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 ${{ inputs.project }} setup' diff --git a/.github/workflows/api-test-lint-deploy.yaml b/.github/workflows/api-test-lint-deploy.yaml index f4547dc9bdd..6c03ab5cc4d 100644 --- a/.github/workflows/api-test-lint-deploy.yaml +++ b/.github/workflows/api-test-lint-deploy.yaml @@ -59,7 +59,7 @@ jobs: node-version: '16' - uses: 'actions/setup-python@v4' with: - python-version: '3.7' + python-version: '3.10' - uses: './.github/actions/python/setup' with: @@ -75,17 +75,13 @@ jobs: os: ['windows-2022', 'ubuntu-22.04', 'macos-latest'] # TODO(mc, 2022-02-24): expand this matrix to 3.8 and 3.9, # preferably in a nightly cronjob on edge or something - python: ['3.7', '3.10'] + python: ['3.10'] with-ot-hardware: ['true', 'false'] exclude: - os: 'windows-2022' with-ot-hardware: 'true' - os: 'macos-latest' with-ot-hardware: 'true' - - os: 'macos-latest' - python: '3.10' - - python: '3.10' - with-ot-hardware: 'true' runs-on: '${{ matrix.os }}' steps: - uses: 'actions/checkout@v3' @@ -152,7 +148,7 @@ 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..65776b1a5cc 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: @@ -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' @@ -164,7 +162,7 @@ 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' 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)" diff --git a/api/Pipfile b/api/Pipfile index ac63c870096..30420dac26c 100755 --- a/api/Pipfile +++ b/api/Pipfile @@ -7,24 +7,24 @@ 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" +mypy = "==0.981" 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" +pytest-xdist = "~=2.5.0" sphinx = "==5.0.1" -twine = "==4.0.2" -wheel = "==0.30.0" -typeguard = "==2.12.1" +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 = ">=3.4.1,<4" -mock = "~=4.0.2" +mock = "~=4.0.3" flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" @@ -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..a519d9462e1 100644 --- a/api/Pipfile.lock +++ b/api/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "e53961988b9cfe876088bf31ed01f5e145545b9b6d014eac255b723c262a245f" + "sha256": "85e6abfa7a1353756769cf234de3045eac2043749097a794e120eb3e32e2fccd" }, "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" + "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363", + "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287" ], "markers": "python_version >= '3.7'", - "version": "==2.13.0" + "version": "==2.14.0" }, "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", - "sha256:0d3d5b7db9ed8a2b11a774db2bbea7ba1884430a205dbd54a32d61d7c2a190fa", - "sha256:1063da2c85b95f2d1a430f1c33b55c9c17ffaf5e612e10aeaad641c55a9e2b9d", - "sha256:12ebea541c44fdc88ccb794a13fe861cc5e35d64ed689513a5c03d05b53b7c82", - "sha256:153e7b6e724761741e0974fc4dcd406d35ba70b92bfe3fedcb497226c93b9da7", - "sha256:15b26ddf78d57f1d143bdf32e820fd8935d36abe8a25eb9ec0b5a71c82eb3895", - "sha256:1872d01ac8c618a8da634e232f24793883d6e456a66593135aeafe3784b0848d", - "sha256:187d18082694a29005ba2944c882344b6748d5be69e3a89bf3cc9d878e548d5a", - "sha256:1b2919306936ac6efb3aed1fbf81039f7087ddadb3160882a57ee2ff74fd2382", - "sha256:232ac332403e37e4a03d209a3f92ed9071f7d3dbda70e2a5e9cff1c4ba9f0678", - "sha256:23e8565ab7ff33218530bc817922fae827420f143479b753104ab801145b1d5b", - "sha256:24817cb02cbef7cd499f7c9a2735286b4782bd47a5b3516a0e84c50eab44b98e", - "sha256:249c6470a2b60935bafd1d1d13cd613f8cd8388d53461c67397ee6a0f5dce741", - "sha256:24a91a981f185721542a0b7c92e9054b7ab4fea0508a795846bc5b0abf8118d4", - "sha256:2502dd2a736c879c0f0d3e2161e74d9907231e25d35794584b1ca5284e43f596", - "sha256:250c9eb0f4600361dd80d46112213dff2286231d92d3e52af1e5a6083d10cad9", - "sha256:278c296c6f96fa686d74eb449ea1697f3c03dc28b75f873b65b5201806346a69", - 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"sha256:ffa565331890b90056c01db69c0fe634a776f8019c143a5ae265f9c6bc4bd6d4" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'", - "version": "==1.15.0" + "markers": "python_version >= '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..