Merge branch 'chore_resolve-630-conflicts' into edge

api-client/src/runs/commands/types.ts

@@ -11,6 +11,7 @@ export interface RunCommandSummary {
   commandType: RunTimeCommand['commandType']
   status: 'queued' | 'running' | 'succeeded' | 'failed'
   createdAt: string
+  intent?: 'protocol' | 'setup'
   params?: any
   // TODO(mc, 2022-02-02): `result` does not exist on RunCommandSummary
   result?: RunTimeCommand['result']

api/buildroot.mk

@@ -26,6 +26,7 @@ ot_api_name := python-opentrons-api
 define PYTHON_OPENTRONS_API_INSTALL_RELEASE_NOTES
 	$(INSTALL) -D -m 0644 $(BR2_EXTERNAL_OPENTRONS_MONOREPO_PATH)/api/release-notes.md $(BINARIES_DIR)/release-notes.md
 endef
+export OPENTRONS_GIT_DIR=$(BR2_EXTERNAL_OPENTRONS_MONOREPO_PATH)
 
 # Calling inner-python-package directly instead of using python-package macro
 # because our directory layout doesn’t conform to buildroot’s expectation of

api/docs/v2/versioning.rst

@@ -271,7 +271,7 @@ If you specify an API version of ``2.13`` or lower, your protocols will continue
   - Motion planning has been improved to avoid certain erroneous downward movements,
     especially when using :py:meth:`.InstrumentContext.aspirate`.
 
-  - :py:attr:`.Labware.tip_length` will raise a useful error if called on labware that is not a tip rack.
+  - :py:meth:`.Labware.reset` and :py:attr:`.Labware.tip_length` will raise useful errors if called on labware that is not a tip rack.
 
 - Removals
 
@@ -295,8 +295,8 @@ If you specify an API version of ``2.13`` or lower, your protocols will continue
 
   - The ``height`` parameter of :py:meth:`.MagneticModuleContext.engage` was removed.
     Use ``offset`` or ``height_from_base`` instead.
-
-  - ``Labware.separate_calibration`` and ``ModuleContext.separate_calibration`` were removed,
+    
+  - ``Labware.separate_calibration`` and :py:meth:`.Labware.set_calibration` were removed,
     since they were holdovers from a calibration system that no longer exists.
 
   - Various methods and setters were removed that could modify tip state outside of

api/release-notes.md

@@ -6,6 +6,27 @@ log][]. For a list of currently known issues, please see the [Opentrons issue tr
 
 ---
 
+## OT-2 Software Changes in 6.3.0
+
+Welcome to the v6.3.0 release of the OT-2 software!
+
+### Improved Features
+
+- The `/calibrations` endpoint now accepts `DELETE` requests.
+
+### Bug Fixes
+
+- Fixed a problem where labware offsets would sometimes be ignored for labware atop a Temperature Module.
+- Calls to the `/commands` endpoint with `waitUntilComplete=true` no longer time out after 30 seconds if you don't specify a timeout interval.
+- Fixed improper pagination and cursor placement for the `/commands` endpoint.
+
+### Known Issues
+
+- Some protocols can't be simulated with the `opentrons_simulate` command-line tool:
+    - JSON protocols created or modified with Protocol Designer v6.0.0 or higher
+    - Python protocols specifying an `apiLevel` of 2.14
+
+---
 ## OT-2 Software Changes in 6.2.1
 
 Welcome to the v6.2.1 release of the OT-2 software! This hotfix release addresses a few problems.

api/setup.py

@@ -23,11 +23,12 @@
 def get_version():
     buildno = os.getenv("BUILD_NUMBER")
     project = os.getenv("OPENTRONS_PROJECT", "robot-stack")
+    git_dir = os.getenv("OPENTRONS_GIT_DIR", None)
     if buildno:
         normalize_opts = {"extra_tag": buildno}
     else:
         normalize_opts = {}
-    return normalize_version("api", project, **normalize_opts)
+    return normalize_version("api", project, git_dir=git_dir, **normalize_opts)
 
 
 VERSION = get_version()

api/src/opentrons/protocol_api/_liquid.py

@@ -10,6 +10,8 @@ class Liquid:
         name: A human-readable name for the liquid.
         description: An optional description.
         display_color: An optional display color for the liquid.
+
+    .. versionadded:: 2.14
     """
 
