Merge branch 'edge' into tip_tracking_for_alternative_configurations

Opentrons · Feb 22, 2024 · 0d1c8c7 · 0d1c8c7
2 parents 7fe6dc6 + c58db57
commit 0d1c8c7
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diff --git a/.github/actions/python/pypi-deploy/action.yaml b/.github/actions/python/pypi-deploy/action.yaml
@@ -28,7 +28,7 @@ runs:
           fi
         fi
         status=0
-        CI=1 QUIET=1 BUILD_NUMBER=${OT_BUILD} make -C ${{ inputs.project }} clean deploy twine_repository_url=${{ inputs.repository_url }} pypi_username=opentrons pypi_password=${{ inputs.password }} || status=$?
+        CI=1 QUIET=1 BUILD_NUMBER=${OT_BUILD} make -C ${{ inputs.project }} clean deploy twine_repository_url=${{ inputs.repository_url }} pypi_username=__token__ pypi_password=${{ inputs.password }} || status=$?
         if [[ ${status} != 0 ]] && [[ ${{ inputs.repository_url }} =~ "test.pypi.org" ]]; then
           echo "upload failures allowed to test pypi"
           exit 0

diff --git a/.github/actions/python/setup/action.yaml b/.github/actions/python/setup/action.yaml
@@ -25,8 +25,10 @@ runs:
       if: ${{ inputs.python-version != 'false' }}
       run: echo "OT_VIRTUALENV_VERSION=${{ inputs.python-version }}" >> $GITHUB_ENV
     - shell: bash
-      run: |
-        npm install --global [email protected]
-        $OT_PYTHON -m pip install pipenv==2023.11.15
+      run: npm install --global [email protected]
+    - shell: bash
+      run: $OT_PYTHON -m pip install --upgrade pip
+    - shell: bash
+      run: $OT_PYTHON -m pip install --user pipenv==2023.12.1
     - shell: bash
-      run: 'make -C ${{ inputs.project }} setup'
+      run: 'make -C ${{ inputs.project }} setup || make -C ${{ inputs.project }} setup'
diff --git a/.github/workflows/api-test-lint-deploy.yaml b/.github/workflows/api-test-lint-deploy.yaml
@@ -165,11 +165,11 @@ jobs:
         with:
           project: 'api'
           repository_url: 'https://test.pypi.org/legacy/'
-          password: '${{ secrets.OT_TEST_PYPI_PASSWORD }}'
+          password: '${{ secrets.TEST_PYPI_DEPLOY_TOKEN_OPENTRONS }}'
       - if: startsWith(env.OT_TAG, 'v')
         name: 'upload to real pypi'
         uses: './.github/actions/python/pypi-deploy'
         with:
           project: 'api'
           repository_url: 'https://upload.pypi.org/legacy/'
-          password: '${{ secrets.OT_PYPI_PASSWORD }}'
+          password: '${{ secrets.PYPI_DEPLOY_TOKEN_OPENTRONS }}'
diff --git a/.github/workflows/notify-server-lint-test.yaml b/.github/workflows/notify-server-lint-test.yaml
diff --git a/.github/workflows/shared-data-test-lint-deploy.yaml b/.github/workflows/shared-data-test-lint-deploy.yaml
@@ -179,14 +179,14 @@ jobs:
         with:
           project: 'shared-data/python'
           repository_url: 'https://test.pypi.org/legacy/'
-          password: '${{ secrets.OT_TEST_PYPI_PASSWORD }}'
+          password: '${{ secrets.TEST_PYPI_DEPLOY_TOKEN_OPENTRONS_SHARED_DATA }}'
       - if: startsWith(env.OT_TAG, 'v')
         name: 'upload to pypi'
         uses: './.github/actions/python/pypi-deploy'
         with:
           project: 'shared-data/python'
           repository_url: 'https://upload.pypi.org/legacy/'
-          password: '${{ secrets.OT_PYPI_PASSWORD }}'
+          password: '${{ secrets.PYPI_DEPLOY_TOKEN_OPENTRONS_SHARED_DATA }}'
 
   publish-switch:
     runs-on: 'ubuntu-latest'

diff --git a/DEV_SETUP.md b/DEV_SETUP.md
@@ -13,7 +13,7 @@ You will need the following tools installed to develop on the Opentrons platform
 - curl
 - ssh
 - Python v3.10
-- Node.js v16
+- Node.js v18
 
 ### macOS
 
@@ -82,10 +82,10 @@ Close and re-open your terminal to confirm `nvs` is installed.
 nvs --version
 ```
 
-Now we can use nvs to install Node.js v16 and switch on `auto` mode, which will make sure Node.js v16 is used any time we're in the `opentrons` project directory.
+Now we can use nvs to install Node.js v18 and switch on `auto` mode, which will make sure Node.js v18 is used any time we're in the `opentrons` project directory.
 
