 +577,7 @@ def load_adapter( # TODO(mm, 2023-06-07): Figure out what to do with this, now that the Flex has non-integer # slot names and labware can be stacked. https://opentrons.atlassian.net/browse/RLAB-354 - @property # type: ignore + @property @requires_version(2, 0) def loaded_labwares(self) -> Dict[int, Labware]: """Get the labwares that have been loaded into the protocol context. @@ -796,7 +796,7 @@ def load_module( # TODO(mm, 2023-06-07): Figure out what to do with this, now that the Flex has non-integer # slot names and labware can be stacked. https://opentrons.atlassian.net/browse/RLAB-354 - @property # type: ignore + @property @requires_version(2, 0) def loaded_modules(self) -> Dict[int, ModuleTypes]: """Get the modules loaded into the protocol context. @@ -911,7 +911,7 @@ def load_instrument( return instrument - @property # type: ignore + @property @requires_version(2, 0) def loaded_instruments(self) -> Dict[str, InstrumentContext]: """Get the instruments that have been loaded into the protocol. @@ -1018,7 +1018,7 @@ def location_cache(self) -> Optional[Location]: def location_cache(self, loc: Optional[Location]) -> None: self._core.set_last_location(loc) - @property # type: ignore + @property @requires_version(2, 0) def deck(self) -> Deck: """An interface to provide information about what's currently loaded on the deck. @@ -1052,7 +1052,7 @@ def deck(self) -> Deck: """ return self._deck - @property # type: ignore + @property @requires_version(2, 0) def fixed_trash(self) -> Union[Labware, TrashBin]: """The trash fixed to slot 12 of an OT-2's deck. @@ -1126,13 +1126,13 @@ def define_liquid( display_color=display_color, ) - @property # type: ignore + @property @requires_version(2, 5) def rail_lights_on(self) -> bool: """Returns True if the rail lights are on""" return self._core.get_rail_lights_on() - @property # type: ignore + @property @requires_version(2, 5) def door_closed(self) -> bool: """Returns True if the robot door is closed""" diff --git a/api/src/opentrons/protocol_engine/state/geometry.py b/api/src/opentrons/protocol_engine/state/geometry.py index 3ae4125abff..bc65a957b18 100644 --- a/api/src/opentrons/protocol_engine/state/geometry.py +++ b/api/src/opentrons/protocol_engine/state/geometry.py @@ -283,7 +283,7 @@ def _normalize_module_calibration_offset( # Since the module was rotated, the calibration offset vector needs to be rotated by 180 degrees along the z axis saved_offset = array([offset.x, offset.y, offset.z]) rotation_matrix = array([[-1, 0, 0], [0, -1, 0], [0, 0, 1]]) - new_offset = dot(saved_offset, rotation_matrix) # type: ignore[no-untyped-call] + new_offset = dot(saved_offset, rotation_matrix) offset = ModuleOffsetVector( x=new_offset[0], y=new_offset[1], z=new_offset[2] ) diff --git a/api/src/opentrons/protocol_engine/state/modules.py b/api/src/opentrons/protocol_engine/state/modules.py index f63cd631204..d7cfeecef14 100644 --- a/api/src/opentrons/protocol_engine/state/modules.py +++ b/api/src/opentrons/protocol_engine/state/modules.py @@ -677,7 +677,7 @@ def get_nominal_module_offset( # Apply the slot transform, if any xform = array(xforms_ser_offset) - xformed = dot(xform, pre_transform) # type: ignore[no-untyped-call] + xformed = dot(xform, pre_transform) return LabwareOffsetVector( x=xformed[0], y=xformed[1], diff --git a/api/src/opentrons/simulate.py b/api/src/opentrons/simulate.py index a0aa5e10077..5e8433debba 100644 --- a/api/src/opentrons/simulate.py +++ b/api/src/opentrons/simulate.py @@ -195,7 +195,7 @@ def handle_command(message: command_types.CommandMessage) -> None: self._logger.setLevel(level) log_handler: Optional[_AccumulatingHandler] = _AccumulatingHandler( - level, log_queue + self._level.upper(), log_queue ) else: log_handler = None diff --git a/api/src/opentrons/system/wifi.py b/api/src/opentrons/system/wifi.py index 24880348f20..c386838726d 100644 --- a/api/src/opentrons/system/wifi.py +++ b/api/src/opentrons/system/wifi.py @@ -2,7 +2,7 @@ import logging import os import shutil -from typing import Generator, Optional, Dict, Any +from typing import Generator, Optional, Dict, Any, TypedDict, List from dataclasses import dataclass from opentrons.config import CONFIG @@ -15,7 +15,17 @@ class ConfigureArgsError(Exception): pass -EAP_CONFIG_SHAPE = { +class EapConfigItem(TypedDict): + name: str + displayName: str + options: List[Dict[str, Any]] + + +class EapConfigShape(TypedDict): + options: List[EapConfigItem] + + +EAP_CONFIG_SHAPE: EapConfigShape = { "options": [ { "name": method.qualified_name(), @@ -186,7 +196,7 @@ def eap_check_config(eap_config: Dict[str, Any]) -> Dict[str, Any]: _eap_check_no_extra_args(eap_config, options) - for opt in options: # type: ignore + for opt in options: # Ignoring most types to do with EAP_CONFIG_SHAPE because of issues # wth type inference for dict comprehensions _eap_check_option_ok(opt, eap_config) diff --git a/api/src/opentrons/types.py b/api/src/opentrons/types.py index 261467fd574..44035851b35 100644 --- a/api/src/opentrons/types.py +++ b/api/src/opentrons/types.py @@ -1,7 +1,7 @@ from __future__ import annotations import enum from math import sqrt, isclose -from typing import TYPE_CHECKING, Any, NamedTuple, Iterable, Union, List +from typing import TYPE_CHECKING, Any, NamedTuple, Iterator, Union, List from opentrons_shared_data.robot.dev_types import RobotType @@ -41,12 +41,12 @@ def __sub__(self, other: Any) -> Point: return NotImplemented return Point(self.x - other.x, self.y - other.y, self.z - other.z) - def __mul__(self, other: Union[int, float]) -> Point: + def __mul__(self, other: Union[int, float]) -> Point: # type: ignore[override] if not isinstance(other, (float, int)): return NotImplemented return Point(self.x * other, self.y * other, self.z * other) - def __rmul__(self, other: Union[int, float]) -> Point: + def __rmul__(self, other: Union[int, float]) -> Point: # type: ignore[override] if not isinstance(other, (float, int)): return NotImplemented return Point(self.x * other, self.y * other, self.z * other) @@ -132,14 +132,16 @@ def point(self) -> Point: def labware(self) -> LabwareLike: return self._labware - def __iter__(self) -> Iterable[Union[Point, LabwareLike]]: - """Iterable interface to support unpacking. Like a tuple.""" - return iter( - ( - self._point, - self._labware, - ) - ) + def __iter__(self) -> Iterator[Union[Point, LabwareLike]]: + """Iterable interface to support unpacking. Like a tuple. + + .. note:: + While type annotations cannot properly support this, it will work in practice: + + point, labware = location + some_function_taking_both(*location) + """ + return iter((self._point, self._labware)) # type: ignore [arg-type] def __eq__(self, other: object) -> bool: return ( diff --git a/api/src/opentrons/util/linal.py b/api/src/opentrons/util/linal.py index 58b293342b1..cc82b5794b2 100644 --- a/api/src/opentrons/util/linal.py +++ b/api/src/opentrons/util/linal.py @@ -33,7 +33,7 @@ def identity_deck_transform() -> DoubleArray: def solve_attitude(expected: SolvePoints, actual: SolvePoints) -> AttitudeMatrix: ex = np.array([list(point) for point in expected]).transpose() ac = np.array([list(point) for point in actual]).transpose() - t = np.dot(ac, inv(ex)) # type: ignore[no-untyped-call] + t = np.dot(ac, inv(ex)) mask_transform = np.array( [[True, True, False], [True, True, False], [False, False, False]] @@ -105,7 +105,7 @@ def solve( # [ y1 y2 y3 ] # [ 1 1 1 ] - transform = np.dot(ac, inv(ex)) # type: ignore[no-untyped-call] + transform = np.dot(ac, inv(ex)) # `dot` in numpy is a misnomer. When both arguments are square, N- # dimensional arrays, the return type is the result of performing matrix # multiplication, rather than the dot-product (so the return here will be @@ -132,21 +132,21 @@ def add_z(xy: DoubleArray, z: float) -> DoubleArray: [ 0 0 0 1 ] """ # First, insert a column of zeros as into the input matrix - interm = insert(xy, 2, [0, 0, 0], axis=1) # type: ignore[no-untyped-call] + interm = insert(xy, 2, [0, 0, 0], axis=1) # Result: # [ 1 0 0 x ] # [ 0 1 0 y ] # [ 0 0 0 1 ] # Then, insert the z row to create a properly formed 3-D transform matrix: - xyz = insert(interm, 2, [0, 0, 1, z], axis=0) # type: ignore[no-untyped-call] + xyz = insert(interm, 2, [0, 0, 1, z], axis=0) # Result: # [ 1 0 0 x ] # [ 0 1 0 y ] # [ 0 0 1 z ] # [ 0 0 0 1 ] - return xyz.round(11) # type: ignore[no-any-return] + return xyz.round(11) def add_matrices( @@ -178,4 +178,4 @@ def apply_reverse( pos: AxisPosition, ) -> Tuple[float, float, float]: """Like apply_transform but inverts the transform first""" - return apply_transform(inv(t), pos) # type: ignore[no-untyped-call] + return apply_transform(inv(t), pos) diff --git a/api/tests/opentrons/config/test_defaults_ot2.py b/api/tests/opentrons/config/test_defaults_ot2.py index df2cd61ce18..77c7c0a3589 100644 --- a/api/tests/opentrons/config/test_defaults_ot2.py +++ b/api/tests/opentrons/config/test_defaults_ot2.py @@ -1,5 +1,5 @@ from opentrons.config.types import CurrentDict -from opentrons.config import robot_configs, defaults_ot2 +from opentrons.config import defaults_ot2 def test_load_currents() -> None: @@ -19,7 +19,4 @@ def test_load_currents() -> None: defaults_ot2._build_hw_versioned_current_dict(default_different_vals, default) == default_different_vals ) - assert ( - robot_configs.defaults_ot2._build_hw_versioned_current_dict(None, default) - == default - ) + assert defaults_ot2._build_hw_versioned_current_dict(None, default) == default diff --git a/api/tests/opentrons/conftest.py b/api/tests/opentrons/conftest.py index f28a0723b01..f1328716f63 100755 --- a/api/tests/opentrons/conftest.py +++ b/api/tests/opentrons/conftest.py @@ -88,7 +88,7 @@ class Bundle(TypedDict): filelike: io.BytesIO binary_zipfile: bytes metadata: Dict[str, str] - bundled_data: Dict[str, str] + bundled_data: Dict[str, bytes] bundled_labware: Dict[str, LabwareDefinition] bundled_python: Dict[str, Any] @@ -498,7 +498,7 @@ def _get_bundle_protocol_fixture(fixture_name: str) -> Bundle: if fixture_name == "simple_bundle": with open(fixture_dir / "protocol.py", "r") as f: result["contents"] = f.read() - with open(fixture_dir / "data.txt", "rb") as f: # type: ignore[assignment] + with open(fixture_dir / "data.txt", "rb") as f: result["bundled_data"] = {"data.txt": f.read()} with open(fixture_dir / "custom_labware.json", "r") as f: custom_labware = json.load(f) diff --git a/api/tests/opentrons/hardware_control/instruments/test_instrument_calibration.py b/api/tests/opentrons/hardware_control/instruments/test_instrument_calibration.py index 6dfc646547e..ac97947bfff 100644 --- a/api/tests/opentrons/hardware_control/instruments/test_instrument_calibration.py +++ b/api/tests/opentrons/hardware_control/instruments/test_instrument_calibration.py @@ -82,10 +82,10 @@ def test_load_tip_length( tipLength=1.23, lastModified=datetime(year=2023, month=1, day=1), uri=LabwareUri("def456"), - source=subject.types.SourceType.factory, + source=subject.SourceType.factory, status=v1_models.CalibrationStatus( markedBad=True, - source=subject.types.SourceType.user, + source=subject.SourceType.user, markedAt=datetime(year=2023, month=2, day=2), ), ) @@ -106,14 +106,14 @@ def test_load_tip_length( assert result == subject.TipLengthCalibration( tip_length=1.23, - source=subject.types.SourceType.factory, + source=subject.SourceType.factory, pipette="abc123", tiprack="asdfghjk", last_modified=datetime(year=2023, month=1, day=1), uri=LabwareUri("def456"), - status=subject.types.CalibrationStatus( + status=subject.CalibrationStatus( markedBad=True, - source=subject.types.SourceType.user, + source=subject.SourceType.user, markedAt=datetime(year=2023, month=2, day=2), ), ) diff --git a/api/tests/opentrons/protocol_api_old/core/simulator/conftest.py b/api/tests/opentrons/protocol_api_old/core/simulator/conftest.py index 015040a39f9..723dc568add 100644 --- a/api/tests/opentrons/protocol_api_old/core/simulator/conftest.py +++ b/api/tests/opentrons/protocol_api_old/core/simulator/conftest.py @@ -117,8 +117,8 @@ def tip_rack(minimal_labware_def: LabwareDefinition) -> LegacyLabwareCore: tip_rack_parameters["isTiprack"] = True tip_rack_parameters["tipLength"] = 123 tip_rack_definition["parameters"] = tip_rack_parameters - tip_rack_definition["wells"]["A1"]["totalLiquidVolume"] = 200 # type: ignore - tip_rack_definition["wells"]["A2"]["totalLiquidVolume"] = 200 # type: ignore + tip_rack_definition["wells"]["A1"]["totalLiquidVolume"] = 200 + tip_rack_definition["wells"]["A2"]["totalLiquidVolume"] = 200 """Labware fixture.""" return LegacyLabwareCore( diff --git a/api/tests/opentrons/protocol_api_old/test_context.py b/api/tests/opentrons/protocol_api_old/test_context.py index abcdd06a6d8..fcb7004d4bc 100644 --- a/api/tests/opentrons/protocol_api_old/test_context.py +++ b/api/tests/opentrons/protocol_api_old/test_context.py @@ -1187,11 +1187,11 @@ def raiser(*args, **kwargs): mod = ctx.load_module("thermocycler") assert isinstance(mod, ThermocyclerContext) - mod._core.flag_unsafe_move = mock.MagicMock(side_effect=raiser) # type: ignore[attr-defined, assignment] + mod._core.flag_unsafe_move = mock.MagicMock(side_effect=raiser) # type: ignore[attr-defined] instr = ctx.load_instrument("p1000_single", "left") with pytest.raises(RuntimeError, match="Cannot"): instr.move_to(Location(Point(0, 0, 0), None)) - mod._core.flag_unsafe_move.assert_called_once_with( # type: ignore[attr-defined] + mod._core.flag_unsafe_move.assert_called_once_with( # type: ignore[attr-defined] # type: ignore[attr-defined] to_loc=Location(Point(0, 0, 0), None), from_loc=Location(Point(0, 0, 0), None) ) diff --git a/api/tests/opentrons/system/test_wifi.py b/api/tests/opentrons/system/test_wifi.py index b6b3a994d68..da807cb2bdb 100644 --- a/api/tests/opentrons/system/test_wifi.py +++ b/api/tests/opentrons/system/test_wifi.py @@ -190,16 +190,16 @@ async def test_key_lifecycle(wifi_keys_tempdir): f.write(str(random.getrandbits(2048))) # TODO(mc, 2021-09-12): use pathlib - with open(path, "rb") as f: # type: ignore[assignment] - add_response = wifi.add_key(fn, f.read()) # type: ignore[arg-type] + with open(path, "rb") as f: + add_response = wifi.add_key(fn, f.read()) assert add_response.created is True assert add_response.key.file == fn results[fn] = add_response # We should not be able to upload a duplicate # TODO(mc, 2021-09-12): use pathlib - with open(os.path.join(source_td, "test1.pem"), "rb") as f: # type: ignore[assignment] - add_response = wifi.add_key("test1.pem", f.read()) # type: ignore[arg-type] + with open(os.path.join(source_td, "test1.pem"), "rb") as f: + add_response = wifi.add_key("test1.pem", f.read()) assert add_response.created is False # We should be able to see them all diff --git a/api/tests/opentrons/util/test_linal.py b/api/tests/opentrons/util/test_linal.py index fa90bfe9a90..38c5cf8e2d3 100755 --- a/api/tests/opentrons/util/test_linal.py +++ b/api/tests/opentrons/util/test_linal.py @@ -25,7 +25,7 @@ def test_solve() -> None: expected2 = np.array( [cos(theta + pi / 2) * scale + 0.5, sin(theta + pi / 2) * scale + 0.25, 1] ) - result = np.dot(X, np.array([[0], [1], [1]])).transpose() # type: ignore[no-untyped-call] + result = np.dot(X, np.array([[0], [1], [1]])).transpose() assert np.isclose(expected2, result).all() @@ -61,5 +61,5 @@ def test_apply_transform() -> None: expected = (round(x - x_delta, 2), round(y - y_delta, 2), round(z)) - result = apply_transform(inv(transform), (1, 2, 3)) # type: ignore[no-untyped-call] + result = apply_transform(inv(transform), (1, 2, 3)) assert np.isclose(result, expected, atol=0.1).all() From d3db24c8c9d9341e5bbc98f8d4c5686899a69705 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Thu, 7 Dec 2023 17:17:50 -0500 Subject: [PATCH 22/60] bump the python version in all the workflows --- .github/workflows/api-test-lint-deploy.yaml | 4 ++-- .github/workflows/docs-build.yaml | 2 +- .github/workflows/g-code-confirm-tests.yaml | 2 +- .github/workflows/g-code-testing-lint-test.yaml | 2 +- .github/workflows/hardware-lint-test.yaml | 2 +- .github/workflows/hardware-testing-protocols.yaml | 2 +- .github/workflows/hardware-testing.yaml | 2 +- .github/workflows/http-docs-build.yaml | 2 +- .github/workflows/notify-server-lint-test.yaml | 2 +- .github/workflows/robot-server-lint-test.yaml | 2 +- .github/workflows/server-utils-lint-test.yaml | 4 ++-- .github/workflows/shared-data-test-lint-deploy.yaml | 4 ++-- .github/workflows/system-server-lint-test.yaml | 4 ++-- .github/workflows/update-server-lint-test.yaml | 4 ++-- .github/workflows/usb-bridge-lint-test.yaml | 4 ++-- 15 files changed, 21 insertions(+), 21 deletions(-) diff --git a/.github/workflows/api-test-lint-deploy.yaml b/.github/workflows/api-test-lint-deploy.yaml index f4547dc9bdd..ebc92d66008 100644 --- a/.github/workflows/api-test-lint-deploy.yaml +++ b/.github/workflows/api-test-lint-deploy.yaml @@ -59,7 +59,7 @@ jobs: node-version: '16' - uses: 'actions/setup-python@v4' with: - python-version: '3.7' + python-version: '3.10' - uses: './.github/actions/python/setup' with: @@ -152,7 +152,7 @@ jobs: node-version: '16' - uses: 'actions/setup-python@v4' with: - python-version: '3.7' + python-version: '3.10' - name: 'set complex environment variables' uses: actions/github-script@v6 with: diff --git a/.github/workflows/docs-build.yaml b/.github/workflows/docs-build.yaml index b954f7d1433..0eea5d6eb7d 100644 --- a/.github/workflows/docs-build.yaml +++ b/.github/workflows/docs-build.yaml @@ -54,7 +54,7 @@ jobs: node-version: '16' - uses: 'actions/setup-python@v3' with: - python-version: '3.7' + python-version: '3.10' - uses: './.github/actions/python/setup' with: project: 'api' diff --git a/.github/workflows/g-code-confirm-tests.yaml b/.github/workflows/g-code-confirm-tests.yaml index 151ae13c3d1..146fa96b9a2 100644 --- a/.github/workflows/g-code-confirm-tests.yaml +++ b/.github/workflows/g-code-confirm-tests.yaml @@ -49,7 +49,7 @@ jobs: node-version: '12' - uses: 'actions/setup-python@v3' with: - python-version: '3.7' + python-version: '3.10' - uses: './.github/actions/python/setup' with: project: 'g-code-testing' diff --git a/.github/workflows/g-code-testing-lint-test.yaml b/.github/workflows/g-code-testing-lint-test.yaml index 3678e5c4a20..6dd00712076 100644 --- a/.github/workflows/g-code-testing-lint-test.yaml +++ b/.github/workflows/g-code-testing-lint-test.yaml @@ -59,7 +59,7 @@ jobs: buildComplexEnvVars(core, context) - uses: 'actions/setup-python@v4' with: - python-version: '3.7' + python-version: '3.10' - uses: './.github/actions/python/setup' with: project: 'g-code-testing' diff --git a/.github/workflows/hardware-lint-test.yaml b/.github/workflows/hardware-lint-test.yaml index 453adba1269..f5e701ea883 100644 --- a/.github/workflows/hardware-lint-test.yaml +++ b/.github/workflows/hardware-lint-test.yaml @@ -55,7 +55,7 @@ jobs: - name: Setup Python uses: 'actions/setup-python@v4' with: - python-version: '3.7' + python-version: '3.10' - name: Setup Hardware Project uses: './.github/actions/python/setup' diff --git a/.github/workflows/hardware-testing-protocols.yaml b/.github/workflows/hardware-testing-protocols.yaml index e962e3811e4..ee59d2dc25c 100644 --- a/.github/workflows/hardware-testing-protocols.yaml +++ b/.github/workflows/hardware-testing-protocols.yaml @@ -50,7 +50,7 @@ jobs: - name: Setup Python uses: 'actions/setup-python@v4' with: - python-version: '3.7' + python-version: '3.10' - name: Setup Project uses: './.github/actions/python/setup' diff --git a/.github/workflows/hardware-testing.yaml b/.github/workflows/hardware-testing.yaml index 3df5507d2b1..6977194ca2a 100644 --- a/.github/workflows/hardware-testing.yaml +++ b/.github/workflows/hardware-testing.yaml @@ -52,7 +52,7 @@ jobs: - name: Setup Python uses: 'actions/setup-python@v4' with: - python-version: '3.7' + python-version: '3.10' - name: Setup Project uses: './.github/actions/python/setup' diff --git a/.github/workflows/http-docs-build.yaml b/.github/workflows/http-docs-build.yaml index e9ad64d75e5..c9ed4eeb250 100644 --- a/.github/workflows/http-docs-build.yaml +++ b/.github/workflows/http-docs-build.yaml @@ -51,7 +51,7 @@ jobs: git checkout ${{ github.ref }} - uses: 'actions/setup-python@v3' with: - python-version: '3.7' + python-version: '3.10' - uses: 'actions/setup-node@v3' with: node-version: '16' diff --git a/.github/workflows/notify-server-lint-test.yaml b/.github/workflows/notify-server-lint-test.yaml index dde68a9f0fa..1f5b7c3fee1 100644 --- a/.github/workflows/notify-server-lint-test.yaml +++ b/.github/workflows/notify-server-lint-test.yaml @@ -54,7 +54,7 @@ jobs: node-version: '16' - uses: 'actions/setup-python@v4' with: - python-version: '3.7' + python-version: '3.10' - uses: './.github/actions/python/setup' with: diff --git a/.github/workflows/robot-server-lint-test.yaml b/.github/workflows/robot-server-lint-test.yaml index d199b09aaa2..ed41189bbca 100644 --- a/.github/workflows/robot-server-lint-test.yaml +++ b/.github/workflows/robot-server-lint-test.yaml @@ -66,7 +66,7 @@ jobs: node-version: '16' - uses: 'actions/setup-python@v4' with: - python-version: '3.7' + python-version: '3.10' - uses: './.github/actions/python/setup' with: diff --git a/.github/workflows/server-utils-lint-test.yaml b/.github/workflows/server-utils-lint-test.yaml index c7039652bf9..c573ab01d19 100644 --- a/.github/workflows/server-utils-lint-test.yaml +++ b/.github/workflows/server-utils-lint-test.yaml @@ -49,7 +49,7 @@ jobs: node-version: '16' - uses: 'actions/setup-python@v4' with: - python-version: '3.7' + python-version: '3.10' - uses: './.github/actions/python/setup' with: @@ -70,7 +70,7 @@ jobs: node-version: '16' - uses: 'actions/setup-python@v4' with: - python-version: '3.7' + python-version: '3.10' - uses: './.github/actions/python/setup' with: project: 'server-utils' diff --git a/.github/workflows/shared-data-test-lint-deploy.yaml b/.github/workflows/shared-data-test-lint-deploy.yaml index f37627b01c7..2b61e5552ca 100644 --- a/.github/workflows/shared-data-test-lint-deploy.yaml +++ b/.github/workflows/shared-data-test-lint-deploy.yaml @@ -54,7 +54,7 @@ jobs: node-version: '16' - uses: 'actions/setup-python@v3' with: - python-version: '3.7' + python-version: '3.10' - uses: './.github/actions/python/setup' with: @@ -164,7 +164,7 @@ jobs: run: sudo apt-get update && sudo apt-get install libudev-dev - uses: 'actions/setup-python@v4' with: - python-version: '3.7' + python-version: '3.10' - uses: './.github/actions/python/setup' with: project: 'shared-data/python' diff --git a/.github/workflows/system-server-lint-test.yaml b/.github/workflows/system-server-lint-test.yaml index 0fecec47e83..d8a9378e3ad 100644 --- a/.github/workflows/system-server-lint-test.yaml +++ b/.github/workflows/system-server-lint-test.yaml @@ -51,7 +51,7 @@ jobs: node-version: '16' - uses: 'actions/setup-python@v4' with: - python-version: '3.7' + python-version: '3.10' - uses: './.github/actions/python/setup' with: @@ -72,7 +72,7 @@ jobs: node-version: '16' - uses: 'actions/setup-python@v4' with: - python-version: '3.7' + python-version: '3.10' - uses: './.github/actions/python/setup' with: project: 'system-server' diff --git a/.github/workflows/update-server-lint-test.yaml b/.github/workflows/update-server-lint-test.yaml index fe908f9f9e6..bb6d616682c 100644 --- a/.github/workflows/update-server-lint-test.yaml +++ b/.github/workflows/update-server-lint-test.yaml @@ -49,7 +49,7 @@ jobs: node-version: '16' - uses: 'actions/setup-python@v4' with: - python-version: '3.7' + python-version: '3.10' - uses: './.github/actions/python/setup' with: @@ -70,7 +70,7 @@ jobs: node-version: '16' - uses: 'actions/setup-python@v4' with: - python-version: '3.7' + python-version: '3.10' - uses: './.github/actions/python/setup' with: project: 'update-server' diff --git a/.github/workflows/usb-bridge-lint-test.yaml b/.github/workflows/usb-bridge-lint-test.yaml index 1ee0d62c53d..13bd040e81a 100644 --- a/.github/workflows/usb-bridge-lint-test.yaml +++ b/.github/workflows/usb-bridge-lint-test.yaml @@ -49,7 +49,7 @@ jobs: node-version: '16' - uses: 'actions/setup-python@v4' with: - python-version: '3.7' + python-version: '3.10' - uses: './.github/actions/python/setup' with: @@ -70,7 +70,7 @@ jobs: node-version: '16' - uses: 'actions/setup-python@v4' with: - python-version: '3.7' + python-version: '3.10' - uses: './.github/actions/python/setup' with: project: 'usb-bridge' From 22ba8405d99313614b4374e9c5463fae8e5114d1 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Tue, 19 Dec 2023 09:54:04 -0500 Subject: [PATCH 23/60] de-default sensor bindings --- hardware/opentrons_hardware/sensors/sensor_abc.