     _id: str

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

@@ -149,7 +149,7 @@ def _map_module(
     engine_state: StateView,
     module_id: str,
 ) -> Optional[Tuple[int, wrapped_deck_conflict.DeckItem]]:
-    module_model = engine_state.modules.get_model(module_id=module_id)
+    module_model = engine_state.modules.get_connected_model(module_id=module_id)
     module_type = module_model.as_type()
     mapped_location = _deck_slot_to_int(
         engine_state.modules.get_location(module_id=module_id)

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

@@ -450,6 +450,9 @@ def get_min_volume(self) -> float:
     def get_max_volume(self) -> float:
         return self._engine_client.state.pipettes.get_maximum_volume(self._pipette_id)
 
+    def get_working_volume(self) -> float:
+        return self._engine_client.state.pipettes.get_working_volume(self._pipette_id)
+
     def get_current_volume(self) -> float:
         try:
             current_volume = self._engine_client.state.pipettes.get_aspirated_volume(

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

@@ -108,7 +108,10 @@ def get_tip_length(self) -> float:
         return self._engine_client.state.labware.get_tip_length(self._labware_id)
 
     def reset_tips(self) -> None:
-        self._engine_client.reset_tips(labware_id=self.labware_id)
+        if self.is_tip_rack():
+            self._engine_client.reset_tips(labware_id=self.labware_id)
+        else:
+            raise TypeError(f"{self.get_display_name()} is not a tip rack.")
 
     def get_next_tip(
         self, num_tips: int, starting_tip: Optional[WellCore]

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

@@ -1,9 +1,23 @@
-from typing import Tuple, List, Optional
+from typing import Dict, Tuple, List, Optional
 
 from opentrons.protocols.api_support.constants import OPENTRONS_NAMESPACE
 from opentrons.protocol_engine.state.labware import LabwareLoadParams
 
 
+# Default versions of Opentrons standard labware definitions in Python Protocol API
+# v2.14 and above. Labware not explicitly listed here default to 1.
+#
+# This will need to be extended t
+_APILEVEL_2_14_OT_DEFAULT_VERSIONS: Dict[str, int] = {
+    # v1 of many labware definitions have wrong `zDimension`s. (Jira RSS-202.)
+    # For "opentrons_96_aluminumblock_generic_pcr_strip_200ul" and
+    # "opentrons_24_aluminumblock_generic_2ml_screwcap", they're wrong enough to
+    # easily cause collisions. (Jira RSS-197.)
+    "opentrons_24_aluminumblock_generic_2ml_screwcap": 2,
+    "opentrons_96_aluminumblock_generic_pcr_strip_200ul": 2,
+}
+
+
 class AmbiguousLoadLabwareParamsError(RuntimeError):
     """Error raised when specific labware parameters cannot be found due to multiple matching labware definitions."""
 
@@ -40,18 +54,35 @@ def matches_params(custom_params: LabwareLoadParams) -> bool:
         params for params in custom_load_labware_params if matches_params(params)
     ]
 
-    # If there is no custom labware for the load name provided earlier, default anything not chosen to
-    # the opentrons defaults. If the provided namespace was OPENTRONS_NAMESPACE, there will be no custom labware
-    # associated with that namespace, meaning `custom_labware_params` will be empty and version will always
-    # default to 1 here
     if not filtered_custom_params:
+        # No custom labware matches the input, but some standard labware might.
+        # Use the Opentrons defaults for anything not explicitly provided.
+        #
+        # If the provided namespace was OPENTRONS_NAMESPACE, there would have been no
+        # custom labware matching that namespace, so we will always take this path in
+        # that case.
         resolved_namespace = namespace if namespace is not None else OPENTRONS_NAMESPACE
-        resolved_version = version if version is not None else 1
+        resolved_version = (
+            version
+            if version is not None
+            else _get_default_version_for_standard_labware(load_name=load_name)
+        )
+
     elif len(filtered_custom_params) > 1:
+        # Multiple custom labware match the input.
         raise AmbiguousLoadLabwareParamsError(
             f"Multiple custom labware associated with load name {load_name}."
         )
+
     else:
+        # Exactly one custom labware matches the input. Return it.
         resolved_namespace = filtered_custom_params[0].namespace
         resolved_version = filtered_custom_params[0].version
+
     return resolved_namespace, resolved_version
+
+
+def _get_default_version_for_standard_labware(load_name: str) -> int:
+    # We know the protocol is running at least apiLevel 2.14 by this point because
+    # apiLevel 2.13 and below has its own separate code path for resolving labware.
+    return _APILEVEL_2_14_OT_DEFAULT_VERSIONS.get(load_name, 1)