 ```shell
-nvs add 16
+nvs add 18
 nvs auto on
 ```
 
@@ -202,7 +202,7 @@ Once you are inside the repository for the first time, you should do two things:
 3. Run `python --version` to confirm your chosen version. If you get the incorrect version and you're using an Apple silicon Mac, try running `eval "$(pyenv init --path)"` and then `pyenv local 3.10.13`. Then check `python --version` again.
 
 ```shell
-# confirm Node v16
+# confirm Node v18
 node --version
 
 # set Python version, and confirm

diff --git a/Makefile b/Makefile
@@ -57,7 +57,8 @@ setup: setup-js setup-py
 # virtual envs using pipenv.
 .PHONY: setup-py-toolchain
 setup-py-toolchain:
-	$(OT_PYTHON) -m pip install pipenv==2023.11.15
+	$(OT_PYTHON) -m pip install --upgrade pip
+	$(OT_PYTHON) -m pip install pipenv==2023.12.1
 
 # front-end dependecies handled by yarn
 .PHONY: setup-js

diff --git a/api/Makefile b/api/Makefile
@@ -19,18 +19,18 @@ sphinx_build_allow_warnings := $(pipenv) run sphinx-build
 
 ot_project := $(OPENTRONS_PROJECT)
 project_rs_default = $(if $(ot_project),$(ot_project),robot-stack)
-project_ot3_default = $(if $(ot_project),$(ot_project),ot3)
+project_ir_default = $(if $(ot_project),$(ot_project),ot3)
 
 # Find the version of the wheel from git using a helper script. We
 # use python here so we can use the same version normalization that will be
 # used to create the wheel.
 wheel_file = dist/$(call python_get_wheelname,api,$(project_rs_default),opentrons,$(BUILD_NUMBER))
 
 # Find the version of the sdist file from git using a helper script.
-sdist_file = dist/$(call python_get_sdistname,api,$(project_ot3_default),opentrons)
+sdist_file = dist/$(call python_get_sdistname,api,$(project_rs_default),opentrons)
 
 # Find the branch, sha, version that will be used to update the VERSION.json file
-version_file = $(call python_get_git_version,api,$(project_ot3_default),opentrons)
+version_file = $(call python_get_git_version,api,$(project_rs_default),opentrons)
 
 # These variables are for simulating python protocols
 sim_log_level ?= info
@@ -100,7 +100,7 @@ wheel:
 
 
 .PHONY: sdist
-sdist: export OPENTRONS_PROJECT=$(project_ot3_default)
+sdist: export OPENTRONS_PROJECT=$(project_rs_default)
 sdist:
 	$(clean_sdist_cmd)
 	$(python) setup.py sdist

diff --git a/api/docs/v2/index.rst b/api/docs/v2/index.rst
@@ -75,13 +75,13 @@ For example, if we wanted to transfer liquid from well A1 to well B1 on a plate,
             # protocol run function
             def run(protocol: protocol_api.ProtocolContext):
                 # labware
-		trash = protocol.load_trash_bin("A3")
                 plate = protocol.load_labware(
                     "corning_96_wellplate_360ul_flat", location="D1"
                 )
                 tiprack = protocol.load_labware(
                     "opentrons_flex_96_tiprack_200ul", location="D2"
                 )
+                trash = protocol.load_trash_bin(location="A3")
             
                 # pipettes
                 left_pipette = protocol.load_instrument(

diff --git a/api/docs/v2/new_examples.rst b/api/docs/v2/new_examples.rst
@@ -92,7 +92,7 @@ This code only loads the instruments and labware listed above, and performs no o
                     load_name="usascientific_12_reservoir_22ml", location="D1"
                 )
                 # load trash bin in deck slot A3
-                trash = protocol.load_trash_bin("A3")
+                trash = protocol.load_trash_bin(location="A3")
                 # Put protocol commands here
     
     .. tab:: OT-2 

diff --git a/api/docs/v2/new_labware.rst b/api/docs/v2/new_labware.rst
@@ -32,6 +32,8 @@ After you've created your labware, save it as a ``.json`` file and add it to the
 
 If other people need to use your custom labware definition, they must also add it to their Opentrons App.
 