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/hardware/opentrons_hardware/sensors/sensor_abc.py b/hardware/opentrons_hardware/sensors/sensor_abc.py index 198fff9884c..67801924328 100644 --- a/hardware/opentrons_hardware/sensors/sensor_abc.py +++ b/hardware/opentrons_hardware/sensors/sensor_abc.py @@ -1,7 +1,7 @@ """Abstract base classes for the sensor drivers.""" from abc import ABC, abstractmethod -from typing import Optional, AsyncIterator +from typing import Optional, AsyncIterator, Sequence from opentrons_hardware.drivers.can_bus.can_messenger import CanMessenger from opentrons_hardware.sensors.sensor_types import BaseSensorType, ThresholdSensorType @@ -88,7 +88,7 @@ async def bind_output( self, can_messenger: CanMessenger, sensor: BaseSensorType, - binding: SensorOutputBinding = SensorOutputBinding.sync, + binding: Optional[Sequence[SensorOutputBinding]], ) -> AsyncIterator[None]: """Send a BindSensorOutputRequest.""" yield From 1af3e928877372dd733b4a0ca2cee097923d1bdc Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Tue, 19 Dec 2023 09:55:20 -0500 Subject: [PATCH 24/60] hardware typing/lint updates --- .../firmware_bindings/utils/binary_serializable.py | 3 +-- .../hardware_control/motion_planning/move_utils.py | 8 ++++---- .../hardware_control/motion_planning/types.py | 2 +- hardware/opentrons_hardware/scripts/can_comm.py | 3 +-- .../scripts/can_log_motion_analyzer.py | 9 +++++---- hardware/opentrons_hardware/scripts/plot_stress_test.py | 2 +- 6 files changed, 13 insertions(+), 14 deletions(-) diff --git a/hardware/opentrons_hardware/firmware_bindings/utils/binary_serializable.py b/hardware/opentrons_hardware/firmware_bindings/utils/binary_serializable.py index 987483b98ff..832c469f42f 100644 --- a/hardware/opentrons_hardware/firmware_bindings/utils/binary_serializable.py +++ b/hardware/opentrons_hardware/firmware_bindings/utils/binary_serializable.py @@ -229,8 +229,7 @@ def build(cls, data: bytes) -> BinarySerializable: ), None, ) - # Mypy is not liking constructing the derived types. - ret_instance = cls(**args) # type: ignore[call-arg] + ret_instance = cls(**args) if message_index is not None: ret_instance.message_index = message_index # type: ignore[attr-defined] return ret_instance diff --git a/hardware/opentrons_hardware/hardware_control/motion_planning/move_utils.py b/hardware/opentrons_hardware/hardware_control/motion_planning/move_utils.py index 4c2a664c601..8792d9fb596 100644 --- a/hardware/opentrons_hardware/hardware_control/motion_planning/move_utils.py +++ b/hardware/opentrons_hardware/hardware_control/motion_planning/move_utils.py @@ -52,7 +52,7 @@ def get_unit_vector( for i in range(len(displacement)): if abs(displacement[i]) < MINIMUM_DISPLACEMENT: displacement[i] = 0 - distance = np.linalg.norm(displacement) # type: ignore[no-untyped-call] + distance = np.linalg.norm(displacement) if not distance or np.array_equal(initial_vectorized, target_vectorized): raise ZeroLengthMoveError(initial, target) unit_vector_ndarray = displacement / distance @@ -432,19 +432,19 @@ def build_blocks( abs(final_speed), max_speed ), f"final speed {final_speed} exceeds max speed {max_speed}" - max_acc = np.array( + max_acc: np.typing.NDArray[np.float64] = np.array( [ constraints[axis].max_acceleration if unit_vector[axis] else 0.0 for axis in unit_vector.keys() ] ) - max_acc_magnitude = np.linalg.norm(max_acc) # type: ignore[no-untyped-call] + max_acc_magnitude = np.linalg.norm(max_acc) acc_v = max_acc_magnitude * vectorize(unit_vector) for a_i, max_acc_i in zip(acc_v, max_acc): if abs(a_i) > max_acc_i: acc_v *= max_acc_i / a_i - max_acceleration = np.linalg.norm(acc_v) # type: ignore[no-untyped-call] + max_acceleration = np.linalg.norm(acc_v) initial_speed_sq = initial_speed**2 final_speed_sq = final_speed**2 diff --git a/hardware/opentrons_hardware/hardware_control/motion_planning/types.py b/hardware/opentrons_hardware/hardware_control/motion_planning/types.py index f78eeb0b22e..f917a0b1697 100644 --- a/hardware/opentrons_hardware/hardware_control/motion_planning/types.py +++ b/hardware/opentrons_hardware/hardware_control/motion_planning/types.py @@ -303,5 +303,5 @@ def vectorize(position: Coordinates[AxisKey, np.float64]) -> "NDArray[np.float64 def is_unit_vector(position: Coordinates[AxisKey, np.float64]) -> bool: """Check whether a coordinate vector has unit magnitude.""" vectorized = vectorize(position) - magnitude = np.linalg.norm(vectorized) # type: ignore[no-untyped-call] + magnitude = np.linalg.norm(vectorized) return cast(bool, np.isclose(magnitude, 1.0)) diff --git a/hardware/opentrons_hardware/scripts/can_comm.py b/hardware/opentrons_hardware/scripts/can_comm.py index f3378301f64..b74e27f5830 100644 --- a/hardware/opentrons_hardware/scripts/can_comm.py +++ b/hardware/opentrons_hardware/scripts/can_comm.py @@ -159,8 +159,7 @@ def prompt_payload( ) except ValueError as e: raise InvalidInput(str(e)) - # Mypy is not liking constructing the derived types. - ret_instance = payload_type(**i) # type: ignore[call-arg] + ret_instance = payload_type(**i) if message_index is not None: ret_instance.message_index = message_index # type: ignore[attr-defined] return ret_instance diff --git a/hardware/opentrons_hardware/scripts/can_log_motion_analyzer.py b/hardware/opentrons_hardware/scripts/can_log_motion_analyzer.py index 8122e7aad95..263cc73f0a6 100755 --- a/hardware/opentrons_hardware/scripts/can_log_motion_analyzer.py +++ b/hardware/opentrons_hardware/scripts/can_log_motion_analyzer.py @@ -25,7 +25,8 @@ from opentrons_hardware.hardware_control.constants import interrupts_per_sec if TYPE_CHECKING: - import matplotlib.pyplot as pp # type: ignore + import matplotlib.pyplot as pp # noqa: F401 + from matplotlib.figure import Figure class IgnoredMessage(BaseException): @@ -583,9 +584,9 @@ def record_filter( yield record -def plot_one(plot: PlotParams) -> "pp.Figure": # noqa: C901 +def plot_one(plot: PlotParams) -> "Figure": # noqa: C901 """Plot a single figure. Requires pyplot.""" - import matplotlib.pyplot as pp + import matplotlib.pyplot as pp # noqa: F811 time_offsets: List[float] = [] absolute_encoder: List[float] = [] @@ -703,7 +704,7 @@ def on_button(event: Any) -> None: def plot_position_errors(plots: List[PlotParams]) -> None: """Plot more than one axis worth of data. Requires pyplot.""" - import matplotlib.pyplot as pp + import matplotlib.pyplot as pp # noqa: F811 for plot in plots: try: diff --git a/hardware/opentrons_hardware/scripts/plot_stress_test.py b/hardware/opentrons_hardware/scripts/plot_stress_test.py index eb51a30ac59..f228cd84ae2 100644 --- a/hardware/opentrons_hardware/scripts/plot_stress_test.py +++ b/hardware/opentrons_hardware/scripts/plot_stress_test.py @@ -3,7 +3,7 @@ from typing import BinaryIO, Iterator, Tuple, Set import argparse -import matplotlib.pyplot as pp # type: ignore +import matplotlib.pyplot as pp from opentrons_hardware.firmware_bindings.constants import NodeId From 03376ab62b8875e2e0f151c537cbbfd587d4a4f3 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Tue, 19 Dec 2023 09:55:38 -0500 Subject: [PATCH 25/60] hardware fixes found by typing/lint updates --- hardware/opentrons_hardware/scripts/load.py | 2 +- hardware/opentrons_hardware/scripts/provision_gripper.py | 4 +--- hardware/opentrons_hardware/scripts/provision_pipette.py | 6 +----- 3 files changed, 3 insertions(+), 9 deletions(-) diff --git a/hardware/opentrons_hardware/scripts/load.py b/hardware/opentrons_hardware/scripts/load.py index 9dff0b42392..cce73a77ba8 100644 --- a/hardware/opentrons_hardware/scripts/load.py +++ b/hardware/opentrons_hardware/scripts/load.py @@ -189,7 +189,7 @@ async def run(self, run_for: float) -> LoadResults: ) try: self._messenger.add_listener(self) - asyncio.wait([self._load_bus()], timeout=run_for) + await asyncio.wait([self._load_bus()], timeout=run_for) except asyncio.TimeoutError: pass except KeyboardInterrupt: diff --git a/hardware/opentrons_hardware/scripts/provision_gripper.py b/hardware/opentrons_hardware/scripts/provision_gripper.py index 2c37612468c..8eca4b79bab 100644 --- a/hardware/opentrons_hardware/scripts/provision_gripper.py +++ b/hardware/opentrons_hardware/scripts/provision_gripper.py @@ -43,9 +43,7 @@ async def flash_serials( ) -> None: """Flash serials in a loop.""" while True: - should_quit = await get_and_update_serial_once(messenger, base_log, trace_log) - if should_quit: - return + await get_and_update_serial_once(messenger, base_log, trace_log) def _read_input_and_confirm(prompt: str) -> str: diff --git a/hardware/opentrons_hardware/scripts/provision_pipette.py b/hardware/opentrons_hardware/scripts/provision_pipette.py index 3f390a5b153..f5b4141f85c 100644 --- a/hardware/opentrons_hardware/scripts/provision_pipette.py +++ b/hardware/opentrons_hardware/scripts/provision_pipette.py @@ -47,11 +47,7 @@ async def flash_serials( ) -> None: """Flash serials in a loop.""" while True: - should_quit = await get_and_update_serial_once( - messenger, which_pipette, base_log, trace_log - ) - if should_quit: - return + await get_and_update_serial_once(messenger, which_pipette, base_log, trace_log) def _read_input_and_confirm(prompt: str) -> str: From a68df58057b0d95a610599389e5576021a03129e Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Tue, 19 Dec 2023 09:55:53 -0500 Subject: [PATCH 26/60] hardware fixes from 3.10 --- .../drivers/can_bus/can_messenger.py | 1 - .../drivers/binary_usb/test_driver.py | 16 +++++++- .../drivers/can_bus/test_can_messenger.py | 38 ++++++++----------- 3 files changed, 30 insertions(+), 25 deletions(-) diff --git a/hardware/opentrons_hardware/drivers/can_bus/can_messenger.py b/hardware/opentrons_hardware/drivers/can_bus/can_messenger.py index 48b85e1ce28..4446b3b0683 100644 --- a/hardware/opentrons_hardware/drivers/can_bus/can_messenger.py +++ b/hardware/opentrons_hardware/drivers/can_bus/can_messenger.py @@ -395,7 +395,6 @@ async def _read_task(self) -> None: log.exception(f"Failed to build from {message}") else: log.error(f"Message {message} is not recognized.") - raise StopAsyncIteration @property def exclusive_writer(self) -> asyncio.Lock: diff --git a/hardware/tests/opentrons_hardware/drivers/binary_usb/test_driver.py b/hardware/tests/opentrons_hardware/drivers/binary_usb/test_driver.py index e02b6caf58e..2148818ecfd 100644 --- a/hardware/tests/opentrons_hardware/drivers/binary_usb/test_driver.py +++ b/hardware/tests/opentrons_hardware/drivers/binary_usb/test_driver.py @@ -56,6 +56,20 @@ def __init__( self, ) -> None: """Open some serial ports to simulate the usb connection.""" + # Note: fork will work on linux. it will definitely not work on windows, and probably + # won't work on OSX because OSX system libraries can start threads and you can't start + # threads from a forked process. + # + # On python 3.7, they hadn't realized this, and fork was the default OSX start method. + # on python 3.8 and subsequent, they had, and so by default OSX uses spawn. + # + # The code in this module sends open fileio objects and/or file descriptors to the subprocess, + # which is only easy on fork. + # + # So here, we're making the start method be fork, which won't work on windows (but it didn't + # before) and will now be pretty unreliable on OSX (which is new, but we only use that for dev + # tests anyway). + self.mp_context = multiprocessing.get_context("fork") self.primary_files_fd = [] # Dict of primary fd to primary file object. self.primary_files = [] self.secondary_names = [] # Dict of primary fd to secondary name. @@ -70,7 +84,7 @@ def __init__( self.device_port = self.secondary_names[0] self.client_port = self.secondary_names[1] - self.proc = multiprocessing.Process( + self.proc = self.mp_context.Process( target=run, args=(self.primary_files_fd, self.primary_files) ) self.proc.start() diff --git a/hardware/tests/opentrons_hardware/drivers/can_bus/test_can_messenger.py b/hardware/tests/opentrons_hardware/drivers/can_bus/test_can_messenger.py index e24f583e12b..1dc685276a6 100644 --- a/hardware/tests/opentrons_hardware/drivers/can_bus/test_can_messenger.py +++ b/hardware/tests/opentrons_hardware/drivers/can_bus/test_can_messenger.py @@ -58,7 +58,7 @@ async def incoming_messages() -> Queue[CanMessage]: @pytest.fixture -def mock_driver(incoming_messages: Queue[CanMessage]) -> AsyncMock: +async def mock_driver(incoming_messages: Queue[CanMessage]) -> AsyncMock: """Mock can driver.""" m = AsyncMock() m.__aiter__.side_effect = lambda: m @@ -67,7 +67,7 @@ def mock_driver(incoming_messages: Queue[CanMessage]) -> AsyncMock: @pytest.fixture -def subject(mock_driver: AsyncMock) -> CanMessenger: +async def subject(mock_driver: AsyncMock) -> CanMessenger: """The test subject.""" return CanMessenger(driver=mock_driver) @@ -106,7 +106,8 @@ async def test_send( message: MessageDefinition, ) -> None: """It should create a can message and use the driver to send the message.""" - await subject.send(node_id, message) + async with subject: + await subject.send(node_id, message) mock_driver.send.assert_called_once_with( message=CanMessage( arbitration_id=ArbitrationId( @@ -157,11 +158,8 @@ async def test_ensure_send( ) ) - """It should create a can message and use the driver to send the message and raise no exception.""" - error, ignore = await asyncio.gather( - subject.ensure_send(node_id, message, expected_nodes=[node_id]), - subject.__aenter__(), - ) + async with subject: + error = await subject.ensure_send(node_id, message, expected_nodes=[node_id]) assert error == ErrorCode.ok mock_driver.send.assert_called_once_with( message=CanMessage( @@ -219,11 +217,8 @@ async def test_ensure_send_error( ) ) - """It should create a can message and use the driver to send the message and raise no exception.""" - error, ignore = await asyncio.gather( - subject.ensure_send(node_id, message, expected_nodes=[node_id]), - subject.__aenter__(), - ) + async with subject: + error = await subject.ensure_send(node_id, message, expected_nodes=[node_id]) assert error == 5 mock_driver.send.assert_called_once_with( message=CanMessage( @@ -290,12 +285,8 @@ async def test_ensure_send_subnodes( data=message.payload.message_index.value.to_bytes(4, "big"), ) ) - - """It should create a can message and use the driver to send the message and raise no exception.""" - error, ignore = await asyncio.gather( - subject.ensure_send(node_id, message, expected_nodes=[node_id]), - subject.__aenter__(), - ) + async with subject: + error = await subject.ensure_send(node_id, message, expected_nodes=[node_id]) assert error == ErrorCode.ok mock_driver.send.assert_called_once_with( message=CanMessage( @@ -332,10 +323,11 @@ async def test_ensure_send_timeout( message: MessageDefinition, ) -> None: """It should create a can message and use the driver to send the message but raise an TimeoutError.""" - error, ignore = await asyncio.gather( - subject.ensure_send(node_id, message, timeout=0.1, expected_nodes=[node_id]), - subject.__aenter__(), - ) + async with subject: + error = await subject.ensure_send( + node_id, message, timeout=0.1, expected_nodes=[node_id] + ) + assert error == ErrorCode.timeout mock_driver.send.assert_called_once_with( message=CanMessage( From 219d461e58458989af0251940259e95017e509ab Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Tue, 19 Dec 2023 10:02:56 -0500 Subject: [PATCH 27/60] notify-server type updates --- notify-server/tests/unit/test_settings.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/notify-server/tests/unit/test_settings.py b/notify-server/tests/unit/test_settings.py index 41ebcf80ede..ebd8077f83a 100644 --- a/notify-server/tests/unit/test_settings.py +++ b/notify-server/tests/unit/test_settings.py @@ -2,7 +2,7 @@ import json import os -from typing import Generator +from typing import Generator, Dict, cast from unittest.mock import patch, MagicMock import pytest from _pytest.fixtures import FixtureRequest @@ -11,9 +11,9 @@ @pytest.fixture -def envvar_patch() -> Generator[MagicMock, None, None]: +def envvar_patch() -> Generator[Dict[str, str], None, None]: """Patch os.environ.""" - with patch.object(os, "environ", new=dict()) as p: + with patch.object(os, "environ", new=cast(Dict[str, str], dict())) as p: yield p From e8eb7ff90d872782e875b91b7d4f858bc2ab5642 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Tue, 19 Dec 2023 10:04:47 -0500 Subject: [PATCH 28/60] shared-data type updates --- shared-data/python/opentrons_shared_data/_version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/shared-data/python/opentrons_shared_data/_version.py b/shared-data/python/opentrons_shared_data/_version.py index 7bf0b94ab04..d5243bca150 100644 --- a/shared-data/python/opentrons_shared_data/_version.py +++ b/shared-data/python/opentrons_shared_data/_version.py @@ -9,7 +9,7 @@ import importlib_metadata as metadata # type: ignore[no-redef] try: - version: str = metadata.version("opentrons_shared_data") # type: ignore[attr-defined] + version: str = metadata.version("opentrons_shared_data") except Exception as e: logging.warning( "Could not determine version for opentrons, may be dev install, using 0.0.0-dev" From 54aa90d78941ffaf5a70b8a765b3c777a81bcec6 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Tue, 19 Dec 2023 10:40:22 -0500 Subject: [PATCH 29/60] update-server deps updates --- update-server/Pipfile.lock | 420 +++++++++++++++++++++++++++++++------ update-server/setup.py | 2 +- 2 files changed, 362 insertions(+), 60 deletions(-) diff --git a/update-server/Pipfile.lock b/update-server/Pipfile.lock index 0cb4b8be550..be1986a7ff5 100644 --- a/update-server/Pipfile.lock +++ b/update-server/Pipfile.lock @@ -29,39 +29,112 @@ "develop": { "aiohttp": { "hashes": [ - "sha256:0419705a36b43c0ac6f15469f9c2a08cad5c939d78bd12a5c23ea167c8253b2b", - "sha256:1812fc4bc6ac1bde007daa05d2d0f61199324e0cc893b11523e646595047ca08", - "sha256:2214b5c0153f45256d5d52d1e0cafe53f9905ed035a142191727a5fb620c03dd", - "sha256:275909137f0c92c61ba6bb1af856a522d5546f1de8ea01e4e726321c697754ac", - "sha256:3983611922b561868428ea1e7269e757803713f55b53502423decc509fef1650", - 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From 35a1008a1f0da9b3dcf386452b602f1e50b1949e Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Tue, 19 Dec 2023 10:40:35 -0500 Subject: [PATCH 30/60] update-server typing fixes --- .../common/name_management/__init__.py | 10 +++----- .../otupdate/common/run_application.py | 12 ++++------ .../otupdate/common/ssh_key_management.py | 24 +++++++------------ .../name_management/test_http_endpoints.py | 10 ++++---- 4 files changed, 22 insertions(+), 34 deletions(-) diff --git a/update-server/otupdate/common/name_management/__init__.py b/update-server/otupdate/common/name_management/__init__.py index c16d5a8d76d..0994cfa1449 100644 --- a/update-server/otupdate/common/name_management/__init__.py +++ b/update-server/otupdate/common/name_management/__init__.py @@ -75,9 +75,7 @@ async def set_name_endpoint(request: web.Request) -> web.Response: """ def build_400(msg: str) -> web.Response: - return web.json_response( # type: ignore[no-untyped-call,no-any-return] - data={"message": msg}, status=400 - ) + return web.json_response(data={"message": msg}, status=400) try: body = await request.json() @@ -97,9 +95,7 @@ def build_400(msg: str) -> web.Response: name_synchronizer = get_name_synchronizer(request) new_name = await name_synchronizer.set_name(new_name=name_to_set) - return web.json_response( # type: ignore[no-untyped-call,no-any-return] - data={"name": new_name}, status=200 - ) + return web.json_response(data={"name": new_name}, status=200) async def get_name_endpoint(request: web.Request) -> web.Response: @@ -111,7 +107,7 @@ async def get_name_endpoint(request: web.Request) -> web.Response: GET /server/name -> 200 OK, {'name': robot name} """ name_synchronizer = get_name_synchronizer(request) - return web.json_response( # type: ignore[no-untyped-call,no-any-return] + return web.json_response( data={"name": await name_synchronizer.get_name()}, status=200 ) diff --git a/update-server/otupdate/common/run_application.py b/update-server/otupdate/common/run_application.py index 18a0cf03d74..ab63803a814 100644 --- a/update-server/otupdate/common/run_application.py +++ b/update-server/otupdate/common/run_application.py @@ -15,15 +15,13 @@ async def run_and_notify_up(app: web.Application, host: str, port: int) -> NoRet This method will only return once the task has been canceled, such as if this process has been signaled to stop. """ - runner = web.AppRunner(app) # type: ignore[no-untyped-call] + runner = web.AppRunner(app) - await runner.setup() # type: ignore[no-untyped-call] + await runner.setup() try: - site = web.TCPSite( # type: ignore[no-untyped-call] - runner=runner, host=host, port=port - ) - await site.start() # type: ignore[no-untyped-call] + site = web.TCPSite(runner=runner, host=host, port=port) + await site.start() systemd.notify_up() @@ -34,4 +32,4 @@ async def run_and_notify_up(app: web.Application, host: str, port: int) -> NoRet await asyncio.sleep(10) finally: - await runner.cleanup() # type: ignore[no-untyped-call] + await runner.cleanup() diff --git a/update-server/otupdate/common/ssh_key_management.py b/update-server/otupdate/common/ssh_key_management.py index fa327806701..adee38b036d 100644 --- a/update-server/otupdate/common/ssh_key_management.py +++ b/update-server/otupdate/common/ssh_key_management.py @@ -39,9 +39,7 @@ async def decorated(request: web.Request) -> web.Response: ), } if not ipaddr_str: - return web.json_response( # type: ignore[no-untyped-call,no-any-return] - data=invalid_req_data, status=403 - ) + return web.json_response(data=invalid_req_data, status=403) try: addr = ipaddress.ip_address(ipaddr_str) except ValueError: @@ -49,9 +47,7 @@ async def decorated(request: web.Request) -> web.Response: raise if not addr.is_link_local: - return web.json_response( # type: ignore[no-untyped-call,no-any-return] - data=invalid_req_data, status=403 - ) + return web.json_response(data=invalid_req_data, status=403) return await handler(request) @@ -106,9 +102,7 @@ def key_present(hashval: str) -> bool: def key_error(error: str, message: str, status: int = 400) -> web.Response: - return web.json_response( # type: ignore[no-untyped-call,no-any-return] - data={"error": error, "message": message}, status=status - ) + return web.json_response(data={"error": error, "message": message}, status=status) @require_linklocal @@ -120,7 +114,7 @@ async def list_keys(request: web.Request) -> web.Response: (or 403 if not from the link-local connection) """ - return web.json_response( # type: ignore[no-untyped-call,no-any-return] + return web.json_response( { "public_keys": [ {"key_md5": details[0], "key": details[1]} for details in get_keys() @@ -173,7 +167,7 @@ async def add(request: web.Request) -> web.Response: with authorized_keys("a") as ak: ak.write(f"{pubkey}\n") - return web.json_response( # type: ignore[no-untyped-call,no-any-return] + return web.json_response( data={"message": f"Added key {hashval}", "key_md5": hashval}, status=201 ) @@ -190,7 +184,7 @@ async def clear(request: web.Request) -> web.Response: with authorized_keys("w") as ak: ak.write("\n".join([]) + "\n") - return web.json_response( # type: ignore[no-untyped-call,no-any-return] + return web.json_response( data={ "message": "Keys cleared. " "Restart robot to take effect", "restart_url": "/server/restart", @@ -217,7 +211,7 @@ async def remove(request: web.Request) -> web.Response: new_keys.append(key) if not found: - return web.json_response( # type: ignore[no-untyped-call,no-any-return] + return web.json_response( data={ "error": "invalid-key-hash", "message": f"No such key md5 {requested_hash}", @@ -228,7 +222,7 @@ async def remove(request: web.Request) -> web.Response: with authorized_keys("w") as ak: ak.write("\n".join(new_keys) + "\n") - return web.json_response( # type: ignore[no-untyped-call,no-any-return] + return web.json_response( data={ "message": f"Key {requested_hash} deleted. " "Restart robot to take effect", "restart_url": "/server/restart", @@ -281,7 +275,7 @@ async def add_from_local(request: web.Request) -> web.Response: LOG.error(f"Could not process ssh public key: {key} {e}") continue - return web.json_response( # type: ignore[no-untyped-call,no-any-return] + return web.json_response( data={"message": f"Added {len(new_keys)} new keys", "key_md5": new_keys}, status=201, ) diff --git a/update-server/tests/common/name_management/test_http_endpoints.py b/update-server/tests/common/name_management/test_http_endpoints.py index 21ebed8f85d..a360760568a 100644 --- a/update-server/tests/common/name_management/test_http_endpoints.py +++ b/update-server/tests/common/name_management/test_http_endpoints.py @@ -15,7 +15,7 @@ async def test_get_name( ) -> None: decoy.when(await mock_name_synchronizer.get_name()).then_return("the returned name") - response = await (test_cli[0].get("/server/name")) # type: ignore[no-untyped-call] + response = await (test_cli[0].get("/server/name")) assert response.status == 200 body = await response.json() @@ -31,7 +31,7 @@ async def test_set_name_valid( "the returned name" ) - response = await test_cli[0].post("/server/name", json={"name": "the input name"}) # type: ignore[no-untyped-call] + response = await test_cli[0].post("/server/name", json={"name": "the input name"}) assert response.status == 200 body = await response.json() @@ -39,15 +39,15 @@ async def test_set_name_valid( async def test_set_name_not_json(test_cli: Tuple[HTTPTestClient, str]) -> None: - response = await test_cli[0].post("/server/name", data="bada bing bada boom") # type: ignore[no-untyped-call] + response = await test_cli[0].post("/server/name", data="bada bing bada boom") assert response.status == 400 async def test_set_name_field_missing(test_cli: Tuple[HTTPTestClient, str]) -> None: - response = await test_cli[0].post("/server/name", json={}) # type: ignore[no-untyped-call] + response = await test_cli[0].post("/server/name", json={}) assert response.status == 400 async def test_set_name_field_not_a_str(test_cli: Tuple[HTTPTestClient, str]) -> None: - response = await test_cli[0].post("/server/name", json={"name": 2}) # type: ignore[no-untyped-call] + response = await test_cli[0].post("/server/name", json={"name": 2}) assert response.status == 400 From c9bf3892abe48d437ba1f46e5c0c2bd9fda1de73 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Tue, 19 Dec 2023 10:40:42 -0500 Subject: [PATCH 31/60] update-server fixes from new typing --- update-server/otupdate/common/update.py | 38 +++++++++++++++++++------ 1 file changed, 29 insertions(+), 9 deletions(-) diff --git a/update-server/otupdate/common/update.py b/update-server/otupdate/common/update.py index 0da8655ae7f..cce77e632dc 100644 --- a/update-server/otupdate/common/update.py +++ b/update-server/otupdate/common/update.py @@ -14,7 +14,7 @@ from typing import Optional from typing_extensions import Protocol -from aiohttp import web, BodyPartReader +from aiohttp import web, BodyPartReader, MultipartReader from . import config, update_actions from .constants import APP_VARIABLE_PREFIX, RESTART_LOCK_NAME @@ -97,6 +97,8 @@ async def status(request: web.Request, session: UpdateSession) -> web.Response: async def _save_file(part: BodyPartReader, path: str) -> None: # making sure directory exists first Path(path).mkdir(parents=True, exist_ok=True) + if not part.name: + raise Exception("Cannot save file with no name") with open(os.path.join(path, part.name), "wb") as write: while not part.at_eof(): chunk = await part.read_chunk() @@ -171,6 +173,21 @@ def validation_done(fut): return validation_future +async def _read_parts_and_find_update( + reader: MultipartReader, session: UpdateSession +) -> Optional[str]: + found: Optional[str] = None + async for part in reader: + if part.name not in VALID_UPDATE_PKG: + LOG.info(f"Unknown field name {part.name} in file_upload, ignoring") + await part.release() + else: + LOG.info(f"Writing {part.name}") + await _save_file(part, session.download_path) + found = part.name + return found + + @require_session async def file_upload(request: web.Request, session: UpdateSession) -> web.Response: """Serves /update/:session/file @@ -187,13 +204,7 @@ async def file_upload(request: web.Request, session: UpdateSession) -> web.Respo status=409, ) reader = await request.multipart() - async for part in reader: - if part.name not in VALID_UPDATE_PKG: - LOG.info(f"Unknown field name {part.name} in file_upload, ignoring") - await part.release() - else: - LOG.info(f"Writing {part.name}") - await _save_file(part, session.download_path) + found_name = await _read_parts_and_find_update(reader, session) maybe_actions = update_actions.UpdateActionsInterface.from_request(request) if not maybe_actions: @@ -205,11 +216,20 @@ async def file_upload(request: web.Request, session: UpdateSession) -> web.Respo status=500, ) + if not found_name: + return web.json_response( + data={ + "error": "no-file-name", + "message": "Request error: no field name for system zip", + }, + status=400, + ) + _begin_validation( session, config.config_from_request(request), asyncio.get_event_loop(), - os.path.join(session.download_path, part.name), + os.path.join(session.download_path, found_name), maybe_actions, ) From a8c4a4c2e6ab80d62af9b3ffc12db04511bb5bc5 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Tue, 19 Dec 2023 10:43:31 -0500 Subject: [PATCH 32/60] same pipenv in action as make --- .github/actions/python/setup/action.