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", @@ -61,10 +60,10 @@ 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", + "pydantic==1.9.2", "pyserial==3.5", "typing-extensions>=4.0.0,<5", "click>=8.0.0,<9", @@ -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/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 41bd554682c..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, @@ -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/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..ae4ad60b9fa 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. @@ -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[ @@ -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/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 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..3b5ac91d5ee 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(), @@ -186,9 +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 - # Ignoring most types to do with EAP_CONFIG_SHAPE because of issues - # wth type inference for dict comprehensions + for opt in options: _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 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/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={}, ) ], ) 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() diff --git a/g-code-testing/Pipfile b/g-code-testing/Pipfile index 1a23292c6f5..026ca783dd5 100644 --- a/g-code-testing/Pipfile +++ b/g-code-testing/Pipfile @@ -11,20 +11,20 @@ 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" -pydantic = "==1.8.2" +anyio = "==3.6.1" +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", sys_platform = "== 'linux'" } +systemd-python = { version = "==234", markers="sys_platform=='linux'" } [dev-packages] diff-match-patch = "==20200713" -pytest = "~=6.1" +pytest = "~=7.1" pytest-aiohttp = "==0.3.0" 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 = "==0.981" flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" @@ -33,4 +33,4 @@ black = "==22.3.0" decoy = "~=1.10.0" [requires] -python_version = "3.7" +python_version = "3.10" diff --git a/g-code-testing/Pipfile.lock b/g-code-testing/Pipfile.lock index a335343967c..805f05c5385 100644 --- a/g-code-testing/Pipfile.lock +++ b/g-code-testing/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": "330370d3fa88efabdd5b0a94b42503ffdfd4cb6265bd50bc398dc4cfcc938939" + "sha256": "791f7b071facb00499fae66b09d598083b98076e85ec26f7c1484d1130e700f9" }, "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": { "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": [ - "sha256:2f8abc20f7248433085eda803936d98992f1343ddb022065779f37c5da0181d0", - "sha256:88d59c13d634dcffe0510be048210188edd79aeccb6a6c9028cdad6f31d730a9" + "sha256:89b2ef2247e3b562a16eef663bc0e2e703ec6468e2fa8a5cd61cd449786d4f6e", + 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b/hardware-testing/Pipfile @@ -4,25 +4,25 @@ 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" [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 = "==0.981" 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" diff --git a/hardware-testing/Pipfile.lock b/hardware-testing/Pipfile.lock index 3ec46749af6..6c717bc2743 100644 --- a/hardware-testing/Pipfile.lock +++ b/hardware-testing/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": "317adb42f71108bc905d9220a1f3438732f3c42c2baadfbbd1d58ab499ef744d" + "sha256": "62d9d88f58594147f78dbda65db2d96b53ac2c07a54eb0b81854c7c7ebe4e247" }, "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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3.4, 3.5'", + "version": "==1.26.18" } } } 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, diff --git a/hardware/Pipfile b/hardware/Pipfile index ef1497cee78..0b302c13e6b 100644 --- a/hardware/Pipfile +++ b/hardware/Pipfile @@ -4,28 +4,28 @@ 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" -pydantic = "==1.8.2" +numpy = 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"sha256:d91d5919357fe7f681a9f2b5b4cb2a5f1ef0a1e9f59c4d8ff0d3491e05c0ffd5" + "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0", + "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef" ], "index": "pypi", - "version": "==4.6.3" - }, - "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/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/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/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/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/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 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: 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 diff --git a/hardware/setup.py b/hardware/setup.py index c874cd55618..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"] @@ -52,7 +52,7 @@ def get_version() -> str: ] EXTRAS = { - "FLEX": ["python-can==3.3.4"], + "FLEX": ["python-can==4.2.2"], } @@ -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/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( 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 diff --git a/notify-server/Pipfile b/notify-server/Pipfile index f3b463c939d..24518fa3fc4 100644 --- a/notify-server/Pipfile +++ b/notify-server/Pipfile @@ -4,29 +4,27 @@ url = "https://pypi.org/simple/" verify_ssl = true [requires] -python_version = "3.7" +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" } -pydantic = "==1.8.2" -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" -mock = "~=4.0.2" -mypy = "==0.800" -pytest = "==6.1.0" +mock = "~=4.0.3" +mypy = "==0.981" +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'" } -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..fa41c21a2f5 100644 --- a/notify-server/Pipfile.lock +++ b/notify-server/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": "ab0997d0755c728a39b26c02efbf824b231f237a6f9e008b6c5ac65a6ba8094f" + "sha256": "ff9059328973547458cf7c1edae2c3171f50e25ed83f236e0b1ec6f3a1f53baa" }, "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": [ - 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"sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef" ], "index": "pypi", - "version": "==4.1.1" - }, - "zipp": { - "hashes": [ - "sha256:9f50f446828eb9d45b267433fd3e9da8d801f614129124863f9c51ebceafb87d", - "sha256:b47250dd24f92b7dd6a0a8fc5244da14608f3ca90a5efcd37a3b1642fac9a375" - ], - "markers": "python_version >= '3.7'", - "version": "==3.7.0" + "markers": "python_version >= '3.8'", + "version": "==4.8.0" } } } 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/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 diff --git a/robot-server/Pipfile b/robot-server/Pipfile index fdc7b17a261..cc242893469 100755 --- a/robot-server/Pipfile +++ b/robot-server/Pipfile @@ -4,57 +4,56 @@ verify_ssl = true name = "pypi" [requires] -python_version = "3.7" +python_version = "3.10" [dev-packages] -robot-server = { 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'" } -pytest = "~=6.1" -pytest-asyncio = "~=0.18" +atomicwrites = { version = "==1.4.0", markers="sys_platform=='win32'" } +colorama = { version = "==0.4.4", markers="sys_platform=='win32'" } +# 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 = "~=2.2.1" -requests = "==2.26.0" -tavern = "~=1.6" -graphviz = "==0.17" -mock = "~=4.0.2" -mypy = "==0.910" +pytest-xdist = "~=2.5.0" +requests = "==2.27.1" +graphviz = "==0.19" +mock = "~=4.0.3" +mypy = "==0.981" 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" 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" } -anyio = "==3.3.0" +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" -systemd-python = { version = "==234", sys_platform = "== 'linux'" } -idna = "==3.2" -click = "==8.0.1" -# 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" +systemd-python = { version = "==234", markers="sys_platform == 'linux'" } +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 