+.. _loading-labware:
+
 ***************
 Loading Labware
 ***************

diff --git a/api/docs/v2/pipettes/partial_tip_pickup.rst b/api/docs/v2/pipettes/partial_tip_pickup.rst
@@ -186,4 +186,4 @@ The major drawback of this configuration, compared to using column 12, is that t
 
 This code first constructs a list of all the wells in row A of the tip rack. Then, when picking up a tip, instead of referencing one of those wells directly, the ``location`` is set to ``row_a.pop()``. This uses the `built-in pop method <https://docs.python.org/3/tutorial/datastructures.html#more-on-lists>`_ to get the last item from the list and remove it from the list. If you keep using this approach to pick up tips, you'll get an error once the tip rack is empty — not from the API, but from Python itself, since you're trying to ``pop`` an item from an empty list.
 
-Additionally, you can't access the rightmost columns in labware in column 3, since they are beyond the movement limit of the pipette. The exact number of inaccessible columns varies by labware type. Any well that is within 29 mm of the right edge of the slot may be inaccessible in a column 12 configuration. Call ``configure_nozzle_layout()`` again to switch to a column 1 layout if you need to pipette in that area.
+Additionally, you can't access the rightmost columns in labware in column 3, since they are beyond the movement limit of the pipette. The exact number of inaccessible columns varies by labware type. Any well that is within 29 mm of the right edge of the slot may be inaccessible in a column 1 configuration. Call ``configure_nozzle_layout()`` again to switch to a column 12 layout if you need to pipette in that area.
diff --git a/api/docs/v2/versioning.rst b/api/docs/v2/versioning.rst
@@ -126,11 +126,6 @@ This table lists the correspondence between Protocol API versions and robot soft
 Changes in API Versions
 =======================
 
-Version 2.17
-------------
-
-- :py:meth:`.dispense` will now raise an error if you try to dispense more than is available.
-
 Version 2.16
 ------------
 

diff --git a/api/src/opentrons/execute.py b/api/src/opentrons/execute.py
@@ -41,7 +41,7 @@
 from opentrons.protocols.api_support.deck_type import (
     guess_from_global_config as guess_deck_type_from_global_config,
     should_load_fixed_trash,
-    should_load_fixed_trash_for_python_protocol,
+    should_load_fixed_trash_labware_for_python_protocol,
 )
 from opentrons.protocols.api_support.types import APIVersion
 from opentrons.protocols.execution import execute as execute_apiv2
@@ -540,7 +540,9 @@ def _create_live_context_pe(
             config=_get_protocol_engine_config(),
             drop_tips_after_run=False,
             post_run_hardware_state=PostRunHardwareState.STAY_ENGAGED_IN_PLACE,
-            load_fixed_trash=should_load_fixed_trash_for_python_protocol(api_version),
+            load_fixed_trash=should_load_fixed_trash_labware_for_python_protocol(
+                api_version
+            ),
         )
     )
 

diff --git a/api/src/opentrons/hardware_control/backends/flex_protocol.py b/api/src/opentrons/hardware_control/backends/flex_protocol.py
@@ -33,10 +33,12 @@
     EstopState,
     HardwareEventHandler,
     HardwareEventUnsubscriber,
+    HepaFanState,
+    HepaUVState,
+    StatusBarState,
 )
 from opentrons.hardware_control.module_control import AttachedModulesControl
 from ..dev_types import OT3AttachedInstruments
-from ..types import StatusBarState
 from .types import HWStopCondition
 