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/actions/python/setup/action.yaml b/.github/actions/python/setup/action.yaml index 6a6b02d9305..7fc81cc258f 100644 --- a/.github/actions/python/setup/action.yaml +++ b/.github/actions/python/setup/action.yaml @@ -27,6 +27,6 @@ runs: - shell: bash run: | npm install --global shx@0.3.3 - $OT_PYTHON -m pip install pipenv==2021.5.29 + $OT_PYTHON -m pip install pipenv==2023.11.15 - shell: bash run: 'make -C ${{ inputs.project }} setup' From cab7ac60f247e73d67467cb5b1a82063a3156108 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Tue, 19 Dec 2023 10:50:48 -0500 Subject: [PATCH 33/60] no more keep-outdated --- scripts/python.mk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/python.mk b/scripts/python.mk index bcc7c49a227..917f6b8b319 100644 --- a/scripts/python.mk +++ b/scripts/python.mk @@ -20,7 +20,7 @@ pip := $(pipenv) run pip pytest := $(pipenv) run py.test pipenv_opts := --dev $(and $(OT_VIRTUALENV_VERSION),--python $(OT_VIRTUALENV_VERSION)) -pipenv_opts += $(and $(CI),--keep-outdated --clear) +pipenv_opts += $(and $(CI),--clear) wheel_opts := $(if $(and $(or $(CI),$(V),$(VERBOSE)),$(not $(QUIET))),,-q) poetry := poetry From a39381ab8ad5919f4d4a1f79350df8a9aad87e2d Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Tue, 19 Dec 2023 10:58:12 -0500 Subject: [PATCH 34/60] update h-t pipfile --- hardware-testing/Pipfile.lock | 128 +++++++++++++++++----------------- 1 file changed, 64 insertions(+), 64 deletions(-) diff --git a/hardware-testing/Pipfile.lock b/hardware-testing/Pipfile.lock index 35bf79f025d..b7d31b5c899 100644 --- a/hardware-testing/Pipfile.lock +++ b/hardware-testing/Pipfile.lock @@ -221,7 +221,7 @@ "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926", "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'", + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==1.16.0" }, "sniffio": { @@ -234,11 +234,11 @@ }, "typing-extensions": { "hashes": [ - "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0", - "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef" + "sha256:23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783", + "sha256:af72aea155e91adfc61c3ae9e0e342dbc0cba726d6cba4b6c72c1f34e47291cd" ], "markers": "python_version >= '3.8'", - "version": "==4.8.0" + "version": "==4.9.0" } }, "develop": { @@ -322,61 +322,61 @@ }, "coverage": { "hashes": [ - "sha256:0cbf38419fb1a347aaf63481c00f0bdc86889d9fbf3f25109cf96c26b403fda1", - "sha256:12d15ab5833a997716d76f2ac1e4b4d536814fc213c85ca72756c19e5a6b3d63", - "sha256:149de1d2401ae4655c436a3dced6dd153f4c3309f599c3d4bd97ab172eaf02d9", - "sha256:1981f785239e4e39e6444c63a98da3a1db8e971cb9ceb50a945ba6296b43f312", - "sha256:2443cbda35df0d35dcfb9bf8f3c02c57c1d6111169e3c85fc1fcc05e0c9f39a3", - "sha256:289fe43bf45a575e3ab10b26d7b6f2ddb9ee2dba447499f5401cfb5ecb8196bb", - "sha256:2f11cc3c967a09d3695d2a6f03fb3e6236622b93be7a4b5dc09166a861be6d25", - "sha256:307adb8bd3abe389a471e649038a71b4eb13bfd6b7dd9a129fa856f5c695cf92", - "sha256:310b3bb9c91ea66d59c53fa4989f57d2436e08f18fb2f421a1b0b6b8cc7fffda", - "sha256:315a989e861031334d7bee1f9113c8770472db2ac484e5b8c3173428360a9148", 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+ "sha256:9437a4074b43c177c92c96d051957592afd85ba00d3e92002c8ef45ee75df438", + "sha256:9e17d9cb06c13b4f2ef570355fa45797d10f19ca71395910b249e3f77942a837", + "sha256:9ede881c7618f9cf93e2df0421ee127afdfd267d1b5d0c59bcea771cf160ea4a", + "sha256:a1f76cfc122c9e0f62dbe0460ec9cc7696fc9a0293931a33b8870f78cf83a327", + "sha256:a2ac4245f18057dfec3b0074c4eb366953bca6787f1ec397c004c78176a23d56", + "sha256:a702e66483b1fe602717020a0e90506e759c84a71dbc1616dd55d29d86a9b91f", + "sha256:ad2453b852a1316c8a103c9c970db8fbc262f4f6b930aa6c606df9b2766eee06", + "sha256:af75cf83c2d57717a8493ed2246d34b1f3398cb8a92b10fd7a1858cad8e78f59", + "sha256:afdcc10c01d0db217fc0a64f58c7edd635b8f27787fea0a3054b856a6dff8717", + "sha256:c59a3e59fb95e6d72e71dc915e6d7fa568863fad0a80b33bc7b82d6e9f844973", + "sha256:cad9afc1644b979211989ec3ff7d82110b2ed52995c2f7263e7841c846a75348", + "sha256:d299d379b676812e142fb57662a8d0d810b859421412b4d7af996154c00c31bb", + "sha256:d31650d313bd90d027f4be7663dfa2241079edd780b56ac416b56eebe0a21aab", + "sha256:d874434e0cb7b90f7af2b6e3309b0733cde8ec1476eb47db148ed7deeb2a9494", + "sha256:db0338c4b0951d93d547e0ff8d8ea340fecf5885f5b00b23be5aa99549e14cfd", + "sha256:df04c64e58df96b4427db8d0559e95e2df3138c9916c96f9f6a4dd220db2fdb7", + "sha256:e995efb191f04b01ced307dbd7407ebf6e6dc209b528d75583277b10fd1800ee", + "sha256:eda7f6e92358ac9e1717ce1f0377ed2b9320cea070906ece4e5c11d172a45a39", + "sha256:ee453085279df1bac0996bc97004771a4a052b1f1e23f6101213e3796ff3cb85", + "sha256:ee6621dccce8af666b8c4651f9f43467bfbf409607c604b840b78f4ff3619aeb", + "sha256:eee5e741b43ea1b49d98ab6e40f7e299e97715af2488d1c77a90de4a663a86e2", + "sha256:f3bfd2c2f0e5384276e12b14882bf2c7621f97c35320c3e7132c156ce18436a1", + "sha256:f501e36ac428c1b334c41e196ff6bd550c0353c7314716e80055b1f0a32ba394", + "sha256:f9191be7af41f0b54324ded600e8ddbcabea23e1e8ba419d9a53b241dece821d", + "sha256:fbd8a5fe6c893de21a3c6835071ec116d79334fbdf641743332e442a3466f7ea", + "sha256:fc200cec654311ca2c3f5ab3ce2220521b3d4732f68e1b1e79bef8fcfc1f2b97", + "sha256:ff4800783d85bff132f2cc7d007426ec698cdce08c3062c8d501ad3f4ea3d16c", + "sha256:ffb0eacbadb705c0a6969b0adf468f126b064f3362411df95f6d4f31c40d31c1", + "sha256:fff0b2f249ac642fd735f009b8363c2b46cf406d3caec00e4deeb79b5ff39b40" ], "markers": "python_version >= '3.8'", - "version": "==7.3.2" + "version": "==7.3.3" }, "flake8": { "hashes": [ @@ -485,11 +485,11 @@ }, "pathspec": { "hashes": [ - "sha256:1d6ed233af05e679efb96b1851550ea95bbb64b7c490b0f5aa52996c11e92a20", - "sha256:e0d8d0ac2f12da61956eb2306b69f9469b42f4deb0f3cb6ed47b9cce9996ced3" + "sha256:a0d503e138a4c123b27490a4f7beda6a01c6f288df0e4a8b79c7eb0dc7b4cc08", + "sha256:a482d51503a1ab33b1c67a6c3813a26953dbdc71c31dacaef9a838c4e29f5712" ], - "markers": "python_version >= '3.7'", - "version": "==0.11.2" + "markers": "python_version >= '3.8'", + "version": "==0.12.1" }, "platformdirs": { "hashes": [ @@ -591,11 +591,11 @@ }, "typing-extensions": { "hashes": [ - "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0", - "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef" + "sha256:23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783", + "sha256:af72aea155e91adfc61c3ae9e0e342dbc0cba726d6cba4b6c72c1f34e47291cd" ], "markers": "python_version >= '3.8'", - "version": "==4.8.0" + "version": "==4.9.0" }, "urllib3": { "hashes": [ From 7f29911a9b5f70051e733d2caaccbce328b13a7c Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Tue, 19 Dec 2023 11:06:26 -0500 Subject: [PATCH 35/60] h-t fxies from typing --- hardware-testing/hardware_testing/gravimetric/__main__.py | 4 ++-- .../hardware_testing/scripts/find_plunger_motion_settings.py | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/hardware-testing/hardware_testing/gravimetric/__main__.py b/hardware-testing/hardware_testing/gravimetric/__main__.py index e7ee0f0f177..54a8278adef 100644 --- a/hardware-testing/hardware_testing/gravimetric/__main__.py +++ b/hardware-testing/hardware_testing/gravimetric/__main__.py @@ -177,8 +177,8 @@ def _get_protocol_context(cls, args: argparse.Namespace) -> ProtocolContext: ) return _ctx - @classmethod # noqa: C901 - def build_run_args(cls, args: argparse.Namespace) -> "RunArgs": + @classmethod + def build_run_args(cls, args: argparse.Namespace) -> "RunArgs": # noqa: C901 """Build.""" _ctx = RunArgs._get_protocol_context(args) operator_name = helpers._get_operator_name(_ctx.is_simulating()) diff --git a/hardware-testing/hardware_testing/scripts/find_plunger_motion_settings.py b/hardware-testing/hardware_testing/scripts/find_plunger_motion_settings.py index 4cb6023ce04..d4e8addcc8b 100644 --- a/hardware-testing/hardware_testing/scripts/find_plunger_motion_settings.py +++ b/hardware-testing/hardware_testing/scripts/find_plunger_motion_settings.py @@ -50,10 +50,10 @@ async def _motion_settings( speed: float, ) -> None: pip_ax = Axis.of_main_tool_actuator(mount) - helpers_ot3.set_gantry_load_per_axis_current_settings_ot3( + await helpers_ot3.set_gantry_load_per_axis_current_settings_ot3( api, axis=pip_ax, hold_current=DEFAULT_HOLD_CURRENT, run_current=current ) - helpers_ot3.set_gantry_load_per_axis_motion_settings_ot3( + await helpers_ot3.set_gantry_load_per_axis_motion_settings_ot3( api, axis=pip_ax, acceleration=acceleration, From 29f423cb66b584c4a5f316896f0559e763d72b3e Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Tue, 19 Dec 2023 11:10:19 -0500 Subject: [PATCH 36/60] h-t needs flex extras --- hardware-testing/Pipfile | 4 +- hardware-testing/Pipfile.lock | 163 +++++++++++++++++++++++++++++++++- 2 files changed, 163 insertions(+), 4 deletions(-) diff --git a/hardware-testing/Pipfile b/hardware-testing/Pipfile index 96d2de6b9bd..acc317ac325 100644 --- a/hardware-testing/Pipfile +++ b/hardware-testing/Pipfile @@ -4,9 +4,9 @@ verify_ssl = true name = "pypi" [packages] -opentrons = {editable = true, path = "./../api"} +opentrons = {editable = true, path = "./../api", extras=['flex-hardware']} opentrons-shared-data = {editable = true, path = "./../shared-data/python"} -opentrons-hardware = {editable = true, path = "./../hardware"} +opentrons-hardware = {editable = true, path = "./../hardware", extras=['FLEX']} hardware-testing = { editable = true, path = "." } pyserial = "==3.5" diff --git a/hardware-testing/Pipfile.lock b/hardware-testing/Pipfile.lock index b7d31b5c899..6c717bc2743 100644 --- a/hardware-testing/Pipfile.lock +++ b/hardware-testing/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "7ca3bff855c6090feac4bf3594ce0b9179f5c105622fb144eed7f35b35cb306d" + "sha256": "62d9d88f58594147f78dbda65db2d96b53ac2c07a54eb0b81854c7c7ebe4e247" }, "pipfile-spec": 6, "requires": { @@ -66,6 +66,68 @@ ], "version": "==3.0.2" }, + "msgpack": { + "hashes": [ + "sha256:04ad6069c86e531682f9e1e71b71c1c3937d6014a7c3e9edd2aa81ad58842862", + "sha256:0bfdd914e55e0d2c9e1526de210f6fe8ffe9705f2b1dfcc4aecc92a4cb4b533d", + "sha256:1dc93e8e4653bdb5910aed79f11e165c85732067614f180f70534f056da97db3", + "sha256:1e2d69948e4132813b8d1131f29f9101bc2c915f26089a6d632001a5c1349672", + "sha256:235a31ec7db685f5c82233bddf9858748b89b8119bf4538d514536c485c15fe0", + "sha256:27dcd6f46a21c18fa5e5deed92a43d4554e3df8d8ca5a47bf0615d6a5f39dbc9", + "sha256:28efb066cde83c479dfe5a48141a53bc7e5f13f785b92ddde336c716663039ee", + "sha256:3476fae43db72bd11f29a5147ae2f3cb22e2f1a91d575ef130d2bf49afd21c46", + "sha256:36e17c4592231a7dbd2ed09027823ab295d2791b3b1efb2aee874b10548b7524", + "sha256:384d779f0d6f1b110eae74cb0659d9aa6ff35aaf547b3955abf2ab4c901c4819", + "sha256:38949d30b11ae5f95c3c91917ee7a6b239f5ec276f271f28638dec9156f82cfc", + "sha256:3967e4ad1aa9da62fd53e346ed17d7b2e922cba5ab93bdd46febcac39be636fc", + "sha256:3e7bf4442b310ff154b7bb9d81eb2c016b7d597e364f97d72b1acc3817a0fdc1", + "sha256:3f0c8c6dfa6605ab8ff0611995ee30d4f9fcff89966cf562733b4008a3d60d82", + "sha256:484ae3240666ad34cfa31eea7b8c6cd2f1fdaae21d73ce2974211df099a95d81", + "sha256:4a7b4f35de6a304b5533c238bee86b670b75b03d31b7797929caa7a624b5dda6", + "sha256:4cb14ce54d9b857be9591ac364cb08dc2d6a5c4318c1182cb1d02274029d590d", + "sha256:4e71bc4416de195d6e9b4ee93ad3f2f6b2ce11d042b4d7a7ee00bbe0358bd0c2", + "sha256:52700dc63a4676669b341ba33520f4d6e43d3ca58d422e22ba66d1736b0a6e4c", + "sha256:572efc93db7a4d27e404501975ca6d2d9775705c2d922390d878fcf768d92c87", + "sha256:576eb384292b139821c41995523654ad82d1916da6a60cff129c715a6223ea84", + "sha256:5b0bf0effb196ed76b7ad883848143427a73c355ae8e569fa538365064188b8e", + "sha256:5b6ccc0c85916998d788b295765ea0e9cb9aac7e4a8ed71d12e7d8ac31c23c95", + "sha256:5ed82f5a7af3697b1c4786053736f24a0efd0a1b8a130d4c7bfee4b9ded0f08f", + "sha256:6d4c80667de2e36970ebf74f42d1088cc9ee7ef5f4e8c35eee1b40eafd33ca5b", + "sha256:730076207cb816138cf1af7f7237b208340a2c5e749707457d70705715c93b93", + "sha256:7687e22a31e976a0e7fc99c2f4d11ca45eff652a81eb8c8085e9609298916dcf", + "sha256:822ea70dc4018c7e6223f13affd1c5c30c0f5c12ac1f96cd8e9949acddb48a61", + "sha256:84b0daf226913133f899ea9b30618722d45feffa67e4fe867b0b5ae83a34060c", + "sha256:85765fdf4b27eb5086f05ac0491090fc76f4f2b28e09d9350c31aac25a5aaff8", + "sha256:8dd178c4c80706546702c59529ffc005681bd6dc2ea234c450661b205445a34d", + "sha256:8f5b234f567cf76ee489502ceb7165c2a5cecec081db2b37e35332b537f8157c", + "sha256:98bbd754a422a0b123c66a4c341de0474cad4a5c10c164ceed6ea090f3563db4", + "sha256:993584fc821c58d5993521bfdcd31a4adf025c7d745bbd4d12ccfecf695af5ba", + "sha256:a40821a89dc373d6427e2b44b572efc36a2778d3f543299e2f24eb1a5de65415", + "sha256:b291f0ee7961a597cbbcc77709374087fa2a9afe7bdb6a40dbbd9b127e79afee", + "sha256:b573a43ef7c368ba4ea06050a957c2a7550f729c31f11dd616d2ac4aba99888d", + "sha256:b610ff0f24e9f11c9ae653c67ff8cc03c075131401b3e5ef4b82570d1728f8a9", + "sha256:bdf38ba2d393c7911ae989c3bbba510ebbcdf4ecbdbfec36272abe350c454075", + "sha256:bfef2bb6ef068827bbd021017a107194956918ab43ce4d6dc945ffa13efbc25f", + "sha256:cab3db8bab4b7e635c1c97270d7a4b2a90c070b33cbc00c99ef3f9be03d3e1f7", + "sha256:cb70766519500281815dfd7a87d3a178acf7ce95390544b8c90587d76b227681", + "sha256:cca1b62fe70d761a282496b96a5e51c44c213e410a964bdffe0928e611368329", + "sha256:ccf9a39706b604d884d2cb1e27fe973bc55f2890c52f38df742bc1d79ab9f5e1", + "sha256:dc43f1ec66eb8440567186ae2f8c447d91e0372d793dfe8c222aec857b81a8cf", + "sha256:dd632777ff3beaaf629f1ab4396caf7ba0bdd075d948a69460d13d44357aca4c", + "sha256:e45ae4927759289c30ccba8d9fdce62bb414977ba158286b5ddaf8df2cddb5c5", + "sha256:e50ebce52f41370707f1e21a59514e3375e3edd6e1832f5e5235237db933c98b", + "sha256:ebbbba226f0a108a7366bf4b59bf0f30a12fd5e75100c630267d94d7f0ad20e5", + "sha256:ec79ff6159dffcc30853b2ad612ed572af86c92b5168aa3fc01a67b0fa40665e", + "sha256:f0936e08e0003f66bfd97e74ee530427707297b0d0361247e9b4f59ab78ddc8b", + "sha256:f26a07a6e877c76a88e3cecac8531908d980d3d5067ff69213653649ec0f60ad", + "sha256:f64e376cd20d3f030190e8c32e1c64582eba56ac6dc7d5b0b49a9d44021b52fd", + "sha256:f6ffbc252eb0d229aeb2f9ad051200668fc3a9aaa8994e49f0cb2ffe2b7867e7", + "sha256:f9a7c509542db4eceed3dcf21ee5267ab565a83555c9b88a8109dcecc4709002", + "sha256:ff1d0899f104f3921d94579a5638847f783c9b04f2d5f229392ca77fba5b82fc" + ], + "markers": "platform_system != 'Windows'", + "version": "==1.0.7" + }, "numpy": { "hashes": [ "sha256:06fa1ed84aa60ea6ef9f91ba57b5ed963c3729534e6e54055fc151fad0423f0a", @@ -110,10 +172,16 @@ }, "opentrons": { "editable": true, + "extras": [ + "flex-hardware" + ], "path": "./../api" }, "opentrons-hardware": { "editable": true, + "extras": [ + "FLEX" + ], "path": "./../hardware" }, "opentrons-shared-data": { @@ -121,6 +189,14 @@ "markers": "python_version >= '3.7'", "path": "./../shared-data/python" }, + "packaging": { + "hashes": [ + "sha256:048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5", + "sha256:8c491190033a9af7e1d931d0b5dacc2ef47509b34dd0de67ed209b5203fc88c7" + ], + "markers": "python_version >= '3.7'", + "version": "==23.2" + }, "pydantic": { "hashes": [ "sha256:1061c6ee6204f4f5a27133126854948e3b3d51fcc16ead2e5d04378c199b2f44", @@ -208,6 +284,13 @@ "index": "pypi", "version": "==3.5" }, + "python-can": { + "hashes": [ + "sha256:6ad50f4613289f3c4d276b6d2ac8901d776dcb929994cce93f55a69e858c595f", + "sha256:7eea9b81b0ff908000a825db024313f622895bd578e8a17433e0474cd7d2da83" + ], + "version": "==4.2.2" + }, "setuptools": { "hashes": [ "sha256:1e8fdff6797d3865f37397be788a4e3cba233608e9b509382a2777d25ebde7f2", @@ -239,6 +322,82 @@ ], "markers": "python_version >= '3.8'", "version": "==4.9.0" + }, + "wrapt": { + "hashes": [ + "sha256:0d2691979e93d06a95a26257adb7bfd0c93818e89b1406f5a28f36e0d8c1e1fc", + "sha256:14d7dc606219cdd7405133c713f2c218d4252f2a469003f8c46bb92d5d095d81", + "sha256:1a5db485fe2de4403f13fafdc231b0dbae5eca4359232d2efc79025527375b09", + "sha256:1acd723ee2a8826f3d53910255643e33673e1d11db84ce5880675954183ec47e", + "sha256:1ca9b6085e4f866bd584fb135a041bfc32cab916e69f714a7d1d397f8c4891ca", + 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], + "markers": "python_version >= '3.6'", + "version": "==1.16.0" } }, "develop": { @@ -578,7 +737,7 @@ "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc", "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f" ], - "markers": "python_version < '3.11'", + "markers": "python_version >= '3.7'", "version": "==2.0.1" }, "types-requests": { From f350cb325fc920ce283ae364511d174f2254611c Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Tue, 19 Dec 2023 16:04:34 -0500 Subject: [PATCH 37/60] r-s deps --- robot-server/Pipfile | 18 +- robot-server/Pipfile.lock | 874 ++++++++++++++++++++++++++------------ 2 files changed, 616 insertions(+), 276 deletions(-) diff --git a/robot-server/Pipfile b/robot-server/Pipfile index 0d2589c252e..ab84bf58dc8 100755 --- a/robot-server/Pipfile +++ b/robot-server/Pipfile @@ -11,13 +11,15 @@ python_version = "3.10" # https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177 atomicwrites = { version = "==1.4.0", markers="sys_platform=='win32'" } colorama = { version = "==0.4.4", markers="sys_platform=='win32'" } -pytest = "~=7.1" +# pytest 7.3.0 dropped attrs, and tavern 1.x at least has some pytest hooks +# that implicitly require the use of attrs in pytest internals +pytest = "<7.3.0,>=7.1.0" +tavern = "~=1.6" pytest-asyncio = "~=0.16" pytest-cov = "==2.10.1" pytest-lazy-fixture = "==0.6.3" pytest-xdist = "~=2.5.0" requests = "==2.27.1" -tavern = "~=1.6" graphviz = "==0.19" mock = "~=4.0.3" mypy = "==0.981" @@ -32,12 +34,14 @@ types-requests = "==2.25.6" types-mock = "==4.0.1" sqlalchemy2-stubs = "==0.0.2a21" python-box = "==5.4.1" +opentrons-hardware = {editable = true, path='../hardware', extras=['FLEX']} +opentrons = { editable = true, path = "../api"} +opentrons-shared-data = { editable = true, path = "../shared-data/python" } +notify-server = { editable = true, path = "../notify-server"} +server-utils = {editable = true, path = "./../server-utils"} +robot-server = { editable = true, path = "."} [packages] -opentrons = { editable = true, path = "../api" } -opentrons-shared-data = { editable = true, path = "../shared-data/python" } -notify-server = { editable = true, path = "../notify-server" } -robot-server = { editable = true, path = "." } anyio = "==3.6.1" fastapi = "==0.68.1" python-dotenv = "==0.19.0" @@ -51,7 +55,5 @@ idna = "==3.3" click = "==8.1.2" numpy = "==1.23.3" zipp = "==3.5.0" -opentrons-hardware = { editable = true, path = "./../hardware" } sqlalchemy = "==1.4.32" aiosqlite = "==0.17.0" -server-utils = {editable = true, path = "./../server-utils"} diff --git a/robot-server/Pipfile.lock b/robot-server/Pipfile.lock index c5c54c750e9..5da49dd795d 100644 --- a/robot-server/Pipfile.lock +++ b/robot-server/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "381b4b6885471b5eff4c6dbcb6612d4c363eaf208379a6d127c53630347ac0b2" + "sha256": "06068f3db988527a2ef06631a6b89ce69d124d3f22759be23f8b2ff789dd3d78" }, "pipfile-spec": 6, "requires": { @@ -16,13 +16,6 @@ ] }, "default": { - "aionotify": { - "hashes": [ - "sha256:385e1becfaac2d9f4326673033d53912ef9565b6febdedbec593ee966df392c6", - "sha256:64b702ad0eb115034533f9f62730a9253b79f5ff0fbf3d100c392124cdf12507" - ], - "version": "==0.2.0" - }, "aiosqlite": { "hashes": [ "sha256:6c49dc6d3405929b1d08eeccc72306d3677503cc5e5e43771efc1e00232e8231", @@ -49,14 +42,6 @@ "markers": "python_version >= '3.7'", "version": "==3.7.2" }, - "attrs": { - "hashes": [ - "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04", - "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015" - ], - "markers": "python_version >= '3.7'", - "version": "==23.1.0" - }, "click": { "hashes": [ "sha256:24e1a4a9ec5bf6299411369b208c1df2188d9eb8d916302fe6bf03faed227f1e", @@ -77,66 +62,67 @@ }, "greenlet": { "hashes": [ - "sha256:0a02d259510b3630f330c86557331a3b0e0c79dac3d166e449a39363beaae174", - "sha256:0b6f9f8ca7093fd4433472fd99b5650f8a26dcd8ba410e14094c1e44cd3ceddd", - 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"sha256:edfad1d29c73f9b863ebe7082ae9321374ccb10879eeabc84ba3b69f2579d537", + "sha256:f2058f813d4f2b5e3a9eb2eb3faf8f1d99b81c3e51aeda4b168406443e8ba809", + "sha256:f6b2d0c6703c988d334f297aa5df18c45e97b0af3679bb75059e0e0bd8b1069d", + "sha256:f8212564d49c50eb4565e502814f694e240c55551a5f1bc841d4fcaabb0a9b8a", + "sha256:ffa565331890b90056c01db69c0fe634a776f8019c143a5ae265f9c6bc4bd6d4" + ], + "markers": "python_version >= '3.6'", + "version": "==1.16.0" + }, + "wsproto": { + "hashes": [ + "sha256:868776f8456997ad0d9720f7322b746bbe9193751b5b290b7f924659377c8c38", + "sha256:d8345d1808dd599b5ffb352c25a367adb6157e664e140dbecba3f9bc007edb9f" + ], + "index": "pypi", + "markers": "python_full_version >= '3.6.1'", + "version": "==1.0.0" } } } From 2209d451bd03951acedd6cee75d63cb787bbdb5a Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Tue, 19 Dec 2023 16:05:13 -0500 Subject: [PATCH 38/60] r-s typechecking updates --- robot-server/robot_server/app_setup.py | 16 ++++++++++------ .../maintenance_runs/router/commands_router.py | 2 +- .../protocols/completed_analysis_store.py | 2 +- .../calibration/pipette_offset/user_flow.py | 2 +- .../robot_server/runs/router/commands_router.py | 2 +- .../service/legacy/models/settings.py | 4 ++-- .../service/legacy/routers/settings.py | 2 +- .../subsystems/firmware_update_manager.py | 8 ++------ robot-server/robot_server/system/time_utils.py | 2 -- 9 files changed, 19 insertions(+), 21 deletions(-) diff --git a/robot-server/robot_server/app_setup.py b/robot-server/robot_server/app_setup.py index 818b66f492a..64ba5b1ecb2 100644 --- a/robot-server/robot_server/app_setup.py +++ b/robot-server/robot_server/app_setup.py @@ -1,6 +1,9 @@ """Main FastAPI application.""" import asyncio import logging +from typing import Optional +from pathlib import Path + from fastapi import FastAPI from fastapi.middleware.cors import CORSMiddleware @@ -55,6 +58,12 @@ async def on_startup() -> None: """Handle app startup.""" settings = get_settings() + if settings.persistence_directory == "automatically_make_temporary": + persistence_directory: Optional[Path] = None + else: + # mypy won't narrow out the sentinel literal from the above if, sadly + persistence_directory = settings.persistence_directory # type: ignore[assignment] + initialize_logging() initialize_task_runner(app_state=app.state) start_initializing_hardware( @@ -65,12 +74,7 @@ async def on_startup() -> None: ], ) start_initializing_persistence( - app_state=app.state, - persistence_directory=( - None - if settings.persistence_directory == "automatically_make_temporary" - else settings.persistence_directory - ), + app_state=app.state, persistence_directory=persistence_directory ) diff --git a/robot-server/robot_server/maintenance_runs/router/commands_router.py b/robot-server/robot_server/maintenance_runs/router/commands_router.py index c0d64f077b6..4dc2901b959 100644 --- a/robot-server/robot_server/maintenance_runs/router/commands_router.py +++ b/robot-server/robot_server/maintenance_runs/router/commands_router.py @@ -182,7 +182,7 @@ async def create_run_command( if waitUntilComplete: timeout_sec = None if timeout is None else timeout / 1000.0 with move_on_after(timeout_sec): - await protocol_engine.wait_for_command(command.id), + await protocol_engine.wait_for_command(command.id) response_data = protocol_engine.state_view.commands.get(command.id) diff --git a/robot-server/robot_server/protocols/completed_analysis_store.py b/robot-server/robot_server/protocols/completed_analysis_store.py index 29ee571d08c..90e779fee16 100644 --- a/robot-server/robot_server/protocols/completed_analysis_store.py +++ b/robot-server/robot_server/protocols/completed_analysis_store.py @@ -301,5 +301,5 @@ def _serialize_completed_analysis_to_json(completed_analysis: CompletedAnalysis) # FastAPI + Pydantic + our customizations serialize these objects # over the `GET /protocols/:id/analyses/:id` endpoint. by_alias=True, - exclude_none=True, + exclude_none=False, ) diff --git a/robot-server/robot_server/robot/calibration/pipette_offset/user_flow.py b/robot-server/robot_server/robot/calibration/pipette_offset/user_flow.py index 111f2e13766..e9fb7beb6f4 100644 --- a/robot-server/robot_server/robot/calibration/pipette_offset/user_flow.py +++ b/robot-server/robot_server/robot/calibration/pipette_offset/user_flow.py @@ -119,7 +119,7 @@ def __init__( if perform_tip_length and has_calibration_block: self._load_calibration_block() - self._has_calibration_block = has_calibration_block + self._has_calibration_block: bool = has_calibration_block else: self._has_calibration_block = False diff --git a/robot-server/robot_server/runs/router/commands_router.py b/robot-server/robot_server/runs/router/commands_router.py index c16fcbd60cc..0c5a9a9444e 100644 --- a/robot-server/robot_server/runs/router/commands_router.py +++ b/robot-server/robot_server/runs/router/commands_router.py @@ -207,7 +207,7 @@ async def create_run_command( if waitUntilComplete: timeout_sec = None if timeout is None else timeout / 1000.0 with move_on_after(timeout_sec): - await protocol_engine.wait_for_command(command.id), + await protocol_engine.wait_for_command(command.id) response_data = protocol_engine.state_view.commands.get(command.id) diff --git a/robot-server/robot_server/service/legacy/models/settings.py b/robot-server/robot_server/service/legacy/models/settings.py index 7d9268b29af..4e9ba6b7251 100644 --- a/robot-server/robot_server/service/legacy/models/settings.py +++ b/robot-server/robot_server/service/legacy/models/settings.py @@ -170,10 +170,10 @@ class BasePipetteSettingFields(BaseModel): # A dynamic model of the possible fields in pipette configuration. It's # generated from pipette_config module. It's derived from an object with the # 'quirks` member. -PipetteSettingsFields = create_model( +PipetteSettingsFields = create_model( # type: ignore[call-overload] "PipetteSettingsFields", __base__=BasePipetteSettingFields, - **{ # type: ignore[arg-type] + **{ conf: (PipetteSettingsField, None) for conf in model_constants.MUTABLE_CONFIGS_V1 if conf != "quirks" diff --git a/robot-server/robot_server/service/legacy/routers/settings.py b/robot-server/robot_server/service/legacy/routers/settings.py index 5e89c478359..dc9c08b293d 100644 --- a/robot-server/robot_server/service/legacy/routers/settings.py +++ b/robot-server/robot_server/service/legacy/routers/settings.py @@ -390,7 +390,7 @@ def _pipette_settings_from_mutable_configs( converted_dict[k] = v.dict_for_encode() elif k == "quirks": converted_dict[k] = {q: b.dict_for_encode() for q, b in v.items()} - fields = PipetteSettingsFields(**converted_dict) # type: ignore + fields = PipetteSettingsFields(**converted_dict) # TODO(mc, 2020-09-17): s/fields/setting_fields (?) # need model and name? diff --git a/robot-server/robot_server/subsystems/firmware_update_manager.py b/robot-server/robot_server/subsystems/firmware_update_manager.py index 75a24798be0..12aacc4feb4 100644 --- a/robot-server/robot_server/subsystems/firmware_update_manager.py +++ b/robot-server/robot_server/subsystems/firmware_update_manager.py @@ -148,9 +148,7 @@ def __init__( self._status_cache_lock = Lock() self._created_at = created_at self._update_id = update_id - # mypy thinks this is assignment to a method, which it is not. that means - # it's ok to assign this and it's also okay to not take a self argument - self._complete_callback = complete_callback # type: ignore[assignment,misc] + self._complete_callback = complete_callback @property def status_cache(self) -> UpdateProgress: @@ -206,9 +204,7 @@ async def _update_task(self) -> None: UpdateProgress(UpdateState.failed, last_progress, be) ) finally: - # mypy continues to think this is a method but it is a function stored in an - # attribute and therefore does not need a self argument - await self._complete_callback() # type: ignore[misc] + await self._complete_callback() def get_handle(self) -> "UpdateProcessHandle": """Get a public handle for the task that is usable elsewhere. diff --git a/robot-server/robot_server/system/time_utils.py b/robot-server/robot_server/system/time_utils.py index 367f084adab..6b617f366d9 100644 --- a/robot-server/robot_server/system/time_utils.py +++ b/robot-server/robot_server/system/time_utils.py @@ -44,7 +44,6 @@ async def _time_status() -> Dict[str, Union[str, bool]]: "timedatectl show", stdout=asyncio.subprocess.PIPE, stderr=asyncio.subprocess.PIPE, - loop=asyncio.get_event_loop(), ) out, err = await proc.communicate() return _str_to_dict(out.decode()) @@ -60,7 +59,6 @@ async def _set_time(time: str) -> Tuple[str, str]: f'date --utc --set "{time}"', stdout=asyncio.subprocess.PIPE, stderr=asyncio.subprocess.PIPE, - loop=asyncio.get_event_loop(), ) out, err = await proc.communicate() return out.decode(), err.decode() From 01000de712f1b1e54158189543ad8d59d48aafad Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Tue, 19 Dec 2023 17:27:55 -0500 Subject: [PATCH 39/60] tavern updates first pass --- .../protocols/test_analyses.tavern.yaml | 1 + .../test_deck_coordinate_load.tavern.yaml | 3 +- .../protocols/test_upload.tavern.yaml | 1 + .../protocols/test_v6_json_upload.tavern.yaml | 118 +++++++++++++-- .../test_json_v6_protocol_run.tavern.yaml | 134 ++++++++++++++++-- .../test_json_v7_protocol_run.tavern.yaml | 134 ++++++++++++++++-- .../integration/test_modules.tavern.yaml | 16 +++ 7 files changed, 366 insertions(+), 41 deletions(-) diff --git a/robot-server/tests/integration/http_api/protocols/test_analyses.tavern.yaml b/robot-server/tests/integration/http_api/protocols/test_analyses.tavern.yaml index a756ea10e1b..47bf0ec5c17 100644 --- a/robot-server/tests/integration/http_api/protocols/test_analyses.tavern.yaml +++ b/robot-server/tests/integration/http_api/protocols/test_analyses.tavern.yaml @@ -45,6 +45,7 @@ stages: createdAt: !anything robotType: !anything metadata: !anything + key: null links: !anything - name: Check that the analysis data is present in /protocols/:id/analyses/:id diff --git a/robot-server/tests/integration/http_api/protocols/test_deck_coordinate_load.tavern.yaml b/robot-server/tests/integration/http_api/protocols/test_deck_coordinate_load.tavern.yaml index f5f4fc91751..802d8fd3262 100644 --- a/robot-server/tests/integration/http_api/protocols/test_deck_coordinate_load.tavern.yaml +++ b/robot-server/tests/integration/http_api/protocols/test_deck_coordinate_load.tavern.yaml @@ -20,11 +20,12 @@ stages: json: data: id: !anystr + key: null protocolType: python files: - name: deck_coordinate_load.py role: main - createdAt: !re_search "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d+\\+\\d{2}:\\d{2}$" + createdAt: !anystr robotType: OT-3 Standard metadata: protocolName: Deck Coordinate PAPIv2 Test diff --git a/robot-server/tests/integration/http_api/protocols/test_upload.tavern.yaml b/robot-server/tests/integration/http_api/protocols/test_upload.tavern.yaml index 63bf756bc8d..c9f0ca73713 100644 --- a/robot-server/tests/integration/http_api/protocols/test_upload.tavern.yaml +++ b/robot-server/tests/integration/http_api/protocols/test_upload.tavern.yaml @@ -20,6 +20,7 @@ stages: data: id: !anystr protocolType: python + key: null files: - name: basic_transfer_standalone.py role: main diff --git a/robot-server/tests/integration/http_api/protocols/test_v6_json_upload.tavern.yaml b/robot-server/tests/integration/http_api/protocols/test_v6_json_upload.tavern.yaml index 13af0f78d84..4cfc73a359c 100644 --- a/robot-server/tests/integration/http_api/protocols/test_v6_json_upload.tavern.yaml +++ b/robot-server/tests/integration/http_api/protocols/test_v6_json_upload.tavern.yaml @@ -39,6 +39,7 @@ stages: json: data: - id: '{protocol_id}' + analyses: [] analysisSummaries: - id: '{analysis_id}' status: completed @@ -65,10 +66,11 @@ stages: author: engineering protocolName: Simple test protocol analyses: [] + key: null analysisSummaries: - id: '{analysis_id}' status: completed - links: + links: referencingRuns: [] - name: Get protocol analysis by ID request: @@ -95,24 +97,28 @@ stages: definitionUri: opentrons/opentrons_1_trash_1100ml_fixed/1 location: slotName: '12' + offsetId: null - id: sourcePlateId loadName: foo_8_plate_33ul definitionUri: example/foo_8_plate_33ul/1 displayName: Source Plate location: moduleId: temperatureModuleId + offsetId: null - id: destPlateId loadName: foo_8_plate_33ul definitionUri: example/foo_8_plate_33ul/1 displayName: Sample Collection Plate location: moduleId: magneticModuleId + offsetId: null - id: tipRackId loadName: opentrons_96_tiprack_10ul definitionUri: opentrons/opentrons_96_tiprack_10ul/1 displayName: Opentrons 96 Tip Rack 10 µL location: slotName: '8' + offsetId: null modules: - id: magneticModuleId serialNumber: !anystr @@ -131,10 +137,14 @@ stages: commandType: home key: !anystr status: succeeded - params: { } + params: + axes: null + skipIfMountPositionOk: null result: { } startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadPipette @@ -148,6 +158,8 @@ stages: pipetteId: pipetteId startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadModule @@ -165,6 +177,8 @@ stages: serialNumber: !anystr startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadModule @@ -182,6 +196,8 @@ stages: serialNumber: !anystr startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -196,10 +212,13 @@ stages: labwareId: sourcePlateId displayName: Source Plate result: + offsetId: null labwareId: sourcePlateId definition: !anydict startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -216,8 +235,11 @@ stages: result: labwareId: destPlateId definition: !anydict + offsetId: null startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -234,8 +256,11 @@ stages: result: labwareId: tipRackId definition: !anydict + offsetId: null startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadLiquid @@ -250,15 +275,21 @@ stages: result: {} startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: home key: !anystr status: succeeded - params: {} + params: + axes: null + skipIfMountPositionOk: null result: {} startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: pickUpTip @@ -275,12 +306,17 @@ stages: y: 0 z: 0 result: - position: { 'x': 146.88, 'y': 246.24, 'z': 64.69 } + position: + x: 146.88 + y: 246.24 + z: 64.69 tipVolume: 10.0 tipLength: 35.910000000000004 tipDiameter: 3.27 startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: aspirate @@ -299,10 +335,15 @@ stages: volume: 5 flowRate: 3 result: - position: { 'x': 16.76, 'y': 75.28, 'z': 157.09 } + position: + x: 16.76 + y: 75.28 + z: 157.09 volume: 5 startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: waitForDuration @@ -310,9 +351,12 @@ stages: status: succeeded params: seconds: 42 + message: null result: {} startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: dispense @@ -330,11 +374,17 @@ stages: z: 1 volume: 4.5 flowRate: 2.5 + pushOut: null result: - position: { 'x': 284.635, 'y': 56.025, 'z': 158.25 } + position: + x: 284.635 + y: 56.025 + z: 158.25 volume: 4.5 startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: touchTip @@ -353,9 +403,14 @@ stages: radius: 0.5 speed: 42.0 result: - position: { 'x': 284.635, 'y': 56.025, 'z': 168.25 } + position: + x: 284.635 + y: 56.025 + z: 168.25 startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: blowout @@ -373,9 +428,14 @@ stages: z: 12 flowRate: 2 result: - position: { 'x': 284.635, 'y': 56.025, 'z': 169.25 } + position: + x: 284.635 + y: 56.025 + z: 169.25 startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: moveToWell @@ -392,11 +452,17 @@ stages: y: 0 z: 0 forceDirect: false + speed: null + minimumZHeight: null result: position: - { 'x': 304.52500000000003, 'y': 56.025, 'z': 182.25 } + x: 304.52500000000003 + y: 56.025 + z: 182.25 startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: moveToWell @@ -417,9 +483,13 @@ stages: speed: 12.3 result: position: - { 'x': 306.52500000000003, 'y': 59.025, 'z': 167.25 } + x: 306.52500000000003 + y: 59.025 + z: 167.25 startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: dropTip @@ -436,10 +506,16 @@ stages: y: 0 z: 0 alternateDropLocation: false + homeAfter: null result: - position: { 'x': 347.84000000000003, 'y': 325.06, 'z': 82.0 } + position: + x: 347.84000000000003 + y: 325.06 + z: 82.0 startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: waitForResume @@ -450,6 +526,8 @@ stages: result: {} startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: moveToCoordinates @@ -465,9 +543,14 @@ stages: forceDirect: true speed: 12.3 result: - position: { 'x': 0.0, 'y': 0.0, 'z': 0.0 } + position: + x: 0.0 + y: 0.0 + z: 0.0 startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: moveRelative @@ -484,6 +567,8 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: moveRelative @@ -500,6 +585,8 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: savePosition @@ -508,6 +595,7 @@ stages: params: pipetteId: pipetteId failOnNotHomed: true + positionId: null result: positionId: !anystr position: @@ -516,6 +604,8 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: moveRelative @@ -532,6 +622,8 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: savePosition @@ -549,6 +641,8 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr + error: null + intent: null errors: [] liquids: - id: waterId diff --git a/robot-server/tests/integration/http_api/runs/test_json_v6_protocol_run.tavern.yaml b/robot-server/tests/integration/http_api/runs/test_json_v6_protocol_run.tavern.yaml index be8bf6369e8..9e07f0482b4 100644 --- a/robot-server/tests/integration/http_api/runs/test_json_v6_protocol_run.tavern.yaml +++ b/robot-server/tests/integration/http_api/runs/test_json_v6_protocol_run.tavern.yaml @@ -31,7 +31,9 @@ stages: json: data: id: !anystr - createdAt: !re_search "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d+\\+\\d{2}:\\d{2}$" + createdAt: !anystr + completedAt: null + startedAt: null status: idle current: True actions: [] @@ -43,6 +45,8 @@ stages: loadName: !anystr definitionUri: opentrons/opentrons_1_trash_1100ml_fixed/1 location: !anydict + displayName: null + offsetId: null labwareOffsets: [] liquids: - id: waterId @@ -102,41 +106,61 @@ stages: key: !anystr commandType: home createdAt: !anystr + completedAt: null + startedAt: null status: queued - params: { } + params: + axes: null + skipIfMountPositionOk: null + intent: null + error: null - id: !anystr key: !anystr commandType: loadPipette createdAt: !anystr + completedAt: null + startedAt: null status: queued params: pipetteName: p10_single mount: left pipetteId: pipetteId + intent: null + error: null - id: !anystr key: !anystr commandType: loadModule createdAt: !anystr + completedAt: null + startedAt: null status: queued params: model: magneticModuleV1 location: slotName: '3' moduleId: magneticModuleId + intent: null + error: null - id: !anystr key: !anystr commandType: loadModule createdAt: !anystr + startedAt: null + completedAt: null status: queued params: model: temperatureModuleV2 location: slotName: '1' moduleId: temperatureModuleId + intent: null + error: null - id: !anystr key: !anystr commandType: loadLabware createdAt: !anystr + startedAt: null + completedAt: null status: queued params: location: @@ -146,10 +170,14 @@ stages: version: 1 labwareId: sourcePlateId displayName: Source Plate + intent: null + error: null - id: !anystr key: !anystr commandType: loadLabware createdAt: !anystr + startedAt: null + completedAt: null status: queued params: location: @@ -159,10 +187,14 @@ stages: version: 1 labwareId: destPlateId displayName: Sample Collection Plate + intent: null + error: null - id: !anystr key: !anystr commandType: loadLabware createdAt: !anystr + startedAt: null + completedAt: null status: queued params: location: @@ -172,8 +204,12 @@ stages: version: 1 labwareId: tipRackId displayName: Opentrons 96 Tip Rack 10 µL + intent: null + error: null - id: !anystr createdAt: !anystr + startedAt: null + completedAt: null commandType: loadLiquid key: !anystr status: queued @@ -183,10 +219,14 @@ stages: volumeByWell: A1: 100 B1: 100 + intent: null + error: null - id: !anystr key: !anystr commandType: pickUpTip createdAt: !anystr + startedAt: null + completedAt: null status: queued params: pipetteId: pipetteId @@ -196,12 +236,16 @@ stages: origin: top offset: x: 0 - 'y': 0 + y: 0 z: 0 + intent: null + error: null - id: !anystr key: !anystr commandType: aspirate createdAt: !anystr + startedAt: null + completedAt: null status: queued params: pipetteId: pipetteId @@ -211,14 +255,18 @@ stages: origin: bottom offset: x: 0 - 'y': 0 + y: 0 z: 2 volume: 5 flowRate: 3 + intent: null + error: null - id: !anystr key: !anystr commandType: dispense createdAt: !anystr + startedAt: null + completedAt: null status: queued params: pipetteId: pipetteId @@ -228,14 +276,19 @@ stages: origin: bottom offset: x: 0 - 'y': 0 + y: 0 z: 1 volume: 4.5 flowRate: 2.5 + pushOut: null + intent: null + error: null - id: !anystr key: !anystr commandType: moveToWell createdAt: !anystr + startedAt: null + completedAt: null status: queued params: pipetteId: pipetteId @@ -245,13 +298,19 @@ stages: origin: top offset: x: 0 - 'y': 0 + y: 0 z: 0 forceDirect: false + speed: null + minimumZHeight: null + intent: null + error: null - id: !anystr key: !anystr commandType: moveToWell createdAt: !anystr + startedAt: null + completedAt: null status: queued params: pipetteId: pipetteId @@ -266,10 +325,14 @@ stages: minimumZHeight: 35 forceDirect: true speed: 12.3 + intent: null + error: null - id: !anystr key: !anystr commandType: dropTip createdAt: !anystr + startedAt: null + completedAt: null status: queued params: pipetteId: pipetteId @@ -282,15 +345,21 @@ stages: y: 0 z: 0 alternateDropLocation: false + homeAfter: null + intent: null + error: null - id: '{setup_command_id}' key: '{setup_command_key}' intent: setup commandType: home + error: null createdAt: '{setup_command_created_at}' startedAt: '{setup_command_started_at}' completedAt: '{setup_command_completed_at}' status: succeeded - params: {} + params: + skipIfMountPositionOk: null + axes: null - name: Play the run request: @@ -305,7 +374,7 @@ stages: data: id: !anystr actionType: play - createdAt: !re_search "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d+\\+\\d{2}:\\d{2}$" + createdAt: !anystr - name: Wait for the protocol to complete max_retries: 10 @@ -339,9 +408,13 @@ stages: commandType: home key: !anystr status: succeeded - params: { } + params: + axes: null + skipIfMountPositionOk: null startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr key: !anystr commandType: loadPipette @@ -349,6 +422,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: pipetteName: p10_single mount: left @@ -360,6 +435,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: model: magneticModuleV1 location: @@ -372,6 +449,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: model: temperatureModuleV2 location: @@ -384,6 +463,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: location: moduleId: temperatureModuleId @@ -399,6 +480,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: location: moduleId: magneticModuleId @@ -414,6 +497,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: location: slotName: '8' @@ -429,6 +514,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: labwareId: sourcePlateId liquidId: waterId @@ -442,6 +529,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: pipetteId: pipetteId labwareId: tipRackId @@ -450,7 +539,7 @@ stages: origin: top offset: x: 0 - 'y': 0 + y: 0 z: 0 - id: !anystr key: !anystr @@ -459,6 +548,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: pipetteId: pipetteId labwareId: sourcePlateId @@ -467,7 +558,7 @@ stages: origin: bottom offset: x: 0 - 'y': 0 + y: 0 z: 2 volume: 5 flowRate: 3 @@ -478,6 +569,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: pipetteId: pipetteId labwareId: destPlateId @@ -486,10 +579,11 @@ stages: origin: bottom offset: x: 0 - 'y': 0 + y: 0 z: 1 volume: 4.5 flowRate: 2.5 + pushOut: null - id: !anystr key: !anystr commandType: moveToWell @@ -497,6 +591,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: pipetteId: pipetteId labwareId: destPlateId @@ -505,9 +601,11 @@ stages: origin: top offset: x: 0 - 'y': 0 + y: 0 z: 0 forceDirect: false + speed: null + minimumZHeight: null - id: !anystr key: !anystr commandType: moveToWell @@ -515,6 +613,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: pipetteId: pipetteId labwareId: destPlateId @@ -535,6 +635,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: pipetteId: pipetteId labwareId: fixedTrash @@ -546,6 +648,7 @@ stages: y: 0 z: 0 alternateDropLocation: false + homeAfter: null - id: '{setup_command_id}' key: '{setup_command_key}' intent: setup @@ -554,4 +657,7 @@ stages: startedAt: '{setup_command_started_at}' completedAt: '{setup_command_completed_at}' status: succeeded - params: {} + error: null + params: + skipIfMountPositionOk: null + axes: null diff --git a/robot-server/tests/integration/http_api/runs/test_json_v7_protocol_run.tavern.yaml b/robot-server/tests/integration/http_api/runs/test_json_v7_protocol_run.tavern.yaml index d1dbef0656e..3d3fbaf06d8 100644 --- a/robot-server/tests/integration/http_api/runs/test_json_v7_protocol_run.tavern.yaml +++ b/robot-server/tests/integration/http_api/runs/test_json_v7_protocol_run.tavern.yaml @@ -31,7 +31,9 @@ stages: json: data: id: !anystr - createdAt: !re_search "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d+\\+\\d{2}:\\d{2}$" + createdAt: !anystr + completedAt: null + startedAt: null status: idle current: True actions: [] @@ -43,6 +45,8 @@ stages: loadName: !anystr definitionUri: opentrons/opentrons_1_trash_1100ml_fixed/1 location: !anydict + displayName: null + offsetId: null labwareOffsets: [] liquids: - id: waterId @@ -102,41 +106,61 @@ stages: key: !anystr commandType: home createdAt: !anystr + startedAt: null + completedAt: null status: queued - params: { } + params: + axes: null + skipIfMountPositionOk: null + intent: null + error: null - id: !anystr key: !anystr commandType: loadPipette createdAt: !anystr + startedAt: null + completedAt: null status: queued params: pipetteName: p10_single mount: left pipetteId: pipetteId + intent: null + error: null - id: !anystr key: !anystr commandType: loadModule createdAt: !anystr + startedAt: null + completedAt: null status: queued params: model: magneticModuleV1 location: slotName: '3' moduleId: magneticModuleId + intent: null + error: null - id: !anystr key: !anystr commandType: loadModule createdAt: !anystr + startedAt: null + completedAt: null status: queued params: model: temperatureModuleV2 location: slotName: '1' moduleId: temperatureModuleId + intent: null + error: null - id: !anystr key: !anystr commandType: loadLabware createdAt: !anystr + startedAt: null + completedAt: null status: queued params: location: @@ -146,10 +170,14 @@ stages: version: 1 labwareId: sourcePlateId displayName: Source Plate + intent: null + error: null - id: !anystr key: !anystr commandType: loadLabware createdAt: !anystr + startedAt: null + completedAt: null status: queued params: location: @@ -159,10 +187,14 @@ stages: version: 1 labwareId: destPlateId displayName: Sample Collection Plate + intent: null + error: null - id: !anystr key: !anystr commandType: loadLabware createdAt: !anystr + startedAt: null + completedAt: null status: queued params: location: @@ -172,8 +204,12 @@ stages: version: 1 labwareId: tipRackId displayName: Opentrons 96 Tip Rack 10 µL + intent: null + error: null - id: !anystr createdAt: !anystr + startedAt: null + completedAt: null commandType: loadLiquid key: !anystr status: queued @@ -183,10 +219,14 @@ stages: volumeByWell: A1: 100 B1: 100 + intent: null + error: null - id: !anystr key: !anystr commandType: pickUpTip createdAt: !anystr + startedAt: null + completedAt: null status: queued params: pipetteId: pipetteId @@ -196,12 +236,16 @@ stages: origin: top offset: x: 0 - 'y': 0 + y: 0 z: 0 + intent: null + error: null - id: !anystr key: !anystr commandType: aspirate createdAt: !anystr + startedAt: null + completedAt: null status: queued params: pipetteId: pipetteId @@ -211,14 +255,18 @@ stages: origin: bottom offset: x: 0 - 'y': 0 + y: 0 z: 2 volume: 5 flowRate: 3 + intent: null + error: null - id: !anystr key: !anystr commandType: dispense createdAt: !anystr + startedAt: null + completedAt: null status: queued params: pipetteId: pipetteId @@ -228,14 +276,19 @@ stages: origin: bottom offset: x: 0 - 'y': 0 + y: 0 z: 1 volume: 4.5 flowRate: 2.5 + pushOut: null + intent: null + error: null - id: !anystr key: !anystr commandType: moveToWell createdAt: !anystr + startedAt: null + completedAt: null status: queued params: pipetteId: pipetteId @@ -245,13 +298,19 @@ stages: origin: top offset: x: 0 - 'y': 0 + y: 0 z: 0 forceDirect: false + speed: null + minimumZHeight: null + intent: null + error: null - id: !anystr key: !anystr commandType: moveToWell createdAt: !anystr + startedAt: null + completedAt: null status: queued params: pipetteId: pipetteId @@ -266,10 +325,14 @@ stages: minimumZHeight: 35 forceDirect: true speed: 12.3 + intent: null + error: null - id: !anystr key: !anystr commandType: dropTip createdAt: !anystr + startedAt: null + completedAt: null status: queued params: pipetteId: pipetteId @@ -282,6 +345,9 @@ stages: y: 0 z: 0 alternateDropLocation: false + homeAfter: null + intent: null + error: null - id: '{setup_command_id}' key: '{setup_command_key}' intent: setup @@ -290,7 +356,10 @@ stages: startedAt: '{setup_command_started_at}' completedAt: '{setup_command_completed_at}' status: succeeded - params: {} + error: null + params: + skipIfMountPositionOk: null + axes: null - name: Play the run request: @@ -305,7 +374,7 @@ stages: data: id: !anystr actionType: play - createdAt: !re_search "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d+\\+\\d{2}:\\d{2}$" + createdAt: !anystr - name: Wait for the protocol to complete max_retries: 10 @@ -341,7 +410,11 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - params: { } + error: null + intent: null + params: + axes: null + skipIfMountPositionOk: null - id: !anystr key: !anystr commandType: loadPipette @@ -349,6 +422,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: pipetteName: p10_single mount: left @@ -360,6 +435,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: model: magneticModuleV1 location: @@ -372,6 +449,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: model: temperatureModuleV2 location: @@ -384,6 +463,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: location: moduleId: temperatureModuleId @@ -399,6 +480,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: location: moduleId: magneticModuleId @@ -414,6 +497,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: location: slotName: '8' @@ -429,6 +514,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: labwareId: sourcePlateId liquidId: waterId @@ -442,6 +529,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: pipetteId: pipetteId labwareId: tipRackId @@ -450,7 +539,7 @@ stages: origin: top offset: x: 0 - 'y': 0 + y: 0 z: 0 - id: !anystr key: !anystr @@ -459,6 +548,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: pipetteId: pipetteId labwareId: sourcePlateId @@ -467,7 +558,7 @@ stages: origin: bottom offset: x: 0 - 'y': 0 + y: 0 z: 2 volume: 5 flowRate: 3 @@ -478,6 +569,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: pipetteId: pipetteId labwareId: destPlateId @@ -486,10 +579,11 @@ stages: origin: bottom offset: x: 0 - 'y': 0 + y: 0 z: 1 volume: 4.5 flowRate: 2.5 + pushOut: null - id: !anystr key: !anystr commandType: moveToWell @@ -497,6 +591,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: pipetteId: pipetteId labwareId: destPlateId @@ -505,9 +601,11 @@ stages: origin: top offset: x: 0 - 'y': 0 + y: 0 z: 0 forceDirect: false + speed: null + minimumZHeight: null - id: !anystr key: !anystr commandType: moveToWell @@ -515,6 +613,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: pipetteId: pipetteId labwareId: destPlateId @@ -535,6 +635,8 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + error: null + intent: null params: pipetteId: pipetteId labwareId: fixedTrash @@ -546,6 +648,7 @@ stages: y: 0 z: 0 alternateDropLocation: false + homeAfter: null - id: '{setup_command_id}' key: '{setup_command_key}' intent: setup @@ -554,4 +657,7 @@ stages: startedAt: '{setup_command_started_at}' completedAt: '{setup_command_completed_at}' status: succeeded - params: { } + error: null + params: + skipIfMountPositionOk: null + axes: null diff --git a/robot-server/tests/integration/test_modules.tavern.yaml b/robot-server/tests/integration/test_modules.tavern.yaml index 93930465eb8..2274ee13218 100644 --- a/robot-server/tests/integration/test_modules.tavern.yaml +++ b/robot-server/tests/integration/test_modules.tavern.yaml @@ -101,11 +101,13 @@ stages: hasAvailableUpdate: !anybool moduleType: thermocyclerModuleType moduleModel: thermocyclerModuleV1 + moduleOffset: null usbPort: port: !anyint hub: !anybool portGroup: !anystr path: !anystr + hubPort: null data: status: !anystr lidStatus: !anystr @@ -115,6 +117,11 @@ stages: currentTemperature: !anyfloat targetTemperature: !anyfloat holdTime: !anyfloat + totalStepCount: null + totalCycleCount: null + currentCycleIndex: null + rampRate: null + currentStepIndex: null - id: !anystr serialNumber: !anystr firmwareVersion: !anystr @@ -122,11 +129,13 @@ stages: hasAvailableUpdate: !anybool moduleType: heaterShakerModuleType moduleModel: heaterShakerModuleV1 + moduleOffset: null usbPort: port: !anyint hub: !anybool portGroup: !anystr path: !anystr + hubPort: null data: status: !anystr labwareLatchStatus: !anystr @@ -134,6 +143,9 @@ stages: temperatureStatus: !anystr currentSpeed: !anyint currentTemperature: !anyfloat + targetSpeed: null + targetTemperature: null + errorDetails: null - id: !anystr serialNumber: !anystr firmwareVersion: !anystr @@ -141,11 +153,13 @@ stages: hasAvailableUpdate: !anybool moduleType: temperatureModuleType moduleModel: temperatureModuleV1 + moduleOffset: null usbPort: port: !anyint hub: !anybool portGroup: !anystr path: !anystr + hubPort: null data: status: !anystr currentTemperature: !anyfloat @@ -157,10 +171,12 @@ stages: hasAvailableUpdate: !anybool moduleType: magneticModuleType moduleModel: magneticModuleV1 + moduleOffset: null usbPort: port: !anyint hub: !anybool portGroup: !anystr + hubPort: null path: !anystr data: status: !anystr From fb4049f03c2484596adecab4b0e90736270f26a5 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Wed, 20 Dec 2023 10:26:12 -0500 Subject: [PATCH 40/60] more tavern updates --- .../runs/test_json_v6_run_failure.tavern.yaml | 14 ++++++++- .../runs/test_papi_v2_run_failure.tavern.yaml | 14 ++++++++- .../runs/test_protocol_run.tavern.yaml | 31 +++++++++++++++++-- ...t_run_queued_protocol_commands.tavern.yaml | 7 +++++ 4 files changed, 61 insertions(+), 5 deletions(-) diff --git a/robot-server/tests/integration/http_api/runs/test_json_v6_run_failure.tavern.yaml b/robot-server/tests/integration/http_api/runs/test_json_v6_run_failure.tavern.yaml index b5796d80d23..07858aa1c93 100644 --- a/robot-server/tests/integration/http_api/runs/test_json_v6_run_failure.tavern.yaml +++ b/robot-server/tests/integration/http_api/runs/test_json_v6_run_failure.tavern.yaml @@ -94,7 +94,11 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - params: {} + params: + skipIfMountPositionOk: null + axes: null + intent: null + error: null - id: !anystr key: !anystr commandType: loadLabware @@ -110,6 +114,8 @@ stages: version: 1 labwareId: tipRackId displayName: Tip Rack + intent: null + error: null - id: !anystr key: !anystr commandType: loadPipette @@ -121,6 +127,8 @@ stages: pipetteName: p10_single mount: left pipetteId: pipetteId + intent: null + error: null - id: !anystr key: !anystr commandType: aspirate @@ -128,6 +136,7 @@ stages: startedAt: !anystr completedAt: !anystr status: failed + intent: null error: id: !anystr errorType: TipNotAttachedError @@ -153,7 +162,10 @@ stages: commandType: pickUpTip createdAt: !anystr completedAt: !anystr + startedAt: null status: failed + intent: null + error: null params: pipetteId: pipetteId labwareId: tipRackId diff --git a/robot-server/tests/integration/http_api/runs/test_papi_v2_run_failure.tavern.yaml b/robot-server/tests/integration/http_api/runs/test_papi_v2_run_failure.tavern.yaml index 14fbb483048..ddb1e3c08fa 100644 --- a/robot-server/tests/integration/http_api/runs/test_papi_v2_run_failure.tavern.yaml +++ b/robot-server/tests/integration/http_api/runs/test_papi_v2_run_failure.tavern.yaml @@ -94,7 +94,11 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - params: {} + intent: null + error: null + params: + skipIfMountPositionOk: null + axes: null - id: !anystr key: !anystr commandType: loadLabware @@ -102,12 +106,16 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + intent: null + error: null params: location: slotName: '1' loadName: opentrons_96_tiprack_300ul namespace: opentrons version: 1 + labwareId: null + displayName: null - id: !anystr key: !anystr commandType: loadPipette @@ -115,9 +123,12 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded + intent: null + error: null params: pipetteName: p300_single mount: right + pipetteId: null - id: !anystr key: !anystr commandType: aspirate @@ -125,6 +136,7 @@ stages: startedAt: !anystr completedAt: !anystr status: failed + intent: null error: id: !anystr errorType: LegacyContextCommandError diff --git a/robot-server/tests/integration/http_api/runs/test_protocol_run.tavern.yaml b/robot-server/tests/integration/http_api/runs/test_protocol_run.tavern.yaml index f5091ab2dea..7dcaaeb1b23 100644 --- a/robot-server/tests/integration/http_api/runs/test_protocol_run.tavern.yaml +++ b/robot-server/tests/integration/http_api/runs/test_protocol_run.tavern.yaml @@ -28,7 +28,9 @@ stages: json: data: id: !anystr - createdAt: !re_search "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d+\\+\\d{2}:\\d{2}$" + createdAt: !anystr + startedAt: null + completedAt: null status: idle current: True actions: [] @@ -40,6 +42,8 @@ stages: loadName: !anystr definitionUri: opentrons/opentrons_1_trash_1100ml_fixed/1 location: !anydict + offsetId: null + displayName: null labwareOffsets: [] protocolId: '{protocol_id}' liquids: [] @@ -86,6 +90,8 @@ stages: data: definitionUri: opentrons/biorad_96_wellplate_200ul_pcr/1 location: + definitionUri: null + moduleModel: null slotName: '1' vector: x: 1.11 @@ -96,10 +102,12 @@ stages: json: data: id: !anystr - createdAt: !re_search "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d+\\+\\d{2}:\\d{2}$" + createdAt: !anystr definitionUri: opentrons/biorad_96_wellplate_200ul_pcr/1 location: slotName: '1' + definitionUri: null + moduleModel: null vector: x: 1.11 y: 2.22 @@ -162,15 +170,23 @@ stages: createdAt: !anystr startedAt: !anystr completedAt: !anystr + intent: null + error: null status: succeeded - params: { } + params: + axes: null + skipIfMountPositionOk: null - id: !anystr key: !anystr commandType: loadLabware status: succeeded + intent: null + error: null params: location: slotName: '1' + labwareId: null + displayName: null loadName: 'biorad_96_wellplate_200ul_pcr' namespace: 'opentrons' version: 1 @@ -193,12 +209,16 @@ stages: key: !anystr commandType: loadLabware status: succeeded + intent: null + error: null params: location: slotName: '1' loadName: 'biorad_96_wellplate_200ul_pcr' namespace: 'opentrons' version: 1 + labwareId: null + displayName: null result: labwareId: !anystr # Labware definitions are inconveniently verbose to test, @@ -244,6 +264,8 @@ stages: definitionUri: opentrons/biorad_96_wellplate_200ul_pcr/1 location: slotName: '1' + moduleModel: null + definitionUri: null vector: x: 1.11 y: 2.22 @@ -254,12 +276,15 @@ stages: loadName: !anystr definitionUri: opentrons/opentrons_1_trash_1100ml_fixed/1 location: !anydict + offsetId: null + displayName: null - id: !anystr loadName: biorad_96_wellplate_200ul_pcr definitionUri: opentrons/biorad_96_wellplate_200ul_pcr/1 location: slotName: '1' offsetId: '{labware_offset_id}' + displayName: null # Changed when the run completed: status: succeeded save: diff --git a/robot-server/tests/integration/http_api/runs/test_run_queued_protocol_commands.tavern.yaml b/robot-server/tests/integration/http_api/runs/test_run_queued_protocol_commands.tavern.yaml index 3434f210bd0..61545e76143 100644 --- a/robot-server/tests/integration/http_api/runs/test_run_queued_protocol_commands.tavern.yaml +++ b/robot-server/tests/integration/http_api/runs/test_run_queued_protocol_commands.tavern.yaml @@ -86,6 +86,8 @@ stages: data: actions: [] createdAt: !re_search "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d+\\+\\d{2}:\\d{2}$" + completedAt: null + startedAt: null current: True errors: [] id: '{run_id}' @@ -95,6 +97,7 @@ stages: modules: [] pipettes: [] status: 'idle' + protocolId: null - name: Play the run request: @@ -149,6 +152,7 @@ stages: commandType: comment status: succeeded intent: protocol + error: null params: message: 'test 1' createdAt: !re_search "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d+\\+\\d{2}:\\d{2}$" @@ -159,6 +163,7 @@ stages: commandType: comment status: succeeded intent: protocol + error: null params: message: 'test 2' createdAt: !re_search "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d+\\+\\d{2}:\\d{2}$" @@ -169,6 +174,7 @@ stages: commandType: comment status: succeeded intent: protocol + error: null params: message: 'test 3' createdAt: !re_search "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d+\\+\\d{2}:\\d{2}$" @@ -179,6 +185,7 @@ stages: commandType: comment status: succeeded intent: protocol + error: null params: message: 'test 4' createdAt: !re_search "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d+\\+\\d{2}:\\d{2}$" From c1cd5305b37d7cb2601075119e40404a08e9c49c Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Wed, 20 Dec 2023 11:27:33 -0500 Subject: [PATCH 41/60] fix the rest of the pydantic issues We now set exclude_unset=True in labware definitions instead of exclude_none, which is much closer to what we want: if you set somethign to none explicitly, then you get the key with a null value but if you load from default, the key doesn't get emitted. The problem is that this applies to defaults that are not null, so we have to explicitly set e.g. the completed analysis status key now. --- robot-server/robot_server/protocols/analysis_models.py | 2 +- robot-server/robot_server/protocols/analysis_store.py | 1 + .../tests/integration/http_api/runs/test_persistence.py | 2 +- robot-server/tests/protocols/test_analysis_store.py | 3 +++ .../tests/protocols/test_completed_analysis_store.py | 3 ++- robot-server/tests/protocols/test_protocols_router.py | 1 + .../opentrons_shared_data/labware/labware_definition.py | 8 ++++++++ 7 files changed, 17 insertions(+), 3 deletions(-) diff --git a/robot-server/robot_server/protocols/analysis_models.py b/robot-server/robot_server/protocols/analysis_models.py index 8caa22f30a7..2053d8ee3e4 100644 --- a/robot-server/robot_server/protocols/analysis_models.py +++ b/robot-server/robot_server/protocols/analysis_models.py @@ -82,7 +82,7 @@ class CompletedAnalysis(BaseModel): # Fields that are currently unique to robot-server, missing from local analysis: id: str = Field(..., description="Unique identifier of this analysis resource") status: Literal[AnalysisStatus.COMPLETED] = Field( - AnalysisStatus.COMPLETED, + ..., description="Status marking the analysis as completed", ) result: AnalysisResult = Field( diff --git a/robot-server/robot_server/protocols/analysis_store.py b/robot-server/robot_server/protocols/analysis_store.py index 8165cf9cf8e..1af59788ed2 100644 --- a/robot-server/robot_server/protocols/analysis_store.py +++ b/robot-server/robot_server/protocols/analysis_store.py @@ -160,6 +160,7 @@ async def update( id=analysis_id, result=result, robotType=robot_type, + status=AnalysisStatus.COMPLETED, commands=commands, labware=labware, modules=modules, diff --git a/robot-server/tests/integration/http_api/runs/test_persistence.py b/robot-server/tests/integration/http_api/runs/test_persistence.py index fa25057c163..6554abdb8fd 100644 --- a/robot-server/tests/integration/http_api/runs/test_persistence.py +++ b/robot-server/tests/integration/http_api/runs/test_persistence.py @@ -285,7 +285,7 @@ async def test_runs_completed_filled_started_at_none_persist( get_run_response = await client.get_run(run_id=run_id) run_data = get_run_response.json()["data"] - assert "startedAt" not in run_data + assert run_data['startedAt'] is None assert datetime.fromisoformat(run_data["completedAt"]).timestamp() == pytest.approx( expected_completed_at.timestamp(), abs=2 ) diff --git a/robot-server/tests/protocols/test_analysis_store.py b/robot-server/tests/protocols/test_analysis_store.py index 06ca93cd218..5f3df46ae8f 100644 --- a/robot-server/tests/protocols/test_analysis_store.py +++ b/robot-server/tests/protocols/test_analysis_store.py @@ -190,6 +190,7 @@ async def test_update_adds_details_and_completes_analysis( assert result == CompletedAnalysis( id="analysis-id", + status=AnalysisStatus.COMPLETED, result=AnalysisResult.OK, robotType="OT-2 Standard", labware=[labware], @@ -211,6 +212,8 @@ async def test_update_adds_details_and_completes_analysis( "loadName": "load-name", "definitionUri": "namespace/load-name/42", "location": {"slotName": "1"}, + "displayName": None, + "offsetId": None } ], "pipettes": [ diff --git a/robot-server/tests/protocols/test_completed_analysis_store.py b/robot-server/tests/protocols/test_completed_analysis_store.py index 76a9d32adc6..349a410ee96 100644 --- a/robot-server/tests/protocols/test_completed_analysis_store.py +++ b/robot-server/tests/protocols/test_completed_analysis_store.py @@ -16,7 +16,7 @@ JsonProtocolConfig, ) from robot_server.protocols.analysis_memcache import MemoryCache -from robot_server.protocols.analysis_models import CompletedAnalysis, AnalysisResult +from robot_server.protocols.analysis_models import CompletedAnalysis, AnalysisResult, AnalysisStatus from robot_server.protocols.protocol_store import ( ProtocolStore, ProtocolResource, @@ -80,6 +80,7 @@ def _completed_analysis_resource( "2", CompletedAnalysis( id=analysis_id, + status=AnalysisStatus.COMPLETED, result=AnalysisResult.OK, pipettes=[], labware=[], diff --git a/robot-server/tests/protocols/test_protocols_router.py b/robot-server/tests/protocols/test_protocols_router.py index fbecaabe425..995ead84a17 100644 --- a/robot-server/tests/protocols/test_protocols_router.py +++ b/robot-server/tests/protocols/test_protocols_router.py @@ -559,6 +559,7 @@ async def test_get_protocol_analyses( """It should get all analyses of a protocol.""" analysis = CompletedAnalysis( id="analysis-id", + status=AnalysisStatus.COMPLETED, result=AnalysisResult.OK, labware=[], pipettes=[], diff --git a/shared-data/python/opentrons_shared_data/labware/labware_definition.py b/shared-data/python/opentrons_shared_data/labware/labware_definition.py index 1b2e68040de..0b2f1db30b0 100644 --- a/shared-data/python/opentrons_shared_data/labware/labware_definition.py +++ b/shared-data/python/opentrons_shared_data/labware/labware_definition.py @@ -326,3 +326,11 @@ class LabwareDefinition(BaseModel): default_factory=None, description="Force, in Newtons, with which the gripper should grip the labware.", ) + + def dict(self, *args: Any, **kwargs: Any) -> Dict[str, Any]: + kwargs['exclude_unset'] = True + return super().dict(*args, **kwargs) + + def json(self, *args: Any, **kwargs: Any) -> str: + kwargs['exclude_unset'] = True + return super().json(*args, **kwargs) From e00b56cd2dad27b1f7642a4eaf130c201504641f Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Wed, 20 Dec 2023 12:35:02 -0500 Subject: [PATCH 42/60] update decoy to get https://github.com/mcous/decoy/pull/201 --- robot-server/Pipfile | 2 +- robot-server/Pipfile.lock | 123 +++++++++--------- .../service/legacy/routers/test_settings.py | 10 +- 3 files changed, 71 insertions(+), 64 deletions(-) diff --git a/robot-server/Pipfile b/robot-server/Pipfile index ab84bf58dc8..cc242893469 100755 --- a/robot-server/Pipfile +++ b/robot-server/Pipfile @@ -27,7 +27,7 @@ flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" flake8-noqa = "~=1.2.1" -decoy = "~=1.10" +decoy = "~=2.1" httpx = "==0.18.*" black = "==22.3.0" types-requests = "==2.25.6" diff --git a/robot-server/Pipfile.lock b/robot-server/Pipfile.lock index 5da49dd795d..094d65ad7ae 100644 --- a/robot-server/Pipfile.lock +++ b/robot-server/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "06068f3db988527a2ef06631a6b89ce69d124d3f22759be23f8b2ff789dd3d78" + "sha256": "808846564361a5e6f5953035846424f4ea2efbd8ea4726358ded3352bf6904a7" }, "pipfile-spec": 6, "requires": { @@ -458,70 +458,70 @@ }, "coverage": { "hashes": [ - "sha256:007a7e49831cfe387473e92e9ff07377f6121120669ddc39674e7244350a6a29", - "sha256:1191270b06ecd68b1d00897b2daddb98e1719f63750969614ceb3438228c088e", - "sha256:1367aa411afb4431ab58fd7ee102adb2665894d047c490649e86219327183134", - "sha256:1f0f8f0c497eb9c9f18f21de0750c8d8b4b9c7000b43996a094290b59d0e7523", - "sha256:222b038f08a7ebed1e4e78ccf3c09a1ca4ac3da16de983e66520973443b546bc", - "sha256:243576944f7c1a1205e5cd658533a50eba662c74f9be4c050d51c69bd4532936", - "sha256:2e9223a18f51d00d3ce239c39fc41410489ec7a248a84fab443fbb39c943616c", - "sha256:307aecb65bb77cbfebf2eb6e12009e9034d050c6c69d8a5f3f737b329f4f15fb", - "sha256:31c0b1b8b5a4aebf8fcd227237fc4263aa7fa0ddcd4d288d42f50eff18b0bac4", - "sha256:3b15e03b8ee6a908db48eccf4e4e42397f146ab1e91c6324da44197a45cb9132", - 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"version": "==7.3.3" + "version": "==7.3.4" }, "decoy": { "hashes": [ - "sha256:57327a6ec24c4f4804d978f9c770cb0ff778d2ed751a45ffc61226bf10fc9f90", - "sha256:dea3634ed92eca686f71e66dfd43350adc1a96c814fb5492a08d3c251c531149" + "sha256:575bdbe81afb4c152cd99a34568a9aa4369461f79d6172c678279c5d5585befe", + "sha256:7ddcc08b8ce991f7705cee76fae9061dcb17352e0a1ca2d9a0d4a0306ebd51cd" ], "index": "pypi", - "markers": "python_version >= '3.6' and python_version < '4.0'", - "version": "==1.11.3" + "markers": "python_version >= '3.7' and python_version < '4.0'", + "version": "==2.1.1" }, "docopt": { "hashes": [ @@ -1446,6 +1446,13 @@ "markers": "python_version >= '3.6'", "version": "==3.5.2" }, + "systemd-python": { + "hashes": [ + "sha256:fd0e44bf70eadae45aadc292cb0a7eb5b0b6372cd1b391228047d33895db83e7" + ], + "markers": "sys_platform == 'linux'", + "version": "==234" + }, "tavern": { "hashes": [ "sha256:736367541c554b4e3c43f0ba20d68225968987a5335007ad68abd9fd29cd8ad3" diff --git a/robot-server/tests/service/legacy/routers/test_settings.py b/robot-server/tests/service/legacy/routers/test_settings.py index 1d422330bc4..0f894eff83b 100644 --- a/robot-server/tests/service/legacy/routers/test_settings.py +++ b/robot-server/tests/service/legacy/routers/test_settings.py @@ -119,7 +119,7 @@ def mock_pipette_data(): def mock_known_pipettes(decoy: Decoy) -> Decoy: with patch( "opentrons_shared_data.pipette.mutable_configurations.known_pipettes", - new=decoy.mock(), + new=decoy.mock(name="opentrons_shared_data.pipette.mutable_configurations.known_pipettes"), ) as m: yield m @@ -128,7 +128,7 @@ def mock_known_pipettes(decoy: Decoy) -> Decoy: def mock_list_mutable_configs(decoy: Decoy) -> Decoy: with patch( "opentrons_shared_data.pipette.mutable_configurations.list_mutable_configs", - new=decoy.mock(), + new=decoy.mock(name="opentrons_shared_data.pipette.mutable_configurations.list_mutable_configs"), ) as m: yield m @@ -137,7 +137,7 @@ def mock_list_mutable_configs(decoy: Decoy) -> Decoy: def mock_list_mutable_configs_with_defaults(decoy: Decoy) -> Decoy: with patch( "opentrons_shared_data.pipette.mutable_configurations.list_mutable_configs_with_defaults", - new=decoy.mock(), + new=decoy.mock(name="opentrons_shared_data.pipette.mutable_configurations.list_mutable_configs_with_defaults"), ) as m: yield m @@ -146,7 +146,7 @@ def mock_list_mutable_configs_with_defaults(decoy: Decoy) -> Decoy: def mock_save_overrides(decoy: Decoy) -> Decoy: with patch( "opentrons_shared_data.pipette.mutable_configurations.save_overrides", - new=decoy.mock(), + new=decoy.mock(name="opentrons_shared_data.pipette.mutable_configurations.save_overrides"), ) as m: yield m @@ -155,7 +155,7 @@ def mock_save_overrides(decoy: Decoy) -> Decoy: def mock_get_opentrons_dir(decoy: Decoy) -> Decoy: with patch( "robot_server.service.legacy.routers.settings.get_opentrons_path", - new=decoy.mock(), + new=decoy.mock(name="robot_server.service.legacy.routers.settings.get_opentrons_path"), ) as m: yield m From d070d6642a29187a1d9252c35eb745bcf1aad96b Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Wed, 20 Dec 2023 12:51:55 -0500 Subject: [PATCH 43/60] api tests no longer need 3.7, perhaps --- .github/workflows/api-test-lint-deploy.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/api-test-lint-deploy.yaml b/.github/workflows/api-test-lint-deploy.yaml index ebc92d66008..3e28cf5bc16 100644 --- a/.github/workflows/api-test-lint-deploy.yaml +++ b/.github/workflows/api-test-lint-deploy.yaml @@ -75,7 +75,7 @@ jobs: os: ['windows-2022', 'ubuntu-22.04', 'macos-latest'] # TODO(mc, 2022-02-24): expand this matrix to 3.8 and 3.9, # preferably in a nightly cronjob on edge or something - python: ['3.7', '3.10'] + python: '3.10' with-ot-hardware: ['true', 'false'] exclude: - os: 'windows-2022' From 06fdb8b2fd804556d7929a4ca136059746e99eda Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Wed, 20 Dec 2023 12:53:38 -0500 Subject: [PATCH 44/60] oops slight updates --- .github/workflows/api-test-lint-deploy.yaml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/.github/workflows/api-test-lint-deploy.yaml b/.github/workflows/api-test-lint-deploy.yaml index 3e28cf5bc16..6c03ab5cc4d 100644 --- a/.github/workflows/api-test-lint-deploy.yaml +++ b/.github/workflows/api-test-lint-deploy.yaml @@ -75,17 +75,13 @@ jobs: os: ['windows-2022', 'ubuntu-22.04', 'macos-latest'] # TODO(mc, 2022-02-24): expand this matrix to 3.8 and 3.9, # preferably in a nightly cronjob on edge or something - python: '3.10' + python: ['3.10'] with-ot-hardware: ['true', 'false'] exclude: - os: 'windows-2022' with-ot-hardware: 'true' - os: 'macos-latest' with-ot-hardware: 'true' - - os: 'macos-latest' - python: '3.10' - - python: '3.10' - with-ot-hardware: 'true' runs-on: '${{ matrix.os }}' steps: - uses: 'actions/checkout@v3' From 86b2ba43d1885b8d79854116daf0d1bbfe0ceef0 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Wed, 20 Dec 2023 13:09:00 -0500 Subject: [PATCH 45/60] specify more labware details in test --- .../opentrons/protocol_api/core/engine/test_labware_core.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/api/tests/opentrons/protocol_api/core/engine/test_labware_core.py b/api/tests/opentrons/protocol_api/core/engine/test_labware_core.py index df29b7c8026..5f84df6f62c 100644 --- a/api/tests/opentrons/protocol_api/core/engine/test_labware_core.py +++ b/api/tests/opentrons/protocol_api/core/engine/test_labware_core.py @@ -80,6 +80,10 @@ def test_set_calibration(subject: LabwareCore) -> None: namespace="hello", parameters=LabwareDefinitionParameters.construct(loadName="world"), # type: ignore[call-arg] ordering=[], + allowedRoles=[], + stackingOffsetWithLabware={}, + stackingOffsetWithModule={}, + gripperOffsets={}, ) ], ) From 76b2244a142c8a9713d481338b2ea052d1503d4e Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Wed, 20 Dec 2023 13:33:29 -0500 Subject: [PATCH 46/60] format robot-server tests --- .../http_api/runs/test_persistence.py | 2 +- .../tests/protocols/test_analysis_store.py | 2 +- .../test_completed_analysis_store.py | 6 +++++- .../service/legacy/routers/test_settings.py | 20 ++++++++++++++----- 4 files changed, 22 insertions(+), 8 deletions(-) diff --git a/robot-server/tests/integration/http_api/runs/test_persistence.py b/robot-server/tests/integration/http_api/runs/test_persistence.py index 6554abdb8fd..b83a23feb51 100644 --- a/robot-server/tests/integration/http_api/runs/test_persistence.py +++ b/robot-server/tests/integration/http_api/runs/test_persistence.py @@ -285,7 +285,7 @@ async def test_runs_completed_filled_started_at_none_persist( get_run_response = await client.get_run(run_id=run_id) run_data = get_run_response.json()["data"] - assert run_data['startedAt'] is None + assert run_data["startedAt"] is None assert datetime.fromisoformat(run_data["completedAt"]).timestamp() == pytest.approx( expected_completed_at.timestamp(), abs=2 ) diff --git a/robot-server/tests/protocols/test_analysis_store.py b/robot-server/tests/protocols/test_analysis_store.py index 5f3df46ae8f..46266a80c90 100644 --- a/robot-server/tests/protocols/test_analysis_store.py +++ b/robot-server/tests/protocols/test_analysis_store.py @@ -213,7 +213,7 @@ async def test_update_adds_details_and_completes_analysis( "definitionUri": "namespace/load-name/42", "location": {"slotName": "1"}, "displayName": None, - "offsetId": None + "offsetId": None, } ], "pipettes": [ diff --git a/robot-server/tests/protocols/test_completed_analysis_store.py b/robot-server/tests/protocols/test_completed_analysis_store.py index 349a410ee96..4b76386acd4 100644 --- a/robot-server/tests/protocols/test_completed_analysis_store.py +++ b/robot-server/tests/protocols/test_completed_analysis_store.py @@ -16,7 +16,11 @@ JsonProtocolConfig, ) from robot_server.protocols.analysis_memcache import MemoryCache -from robot_server.protocols.analysis_models import CompletedAnalysis, AnalysisResult, AnalysisStatus +from robot_server.protocols.analysis_models import ( + CompletedAnalysis, + AnalysisResult, + AnalysisStatus, +) from robot_server.protocols.protocol_store import ( ProtocolStore, ProtocolResource, diff --git a/robot-server/tests/service/legacy/routers/test_settings.py b/robot-server/tests/service/legacy/routers/test_settings.py index 0f894eff83b..dbe99c2ba09 100644 --- a/robot-server/tests/service/legacy/routers/test_settings.py +++ b/robot-server/tests/service/legacy/routers/test_settings.py @@ -119,7 +119,9 @@ def mock_pipette_data(): def mock_known_pipettes(decoy: Decoy) -> Decoy: with patch( "opentrons_shared_data.pipette.mutable_configurations.known_pipettes", - new=decoy.mock(name="opentrons_shared_data.pipette.mutable_configurations.known_pipettes"), + new=decoy.mock( + name="opentrons_shared_data.pipette.mutable_configurations.known_pipettes" + ), ) as m: yield m @@ -128,7 +130,9 @@ def mock_known_pipettes(decoy: Decoy) -> Decoy: def mock_list_mutable_configs(decoy: Decoy) -> Decoy: with patch( "opentrons_shared_data.pipette.mutable_configurations.list_mutable_configs", - new=decoy.mock(name="opentrons_shared_data.pipette.mutable_configurations.list_mutable_configs"), + new=decoy.mock( + name="opentrons_shared_data.pipette.mutable_configurations.list_mutable_configs" + ), ) as m: yield m @@ -137,7 +141,9 @@ def mock_list_mutable_configs(decoy: Decoy) -> Decoy: def mock_list_mutable_configs_with_defaults(decoy: Decoy) -> Decoy: with patch( "opentrons_shared_data.pipette.mutable_configurations.list_mutable_configs_with_defaults", - new=decoy.mock(name="opentrons_shared_data.pipette.mutable_configurations.list_mutable_configs_with_defaults"), + new=decoy.mock( + name="opentrons_shared_data.pipette.mutable_configurations.list_mutable_configs_with_defaults" + ), ) as m: yield m @@ -146,7 +152,9 @@ def mock_list_mutable_configs_with_defaults(decoy: Decoy) -> Decoy: def mock_save_overrides(decoy: Decoy) -> Decoy: with patch( "opentrons_shared_data.pipette.mutable_configurations.save_overrides", - new=decoy.mock(name="opentrons_shared_data.pipette.mutable_configurations.save_overrides"), + new=decoy.mock( + name="opentrons_shared_data.pipette.mutable_configurations.save_overrides" + ), ) as m: yield m @@ -155,7 +163,9 @@ def mock_save_overrides(decoy: Decoy) -> Decoy: def mock_get_opentrons_dir(decoy: Decoy) -> Decoy: with patch( "robot_server.service.legacy.routers.settings.get_opentrons_path", - new=decoy.mock(name="robot_server.service.legacy.routers.settings.get_opentrons_path"), + new=decoy.mock( + name="robot_server.service.legacy.routers.settings.get_opentrons_path" + ), ) as m: yield m From 5693a8f5eaff8fce28bfd35c81d4b05455ec1d39 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Wed, 20 Dec 2023 14:34:40 -0500 Subject: [PATCH 47/60] fix r-s tests after rebase --- .../protocols/test_v6_json_upload.tavern.yaml | 1 + .../test_v8_json_upload_flex.tavern.yaml | 80 +++++++++++++++++- .../test_v8_json_upload_ot2.tavern.yaml | 82 ++++++++++++++++++- .../test_maintenance_run_creation.tavern.yaml | 3 +- .../test_deck_configuration.tavern.yaml | 20 +++-- .../test_completed_analysis_store.py | 1 + 6 files changed, 174 insertions(+), 13 deletions(-) diff --git a/robot-server/tests/integration/http_api/protocols/test_v6_json_upload.tavern.yaml b/robot-server/tests/integration/http_api/protocols/test_v6_json_upload.tavern.yaml index 4cfc73a359c..9f8d37c5742 100644 --- a/robot-server/tests/integration/http_api/protocols/test_v6_json_upload.tavern.yaml +++ b/robot-server/tests/integration/http_api/protocols/test_v6_json_upload.tavern.yaml @@ -98,6 +98,7 @@ stages: location: slotName: '12' offsetId: null + displayName: null - id: sourcePlateId loadName: foo_8_plate_33ul definitionUri: example/foo_8_plate_33ul/1 diff --git a/robot-server/tests/integration/http_api/protocols/test_v8_json_upload_flex.tavern.yaml b/robot-server/tests/integration/http_api/protocols/test_v8_json_upload_flex.tavern.yaml index 636cd055090..84e2b2794cf 100644 --- a/robot-server/tests/integration/http_api/protocols/test_v8_json_upload_flex.tavern.yaml +++ b/robot-server/tests/integration/http_api/protocols/test_v8_json_upload_flex.tavern.yaml @@ -66,6 +66,7 @@ stages: author: engineering protocolName: Simple test protocol analyses: [] + key: null analysisSummaries: - id: '{analysis_id}' status: completed @@ -97,24 +98,28 @@ stages: displayName: Source Plate location: moduleId: temperatureModuleId + offsetId: null - id: destPlateId loadName: armadillo_96_wellplate_200ul_pcr_full_skirt definitionUri: opentrons/armadillo_96_wellplate_200ul_pcr_full_skirt/1 displayName: Sample Collection Plate location: moduleId: magneticModuleId + offsetId: null - id: tipRackId loadName: opentrons_96_tiprack_1000ul definitionUri: opentrons/opentrons_96_tiprack_1000ul/1 displayName: Opentrons 96 Tip Rack 1000 µL location: slotName: 'B2' + offsetId: null - id: fixedTrash loadName: opentrons_1_trash_1100ml_fixed definitionUri: opentrons/opentrons_1_trash_1100ml_fixed/1 displayName: Trash location: slotName: 'A3' + offsetId: null modules: - id: magneticModuleId serialNumber: !anystr @@ -133,10 +138,14 @@ stages: commandType: home key: !anystr status: succeeded - params: { } + params: + skipIfMountPositionOk: null + axes: null result: { } startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadPipette @@ -150,6 +159,8 @@ stages: pipetteId: pipetteId startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadModule @@ -167,6 +178,8 @@ stages: serialNumber: !anystr startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadModule @@ -184,6 +197,8 @@ stages: serialNumber: !anystr startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -200,8 +215,11 @@ stages: result: labwareId: sourcePlateId definition: !anydict + offsetId: null startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -218,8 +236,11 @@ stages: result: labwareId: destPlateId definition: !anydict + offsetId: null startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -236,8 +257,11 @@ stages: result: labwareId: tipRackId definition: !anydict + offsetId: null startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -254,8 +278,11 @@ stages: result: labwareId: fixedTrash definition: !anydict + offsetId: null startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadLiquid @@ -270,15 +297,21 @@ stages: result: {} startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: home key: !anystr status: succeeded - params: {} + params: + skipIfMountPositionOk: null + axes: null result: {} startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: pickUpTip @@ -301,6 +334,8 @@ stages: tipDiameter: 7.23 startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: aspirate @@ -323,6 +358,8 @@ stages: volume: 5.0 startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: waitForDuration @@ -330,9 +367,12 @@ stages: status: succeeded params: seconds: 42.0 + message: null result: {} startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: dispense @@ -350,11 +390,14 @@ stages: z: 1.0 volume: 4.5 flowRate: 2.5 + pushOut: null result: position: { 'x': 341.205, 'y': 65.115, 'z': 84.3 } volume: 4.5 startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: touchTip @@ -376,6 +419,8 @@ stages: position: { 'x': 341.205, 'y': 65.115, 'z': 94.3 } startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: blowout @@ -396,6 +441,8 @@ stages: position: { 'x': 341.205, 'y': 65.115, 'z': 95.3 } startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: moveToCoordinates @@ -408,10 +455,14 @@ stages: y: 100.0 z: 100.0 forceDirect: false + minimumZHeight: null + speed: null result: position: { 'x': 100.0, 'y': 100.0, 'z': 100.0 } startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: moveToWell @@ -429,11 +480,14 @@ stages: z: 0 forceDirect: false speed: 12.3 + minimumZHeight: null result: position: { 'x': 350.205, 'y': 65.115, 'z': 98.25 } startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: moveToWell @@ -451,11 +505,14 @@ stages: z: 10.0 minimumZHeight: 35.0 forceDirect: true + speed: null result: position: { 'x': 352.205, 'y': 68.115, 'z': 93.3 } startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: dropTip @@ -472,10 +529,13 @@ stages: y: 0 z: 0 alternateDropLocation: false + homeAfter: null result: position: { 'x': 410.84000000000003, 'y': 374.56, 'z': 82.0 } startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: waitForResume @@ -486,6 +546,8 @@ stages: result: {} startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: moveToCoordinates @@ -499,10 +561,13 @@ stages: z: 0.0 minimumZHeight: 35.0 forceDirect: true + speed: null result: position: { 'x': 0.0, 'y': 0.0, 'z': 0.0 } startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: moveRelative @@ -519,6 +584,8 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: moveRelative @@ -535,6 +602,8 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: savePosition @@ -543,6 +612,7 @@ stages: params: pipetteId: pipetteId failOnNotHomed: true + positionId: null result: positionId: !anystr position: @@ -551,6 +621,8 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: moveRelative @@ -567,6 +639,8 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: savePosition @@ -584,6 +658,8 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr + error: null + intent: null errors: [] liquids: - id: waterId diff --git a/robot-server/tests/integration/http_api/protocols/test_v8_json_upload_ot2.tavern.yaml b/robot-server/tests/integration/http_api/protocols/test_v8_json_upload_ot2.tavern.yaml index 48fb8200d61..6e0f018af08 100644 --- a/robot-server/tests/integration/http_api/protocols/test_v8_json_upload_ot2.tavern.yaml +++ b/robot-server/tests/integration/http_api/protocols/test_v8_json_upload_ot2.tavern.yaml @@ -65,6 +65,7 @@ stages: author: engineering protocolName: Simple test protocol analyses: [] + key: null analysisSummaries: - id: '{analysis_id}' status: completed @@ -96,24 +97,28 @@ stages: displayName: Source Plate location: moduleId: temperatureModuleId + offsetId: null - id: destPlateId loadName: armadillo_96_wellplate_200ul_pcr_full_skirt definitionUri: opentrons/armadillo_96_wellplate_200ul_pcr_full_skirt/1 displayName: Sample Collection Plate location: moduleId: magneticModuleId + offsetId: null - id: tipRackId loadName: opentrons_96_tiprack_10ul definitionUri: opentrons/opentrons_96_tiprack_10ul/1 displayName: Opentrons 96 Tip Rack 10 µL location: slotName: '8' + offsetId: null - id: fixedTrash loadName: opentrons_1_trash_1100ml_fixed definitionUri: opentrons/opentrons_1_trash_1100ml_fixed/1 displayName: Trash location: slotName: '12' + offsetId: null modules: - id: magneticModuleId serialNumber: !anystr @@ -132,10 +137,14 @@ stages: commandType: home key: !anystr status: succeeded - params: { } + params: + skipIfMountPositionOk: null + axes: null result: { } startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadPipette @@ -149,6 +158,8 @@ stages: pipetteId: pipetteId startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadModule @@ -166,6 +177,8 @@ stages: serialNumber: !anystr startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadModule @@ -183,6 +196,8 @@ stages: serialNumber: !anystr startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -199,8 +214,11 @@ stages: result: labwareId: sourcePlateId definition: !anydict + offsetId: null startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -217,8 +235,11 @@ stages: result: labwareId: destPlateId definition: !anydict + offsetId: null startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -235,8 +256,11 @@ stages: result: labwareId: tipRackId definition: !anydict + offsetId: null startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -253,8 +277,11 @@ stages: result: labwareId: fixedTrash definition: !anydict + offsetId: null startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: loadLiquid @@ -269,15 +296,21 @@ stages: result: {} startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: home key: !anystr status: succeeded - params: {} + params: + skipIfMountPositionOk: null + axes: null result: {} startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: pickUpTip @@ -300,6 +333,8 @@ stages: tipDiameter: 3.27 startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: aspirate @@ -322,6 +357,8 @@ stages: volume: 5.0 startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: waitForDuration @@ -329,9 +366,12 @@ stages: status: succeeded params: seconds: 42.0 + message: null result: {} startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: dispense @@ -349,11 +389,14 @@ stages: z: 1.0 volume: 4.5 flowRate: 2.5 + pushOut: null result: position: { 'x': 280.805, 'y': 65.115, 'z': 84.3 } volume: 4.5 startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: touchTip @@ -370,10 +413,13 @@ stages: y: 0.0 z: 11.0 radius: 1.0 + speed: null result: position: { 'x': 280.805, 'y': 65.115, 'z': 94.3 } startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: blowout @@ -394,6 +440,8 @@ stages: position: { 'x': 280.805, 'y': 65.115, 'z': 95.3 } startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: moveToCoordinates @@ -406,10 +454,14 @@ stages: y: 100.0 z: 100.0 forceDirect: false + minimumZHeight: null + speed: null result: position: {'x': 100.0, 'y': 100.0, 'z': 100.0} startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: moveToWell @@ -426,11 +478,15 @@ stages: y: 0 z: 0 forceDirect: false + speed: null + minimumZHeight: null result: position: { 'x': 289.805, 'y': 65.115, 'z': 98.25 } startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: moveToWell @@ -448,11 +504,14 @@ stages: z: 10.0 minimumZHeight: 35.0 forceDirect: true + speed: null result: position: { 'x': 291.805, 'y': 68.115, 'z': 93.3 } startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: dropTip @@ -469,10 +528,13 @@ stages: y: 0 z: 0 alternateDropLocation: false + homeAfter: null result: position: { 'x': 347.84000000000003, 'y': 325.06, 'z': 82.0 } startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: waitForResume @@ -483,6 +545,8 @@ stages: result: {} startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: moveToCoordinates @@ -496,10 +560,13 @@ stages: z: 0.0 minimumZHeight: 35.0 forceDirect: true + speed: null result: position: { 'x': 0.0, 'y': 0.0, 'z': 0.0 } startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: moveRelative @@ -516,6 +583,8 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: moveRelative @@ -532,6 +601,8 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: savePosition @@ -540,6 +611,7 @@ stages: params: pipetteId: pipetteId failOnNotHomed: true + positionId: null result: positionId: !anystr position: @@ -548,6 +620,8 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: moveRelative @@ -564,6 +638,8 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr + error: null + intent: null - id: !anystr createdAt: !anystr commandType: savePosition @@ -581,6 +657,8 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr + error: null + intent: null errors: [] liquids: - id: waterId diff --git a/robot-server/tests/integration/http_api/runs/test_maintenance_run_creation.tavern.yaml b/robot-server/tests/integration/http_api/runs/test_maintenance_run_creation.tavern.yaml index 7b7d7930f22..23be48f9fb0 100644 --- a/robot-server/tests/integration/http_api/runs/test_maintenance_run_creation.tavern.yaml +++ b/robot-server/tests/integration/http_api/runs/test_maintenance_run_creation.tavern.yaml @@ -12,7 +12,8 @@ stages: response: json: data: [] - links: {} + links: + current: null meta: cursor: 0 totalLength: 0 diff --git a/robot-server/tests/integration/http_api/test_deck_configuration.tavern.yaml b/robot-server/tests/integration/http_api/test_deck_configuration.tavern.yaml index 21be55b752f..63b3f27fdfd 100644 --- a/robot-server/tests/integration/http_api/test_deck_configuration.tavern.yaml +++ b/robot-server/tests/integration/http_api/test_deck_configuration.tavern.yaml @@ -5,6 +5,17 @@ marks: - usefixtures: - ot3_server_base_url +# lastModifiedAt is deliberately omitted from this expected object. +# This requires turning off strict json checking. +# A lastModifiedAt that's omitted or null means the deck configuration has never been set. +# +# Unfortunately, this makes this test order-dependent with any other tests +# that modify the deck configuration, even if they try to restore the original value +# after they're done. We probably need some kind of deck configuration factory-reset. +strict: + - headers:off + - json:off + stages: - name: Get the deck configuration and make sure there's a default request: @@ -12,14 +23,7 @@ stages: response: json: data: - # lastModifiedAt is deliberately omitted from this expected object. - # A lastModifiedAt that's omitted or null means the deck configuration has never been set. - # - # Unfortunately, this makes this test order-dependent with any other tests - # that modify the deck configuration, even if they try to restore the original value - # after they're done. We probably need some kind of deck configuration factory-reset. - # - # lastModifiedAt: null + cutoutFixtures: &expectedDefaultCutoutFixtures - cutoutFixtureId: singleLeftSlot cutoutId: cutoutA1 diff --git a/robot-server/tests/protocols/test_completed_analysis_store.py b/robot-server/tests/protocols/test_completed_analysis_store.py index 4b76386acd4..fe1845e444c 100644 --- a/robot-server/tests/protocols/test_completed_analysis_store.py +++ b/robot-server/tests/protocols/test_completed_analysis_store.py @@ -159,6 +159,7 @@ async def test_get_by_analysis_id_as_document( "id": "analysis-id", "result": "ok", "status": "completed", + "robotType": None, "commands": [], "errors": [], "labware": [], From d994e7da15c147bcc694a1a8d54e616ba3f31334 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Wed, 20 Dec 2023 14:44:00 -0500 Subject: [PATCH 48/60] system-server fixups --- system-server/Pipfile | 2 +- system-server/Pipfile.lock | 151 +++++++++++++----------- system-server/system_server/_version.py | 2 +- 3 files changed, 81 insertions(+), 74 deletions(-) diff --git a/system-server/Pipfile b/system-server/Pipfile index dc6c390d9f8..2c911138d3f 100644 --- a/system-server/Pipfile +++ b/system-server/Pipfile @@ -20,7 +20,7 @@ flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" flake8-noqa = "~=1.2.1" -pytest = "~=7.1" +pytest = "<7.3.0,>=7.1" pytest-asyncio = "==0.18" pytest-cov = "==2.10.1" pytest-lazy-fixture = "==0.6.3" diff --git a/system-server/Pipfile.lock b/system-server/Pipfile.lock index 32424cb43b7..493dd5be346 100644 --- a/system-server/Pipfile.lock +++ b/system-server/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "4707d9057be5081ab3f2a89b0d9e69d5951ad7a5204388394af2fb4f7c01e873" + "sha256": "2785838ab3d5199201cc286ff042bbcf191c1a642d0ba0f4f5a980c5f04e710e" }, "pipfile-spec": 6, "requires": { @@ -60,66 +60,67 @@ }, "greenlet": { "hashes": [ - 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(platform_machine == 'amd64' or (platform_machine == 'AMD64' or (platform_machine == 'win32' or platform_machine == 'WIN32')))))", - "version": "==3.0.1" + "version": "==3.0.2" }, "h11": { "hashes": [ @@ -285,14 +286,20 @@ "editable": true, "path": "." }, + "systemd-python": { + "hashes": [ + "sha256:fd0e44bf70eadae45aadc292cb0a7eb5b0b6372cd1b391228047d33895db83e7" + ], + "version": "==234" + }, "typing-extensions": { "hashes": [ - "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0", - "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef" + "sha256:23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783", + "sha256:af72aea155e91adfc61c3ae9e0e342dbc0cba726d6cba4b6c72c1f34e47291cd" ], "index": "pypi", "markers": "python_version >= '3.8'", - "version": "==4.8.0" + "version": "==4.9.0" }, "uvicorn": { "hashes": [ @@ -614,11 +621,11 @@ }, "pathspec": { "hashes": [ - "sha256:1d6ed233af05e679efb96b1851550ea95bbb64b7c490b0f5aa52996c11e92a20", - "sha256:e0d8d0ac2f12da61956eb2306b69f9469b42f4deb0f3cb6ed47b9cce9996ced3" + "sha256:a0d503e138a4c123b27490a4f7beda6a01c6f288df0e4a8b79c7eb0dc7b4cc08", + "sha256:a482d51503a1ab33b1c67a6c3813a26953dbdc71c31dacaef9a838c4e29f5712" ], - "markers": "python_version >= '3.7'", - "version": "==0.11.2" + "markers": "python_version >= '3.8'", + "version": "==0.12.1" }, "pbr": { "hashes": [ @@ -731,12 +738,12 @@ }, "pytest": { "hashes": [ - "sha256:0d009c083ea859a71b76adf7c1d502e4bc170b80a8ef002da5806527b9591fac", - "sha256:d989d136982de4e3b29dabcc838ad581c64e8ed52c11fbe86ddebd9da0818cd5" + "sha256:130328f552dcfac0b1cec75c12e3f005619dc5f874f0a06e8ff7263f0ee6225e", + "sha256:c99ab0c73aceb050f68929bc93af19ab6db0558791c6a0715723abe9d0ade9d4" ], "index": "pypi", "markers": "python_version >= '3.7'", - "version": "==7.4.3" + "version": "==7.2.2" }, "pytest-asyncio": { "hashes": [ @@ -1000,12 +1007,12 @@ }, "typing-extensions": { "hashes": [ - "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0", - "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef" + "sha256:23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783", + "sha256:af72aea155e91adfc61c3ae9e0e342dbc0cba726d6cba4b6c72c1f34e47291cd" ], "index": "pypi", "markers": "python_version >= '3.8'", - "version": "==4.8.0" + "version": "==4.9.0" }, "urllib3": { "hashes": [ diff --git a/system-server/system_server/_version.py b/system-server/system_server/_version.py index 389fea511a2..e0df4605660 100644 --- a/system-server/system_server/_version.py +++ b/system-server/system_server/_version.py @@ -9,7 +9,7 @@ import importlib_metadata as metadata # type: ignore[no-redef] try: - version: str = metadata.version("system_server") # type: ignore[attr-defined] + version: str = metadata.version("system_server") except Exception as e: logging.warning( "Could not determine version for system_server, may be dev install, using 0.0.0-dev" From a9eb1a752fd03a81f545efb64183586f067f4210 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Wed, 20 Dec 2023 14:46:16 -0500 Subject: [PATCH 49/60] fix up server-utils typing --- server-utils/server_utils/util.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/server-utils/server_utils/util.py b/server-utils/server_utils/util.py index f15e83bafc1..631b4b6c979 100644 --- a/server-utils/server_utils/util.py +++ b/server-utils/server_utils/util.py @@ -7,7 +7,7 @@ from functools import wraps from pathlib import Path from types import TracebackType -from typing import cast, Any, Awaitable, Callable, Optional, Type, TypeVar +from typing import cast, Any, Coroutine, Callable, Optional, Type, TypeVar from typing_extensions import Final from datetime import datetime, timezone @@ -56,7 +56,7 @@ def save_upload(directory: Path, upload_file: UploadFile) -> FileMeta: _CALL_ONCE_TASK_ATTR: Final = "_call_once_task" -AsyncFuncT = TypeVar("AsyncFuncT", bound=Callable[..., Awaitable[Any]]) +AsyncFuncT = TypeVar("AsyncFuncT", bound=Callable[..., Coroutine[Any, Any, Any]]) def call_once(fn: AsyncFuncT) -> AsyncFuncT: From 47685e405c67dad03ba0073cab6dbf7ce9cf1f1d Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Wed, 20 Dec 2023 14:47:02 -0500 Subject: [PATCH 50/60] s-d typing fixups --- .../opentrons_shared_data/labware/labware_definition.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/shared-data/python/opentrons_shared_data/labware/labware_definition.py b/shared-data/python/opentrons_shared_data/labware/labware_definition.py index 0b2f1db30b0..e884b9e9623 100644 --- a/shared-data/python/opentrons_shared_data/labware/labware_definition.py +++ b/shared-data/python/opentrons_shared_data/labware/labware_definition.py @@ -6,7 +6,7 @@ from __future__ import annotations from enum import Enum -from typing import TYPE_CHECKING, Dict, List, Optional, Union +from typing import TYPE_CHECKING, Dict, List, Optional, Union, Any from pydantic import ( BaseModel, @@ -328,9 +328,9 @@ class LabwareDefinition(BaseModel): ) def dict(self, *args: Any, **kwargs: Any) -> Dict[str, Any]: - kwargs['exclude_unset'] = True + kwargs["exclude_unset"] = True return super().dict(*args, **kwargs) def json(self, *args: Any, **kwargs: Any) -> str: - kwargs['exclude_unset'] = True + kwargs["exclude_unset"] = True return super().json(*args, **kwargs) From 35f7ea5060be3ed3fc34b478fc01ee5a57b92f4e Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Wed, 20 Dec 2023 14:56:47 -0500 Subject: [PATCH 51/60] get tip presence impl --- .../opentrons/protocol_engine/execution/tip_handler.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/api/src/opentrons/protocol_engine/execution/tip_handler.py b/api/src/opentrons/protocol_engine/execution/tip_handler.py index b628c8ef35d..51cf4708377 100644 --- a/api/src/opentrons/protocol_engine/execution/tip_handler.py +++ b/api/src/opentrons/protocol_engine/execution/tip_handler.py @@ -339,6 +339,14 @@ async def verify_tip_presence( This should not be called when using virtual pipettes. """ + async def get_tip_presence(self, pipette_id: str) -> TipPresenceStatus: + """Get tip presence. + + This is a check to the physical machine's sensors and should not be + called on a virtual pipette. + """ + raise RuntimeError("Do not call VirtualTipHandler.get_tip_presence") + def create_tip_handler( state_view: StateView, hardware_api: HardwareControlAPI From 3c2563da4b7022623dd28c3a5cba38710f9d0d22 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Wed, 20 Dec 2023 14:57:41 -0500 Subject: [PATCH 52/60] another moved noqa --- api/src/opentrons/protocol_api/instrument_context.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/api/src/opentrons/protocol_api/instrument_context.py b/api/src/opentrons/protocol_api/instrument_context.py index d3cd6777fda..ae4ad60b9fa 100644 --- a/api/src/opentrons/protocol_api/instrument_context.py +++ b/api/src/opentrons/protocol_api/instrument_context.py @@ -275,8 +275,8 @@ def aspirate( return self - @requires_version(2, 0) # noqa: C901 - def dispense( + @requires_version(2, 0) + def dispense( # noqa: C901 self, volume: Optional[float] = None, location: Optional[ From 4f79f6a9ec40138fdd8478449d63809d8a4b61b9 Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Wed, 20 Dec 2023 15:03:49 -0500 Subject: [PATCH 53/60] no more s-d tests on 3.7 --- .github/workflows/shared-data-test-lint-deploy.yaml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/shared-data-test-lint-deploy.yaml b/.github/workflows/shared-data-test-lint-deploy.yaml index 2b61e5552ca..65776b1a5cc 100644 --- a/.github/workflows/shared-data-test-lint-deploy.yaml +++ b/.github/workflows/shared-data-test-lint-deploy.yaml @@ -71,10 +71,8 @@ jobs: os: ['windows-2022', 'ubuntu-22.04', 'macos-latest'] # TODO(mc, 2022-02-24): expand this matrix to 3.8 and 3.9, # preferably in a nightly cronjob on edge or something - python: ['3.7', '3.10'] - exclude: - - os: 'macos-latest' - python: '3.10' + python: ['3.10'] + runs-on: '${{ matrix.os }}' steps: - uses: 'actions/checkout@v3' From d82f20d976c9a2f8ac9607785a2b0fb9fdccdaea Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Wed, 20 Dec 2023 16:45:45 -0500 Subject: [PATCH 54/60] just dont touch app-testing --- app-testing/Pipfile | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/app-testing/Pipfile b/app-testing/Pipfile index 64274bc892a..12dfe7880a0 100644 --- a/app-testing/Pipfile +++ b/app-testing/Pipfile @@ -4,21 +4,21 @@ url = "https://pypi.org/simple" verify_ssl = true [packages] -pytest = "==7.1.1" +pytest = "==7.2.0" black = "==22.12.0" selenium = "==4.7.2" -importlib-metadata = "==4.11.3" -requests = "==2.27.1" +importlib-metadata = "==5.0.0" +requests = "==2.28.1" python-dotenv = "==0.21.0" -pytest-xdist = "==2.5.0" -mypy = "==0.942" +pytest-xdist = "==3.0.2" +mypy = "==0.991" types-requests = "==2.28.11.5" rich = "==13.0.0" -atomicwrites = "==1.4.0" +atomicwrites = "==1.4.1" pyreadline3 = "==3.4.1" pydantic = "==1.10.4" pygithub = "==1.57" ruff = "==0.0.236" [requires] -python_version = "3.10" +python_version = "3.11" From a0e854413bc8877ae9c53a6170b5db121554fe1d Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Thu, 21 Dec 2023 09:39:44 -0500 Subject: [PATCH 55/60] back to more recent sphinx --- api/Pipfile | 4 +- api/Pipfile.lock | 175 ++++++++++++++++++++++++----------------------- 2 files changed, 90 insertions(+), 89 deletions(-) diff --git a/api/Pipfile b/api/Pipfile index a2cf4813902..30420dac26c 100755 --- a/api/Pipfile +++ b/api/Pipfile @@ -17,13 +17,13 @@ pytest-asyncio = "~=0.16" pytest-cov = "==2.10.1" pytest-lazy-fixture = "==0.6.3" pytest-xdist = "~=2.5.0" -sphinx = "==4.4.0" +sphinx = "==5.0.1" twine = "==4.0.0" wheel = "==0.37.0" typeguard = "==2.13.1" sphinx-substitution-extensions = "==2020.9.30.0" sphinxext-opengraph = "==0.8.1" -sphinx-tabs = ">=3.4.0,<4" +sphinx-tabs = ">=3.4.1,<4" mock = "~=4.0.3" flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" diff --git a/api/Pipfile.lock b/api/Pipfile.lock index 2d9dc89bf38..a519d9462e1 100644 --- a/api/Pipfile.lock +++ b/api/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "4e0f3375a8c869d73bc486d144b4bfb9a158ffca346fb192d6cfde548f413f9f" + "sha256": "85e6abfa7a1353756769cf234de3045eac2043749097a794e120eb3e32e2fccd" }, "pipfile-spec": 6, "requires": {}, @@ -56,11 +56,11 @@ }, "babel": { "hashes": [ - "sha256:33e0952d7dd6374af8dbf6768cc4ddf3ccfefc244f9986d4074704f2fbd18900", - "sha256:7077a4984b02b6727ac10f1f7294484f737443d7e2e66c5e4380e41a3ae0b4ed" + "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363", + "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287" ], "markers": "python_version >= '3.7'", - "version": "==2.13.1" + "version": "==2.14.0" }, "black": { "hashes": [ @@ -319,11 +319,11 @@ }, "docutils": { "hashes": [ - "sha256:686577d2e4c32380bb50cbb22f575ed742d58168cee37e99117a854bcd88f125", - "sha256:cf316c8370a737a022b72b56874f6602acf974a37a9fba42ec2876387549fc61" + "sha256:23010f129180089fbcd3bc08cfefccb3b890b0050e1ca00c867036e9d161b98c", + "sha256:679987caf361a7539d76e584cbeddc311e3aee937877c87346f31debc63e9d06" ], "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'", - 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"version": "==4.8.0" + "version": "==4.9.0" }, "urllib3": { "hashes": [ From 640d04d8d0b6bd3ae2087f0cd1f2d8bbe884f24f Mon Sep 17 00:00:00 2001 From: Seth Foster Date: Tue, 2 Jan 2024 10:01:54 -0500 Subject: [PATCH 56/60] update setup py metadata --- api/setup.py | 3 +-- hardware/setup.py | 4 ++-- robot-server/setup.py | 4 ++-- server-utils/setup.py | 4 ++-- shared-data/python/setup.py | 3 +-- usb-bridge/setup.py | 3 +-- 6 files changed, 9 insertions(+), 12 deletions(-) diff --git a/api/setup.py b/api/setup.py index 9e251fc1f0d..818a3c88ee7 100755 --- a/api/setup.py +++ b/api/setup.py @@ -46,7 +46,6 @@ def get_version(): "Intended Audience :: Science/Research", "Programming Language :: Python", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", @@ -88,7 +87,7 @@ def read(*parts): if __name__ == "__main__": setup( - python_requires=">=3.7", + python_requires=">=3.8", name=DISTNAME, description=DESCRIPTION, license=LICENSE, diff --git a/hardware/setup.py b/hardware/setup.py index 1195e9ea727..b463a3fbd20 100644 --- a/hardware/setup.py +++ b/hardware/setup.py @@ -40,7 +40,7 @@ def get_version() -> str: "Intended Audience :: Science/Research", "Programming Language :: Python", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.10", "Topic :: Scientific/Engineering", ] KEYWORDS = ["robots", "protocols", "synbio", "pcr", "automation", "lab"] @@ -67,7 +67,7 @@ def read(*parts: str) -> str: if __name__ == "__main__": setup( - python_requires=">=3.7", + python_requires="~=3.10", name=DISTNAME, description=DESCRIPTION, license=LICENSE, diff --git a/robot-server/setup.py b/robot-server/setup.py index 6cfdd9ad421..5862f0c244e 100755 --- a/robot-server/setup.py +++ b/robot-server/setup.py @@ -45,7 +45,7 @@ def get_version(): "Intended Audience :: Science/Research", "Programming Language :: Python", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.10", "Topic :: Scientific/Engineering", ] KEYWORDS = ["robots", "protocols", "synbio", "pcr", "automation", "lab"] @@ -81,7 +81,7 @@ def read(*parts): if __name__ == "__main__": setup( - python_requires=">=3.7", + python_requires="~=3.10", name=DISTNAME, description=DESCRIPTION, license=LICENSE, diff --git a/server-utils/setup.py b/server-utils/setup.py index 2728aa4c86a..47204f4168d 100755 --- a/server-utils/setup.py +++ b/server-utils/setup.py @@ -44,7 +44,7 @@ def get_version(): "Intended Audience :: Science/Research", "Programming Language :: Python", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.10", "Topic :: Scientific/Engineering", ] KEYWORDS = ["robots", "protocols", "synbio", "pcr", "automation", "lab"] @@ -76,7 +76,7 @@ def read(*parts): if __name__ == "__main__": setup( - python_requires=">=3.7", + python_requires="~=3.10", name=DISTNAME, description=DESCRIPTION, license=LICENSE, diff --git a/shared-data/python/setup.py b/shared-data/python/setup.py index 4dbcb119f69..48c31471d34 100644 --- a/shared-data/python/setup.py +++ b/shared-data/python/setup.py @@ -130,7 +130,6 @@ def get_version(): "Intended Audience :: Science/Research", "Programming Language :: Python", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", @@ -152,7 +151,7 @@ def get_version(): if __name__ == "__main__": setup( - python_requires=">=3.7", + python_requires=">=3.8", name=DISTNAME, description=DESCRIPTION, license=LICENSE, diff --git a/usb-bridge/setup.py b/usb-bridge/setup.py index 97c0f505951..583361428d8 100644 --- a/usb-bridge/setup.py +++ b/usb-bridge/setup.py @@ -37,7 +37,6 @@ def get_version(): 'Intended Audience :: Science/Research', 'Programming Language :: Python', 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.7', 'Programming Language :: Python :: 3.10', 'Topic :: Scientific/Engineering', ] @@ -62,7 +61,7 @@ def read(*parts): if __name__ == "__main__": setup( - python_requires='>=3.7', + python_requires='~=3.10', name=DISTNAME, description=DESCRIPTION, license=LICENSE, From 59ecbb60c7e6b6ae2d009da6086a5206c74a385f Mon Sep 17 00:00:00 2001 From: Max Marrone Date: Tue, 2 Jan 2024 13:14:57 -0500 Subject: [PATCH 57/60] Revert null/omitted test changes. --- .../protocols/test_analyses.tavern.yaml | 1 - .../test_deck_coordinate_load.tavern.yaml | 1 - .../protocols/test_upload.tavern.yaml | 1 - .../protocols/test_v6_json_upload.tavern.yaml | 119 ++-------------- .../test_v8_json_upload_flex.tavern.yaml | 80 +---------- .../test_v8_json_upload_ot2.tavern.yaml | 82 +---------- .../test_json_v6_protocol_run.tavern.yaml | 130 ++---------------- .../runs/test_json_v6_run_failure.tavern.yaml | 14 +- .../test_json_v7_protocol_run.tavern.yaml | 130 ++---------------- .../test_maintenance_run_creation.tavern.yaml | 3 +- .../runs/test_papi_v2_run_failure.tavern.yaml | 14 +- .../http_api/runs/test_persistence.py | 2 +- .../runs/test_protocol_run.tavern.yaml | 27 +--- ...t_run_queued_protocol_commands.tavern.yaml | 7 - .../test_deck_configuration.tavern.yaml | 20 ++- .../integration/test_modules.tavern.yaml | 16 --- .../tests/protocols/test_analysis_store.py | 2 - .../test_completed_analysis_store.py | 1 - 18 files changed, 53 insertions(+), 597 deletions(-) diff --git a/robot-server/tests/integration/http_api/protocols/test_analyses.tavern.yaml b/robot-server/tests/integration/http_api/protocols/test_analyses.tavern.yaml index 47bf0ec5c17..a756ea10e1b 100644 --- a/robot-server/tests/integration/http_api/protocols/test_analyses.tavern.yaml +++ b/robot-server/tests/integration/http_api/protocols/test_analyses.tavern.yaml @@ -45,7 +45,6 @@ stages: createdAt: !anything robotType: !anything metadata: !anything - key: null links: !anything - name: Check that the analysis data is present in /protocols/:id/analyses/:id diff --git a/robot-server/tests/integration/http_api/protocols/test_deck_coordinate_load.tavern.yaml b/robot-server/tests/integration/http_api/protocols/test_deck_coordinate_load.tavern.yaml index 802d8fd3262..a7458e9dfc3 100644 --- a/robot-server/tests/integration/http_api/protocols/test_deck_coordinate_load.tavern.yaml +++ b/robot-server/tests/integration/http_api/protocols/test_deck_coordinate_load.tavern.yaml @@ -20,7 +20,6 @@ stages: json: data: id: !anystr - key: null protocolType: python files: - name: deck_coordinate_load.py diff --git a/robot-server/tests/integration/http_api/protocols/test_upload.tavern.yaml b/robot-server/tests/integration/http_api/protocols/test_upload.tavern.yaml index c9f0ca73713..63bf756bc8d 100644 --- a/robot-server/tests/integration/http_api/protocols/test_upload.tavern.yaml +++ b/robot-server/tests/integration/http_api/protocols/test_upload.tavern.yaml @@ -20,7 +20,6 @@ stages: data: id: !anystr protocolType: python - key: null files: - name: basic_transfer_standalone.py role: main diff --git a/robot-server/tests/integration/http_api/protocols/test_v6_json_upload.tavern.yaml b/robot-server/tests/integration/http_api/protocols/test_v6_json_upload.tavern.yaml index 9f8d37c5742..13af0f78d84 100644 --- a/robot-server/tests/integration/http_api/protocols/test_v6_json_upload.tavern.yaml +++ b/robot-server/tests/integration/http_api/protocols/test_v6_json_upload.tavern.yaml @@ -39,7 +39,6 @@ stages: json: data: - id: '{protocol_id}' - analyses: [] analysisSummaries: - id: '{analysis_id}' status: completed @@ -66,11 +65,10 @@ stages: author: engineering protocolName: Simple test protocol analyses: [] - key: null analysisSummaries: - id: '{analysis_id}' status: completed - links: + links: referencingRuns: [] - name: Get protocol analysis by ID request: @@ -97,29 +95,24 @@ stages: definitionUri: opentrons/opentrons_1_trash_1100ml_fixed/1 location: slotName: '12' - offsetId: null - displayName: null - id: sourcePlateId loadName: foo_8_plate_33ul definitionUri: example/foo_8_plate_33ul/1 displayName: Source Plate location: moduleId: temperatureModuleId - offsetId: null - id: destPlateId loadName: foo_8_plate_33ul definitionUri: example/foo_8_plate_33ul/1 displayName: Sample Collection Plate location: moduleId: magneticModuleId - offsetId: null - id: tipRackId loadName: opentrons_96_tiprack_10ul definitionUri: opentrons/opentrons_96_tiprack_10ul/1 displayName: Opentrons 96 Tip Rack 10 µL location: slotName: '8' - offsetId: null modules: - id: magneticModuleId serialNumber: !anystr @@ -138,14 +131,10 @@ stages: commandType: home key: !anystr status: succeeded - params: - axes: null - skipIfMountPositionOk: null + params: { } result: { } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadPipette @@ -159,8 +148,6 @@ stages: pipetteId: pipetteId startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadModule @@ -178,8 +165,6 @@ stages: serialNumber: !anystr startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadModule @@ -197,8 +182,6 @@ stages: serialNumber: !anystr startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -213,13 +196,10 @@ stages: labwareId: sourcePlateId displayName: Source Plate result: - offsetId: null labwareId: sourcePlateId definition: !anydict startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -236,11 +216,8 @@ stages: result: labwareId: destPlateId definition: !anydict - offsetId: null startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -257,11 +234,8 @@ stages: result: labwareId: tipRackId definition: !anydict - offsetId: null startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadLiquid @@ -276,21 +250,15 @@ stages: result: {} startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: home key: !anystr status: succeeded - params: - axes: null - skipIfMountPositionOk: null + params: {} result: {} startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: pickUpTip @@ -307,17 +275,12 @@ stages: y: 0 z: 0 result: - position: - x: 146.88 - y: 246.24 - z: 64.69 + position: { 'x': 146.88, 'y': 246.24, 'z': 64.69 } tipVolume: 10.0 tipLength: 35.910000000000004 tipDiameter: 3.27 startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: aspirate @@ -336,15 +299,10 @@ stages: volume: 5 flowRate: 3 result: - position: - x: 16.76 - y: 75.28 - z: 157.09 + position: { 'x': 16.76, 'y': 75.28, 'z': 157.09 } volume: 5 startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: waitForDuration @@ -352,12 +310,9 @@ stages: status: succeeded params: seconds: 42 - message: null result: {} startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: dispense @@ -375,17 +330,11 @@ stages: z: 1 volume: 4.5 flowRate: 2.5 - pushOut: null result: - position: - x: 284.635 - y: 56.025 - z: 158.25 + position: { 'x': 284.635, 'y': 56.025, 'z': 158.25 } volume: 4.5 startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: touchTip @@ -404,14 +353,9 @@ stages: radius: 0.5 speed: 42.0 result: - position: - x: 284.635 - y: 56.025 - z: 168.25 + position: { 'x': 284.635, 'y': 56.025, 'z': 168.25 } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: blowout @@ -429,14 +373,9 @@ stages: z: 12 flowRate: 2 result: - position: - x: 284.635 - y: 56.025 - z: 169.25 + position: { 'x': 284.635, 'y': 56.025, 'z': 169.25 } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: moveToWell @@ -453,17 +392,11 @@ stages: y: 0 z: 0 forceDirect: false - speed: null - minimumZHeight: null result: position: - x: 304.52500000000003 - y: 56.025 - z: 182.25 + { 'x': 304.52500000000003, 'y': 56.025, 'z': 182.25 } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: moveToWell @@ -484,13 +417,9 @@ stages: speed: 12.3 result: position: - x: 306.52500000000003 - y: 59.025 - z: 167.25 + { 'x': 306.52500000000003, 'y': 59.025, 'z': 167.25 } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: dropTip @@ -507,16 +436,10 @@ stages: y: 0 z: 0 alternateDropLocation: false - homeAfter: null result: - position: - x: 347.84000000000003 - y: 325.06 - z: 82.0 + position: { 'x': 347.84000000000003, 'y': 325.06, 'z': 82.0 } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: waitForResume @@ -527,8 +450,6 @@ stages: result: {} startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: moveToCoordinates @@ -544,14 +465,9 @@ stages: forceDirect: true speed: 12.3 result: - position: - x: 0.0 - y: 0.0 - z: 0.0 + position: { 'x': 0.0, 'y': 0.0, 'z': 0.0 } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: moveRelative @@ -568,8 +484,6 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: moveRelative @@ -586,8 +500,6 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: savePosition @@ -596,7 +508,6 @@ stages: params: pipetteId: pipetteId failOnNotHomed: true - positionId: null result: positionId: !anystr position: @@ -605,8 +516,6 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: moveRelative @@ -623,8 +532,6 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: savePosition @@ -642,8 +549,6 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr - error: null - intent: null errors: [] liquids: - id: waterId diff --git a/robot-server/tests/integration/http_api/protocols/test_v8_json_upload_flex.tavern.yaml b/robot-server/tests/integration/http_api/protocols/test_v8_json_upload_flex.tavern.yaml index 84e2b2794cf..636cd055090 100644 --- a/robot-server/tests/integration/http_api/protocols/test_v8_json_upload_flex.tavern.yaml +++ b/robot-server/tests/integration/http_api/protocols/test_v8_json_upload_flex.tavern.yaml @@ -66,7 +66,6 @@ stages: author: engineering protocolName: Simple test protocol analyses: [] - key: null analysisSummaries: - id: '{analysis_id}' status: completed @@ -98,28 +97,24 @@ stages: displayName: Source Plate location: moduleId: temperatureModuleId - offsetId: null - id: destPlateId loadName: armadillo_96_wellplate_200ul_pcr_full_skirt definitionUri: opentrons/armadillo_96_wellplate_200ul_pcr_full_skirt/1 displayName: Sample Collection Plate location: moduleId: magneticModuleId - offsetId: null - id: tipRackId loadName: opentrons_96_tiprack_1000ul definitionUri: opentrons/opentrons_96_tiprack_1000ul/1 displayName: Opentrons 96 Tip Rack 1000 µL location: slotName: 'B2' - offsetId: null - id: fixedTrash loadName: opentrons_1_trash_1100ml_fixed definitionUri: opentrons/opentrons_1_trash_1100ml_fixed/1 displayName: Trash location: slotName: 'A3' - offsetId: null modules: - id: magneticModuleId serialNumber: !anystr @@ -138,14 +133,10 @@ stages: commandType: home key: !anystr status: succeeded - params: - skipIfMountPositionOk: null - axes: null + params: { } result: { } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadPipette @@ -159,8 +150,6 @@ stages: pipetteId: pipetteId startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadModule @@ -178,8 +167,6 @@ stages: serialNumber: !anystr startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadModule @@ -197,8 +184,6 @@ stages: serialNumber: !anystr startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -215,11 +200,8 @@ stages: result: labwareId: sourcePlateId definition: !anydict - offsetId: null startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -236,11 +218,8 @@ stages: result: labwareId: destPlateId definition: !anydict - offsetId: null startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -257,11 +236,8 @@ stages: result: labwareId: tipRackId definition: !anydict - offsetId: null startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -278,11 +254,8 @@ stages: result: labwareId: fixedTrash definition: !anydict - offsetId: null startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadLiquid @@ -297,21 +270,15 @@ stages: result: {} startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: home key: !anystr status: succeeded - params: - skipIfMountPositionOk: null - axes: null + params: {} result: {} startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: pickUpTip @@ -334,8 +301,6 @@ stages: tipDiameter: 7.23 startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: aspirate @@ -358,8 +323,6 @@ stages: volume: 5.0 startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: waitForDuration @@ -367,12 +330,9 @@ stages: status: succeeded params: seconds: 42.0 - message: null result: {} startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: dispense @@ -390,14 +350,11 @@ stages: z: 1.0 volume: 4.5 flowRate: 2.5 - pushOut: null result: position: { 'x': 341.205, 'y': 65.115, 'z': 84.3 } volume: 4.5 startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: touchTip @@ -419,8 +376,6 @@ stages: position: { 'x': 341.205, 'y': 65.115, 'z': 94.3 } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: blowout @@ -441,8 +396,6 @@ stages: position: { 'x': 341.205, 'y': 65.115, 'z': 95.3 } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: moveToCoordinates @@ -455,14 +408,10 @@ stages: y: 100.0 z: 100.0 forceDirect: false - minimumZHeight: null - speed: null result: position: { 'x': 100.0, 'y': 100.0, 'z': 100.0 } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: moveToWell @@ -480,14 +429,11 @@ stages: z: 0 forceDirect: false speed: 12.3 - minimumZHeight: null result: position: { 'x': 350.205, 'y': 65.115, 'z': 98.25 } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: moveToWell @@ -505,14 +451,11 @@ stages: z: 10.0 minimumZHeight: 35.0 forceDirect: true - speed: null result: position: { 'x': 352.205, 'y': 68.115, 'z': 93.3 } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: dropTip @@ -529,13 +472,10 @@ stages: y: 0 z: 0 alternateDropLocation: false - homeAfter: null result: position: { 'x': 410.84000000000003, 'y': 374.56, 'z': 82.0 } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: waitForResume @@ -546,8 +486,6 @@ stages: result: {} startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: moveToCoordinates @@ -561,13 +499,10 @@ stages: z: 0.0 minimumZHeight: 35.0 forceDirect: true - speed: null result: position: { 'x': 0.0, 'y': 0.0, 'z': 0.0 } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: moveRelative @@ -584,8 +519,6 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: moveRelative @@ -602,8 +535,6 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: savePosition @@ -612,7 +543,6 @@ stages: params: pipetteId: pipetteId failOnNotHomed: true - positionId: null result: positionId: !anystr position: @@ -621,8 +551,6 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: moveRelative @@ -639,8 +567,6 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: savePosition @@ -658,8 +584,6 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr - error: null - intent: null errors: [] liquids: - id: waterId diff --git a/robot-server/tests/integration/http_api/protocols/test_v8_json_upload_ot2.tavern.yaml b/robot-server/tests/integration/http_api/protocols/test_v8_json_upload_ot2.tavern.yaml index 6e0f018af08..48fb8200d61 100644 --- a/robot-server/tests/integration/http_api/protocols/test_v8_json_upload_ot2.tavern.yaml +++ b/robot-server/tests/integration/http_api/protocols/test_v8_json_upload_ot2.tavern.yaml @@ -65,7 +65,6 @@ stages: author: engineering protocolName: Simple test protocol analyses: [] - key: null analysisSummaries: - id: '{analysis_id}' status: completed @@ -97,28 +96,24 @@ stages: displayName: Source Plate location: moduleId: temperatureModuleId - offsetId: null - id: destPlateId loadName: armadillo_96_wellplate_200ul_pcr_full_skirt definitionUri: opentrons/armadillo_96_wellplate_200ul_pcr_full_skirt/1 displayName: Sample Collection Plate location: moduleId: magneticModuleId - offsetId: null - id: tipRackId loadName: opentrons_96_tiprack_10ul definitionUri: opentrons/opentrons_96_tiprack_10ul/1 displayName: Opentrons 96 Tip Rack 10 µL location: slotName: '8' - offsetId: null - id: fixedTrash loadName: opentrons_1_trash_1100ml_fixed definitionUri: opentrons/opentrons_1_trash_1100ml_fixed/1 displayName: Trash location: slotName: '12' - offsetId: null modules: - id: magneticModuleId serialNumber: !anystr @@ -137,14 +132,10 @@ stages: commandType: home key: !anystr status: succeeded - params: - skipIfMountPositionOk: null - axes: null + params: { } result: { } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadPipette @@ -158,8 +149,6 @@ stages: pipetteId: pipetteId startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadModule @@ -177,8 +166,6 @@ stages: serialNumber: !anystr startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadModule @@ -196,8 +183,6 @@ stages: serialNumber: !anystr startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -214,11 +199,8 @@ stages: result: labwareId: sourcePlateId definition: !anydict - offsetId: null startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -235,11 +217,8 @@ stages: result: labwareId: destPlateId definition: !anydict - offsetId: null startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -256,11 +235,8 @@ stages: result: labwareId: tipRackId definition: !anydict - offsetId: null startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadLabware @@ -277,11 +253,8 @@ stages: result: labwareId: fixedTrash definition: !anydict - offsetId: null startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: loadLiquid @@ -296,21 +269,15 @@ stages: result: {} startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: home key: !anystr status: succeeded - params: - skipIfMountPositionOk: null - axes: null + params: {} result: {} startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: pickUpTip @@ -333,8 +300,6 @@ stages: tipDiameter: 3.27 startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: aspirate @@ -357,8 +322,6 @@ stages: volume: 5.0 startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: waitForDuration @@ -366,12 +329,9 @@ stages: status: succeeded params: seconds: 42.0 - message: null result: {} startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: dispense @@ -389,14 +349,11 @@ stages: z: 1.0 volume: 4.5 flowRate: 2.5 - pushOut: null result: position: { 'x': 280.805, 'y': 65.115, 'z': 84.3 } volume: 4.5 startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: touchTip @@ -413,13 +370,10 @@ stages: y: 0.0 z: 11.0 radius: 1.0 - speed: null result: position: { 'x': 280.805, 'y': 65.115, 'z': 94.3 } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: blowout @@ -440,8 +394,6 @@ stages: position: { 'x': 280.805, 'y': 65.115, 'z': 95.3 } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: moveToCoordinates @@ -454,14 +406,10 @@ stages: y: 100.0 z: 100.0 forceDirect: false - minimumZHeight: null - speed: null result: position: {'x': 100.0, 'y': 100.0, 'z': 100.0} startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: moveToWell @@ -478,15 +426,11 @@ stages: y: 0 z: 0 forceDirect: false - speed: null - minimumZHeight: null result: position: { 'x': 289.805, 'y': 65.115, 'z': 98.25 } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: moveToWell @@ -504,14 +448,11 @@ stages: z: 10.0 minimumZHeight: 35.0 forceDirect: true - speed: null result: position: { 'x': 291.805, 'y': 68.115, 'z': 93.3 } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: dropTip @@ -528,13 +469,10 @@ stages: y: 0 z: 0 alternateDropLocation: false - homeAfter: null result: position: { 'x': 347.84000000000003, 'y': 325.06, 'z': 82.0 } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: waitForResume @@ -545,8 +483,6 @@ stages: result: {} startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: moveToCoordinates @@ -560,13 +496,10 @@ stages: z: 0.0 minimumZHeight: 35.0 forceDirect: true - speed: null result: position: { 'x': 0.0, 'y': 0.0, 'z': 0.0 } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: moveRelative @@ -583,8 +516,6 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: moveRelative @@ -601,8 +532,6 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: savePosition @@ -611,7 +540,6 @@ stages: params: pipetteId: pipetteId failOnNotHomed: true - positionId: null result: positionId: !anystr position: @@ -620,8 +548,6 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: moveRelative @@ -638,8 +564,6 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr createdAt: !anystr commandType: savePosition @@ -657,8 +581,6 @@ stages: z: !anyfloat startedAt: !anystr completedAt: !anystr - error: null - intent: null errors: [] liquids: - id: waterId diff --git a/robot-server/tests/integration/http_api/runs/test_json_v6_protocol_run.tavern.yaml b/robot-server/tests/integration/http_api/runs/test_json_v6_protocol_run.tavern.yaml index 9e07f0482b4..35d815286dc 100644 --- a/robot-server/tests/integration/http_api/runs/test_json_v6_protocol_run.tavern.yaml +++ b/robot-server/tests/integration/http_api/runs/test_json_v6_protocol_run.tavern.yaml @@ -32,8 +32,6 @@ stages: data: id: !anystr createdAt: !anystr - completedAt: null - startedAt: null status: idle current: True actions: [] @@ -45,8 +43,6 @@ stages: loadName: !anystr definitionUri: opentrons/opentrons_1_trash_1100ml_fixed/1 location: !anydict - displayName: null - offsetId: null labwareOffsets: [] liquids: - id: waterId @@ -106,61 +102,41 @@ stages: key: !anystr commandType: home createdAt: !anystr - completedAt: null - startedAt: null status: queued - params: - axes: null - skipIfMountPositionOk: null - intent: null - error: null + params: { } - id: !anystr key: !anystr commandType: loadPipette createdAt: !anystr - completedAt: null - startedAt: null status: queued params: pipetteName: p10_single mount: left pipetteId: pipetteId - intent: null - error: null - id: !anystr key: !anystr commandType: loadModule createdAt: !anystr - completedAt: null - startedAt: null status: queued params: model: magneticModuleV1 location: slotName: '3' moduleId: magneticModuleId - intent: null - error: null - id: !anystr key: !anystr commandType: loadModule createdAt: !anystr - startedAt: null - completedAt: null status: queued params: model: temperatureModuleV2 location: slotName: '1' moduleId: temperatureModuleId - intent: null - error: null - id: !anystr key: !anystr commandType: loadLabware createdAt: !anystr - startedAt: null - completedAt: null status: queued params: location: @@ -170,14 +146,10 @@ stages: version: 1 labwareId: sourcePlateId displayName: Source Plate - intent: null - error: null - id: !anystr key: !anystr commandType: loadLabware createdAt: !anystr - startedAt: null - completedAt: null status: queued params: location: @@ -187,14 +159,10 @@ stages: version: 1 labwareId: destPlateId displayName: Sample Collection Plate - intent: null - error: null - id: !anystr key: !anystr commandType: loadLabware createdAt: !anystr - startedAt: null - completedAt: null status: queued params: location: @@ -204,12 +172,8 @@ stages: version: 1 labwareId: tipRackId displayName: Opentrons 96 Tip Rack 10 µL - intent: null - error: null - id: !anystr createdAt: !anystr - startedAt: null - completedAt: null commandType: loadLiquid key: !anystr status: queued @@ -219,14 +183,10 @@ stages: volumeByWell: A1: 100 B1: 100 - intent: null - error: null - id: !anystr key: !anystr commandType: pickUpTip createdAt: !anystr - startedAt: null - completedAt: null status: queued params: pipetteId: pipetteId @@ -236,16 +196,12 @@ stages: origin: top offset: x: 0 - y: 0 + 'y': 0 z: 0 - intent: null - error: null - id: !anystr key: !anystr commandType: aspirate createdAt: !anystr - startedAt: null - completedAt: null status: queued params: pipetteId: pipetteId @@ -255,18 +211,14 @@ stages: origin: bottom offset: x: 0 - y: 0 + 'y': 0 z: 2 volume: 5 flowRate: 3 - intent: null - error: null - id: !anystr key: !anystr commandType: dispense createdAt: !anystr - startedAt: null - completedAt: null status: queued params: pipetteId: pipetteId @@ -276,19 +228,14 @@ stages: origin: bottom offset: x: 0 - y: 0 + 'y': 0 z: 1 volume: 4.5 flowRate: 2.5 - pushOut: null - intent: null - error: null - id: !anystr key: !anystr commandType: moveToWell createdAt: !anystr - startedAt: null - completedAt: null status: queued params: pipetteId: pipetteId @@ -298,19 +245,13 @@ stages: origin: top offset: x: 0 - y: 0 + 'y': 0 z: 0 forceDirect: false - speed: null - minimumZHeight: null - intent: null - error: null - id: !anystr key: !anystr commandType: moveToWell createdAt: !anystr - startedAt: null - completedAt: null status: queued params: pipetteId: pipetteId @@ -325,14 +266,10 @@ stages: minimumZHeight: 35 forceDirect: true speed: 12.3 - intent: null - error: null - id: !anystr key: !anystr commandType: dropTip createdAt: !anystr - startedAt: null - completedAt: null status: queued params: pipetteId: pipetteId @@ -345,21 +282,15 @@ stages: y: 0 z: 0 alternateDropLocation: false - homeAfter: null - intent: null - error: null - id: '{setup_command_id}' key: '{setup_command_key}' intent: setup commandType: home - error: null createdAt: '{setup_command_created_at}' startedAt: '{setup_command_started_at}' completedAt: '{setup_command_completed_at}' status: succeeded - params: - skipIfMountPositionOk: null - axes: null + params: {} - name: Play the run request: @@ -408,13 +339,9 @@ stages: commandType: home key: !anystr status: succeeded - params: - axes: null - skipIfMountPositionOk: null + params: { } startedAt: !anystr completedAt: !anystr - error: null - intent: null - id: !anystr key: !anystr commandType: loadPipette @@ -422,8 +349,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: pipetteName: p10_single mount: left @@ -435,8 +360,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: model: magneticModuleV1 location: @@ -449,8 +372,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: model: temperatureModuleV2 location: @@ -463,8 +384,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: location: moduleId: temperatureModuleId @@ -480,8 +399,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: location: moduleId: magneticModuleId @@ -497,8 +414,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: location: slotName: '8' @@ -514,8 +429,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: labwareId: sourcePlateId liquidId: waterId @@ -529,8 +442,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: pipetteId: pipetteId labwareId: tipRackId @@ -539,7 +450,7 @@ stages: origin: top offset: x: 0 - y: 0 + 'y': 0 z: 0 - id: !anystr key: !anystr @@ -548,8 +459,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: pipetteId: pipetteId labwareId: sourcePlateId @@ -558,7 +467,7 @@ stages: origin: bottom offset: x: 0 - y: 0 + 'y': 0 z: 2 volume: 5 flowRate: 3 @@ -569,8 +478,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: pipetteId: pipetteId labwareId: destPlateId @@ -579,11 +486,10 @@ stages: origin: bottom offset: x: 0 - y: 0 + 'y': 0 z: 1 volume: 4.5 flowRate: 2.5 - pushOut: null - id: !anystr key: !anystr commandType: moveToWell @@ -591,8 +497,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: pipetteId: pipetteId labwareId: destPlateId @@ -601,11 +505,9 @@ stages: origin: top offset: x: 0 - y: 0 + 'y': 0 z: 0 forceDirect: false - speed: null - minimumZHeight: null - id: !anystr key: !anystr commandType: moveToWell @@ -613,8 +515,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: pipetteId: pipetteId labwareId: destPlateId @@ -635,8 +535,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: pipetteId: pipetteId labwareId: fixedTrash @@ -648,7 +546,6 @@ stages: y: 0 z: 0 alternateDropLocation: false - homeAfter: null - id: '{setup_command_id}' key: '{setup_command_key}' intent: setup @@ -657,7 +554,4 @@ stages: startedAt: '{setup_command_started_at}' completedAt: '{setup_command_completed_at}' status: succeeded - error: null - params: - skipIfMountPositionOk: null - axes: null + params: {} diff --git a/robot-server/tests/integration/http_api/runs/test_json_v6_run_failure.tavern.yaml b/robot-server/tests/integration/http_api/runs/test_json_v6_run_failure.tavern.yaml index 07858aa1c93..b5796d80d23 100644 --- a/robot-server/tests/integration/http_api/runs/test_json_v6_run_failure.tavern.yaml +++ b/robot-server/tests/integration/http_api/runs/test_json_v6_run_failure.tavern.yaml @@ -94,11 +94,7 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - params: - skipIfMountPositionOk: null - axes: null - intent: null - error: null + params: {} - id: !anystr key: !anystr commandType: loadLabware @@ -114,8 +110,6 @@ stages: version: 1 labwareId: tipRackId displayName: Tip Rack - intent: null - error: null - id: !anystr key: !anystr commandType: loadPipette @@ -127,8 +121,6 @@ stages: pipetteName: p10_single mount: left pipetteId: pipetteId - intent: null - error: null - id: !anystr key: !anystr commandType: aspirate @@ -136,7 +128,6 @@ stages: startedAt: !anystr completedAt: !anystr status: failed - intent: null error: id: !anystr errorType: TipNotAttachedError @@ -162,10 +153,7 @@ stages: commandType: pickUpTip createdAt: !anystr completedAt: !anystr - startedAt: null status: failed - intent: null - error: null params: pipetteId: pipetteId labwareId: tipRackId diff --git a/robot-server/tests/integration/http_api/runs/test_json_v7_protocol_run.tavern.yaml b/robot-server/tests/integration/http_api/runs/test_json_v7_protocol_run.tavern.yaml index 3d3fbaf06d8..bd11483d511 100644 --- a/robot-server/tests/integration/http_api/runs/test_json_v7_protocol_run.tavern.yaml +++ b/robot-server/tests/integration/http_api/runs/test_json_v7_protocol_run.tavern.yaml @@ -32,8 +32,6 @@ stages: data: id: !anystr createdAt: !anystr - completedAt: null - startedAt: null status: idle current: True actions: [] @@ -45,8 +43,6 @@ stages: loadName: !anystr definitionUri: opentrons/opentrons_1_trash_1100ml_fixed/1 location: !anydict - displayName: null - offsetId: null labwareOffsets: [] liquids: - id: waterId @@ -106,61 +102,41 @@ stages: key: !anystr commandType: home createdAt: !anystr - startedAt: null - completedAt: null status: queued - params: - axes: null - skipIfMountPositionOk: null - intent: null - error: null + params: { } - id: !anystr key: !anystr commandType: loadPipette createdAt: !anystr - startedAt: null - completedAt: null status: queued params: pipetteName: p10_single mount: left pipetteId: pipetteId - intent: null - error: null - id: !anystr key: !anystr commandType: loadModule createdAt: !anystr - startedAt: null - completedAt: null status: queued params: model: magneticModuleV1 location: slotName: '3' moduleId: magneticModuleId - intent: null - error: null - id: !anystr key: !anystr commandType: loadModule createdAt: !anystr - startedAt: null - completedAt: null status: queued params: model: temperatureModuleV2 location: slotName: '1' moduleId: temperatureModuleId - intent: null - error: null - id: !anystr key: !anystr commandType: loadLabware createdAt: !anystr - startedAt: null - completedAt: null status: queued params: location: @@ -170,14 +146,10 @@ stages: version: 1 labwareId: sourcePlateId displayName: Source Plate - intent: null - error: null - id: !anystr key: !anystr commandType: loadLabware createdAt: !anystr - startedAt: null - completedAt: null status: queued params: location: @@ -187,14 +159,10 @@ stages: version: 1 labwareId: destPlateId displayName: Sample Collection Plate - intent: null - error: null - id: !anystr key: !anystr commandType: loadLabware createdAt: !anystr - startedAt: null - completedAt: null status: queued params: location: @@ -204,12 +172,8 @@ stages: version: 1 labwareId: tipRackId displayName: Opentrons 96 Tip Rack 10 µL - intent: null - error: null - id: !anystr createdAt: !anystr - startedAt: null - completedAt: null commandType: loadLiquid key: !anystr status: queued @@ -219,14 +183,10 @@ stages: volumeByWell: A1: 100 B1: 100 - intent: null - error: null - id: !anystr key: !anystr commandType: pickUpTip createdAt: !anystr - startedAt: null - completedAt: null status: queued params: pipetteId: pipetteId @@ -236,16 +196,12 @@ stages: origin: top offset: x: 0 - y: 0 + 'y': 0 z: 0 - intent: null - error: null - id: !anystr key: !anystr commandType: aspirate createdAt: !anystr - startedAt: null - completedAt: null status: queued params: pipetteId: pipetteId @@ -255,18 +211,14 @@ stages: origin: bottom offset: x: 0 - y: 0 + 'y': 0 z: 2 volume: 5 flowRate: 3 - intent: null - error: null - id: !anystr key: !anystr commandType: dispense createdAt: !anystr - startedAt: null - completedAt: null status: queued params: pipetteId: pipetteId @@ -276,19 +228,14 @@ stages: origin: bottom offset: x: 0 - y: 0 + 'y': 0 z: 1 volume: 4.5 flowRate: 2.5 - pushOut: null - intent: null - error: null - id: !anystr key: !anystr commandType: moveToWell createdAt: !anystr - startedAt: null - completedAt: null status: queued params: pipetteId: pipetteId @@ -298,19 +245,13 @@ stages: origin: top offset: x: 0 - y: 0 + 'y': 0 z: 0 forceDirect: false - speed: null - minimumZHeight: null - intent: null - error: null - id: !anystr key: !anystr commandType: moveToWell createdAt: !anystr - startedAt: null - completedAt: null status: queued params: pipetteId: pipetteId @@ -325,14 +266,10 @@ stages: minimumZHeight: 35 forceDirect: true speed: 12.3 - intent: null - error: null - id: !anystr key: !anystr commandType: dropTip createdAt: !anystr - startedAt: null - completedAt: null status: queued params: pipetteId: pipetteId @@ -345,9 +282,6 @@ stages: y: 0 z: 0 alternateDropLocation: false - homeAfter: null - intent: null - error: null - id: '{setup_command_id}' key: '{setup_command_key}' intent: setup @@ -356,10 +290,7 @@ stages: startedAt: '{setup_command_started_at}' completedAt: '{setup_command_completed_at}' status: succeeded - error: null - params: - skipIfMountPositionOk: null - axes: null + params: {} - name: Play the run request: @@ -410,11 +341,7 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null - params: - axes: null - skipIfMountPositionOk: null + params: { } - id: !anystr key: !anystr commandType: loadPipette @@ -422,8 +349,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: pipetteName: p10_single mount: left @@ -435,8 +360,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: model: magneticModuleV1 location: @@ -449,8 +372,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: model: temperatureModuleV2 location: @@ -463,8 +384,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: location: moduleId: temperatureModuleId @@ -480,8 +399,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: location: moduleId: magneticModuleId @@ -497,8 +414,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: location: slotName: '8' @@ -514,8 +429,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: labwareId: sourcePlateId liquidId: waterId @@ -529,8 +442,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: pipetteId: pipetteId labwareId: tipRackId @@ -539,7 +450,7 @@ stages: origin: top offset: x: 0 - y: 0 + 'y': 0 z: 0 - id: !anystr key: !anystr @@ -548,8 +459,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: pipetteId: pipetteId labwareId: sourcePlateId @@ -558,7 +467,7 @@ stages: origin: bottom offset: x: 0 - y: 0 + 'y': 0 z: 2 volume: 5 flowRate: 3 @@ -569,8 +478,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: pipetteId: pipetteId labwareId: destPlateId @@ -579,11 +486,10 @@ stages: origin: bottom offset: x: 0 - y: 0 + 'y': 0 z: 1 volume: 4.5 flowRate: 2.5 - pushOut: null - id: !anystr key: !anystr commandType: moveToWell @@ -591,8 +497,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: pipetteId: pipetteId labwareId: destPlateId @@ -601,11 +505,9 @@ stages: origin: top offset: x: 0 - y: 0 + 'y': 0 z: 0 forceDirect: false - speed: null - minimumZHeight: null - id: !anystr key: !anystr commandType: moveToWell @@ -613,8 +515,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: pipetteId: pipetteId labwareId: destPlateId @@ -635,8 +535,6 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - error: null - intent: null params: pipetteId: pipetteId labwareId: fixedTrash @@ -648,7 +546,6 @@ stages: y: 0 z: 0 alternateDropLocation: false - homeAfter: null - id: '{setup_command_id}' key: '{setup_command_key}' intent: setup @@ -657,7 +554,4 @@ stages: startedAt: '{setup_command_started_at}' completedAt: '{setup_command_completed_at}' status: succeeded - error: null - params: - skipIfMountPositionOk: null - axes: null + params: { } diff --git a/robot-server/tests/integration/http_api/runs/test_maintenance_run_creation.tavern.yaml b/robot-server/tests/integration/http_api/runs/test_maintenance_run_creation.tavern.yaml index 23be48f9fb0..7b7d7930f22 100644 --- a/robot-server/tests/integration/http_api/runs/test_maintenance_run_creation.tavern.yaml +++ b/robot-server/tests/integration/http_api/runs/test_maintenance_run_creation.tavern.yaml @@ -12,8 +12,7 @@ stages: response: json: data: [] - links: - current: null + links: {} meta: cursor: 0 totalLength: 0 diff --git a/robot-server/tests/integration/http_api/runs/test_papi_v2_run_failure.tavern.yaml b/robot-server/tests/integration/http_api/runs/test_papi_v2_run_failure.tavern.yaml index ddb1e3c08fa..14fbb483048 100644 --- a/robot-server/tests/integration/http_api/runs/test_papi_v2_run_failure.tavern.yaml +++ b/robot-server/tests/integration/http_api/runs/test_papi_v2_run_failure.tavern.yaml @@ -94,11 +94,7 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - intent: null - error: null - params: - skipIfMountPositionOk: null - axes: null + params: {} - id: !anystr key: !anystr commandType: loadLabware @@ -106,16 +102,12 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - intent: null - error: null params: location: slotName: '1' loadName: opentrons_96_tiprack_300ul namespace: opentrons version: 1 - labwareId: null - displayName: null - id: !anystr key: !anystr commandType: loadPipette @@ -123,12 +115,9 @@ stages: startedAt: !anystr completedAt: !anystr status: succeeded - intent: null - error: null params: pipetteName: p300_single mount: right - pipetteId: null - id: !anystr key: !anystr commandType: aspirate @@ -136,7 +125,6 @@ stages: startedAt: !anystr completedAt: !anystr status: failed - intent: null error: id: !anystr errorType: LegacyContextCommandError diff --git a/robot-server/tests/integration/http_api/runs/test_persistence.py b/robot-server/tests/integration/http_api/runs/test_persistence.py index b83a23feb51..fa25057c163 100644 --- a/robot-server/tests/integration/http_api/runs/test_persistence.py +++ b/robot-server/tests/integration/http_api/runs/test_persistence.py @@ -285,7 +285,7 @@ async def test_runs_completed_filled_started_at_none_persist( get_run_response = await client.get_run(run_id=run_id) run_data = get_run_response.json()["data"] - assert run_data["startedAt"] is None + assert "startedAt" not in run_data assert datetime.fromisoformat(run_data["completedAt"]).timestamp() == pytest.approx( expected_completed_at.timestamp(), abs=2 ) diff --git a/robot-server/tests/integration/http_api/runs/test_protocol_run.tavern.yaml b/robot-server/tests/integration/http_api/runs/test_protocol_run.tavern.yaml index 7dcaaeb1b23..e0521f3e655 100644 --- a/robot-server/tests/integration/http_api/runs/test_protocol_run.tavern.yaml +++ b/robot-server/tests/integration/http_api/runs/test_protocol_run.tavern.yaml @@ -29,8 +29,6 @@ stages: data: id: !anystr createdAt: !anystr - startedAt: null - completedAt: null status: idle current: True actions: [] @@ -42,8 +40,6 @@ stages: loadName: !anystr definitionUri: opentrons/opentrons_1_trash_1100ml_fixed/1 location: !anydict - offsetId: null - displayName: null labwareOffsets: [] protocolId: '{protocol_id}' liquids: [] @@ -90,8 +86,6 @@ stages: data: definitionUri: opentrons/biorad_96_wellplate_200ul_pcr/1 location: - definitionUri: null - moduleModel: null slotName: '1' vector: x: 1.11 @@ -106,8 +100,6 @@ stages: definitionUri: opentrons/biorad_96_wellplate_200ul_pcr/1 location: slotName: '1' - definitionUri: null - moduleModel: null vector: x: 1.11 y: 2.22 @@ -170,23 +162,15 @@ stages: createdAt: !anystr startedAt: !anystr completedAt: !anystr - intent: null - error: null status: succeeded - params: - axes: null - skipIfMountPositionOk: null + params: { } - id: !anystr key: !anystr commandType: loadLabware status: succeeded - intent: null - error: null params: location: slotName: '1' - labwareId: null - displayName: null loadName: 'biorad_96_wellplate_200ul_pcr' namespace: 'opentrons' version: 1 @@ -209,16 +193,12 @@ stages: key: !anystr commandType: loadLabware status: succeeded - intent: null - error: null params: location: slotName: '1' loadName: 'biorad_96_wellplate_200ul_pcr' namespace: 'opentrons' version: 1 - labwareId: null - displayName: null result: labwareId: !anystr # Labware definitions are inconveniently verbose to test, @@ -264,8 +244,6 @@ stages: definitionUri: opentrons/biorad_96_wellplate_200ul_pcr/1 location: slotName: '1' - moduleModel: null - definitionUri: null vector: x: 1.11 y: 2.22 @@ -276,15 +254,12 @@ stages: loadName: !anystr definitionUri: opentrons/opentrons_1_trash_1100ml_fixed/1 location: !anydict - offsetId: null - displayName: null - id: !anystr loadName: biorad_96_wellplate_200ul_pcr definitionUri: opentrons/biorad_96_wellplate_200ul_pcr/1 location: slotName: '1' offsetId: '{labware_offset_id}' - displayName: null # Changed when the run completed: status: succeeded save: diff --git a/robot-server/tests/integration/http_api/runs/test_run_queued_protocol_commands.tavern.yaml b/robot-server/tests/integration/http_api/runs/test_run_queued_protocol_commands.tavern.yaml index 61545e76143..3434f210bd0 100644 --- a/robot-server/tests/integration/http_api/runs/test_run_queued_protocol_commands.tavern.yaml +++ b/robot-server/tests/integration/http_api/runs/test_run_queued_protocol_commands.tavern.yaml @@ -86,8 +86,6 @@ stages: data: actions: [] createdAt: !re_search "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d+\\+\\d{2}:\\d{2}$" - completedAt: null - startedAt: null current: True errors: [] id: '{run_id}' @@ -97,7 +95,6 @@ stages: modules: [] pipettes: [] status: 'idle' - protocolId: null - name: Play the run request: @@ -152,7 +149,6 @@ stages: commandType: comment status: succeeded intent: protocol - error: null params: message: 'test 1' createdAt: !re_search "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d+\\+\\d{2}:\\d{2}$" @@ -163,7 +159,6 @@ stages: commandType: comment status: succeeded intent: protocol - error: null params: message: 'test 2' createdAt: !re_search "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d+\\+\\d{2}:\\d{2}$" @@ -174,7 +169,6 @@ stages: commandType: comment status: succeeded intent: protocol - error: null params: message: 'test 3' createdAt: !re_search "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d+\\+\\d{2}:\\d{2}$" @@ -185,7 +179,6 @@ stages: commandType: comment status: succeeded intent: protocol - error: null params: message: 'test 4' createdAt: !re_search "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d+\\+\\d{2}:\\d{2}$" diff --git a/robot-server/tests/integration/http_api/test_deck_configuration.tavern.yaml b/robot-server/tests/integration/http_api/test_deck_configuration.tavern.yaml index 63b3f27fdfd..21be55b752f 100644 --- a/robot-server/tests/integration/http_api/test_deck_configuration.tavern.yaml +++ b/robot-server/tests/integration/http_api/test_deck_configuration.tavern.yaml @@ -5,17 +5,6 @@ marks: - usefixtures: - ot3_server_base_url -# lastModifiedAt is deliberately omitted from this expected object. -# This requires turning off strict json checking. -# A lastModifiedAt that's omitted or null means the deck configuration has never been set. -# -# Unfortunately, this makes this test order-dependent with any other tests -# that modify the deck configuration, even if they try to restore the original value -# after they're done. We probably need some kind of deck configuration factory-reset. -strict: - - headers:off - - json:off - stages: - name: Get the deck configuration and make sure there's a default request: @@ -23,7 +12,14 @@ stages: response: json: data: - + # lastModifiedAt is deliberately omitted from this expected object. + # A lastModifiedAt that's omitted or null means the deck configuration has never been set. + # + # Unfortunately, this makes this test order-dependent with any other tests + # that modify the deck configuration, even if they try to restore the original value + # after they're done. We probably need some kind of deck configuration factory-reset. + # + # lastModifiedAt: null cutoutFixtures: &expectedDefaultCutoutFixtures - cutoutFixtureId: singleLeftSlot cutoutId: cutoutA1 diff --git a/robot-server/tests/integration/test_modules.tavern.yaml b/robot-server/tests/integration/test_modules.tavern.yaml index 2274ee13218..93930465eb8 100644 --- a/robot-server/tests/integration/test_modules.tavern.yaml +++ b/robot-server/tests/integration/test_modules.tavern.yaml @@ -101,13 +101,11 @@ stages: hasAvailableUpdate: !anybool moduleType: thermocyclerModuleType moduleModel: thermocyclerModuleV1 - moduleOffset: null usbPort: port: !anyint hub: !anybool portGroup: !anystr path: !anystr - hubPort: null data: status: !anystr lidStatus: !anystr @@ -117,11 +115,6 @@ stages: currentTemperature: !anyfloat targetTemperature: !anyfloat holdTime: !anyfloat - totalStepCount: null - totalCycleCount: null - currentCycleIndex: null - rampRate: null - currentStepIndex: null - id: !anystr serialNumber: !anystr firmwareVersion: !anystr @@ -129,13 +122,11 @@ stages: hasAvailableUpdate: !anybool moduleType: heaterShakerModuleType moduleModel: heaterShakerModuleV1 - moduleOffset: null usbPort: port: !anyint hub: !anybool portGroup: !anystr path: !anystr - hubPort: null data: status: !anystr labwareLatchStatus: !anystr @@ -143,9 +134,6 @@ stages: temperatureStatus: !anystr currentSpeed: !anyint currentTemperature: !anyfloat - targetSpeed: null - targetTemperature: null - errorDetails: null - id: !anystr serialNumber: !anystr firmwareVersion: !anystr @@ -153,13 +141,11 @@ stages: hasAvailableUpdate: !anybool moduleType: temperatureModuleType moduleModel: temperatureModuleV1 - moduleOffset: null usbPort: port: !anyint hub: !anybool portGroup: !anystr path: !anystr - hubPort: null data: status: !anystr currentTemperature: !anyfloat @@ -171,12 +157,10 @@ stages: hasAvailableUpdate: !anybool moduleType: magneticModuleType moduleModel: magneticModuleV1 - moduleOffset: null usbPort: port: !anyint hub: !anybool portGroup: !anystr - hubPort: null path: !anystr data: status: !anystr diff --git a/robot-server/tests/protocols/test_analysis_store.py b/robot-server/tests/protocols/test_analysis_store.py index 46266a80c90..7207e15ff60 100644 --- a/robot-server/tests/protocols/test_analysis_store.py +++ b/robot-server/tests/protocols/test_analysis_store.py @@ -212,8 +212,6 @@ async def test_update_adds_details_and_completes_analysis( "loadName": "load-name", "definitionUri": "namespace/load-name/42", "location": {"slotName": "1"}, - "displayName": None, - "offsetId": None, } ], "pipettes": [ diff --git a/robot-server/tests/protocols/test_completed_analysis_store.py b/robot-server/tests/protocols/test_completed_analysis_store.py index fe1845e444c..4b76386acd4 100644 --- a/robot-server/tests/protocols/test_completed_analysis_store.py +++ b/robot-server/tests/protocols/test_completed_analysis_store.py @@ -159,7 +159,6 @@ async def test_get_by_analysis_id_as_document( "id": "analysis-id", "result": "ok", "status": "completed", - "robotType": None, "commands": [], "errors": [], "labware": [], From f9b09eb2c6e4272da006c3662deb8f30bdfdb590 Mon Sep 17 00:00:00 2001 From: Max Marrone Date: Wed, 3 Jan 2024 11:29:35 -0500 Subject: [PATCH 58/60] Revert the new null/omitted workaround. --- .../robot_server/protocols/completed_analysis_store.py | 2 +- .../labware/labware_definition.py | 10 +--------- 2 files changed, 2 insertions(+), 10 deletions(-) diff --git a/robot-server/robot_server/protocols/completed_analysis_store.py b/robot-server/robot_server/protocols/completed_analysis_store.py index 90e779fee16..29ee571d08c 100644 --- a/robot-server/robot_server/protocols/completed_analysis_store.py +++ b/robot-server/robot_server/protocols/completed_analysis_store.py @@ -301,5 +301,5 @@ def _serialize_completed_analysis_to_json(completed_analysis: CompletedAnalysis) # FastAPI + Pydantic + our customizations serialize these objects # over the `GET /protocols/:id/analyses/:id` endpoint. by_alias=True, - exclude_none=False, + exclude_none=True, ) diff --git a/shared-data/python/opentrons_shared_data/labware/labware_definition.py b/shared-data/python/opentrons_shared_data/labware/labware_definition.py index e884b9e9623..1b2e68040de 100644 --- a/shared-data/python/opentrons_shared_data/labware/labware_definition.py +++ b/shared-data/python/opentrons_shared_data/labware/labware_definition.py @@ -6,7 +6,7 @@ from __future__ import annotations from enum import Enum -from typing import TYPE_CHECKING, Dict, List, Optional, Union, Any +from typing import TYPE_CHECKING, Dict, List, Optional, Union from pydantic import ( BaseModel, @@ -326,11 +326,3 @@ class LabwareDefinition(BaseModel): default_factory=None, description="Force, in Newtons, with which the gripper should grip the labware.", ) - - def dict(self, *args: Any, **kwargs: Any) -> Dict[str, Any]: - kwargs["exclude_unset"] = True - return super().dict(*args, **kwargs) - - def json(self, *args: Any, **kwargs: Any) -> str: - kwargs["exclude_unset"] = True - return super().json(*args, **kwargs) From 82c88e7087e75cfff994e7d9f4c2a542fc61d80e Mon Sep 17 00:00:00 2001 From: Max Marrone Date: Wed, 3 Jan 2024 14:52:21 -0500 Subject: [PATCH 59/60] Fix the old null/omitted workaround. Add the missing .json() override to BaseResponseBody. --- robot-server/robot_server/service/json_api/response.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/robot-server/robot_server/service/json_api/response.py b/robot-server/robot_server/service/json_api/response.py index ce75ccea9bf..7bc0f6083fd 100644 --- a/robot-server/robot_server/service/json_api/response.py +++ b/robot-server/robot_server/service/json_api/response.py @@ -39,6 +39,11 @@ def dict(self, *args: Any, **kwargs: Any) -> Dict[str, Any]: kwargs["exclude_none"] = True return super().dict(*args, **kwargs) + def json(self, *args: Any, **kwargs: Any) -> str: + """See notes in `.dict()`.""" + kwargs["exclude_none"] = True + return super().json(*args, **kwargs) + class SimpleBody(BaseResponseBody, GenericModel, Generic[ResponseDataT]): """A response that returns a single resource.""" From 5a41e94f8e02affbb2e31c71980d069d95b3d730 Mon Sep 17 00:00:00 2001 From: Max Marrone Date: Wed, 3 Jan 2024 16:00:54 -0500 Subject: [PATCH 60/60] Delete outdated comment. --- api/src/opentrons/system/wifi.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/api/src/opentrons/system/wifi.py b/api/src/opentrons/system/wifi.py index c386838726d..3b5ac91d5ee 100644 --- a/api/src/opentrons/system/wifi.py +++ b/api/src/opentrons/system/wifi.py @@ -197,8 +197,6 @@ def eap_check_config(eap_config: Dict[str, Any]) -> Dict[str, Any]: _eap_check_no_extra_args(eap_config, options) for opt in options: - # Ignoring most types to do with EAP_CONFIG_SHAPE because of issues - # wth type inference for dict comprehensions _eap_check_option_ok(opt, eap_config) if opt["type"] == "file" and opt["name"] in eap_config: # Special work for file: rewrite from key id to path