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

@@ -67,7 +67,7 @@ def module_id(self) -> str:
     def get_model(self) -> ModuleModel:
         """Get the module's model identifier."""
         return module_model_from_string(
-            self._engine_client.state.modules.get_model(self.module_id)
+            self._engine_client.state.modules.get_connected_model(self.module_id)
         )
 
     def get_serial_number(self) -> str:

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

@@ -170,6 +170,10 @@ def get_min_volume(self) -> float:
     def get_max_volume(self) -> float:
         ...
 
+    @abstractmethod
+    def get_working_volume(self) -> float:
+        ...
+
     @abstractmethod
     def get_current_volume(self) -> float:
         ...

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

@@ -390,6 +390,10 @@ def get_max_volume(self) -> float:
         """Get the max volume."""
         return self.get_hardware_state()["max_volume"]
 
+    def get_working_volume(self) -> float:
+        """Get the working volume."""
+        return self.get_hardware_state()["working_volume"]
+
     def get_current_volume(self) -> float:
         """Get the current volume."""
         return self.get_hardware_state()["current_volume"]

api/src/opentrons/protocol_api/core/legacy_simulator/legacy_instrument_core.py

@@ -293,6 +293,9 @@ def get_min_volume(self) -> float:
     def get_max_volume(self) -> float:
         return self._pipette_dict["max_volume"]
 
+    def get_working_volume(self) -> float:
+        return self._pipette_dict["working_volume"]
+
     def get_current_volume(self) -> float:
         return self._pipette_dict["current_volume"]
 

api/src/opentrons/protocol_api/instrument_context.py

@@ -1179,7 +1179,7 @@ def transfer(
             )
             max_volume = min(next_tip.max_volume, self.max_volume)
         else:
-            max_volume = self.hw_pipette["working_volume"]
+            max_volume = self._core.get_working_volume()
 
         touch_tip = None
         if kwargs.get("touch_tip"):

api/src/opentrons/protocol_api/labware.py

@@ -215,8 +215,8 @@ def load_liquid(self, liquid: Liquid, volume: float) -> None:
         """
         Load a liquid into a well.
 
-        :param liquid: The type of liquid to load into the well.
-        :param volume: The volume of liquid to load, in µL.
+        :param Liquid liquid: The liquid to load into the well.
+        :param float volume: The volume of liquid to load, in µL.
         """
         self._core.load_liquid(
             liquid=liquid,
@@ -313,6 +313,9 @@ def __init__(
 
     @property
     def separate_calibration(self) -> bool:
+        if self._api_version >= ENGINE_CORE_API_VERSION:
+            raise APIVersionError("Labware.separate_calibration has been removed")
+
         _log.warning(
             "Labware.separate_calibrations is a deprecated internal property."
             " It no longer has meaning, but will always return `False`"
@@ -432,8 +435,16 @@ def magdeck_engage_height(self) -> Optional[float]:
 
     def set_calibration(self, delta: Point) -> None:
         """
-        Called by save calibration in order to update the offset on the object.
+        An internal, deprecated method used for updating the offset on the object.
+
+        .. deprecated:: 2.14
         """
+        if self._api_version >= ENGINE_CORE_API_VERSION:
+            raise APIVersionError(
+                "Labware.set_calibration() is not supported when apiLevel is 2.14 or higher."
+                " Use a lower apiLevel"
+                " or use the Opentrons App's Labware Position Check."
+            )
         self._core.set_calibration(delta)
 
     @requires_version(2, 12)
@@ -874,7 +885,12 @@ def return_tips(self, start_well: Well, num_channels: int = 1) -> None:
 
     @requires_version(2, 0)
     def reset(self) -> None:
-        """Reset all tips in a tiprack."""
+        """Reset all tips in a tip rack.
+
+        .. versionchanged:: 2.14
+            This method will raise an exception if you call it on a labware that isn't
+            a tip rack. Formerly, it would do nothing.
+        """
         self._core.reset_tips()
 
 

api/src/opentrons/protocol_api/module_contexts.py

@@ -124,14 +124,10 @@ def load_labware(
     ) -> Labware:
         """Load a labware onto the module using its load parameters.
 