7e977d6f731..094d65ad7ae 100644 --- a/robot-server/Pipfile.lock +++ b/robot-server/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": "dff9b5c0c0a442a884ac96695c64e24d61436e1b470c008871d531a9c01f2be9" + "sha256": "808846564361a5e6f5953035846424f4ea2efbd8ea4726358ded3352bf6904a7" }, "pipfile-spec": 6, "requires": { - "python_version": "3.7" + "python_version": 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"wsproto": { "hashes": [ "sha256:868776f8456997ad0d9720f7322b746bbe9193751b5b290b7f924659377c8c38", "sha256:d8345d1808dd599b5ffb352c25a367adb6157e664e140dbecba3f9bc007edb9f" ], "index": "pypi", + "markers": "python_full_version >= '3.6.1'", "version": "==1.0.0" - }, - "zipp": { - "hashes": [ - "sha256:957cfda87797e389580cb8b9e3870841ca991e2125350677b2ca83a0e99390a3", - "sha256:f5812b1e007e48cff63449a5e9f4e7ebea716b4111f9c4f9a645f91d579bf0c4" - ], - "index": "pypi", - "version": "==3.5.0" } } } 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/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/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/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.""" 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() diff --git a/robot-server/setup.py b/robot-server/setup.py index 18a5ddb34df..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"] @@ -56,11 +56,11 @@ 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", - "pydantic==1.8.2", + "pydantic==1.9.2", "typing-extensions>=4.0.0,<5", "uvicorn==0.14.0", "wsproto==1.0.0", @@ -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/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..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 @@ -24,7 +24,7 @@ stages: 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}$" + createdAt: !anystr robotType: OT-3 Standard metadata: protocolName: Deck Coordinate PAPIv2 Test diff --git a/robot-server/tests/integration/http_api/runs/test_json_v6_protocol_run.tavern.yaml b/robot-server/tests/integration/http_api/runs/test_json_v6_protocol_run.tavern.yaml index be8bf6369e8..35d815286dc 100644 --- a/robot-server/tests/integration/http_api/runs/test_json_v6_protocol_run.tavern.yaml +++ b/robot-server/tests/integration/http_api/runs/test_json_v6_protocol_run.tavern.yaml @@ -31,7 +31,7 @@ stages: json: data: id: !anystr - createdAt: !re_search "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d+\\+\\d{2}:\\d{2}$" + createdAt: !anystr status: idle current: True actions: [] @@ -305,7 +305,7 @@ 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}$" + createdAt: !anystr - name: Wait for the protocol to complete max_retries: 10 diff --git a/robot-server/tests/integration/http_api/runs/test_json_v7_protocol_run.tavern.yaml b/robot-server/tests/integration/http_api/runs/test_json_v7_protocol_run.tavern.yaml index d1dbef0656e..bd11483d511 100644 --- a/robot-server/tests/integration/http_api/runs/test_json_v7_protocol_run.tavern.yaml +++ b/robot-server/tests/integration/http_api/runs/test_json_v7_protocol_run.tavern.yaml @@ -31,7 +31,7 @@ stages: json: data: id: !anystr - createdAt: !re_search "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d+\\+\\d{2}:\\d{2}$" + createdAt: !anystr status: idle current: True actions: [] @@ -305,7 +305,7 @@ 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}$" + createdAt: !anystr - name: Wait for the protocol to complete max_retries: 10 diff --git a/robot-server/tests/integration/http_api/runs/test_protocol_run.tavern.yaml b/robot-server/tests/integration/http_api/runs/test_protocol_run.tavern.yaml index f5091ab2dea..e0521f3e655 100644 --- a/robot-server/tests/integration/http_api/runs/test_protocol_run.tavern.yaml +++ b/robot-server/tests/integration/http_api/runs/test_protocol_run.tavern.yaml @@ -28,7 +28,7 @@ stages: json: data: id: !anystr - createdAt: !re_search "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d+\\+\\d{2}:\\d{2}$" + createdAt: !anystr status: idle current: True actions: [] @@ -96,7 +96,7 @@ 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' diff --git a/robot-server/tests/protocols/test_analysis_store.py b/robot-server/tests/protocols/test_analysis_store.py index 06ca93cd218..7207e15ff60 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], diff --git a/robot-server/tests/protocols/test_completed_analysis_store.py b/robot-server/tests/protocols/test_completed_analysis_store.py index 76a9d32adc6..