 Cls = TypeVar("Cls")
@@ -417,3 +419,17 @@ def check_gripper_position_within_bounds(
         hard_limit_upper: float,
     ) -> None:
         ...
+
+    async def set_hepa_fan_state(self, fan_on: bool, duty_cycle: int) -> bool:
+        """Sets the state and duty cycle of the Hepa/UV module."""
+        ...
+
+    async def get_hepa_fan_state(self) -> Optional[HepaFanState]:
+        ...
+
+    async def set_hepa_uv_state(self, light_on: bool, uv_duration_s: int) -> bool:
+        """Sets the state and duration (seconds) of the UV light for the Hepa/UV module."""
+        ...
+
+    async def get_hepa_uv_state(self) -> Optional[HepaUVState]:
+        ...
diff --git a/api/src/opentrons/hardware_control/backends/ot3controller.py b/api/src/opentrons/hardware_control/backends/ot3controller.py
@@ -169,6 +169,12 @@
 from opentrons_hardware.hardware_control.gripper_settings import (
     get_gripper_jaw_state,
 )
+from opentrons_hardware.hardware_control.hepa_uv_settings import (
+    set_hepa_fan_state as set_hepa_fan_state_fw,
+    get_hepa_fan_state as get_hepa_fan_state_fw,
+    set_hepa_uv_state as set_hepa_uv_state_fw,
+    get_hepa_uv_state as get_hepa_uv_state_fw,
+)
 
 from opentrons_hardware.drivers.gpio import OT3GPIO, RemoteOT3GPIO
 from opentrons_shared_data.pipette.dev_types import PipetteName
@@ -193,7 +199,7 @@
     AttachedGripper,
     OT3AttachedInstruments,
 )
-from ..types import StatusBarState
+from ..types import HepaFanState, HepaUVState, StatusBarState
 
 from .types import HWStopCondition
 from .flex_protocol import FlexBackend
@@ -1570,3 +1576,32 @@ def check_gripper_position_within_bounds(
                     "actual-jaw-width": current_gripper_position,
                 },
             )
+
+    async def set_hepa_fan_state(self, fan_on: bool, duty_cycle: int) -> bool:
+        return await set_hepa_fan_state_fw(self._messenger, fan_on, duty_cycle)
+
+    async def get_hepa_fan_state(self) -> Optional[HepaFanState]:
+        res = await get_hepa_fan_state_fw(self._messenger)
+        return (
+            HepaFanState(
+                fan_on=res.fan_on,
+                duty_cycle=res.duty_cycle,
+            )
+            if res
+            else None
+        )
+
+    async def set_hepa_uv_state(self, light_on: bool, uv_duration_s: int) -> bool:
+        return await set_hepa_uv_state_fw(self._messenger, light_on, uv_duration_s)
+
+    async def get_hepa_uv_state(self) -> Optional[HepaUVState]:
+        res = await get_hepa_uv_state_fw(self._messenger)
+        return (
+            HepaUVState(
+                light_on=res.uv_light_on,
+                uv_duration_s=res.uv_duration_s,
+                remaining_time_s=res.remaining_time_s,
+            )
+            if res
+            else None
+        )
diff --git a/api/src/opentrons/hardware_control/backends/ot3simulator.py b/api/src/opentrons/hardware_control/backends/ot3simulator.py
@@ -25,6 +25,8 @@
 from opentrons.hardware_control.types import (
     BoardRevision,
     Axis,
+    HepaFanState,
+    HepaUVState,
     OT3Mount,
     OT3AxisMap,
     CurrentConfig,
@@ -803,3 +805,15 @@ def check_gripper_position_within_bounds(
         # This is a (pretty bad) simulation of the gripper actually gripping something,
         # but it should work.
         self._encoder_position[Axis.G] = (hard_limit_upper - jaw_width) / 2
+
+    async def set_hepa_fan_state(self, fan_on: bool, duty_cycle: int) -> bool:
+        return False
+
+    async def get_hepa_fan_state(self) -> Optional[HepaFanState]:
+        return None
+
+    async def set_hepa_uv_state(self, light_on: bool, timeout_s: int) -> bool:
+        return False
+
+    async def get_hepa_uv_state(self) -> Optional[HepaUVState]:
+        return None
diff --git a/api/src/opentrons/hardware_control/backends/ot3utils.py b/api/src/opentrons/hardware_control/backends/ot3utils.py
@@ -351,8 +351,13 @@ def motor_nodes(devices: Set[FirmwareTarget]) -> Set[NodeId]:
         NodeId.head_bootloader,
         NodeId.gripper_bootloader,
     }
+    hepa_uv_nodes = {
+        NodeId.hepa_uv,
+        NodeId.hepa_uv_bootloader,
+    }
     # remove any bootloader nodes
     motor_nodes -= bootloader_nodes
+    motor_nodes -= hepa_uv_nodes
     # filter out usb nodes
     return {NodeId(target) for target in motor_nodes if target in NodeId}
 

