Merge remote-tracking branch 'origin/chore_release-7.2.0' into pick_u…

…p_tip_testing

.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

.github/actions/python/setup/action.yaml

@@ -27,6 +27,7 @@ runs:
     - shell: bash
       run: |
         npm install --global [email protected]
-        $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
     - shell: bash
       run: 'make -C ${{ inputs.project }} setup'

.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 }}'

.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'

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

Makefile

@@ -65,7 +65,8 @@ PYTHON_SETUP_TARGETS := $(addsuffix -py-setup, $(PYTHON_DIRS))
 
 .PHONY: setup-py
 setup-py:
-	$(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
 	$(MAKE) $(PYTHON_SETUP_TARGETS)
 
 

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

api/docs/v2/index.rst

@@ -75,6 +75,7 @@ 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"
                 )

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
+            ),
         )
     )
 

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}
 

api/src/opentrons/protocol_api/core/engine/protocol.py

@@ -134,9 +134,14 @@ def _load_fixed_trash(self) -> None:
     def append_disposal_location(
         self,
         disposal_location: Union[Labware, TrashBin, WasteChute],
-        skip_add_to_engine: bool = False,
     ) -> None:
-        """Append a disposal location object to the core"""
+        """Append a disposal location object to the core."""
+        self._disposal_locations.append(disposal_location)
+
+    def add_disposal_location_to_engine(
+        self, disposal_location: Union[TrashBin, WasteChute]
+    ) -> None:
+        """Verify and add disposal location to engine store and append it to the core."""
         if isinstance(disposal_location, TrashBin):
             self._engine_client.state.addressable_areas.raise_if_area_not_in_deck_configuration(
                 disposal_location.area_name
@@ -152,8 +157,7 @@ def append_disposal_location(
                 existing_labware_ids=list(self._labware_cores_by_id.keys()),
                 existing_module_ids=list(self._module_cores_by_id.keys()),
             )
-            if not skip_add_to_engine:
-                self._engine_client.add_addressable_area(disposal_location.area_name)
+            self._engine_client.add_addressable_area(disposal_location.area_name)
         elif isinstance(disposal_location, WasteChute):
             # TODO(jbl 2024-01-25) hardcoding this specific addressable area should be refactored
             #   when analysis is fixed up
@@ -166,9 +170,8 @@ def append_disposal_location(
             self._engine_client.state.addressable_areas.raise_if_area_not_in_deck_configuration(
                 "1ChannelWasteChute"
             )
-            if not skip_add_to_engine:
-                self._engine_client.add_addressable_area("1ChannelWasteChute")
-        self._disposal_locations.append(disposal_location)
+            self._engine_client.add_addressable_area("1ChannelWasteChute")
+        self.append_disposal_location(disposal_location)
 
     def get_disposal_locations(self) -> List[Union[Labware, TrashBin, WasteChute]]:
         """Get disposal locations."""

api/src/opentrons/protocol_api/core/legacy/legacy_protocol_core.py

@@ -136,14 +136,18 @@ def is_simulating(self) -> bool:
     def append_disposal_location(
         self,
         disposal_location: Union[Labware, TrashBin, WasteChute],
-        skip_add_to_engine: bool = False,
     ) -> None:
         if isinstance(disposal_location, (TrashBin, WasteChute)):
             raise APIVersionError(
                 "Trash Bin and Waste Chute Disposal locations are not supported in this API Version."
             )
         self._disposal_locations.append(disposal_location)
 
+    def add_disposal_location_to_engine(
+        self, disposal_location: Union[TrashBin, WasteChute]
+    ) -> None:
+        assert False, "add_disposal_location_to_engine only supported on engine core"
+
     def add_labware_definition(
         self,
         definition: LabwareDefinition,

api/src/opentrons/protocol_api/core/protocol.py

@@ -65,11 +65,17 @@ def add_labware_definition(
     def append_disposal_location(
         self,
         disposal_location: Union[Labware, TrashBin, WasteChute],
-        skip_add_to_engine: bool = False,
     ) -> None:
         """Append a disposal location object to the core"""
         ...
 
+    @abstractmethod
+    def add_disposal_location_to_engine(
+        self, disposal_location: Union[TrashBin, WasteChute]
+    ) -> None:
+        """Verify and add disposal location to engine store and append it to the core."""
+        ...
+
     @abstractmethod
     def load_labware(
         self,

api/src/opentrons/protocol_api/create_protocol_context.py

@@ -15,10 +15,14 @@
 from opentrons.protocol_engine import ProtocolEngine
 from opentrons.protocol_engine.clients import SyncClient, ChildThreadTransport
 from opentrons.protocols.api_support.types import APIVersion
+from opentrons.protocols.api_support.deck_type import (
+    should_load_fixed_trash_area_for_python_protocol,
+)
 from opentrons.protocols.api_support.definitions import MAX_SUPPORTED_VERSION
 
 from .protocol_context import ProtocolContext
 from .deck import Deck
+from ._trash_bin import TrashBin
 
 from .core.common import ProtocolCore as AbstractProtocolCore
 from .core.legacy.deck import Deck as LegacyDeck
@@ -148,7 +152,7 @@ def create_protocol_context(
     # this swap may happen once `ctx.move_labware` off-deck is implemented
     deck = None if isinstance(core, ProtocolCore) else cast(Deck, core.get_deck())
 