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 +from robot_server.protocols.analysis_models import ( + CompletedAnalysis, + AnalysisResult, + AnalysisStatus, +) from robot_server.protocols.protocol_store import ( ProtocolStore, ProtocolResource, @@ -80,6 +84,7 @@ 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/robot-server/tests/service/legacy/routers/test_settings.py b/robot-server/tests/service/legacy/routers/test_settings.py index 1d422330bc4..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(), + 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(), + 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(), + 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(), + 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(), + new=decoy.mock( + name="robot_server.service.legacy.routers.settings.get_opentrons_path" + ), ) as m: yield m 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..917f6b8b319 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 @@ -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 diff --git a/server-utils/Pipfile b/server-utils/Pipfile index fce71d9e3c3..ae589d277a7 100755 --- a/server-utils/Pipfile +++ b/server-utils/Pipfile @@ -4,22 +4,22 @@ verify_ssl = true name = "pypi" [requires] -python_version = "3.7" +python_version = "3.10" [dev-packages] 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'" } -pytest = "~=6.1" -pytest-asyncio = "~=0.18" +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" 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 = "==0.981" 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 = "==3.3.0" -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", sys_platform = "== 'linux'" } -idna = "==3.2" -sqlalchemy = "==1.4.32" -aiosqlite = "==0.17.0" +idna = "==3.3" diff --git a/server-utils/Pipfile.lock b/server-utils/Pipfile.lock index 9c0ad3ac5ad..7f8c62a76ed 100644 --- a/server-utils/Pipfile.lock +++ b/server-utils/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": "6c0dfa476e6a1f837719069be4cce9505c07cab2aba9f226825e9a70da9b016b" + "sha256": "cc50e1adfd1023979f6306f3470f3e3f51cfc9b8defa50cac882385f9d05f71e" }, "pipfile-spec": 6, "requires": { - "python_version": "3.7" + "python_version": "3.10" }, "sources": [ { @@ -16,282 +16,14 @@ ] }, "default": { - "aiosqlite": { - "hashes": [ - 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- "sha256:b8aa58f8cf793ffd8782d3d8cb19e66ef36f7aba4353eec859e74678b01b07a7" + "sha256:68d7c56fd5a8999887728ef304a6d12edc7be74f1cfa47714fc8b414525c9a61", + "sha256:f22fa1e554c9ddfd16e6e41ac79759e17be9e492b3587efa038054674760e72d" ], "index": "pypi", - "version": "==2.26.0" + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'", + "version": "==2.27.1" }, "rfc3986": { "extras": [ @@ -920,7 +671,7 @@ "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" }, "sqlalchemy2-stubs": { @@ -929,6 +680,7 @@ "sha256:bd4a3d5ca7ff9d01b2245e1b26304d6b2ec4daf43a01faf40db9e09245679433" ], "index": "pypi", + "markers": "python_version >= '3.6'", "version": "==0.0.2a21" }, "starlette": { @@ -939,14 +691,6 @@ "markers": 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python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'", - "version": "==1.26.15" + "version": "==1.26.18" }, "uvicorn": { "hashes": [ "sha256:2a76bb359171a504b3d1c853409af3adbfa5cef374a4a59e5881945a97a93eae", "sha256:45ad7dfaaa7d55cab4cd1e85e03f27e9d60bc067ddc59db52a2b0aeca8870292" ], - "index": "pypi", "version": "==0.14.0" }, "wsproto": { @@ -1036,16 +743,8 @@ "sha256:868776f8456997ad0d9720f7322b746bbe9193751b5b290b7f924659377c8c38", "sha256:d8345d1808dd599b5ffb352c25a367adb6157e664e140dbecba3f9bc007edb9f" ], - "index": "pypi", + "markers": "python_full_version >= '3.6.1'", "version": "==1.0.0" - }, - "zipp": { - "hashes": [ - "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b", - "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556" - ], - "markers": "python_version >= '3.7'", - "version": "==3.15.0" } } } 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: diff --git a/server-utils/setup.py b/server-utils/setup.py index b049bc315a3..47204f4168d 100755 --- a/server-utils/setup.py +++ b/server-utils/setup.py @@ -44,18 +44,18 @@ 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"] 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", - "pydantic==1.8.2", + "pydantic==1.9.2", "typing-extensions>=4.0.0,<5", "uvicorn==0.14.0", "wsproto==1.0.0", @@ -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/Pipfile b/shared-data/python/Pipfile index 07b539b1774..3bc47618711 100644 --- a/shared-data/python/Pipfile +++ b/shared-data/python/Pipfile @@ -4,23 +4,23 @@ verify_ssl = true name = "pypi" [dev-packages] -mypy = "==0.800" +mypy = "==0.981" 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" # 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..13cfff4c0b2 100644 --- a/shared-data/python/Pipfile.lock +++ b/shared-data/python/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "42d3f5bc6e1a22e3c568c41e9cf4a70127eece0a90b366542520cf2c6ab9bb75" + "sha256": 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>= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'", - "version": "==1.26.9" - }, - "webencodings": { - "hashes": [ - "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78", - "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923" + "sha256:55901e917a5896a349ff771be919f8bd99aff50b79fe58fec595eb37bbc56bb3", + "sha256:df7aa8afb0148fa78488e7899b2c59b5f4ffcfa82e6c54ccb9dd37c1d7b52d54" ], - "version": "==0.5.1" + "markers": "python_version >= '3.8'", + "version": "==2.1.0" }, "wheel": { "hashes": [ - "sha256:9515fe0a94e823fd90b08d22de45d7bde57c90edce705b22f5e1ecf7e1b653c8", - "sha256:e721e53864f084f956f40f96124a74da0631ac13fbbd1ba99e8e2b5e9cafdf64" + "sha256:4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a", + "sha256:e9a504e793efbca1b8e0e9cb979a249cf4a0a7b5b8c9e8b65a5e39d49529c1c4" ], "index": "pypi", - "version": "==0.30.0" + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'", + "version": "==0.37.1" }, "zipp": { "hashes": [ - "sha256:9f50f446828eb9d45b267433fd3e9da8d801f614129124863f9c51ebceafb87d", - "sha256:b47250dd24f92b7dd6a0a8fc5244da14608f3ca90a5efcd37a3b1642fac9a375" + "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31", + "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0" ], - "markers": "python_version >= '3.7'", - "version": "==3.7.0" + "markers": "python_version >= '3.8'", + "version": "==3.17.0" } } } 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" diff --git a/shared-data/python/setup.py b/shared-data/python/setup.py index ab592c2e944..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", @@ -142,17 +141,17 @@ 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", - "pydantic==1.8.2", + "pydantic==1.9.2", ] if __name__ == "__main__": setup( - python_requires=">=3.7", + python_requires=">=3.8", name=DISTNAME, description=DESCRIPTION, license=LICENSE, diff --git a/system-server/Pipfile b/system-server/Pipfile index 8ee68d02103..2c911138d3f 100644 --- a/system-server/Pipfile +++ b/system-server/Pipfile @@ -6,43 +6,40 @@ 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" -systemd-python = { version = "==234", 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} [dev-packages] -system_server = {path = ".", editable = true} flake8 = "~=3.9.0" flake8-annotations = "~=2.6.2" flake8-docstrings = "~=1.6.0" flake8-noqa = "~=1.2.1" -pytest = "~=6.1" +pytest = "<7.3.0,>=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'" } +atomicwrites = { version = "==1.4.0", markers="sys_platform=='win32'" } +colorama = { version = "==0.4.4", markers="sys_platform=='win32'" } sqlalchemy2-stubs = "==0.0.2a21" -mypy = "==0.910" +mypy = "==0.981" 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/system-server/Pipfile.lock b/system-server/Pipfile.lock index 00a0d864ed3..493dd5be346 100644 --- a/system-server/Pipfile.lock +++ b/system-server/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": "f8557d4a9b2a3206fb84ee900cd093611cb108d2b71b5602ad15cbe38b389540" + "sha256": "2785838ab3d5199201cc286ff042bbcf191c1a642d0ba0f4f5a980c5f04e710e" }, "pipfile-spec": 6, "requires": { - "python_version": "3.7" + "python_version": "3.10" }, "sources": [ { @@ -16,29 +16,38 @@ ] }, "default": { + "aiosqlite": { + "hashes": [ + "sha256:6c49dc6d3405929b1d08eeccc72306d3677503cc5e5e43771efc1e00232e8231", + "sha256:f0e6acc24bc4864149267ac82fb46dfb3be4455f99fe21df82609cc6e6baee51" + ], + "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", + 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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" diff --git a/update-server/Pipfile b/update-server/Pipfile index 50ff797de6c..ef6739e8470 100644 --- a/update-server/Pipfile +++ b/update-server/Pipfile @@ -4,7 +4,6 @@ verify_ssl = true name = "pypi" [packages] -aiohttp = "==3.4.4" typing-extensions = "==3.10.0.0" [dev-packages] @@ -13,19 +12,19 @@ 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" +atomicwrites = {version="==1.4.0", markers="sys_platform=='win32'"} +colorama = {version="==0.4.4", markers="sys_platform=='win32'"} +mypy = "==0.981" black = "==22.3.0" decoy = "~=1.10" [requires] -python_version = "3.7" +python_version = "3.10" diff --git a/update-server/Pipfile.lock b/update-server/Pipfile.lock index cced41f3d19..be1986a7ff5 100644 --- a/update-server/Pipfile.lock +++ b/update-server/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": "62e7113800829936d95ee7f0b54803dfb95e2040c6f1b6b84a4c0b3876d2d6c8" + "sha256": 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"sha256:ec61d826d80fc293ed46c9dd26995921e3a82146feacd952ef0757236fc137be", + "sha256:ee04010f26d5102399bd17f8df8bc38dc7ccd7701dc77f4a68c5b8d733406958", + "sha256:f3bc6af6e2b8f92eced34ef6a96ffb248e863af20ef4fde9448cc8c9b858b749", + "sha256:f7d6b36dd2e029b6bcb8a13cf19664c7b8e19ab3a58e0fefbb5b8461447ed5ec" ], "markers": "python_version >= '3.7'", - "version": "==3.8.0" + "version": "==1.9.4" } } } 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/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, ) diff --git a/update-server/setup.py b/update-server/setup.py index 768fe81e1d3..5137d4dcb6e 100644 --- a/update-server/setup.py +++ b/update-server/setup.py @@ -46,7 +46,7 @@ def get_version(): "A server to update software and firmware on Opentrons robots") PACKAGES = find_packages(where='.', exclude=["tests.*", "tests"]) INSTALL_REQUIRES = [ - 'aiohttp==3.4.4', + 'aiohttp==3.8.4', ] 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 diff --git a/usb-bridge/Pipfile b/usb-bridge/Pipfile index 23b79bb6716..992d36a32b6 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" +atomicwrites = {version="==1.4.0", markers="sys_platform=='win32'"} +colorama = {version="==0.4.4", markers="sys_platform=='win32'"} +mypy = "==0.981" 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" diff --git a/usb-bridge/Pipfile.lock b/usb-bridge/Pipfile.lock index 696341f437e..58e4e5df515 100644 --- a/usb-bridge/Pipfile.lock +++ b/usb-bridge/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": "5f8ac3a6a4adb5b7e0e6083b3b4498cb09e025459845b93ae748b4912a32f903" + "sha256": "adbb22a527580a6b606220ad427fc699d6e46a1507ddfc0f325720c6ded1e2cb" }, "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, 3.3'", + "version": "==1.16.0" }, "typing-extensions": { 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python_requires='~=3.10', name=DISTNAME, description=DESCRIPTION, license=LICENSE,