diff --git a/api/src/opentrons/hardware_control/instruments/ot2/pipette_handler.py b/api/src/opentrons/hardware_control/instruments/ot2/pipette_handler.py
@@ -771,7 +771,7 @@ def plan_check_pick_up_tip(  # type: ignore[no-untyped-def]
         if instrument.has_tip:
             raise UnexpectedTipAttachError("pick_up_tip", instrument.name, mount.name)
         self._ihp_log.debug(f"Picking up tip on {mount.name}")
-
+        tip_count = instrument.nozzle_manager.current_configuration.tip_count
         if presses is None or presses < 0:
             checked_presses = instrument.pick_up_configurations.press_fit.presses
         else:
@@ -782,17 +782,20 @@ def plan_check_pick_up_tip(  # type: ignore[no-untyped-def]
         else:
             check_incr = increment
 
-        pick_up_speed = instrument.pick_up_configurations.press_fit.speed
+        pick_up_speed = instrument.pick_up_configurations.press_fit.speed_by_tip_count[
+            tip_count
+        ]
+        pick_up_distance = (
+            instrument.pick_up_configurations.press_fit.distance_by_tip_count[tip_count]
+        )
 
         def build_presses() -> Iterator[Tuple[float, float]]:
             # Press the nozzle into the tip <presses> number of times,
             # moving further by <increment> mm after each press
             for i in range(checked_presses):
                 # move nozzle down into the tip
-                press_dist = (
-                    -1.0 * instrument.pick_up_configurations.press_fit.distance
-                    + -1.0 * check_incr * i
-                )
+
+                press_dist = -1.0 * pick_up_distance + -1.0 * check_incr * i
                 # move nozzle back up
                 backup_dist = -press_dist
                 yield (press_dist, backup_dist)
@@ -814,7 +817,7 @@ def add_tip_to_instr() -> None:
                                 Axis.by_mount(
                                     mount
                                 ): instrument.pick_up_configurations.press_fit.current_by_tip_count[
-                                    instrument.nozzle_manager.current_configuration.tip_count
+                                    tip_count
                                 ]
                             },
                             speed=pick_up_speed,
@@ -824,9 +827,7 @@ def add_tip_to_instr() -> None:
                         for press_dist, backup_dist in build_presses()
                     ],
                     shake_off_list=self._build_pickup_shakes(instrument),
-                    retract_target=instrument.pick_up_configurations.press_fit.distance
-                    + check_incr * checked_presses
-                    + 2,
+                    retract_target=pick_up_distance + check_incr * checked_presses + 2,
                 ),
                 add_tip_to_instr,
             )
@@ -855,9 +856,7 @@ def add_tip_to_instr() -> None:
                         for press_dist, backup_dist in build_presses()
                     ],
                     shake_off_list=self._build_pickup_shakes(instrument),
-                    retract_target=instrument.pick_up_configurations.press_fit.distance
-                    + check_incr * checked_presses
-                    + 2,
+                    retract_target=pick_up_distance + check_incr * checked_presses + 2,
                 ),
                 add_tip_to_instr,
             )
Original file line number	Diff line number	Diff line change
Expand Up		@@ -186,4 +186,4 @@ The major drawback of this configuration, compared to using column 12, is that t

		This code first constructs a list of all the wells in row A of the tip rack. Then, when picking up a tip, instead of referencing one of those wells directly, the ``location`` is set to ``row_a.pop()``. This uses the `built-in pop method <https://docs.python.org/3/tutorial/datastructures.html#more-on-lists>`_ to get the last item from the list and remove it from the list. If you keep using this approach to pick up tips, you'll get an error once the tip rack is empty — not from the API, but from Python itself, since you're trying to ``pop`` an item from an empty list.

		Additionally, you can't access the rightmost columns in labware in column 3, since they are beyond the movement limit of the pipette. The exact number of inaccessible columns varies by labware type. Any well that is within 29 mm of the right edge of the slot may be inaccessible in a column 12 configuration. Call ``configure_nozzle_layout()`` again to switch to a column 1 layout if you need to pipette in that area.
		Additionally, you can't access the rightmost columns in labware in column 3, since they are beyond the movement limit of the pipette. The exact number of inaccessible columns varies by labware type. Any well that is within 29 mm of the right edge of the slot may be inaccessible in a column 1 configuration. Call ``configure_nozzle_layout()`` again to switch to a column 12 layout if you need to pipette in that area.