-    return ProtocolContext(
+    context = ProtocolContext(
         api_version=api_version,
         # TODO(mm, 2023-05-11): This cast shouldn't be necessary.
         # Fix this by making the appropriate TypeVars covariant?
@@ -158,3 +162,18 @@ def create_protocol_context(
         deck=deck,
         bundled_data=bundled_data,
     )
+    # If we're loading an engine based core into the context, and we're on api level 2.16 or above, on an OT-2 we need
+    # to insert a fixed trash addressable area into the protocol engine, for correctness in anything that relies on
+    # knowing what addressable areas have been loaded (and any checks involving trash geometry). Because the method
+    # that uses this in the core relies on the sync client and this code will run in the main thread (which if called
+    # will cause a deadlock), we're directly calling the protocol engine method here where we have access to it.
+    if (
+        protocol_engine is not None
+        and should_load_fixed_trash_area_for_python_protocol(
+            api_version=api_version,
+            robot_type=protocol_engine.state_view.config.robot_type,
+        )
+    ):
+        assert isinstance(context.fixed_trash, TrashBin)
+        protocol_engine.add_addressable_area(context.fixed_trash.area_name)
+    return context

api/src/opentrons/protocol_api/protocol_context.py

@@ -26,7 +26,8 @@
 from opentrons.protocols.api_support import instrument as instrument_support
 from opentrons.protocols.api_support.deck_type import (
     NoTrashDefinedError,
-    should_load_fixed_trash_for_python_protocol,
+    should_load_fixed_trash_labware_for_python_protocol,
+    should_load_fixed_trash_area_for_python_protocol,
 )
 from opentrons.protocols.api_support.types import APIVersion
 from opentrons.protocols.api_support.util import (
@@ -159,22 +160,19 @@ def __init__(
         # protocols after 2.16 expect trash to exist as either a TrashBin or WasteChute object.
 
         self._load_fixed_trash()
-        if should_load_fixed_trash_for_python_protocol(self._api_version):
+        if should_load_fixed_trash_labware_for_python_protocol(self._api_version):
             self._core.append_disposal_location(self.fixed_trash)
-        elif (
-            self._api_version >= APIVersion(2, 16)
-            and self._core.robot_type == "OT-2 Standard"
+        elif should_load_fixed_trash_area_for_python_protocol(
+            self._api_version, self._core.robot_type
         ):
             _fixed_trash_trashbin = TrashBin(
                 location=DeckSlotName.FIXED_TRASH, addressable_area_name="fixedTrash"
             )
-            # We have to skip adding this fixed trash bin to engine because this __init__ is called in the main thread
-            # and any calls to sync client will cause a deadlock. This means that OT-2 fixed trashes are not added to
-            # the engine store until one is first referenced. This should have minimal consequences for OT-2 given that
-            # we do not need to worry about the 96 channel pipette and partial tip configuration with that pipette.
-            self._core.append_disposal_location(
-                _fixed_trash_trashbin, skip_add_to_engine=True
-            )
+            # We are just appending the fixed trash to the core's internal list here, not adding it to the engine via
+            # the core, since that method works through the SyncClient and if called from here, will cause protocols
+            # to deadlock. Instead, that method is called in protocol engine directly in create_protocol_context after
+            # ProtocolContext is initialized.
+            self._core.append_disposal_location(_fixed_trash_trashbin)
 
         self._commands: List[str] = []
         self._unsubscribe_commands: Optional[Callable[[], None]] = None
@@ -517,7 +515,7 @@ def load_trash_bin(self, location: DeckLocation) -> TrashBin:
         trash_bin = TrashBin(
             location=slot_name, addressable_area_name=addressable_area_name
         )
-        self._core.append_disposal_location(trash_bin)
+        self._core.add_disposal_location_to_engine(trash_bin)
         return trash_bin
 
     @requires_version(2, 16)
@@ -534,7 +532,7 @@ def load_waste_chute(
         API will raise an error.
         """
         waste_chute = WasteChute()
-        self._core.append_disposal_location(waste_chute)
+        self._core.add_disposal_location_to_engine(waste_chute)
         return waste_chute
 
     @requires_version(2, 15)

api/src/opentrons/protocol_engine/state/commands.py

@@ -152,6 +152,9 @@ class CommandState:
     are stored on the individual commands themselves.
     """
 
+    failed_command: Optional[CommandEntry]
+    """The command, if any, that made the run fail and the index in the command list."""
+
     finish_error: Optional[ErrorOccurrence]
     """The error that happened during the post-run finish steps (homing & dropping tips), if any."""
 
@@ -189,6 +192,7 @@ def __init__(
             commands_by_id=OrderedDict(),
             run_error=None,
             finish_error=None,
+            failed_command=None,
             run_completed_at=None,
             run_started_at=None,
             latest_command_hash=None,
@@ -281,6 +285,7 @@ def handle_action(self, action: Action) -> None:  # noqa: C901
                 ),
             )
 
+            self._state.failed_command = self._state.commands_by_id[action.command_id]
             if prev_entry.command.intent == CommandIntent.SETUP:
                 other_command_ids_to_fail = [
                     *[i for i in self._state.queued_setup_command_ids],
@@ -464,6 +469,12 @@ def get_slice(
                 cursor = commands_by_id[running_command_id].index
             elif len(queued_command_ids) > 0:
                 cursor = commands_by_id[queued_command_ids.head()].index - 1
+            elif (
+                self._state.run_result
+                and self._state.run_result == RunResult.FAILED
+                and self._state.failed_command
+            ):
+                cursor = self._state.failed_command.index
             else:
                 cursor = total_length - length