-        :param name: The name of the labware object.
-        :param str label: An optional display name to give the labware.
-                          If specified, this is the name the labware will use
-                          in the run log and the calibration view in the Opentrons App.
-        :param str namespace: The namespace the labware definition belongs to.
-                              If unspecified, will search 'opentrons' then 'custom_beta'
-        :param int version: The version of the labware definition.
-                            If unspecified, will use version 1.
+        The parameters of this function behave like those of
+        :py:obj:`ProtocolContext.load_labware` (which loads labware directly
+        onto the deck). Note that the parameter ``name`` here corresponds to
+        ``load_name`` on the ``ProtocolContext`` function.
 
         :returns: The initialized and loaded labware object.
 
@@ -345,12 +341,14 @@ def calibrate(self) -> None:
         .. deprecated:: 2.14
             This method is unnecessary; remove any usage.
         """
-        _log.warning(
-            "`MagneticModuleContext.calibrate` doesn't do anything useful"
-            " and will no-op in Protocol API version 2.14 and higher."
-        )
         if self._api_version < ENGINE_CORE_API_VERSION:
+            _log.warning(
+                "`MagneticModuleContext.calibrate` doesn't do anything useful"
+                " and will be removed in Protocol API version 2.14 and higher."
+            )
             self._core._sync_module_hardware.calibrate()  # type: ignore[attr-defined]
+        else:
+            raise APIVersionError("`MagneticModuleContext.calibrate` has been removed.")
 
     @publish(command=cmds.magdeck_engage)
     @requires_version(2, 0)

api/src/opentrons/protocol_api/protocol_context.py

@@ -298,18 +298,32 @@ def load_labware(
         This function returns the created and initialized labware for use
         later in the protocol.
 
-        :param load_name: A string to use for looking up a labware definition
-        :param location: The slot into which to load the labware such as
-                         1 or '1'
+        :param str load_name: A string to use for looking up a labware definition.
+            You can find the ``load_name`` for any standard labware on the Opentrons
+            `Labware Library <https://labware.opentrons.com>`_.
+
+        :param location: The slot into which to load the labware,
+            such as ``1`` or ``"1"``.
+
         :type location: int or str
-        :param str label: An optional special name to give the labware. If
-                          specified, this is the name the labware will appear
-                          as in the run log and the calibration view in the
-                          Opentrons app.
-        :param str namespace: The namespace the labware definition belongs to.
-            If unspecified, will search 'opentrons' then 'custom_beta'
-        :param int version: The version of the labware definition. If
-            unspecified, will use version 1.
+
+        :param str label: An optional special name to give the labware. If specified, this
+            is the name the labware will appear as in the run log and the calibration
+            view in the Opentrons app.
+
+        :param str namespace: The namespace that the labware definition belongs to.
+            If unspecified, will search both:
+
+              * ``"opentrons"``, to load standard Opentrons labware definitions.
+              * ``"custom_beta"``, to load custom labware definitions created with the
+                `Custom Labware Creator <https://labware.opentrons.com/create>`_.
+
+            You might need to specify an explicit ``namespace`` if you have a custom
+            definition whose ``load_name`` is the same as an Opentrons standard
+            definition, and you want to explicitly choose one or the other.
+
+        :param version: The version of the labware definition. You should normally
+            leave this unspecified to let the implementation choose a good default.
         """
         load_name = validation.ensure_lowercase_name(load_name)
         deck_slot = validation.ensure_deck_slot(location)
@@ -795,6 +809,8 @@ def define_liquid(
         :param str name: A human-readable name for the liquid.
         :param str description: An optional description of the liquid.
         :param str display_color: An optional hex color code, with hash included, to represent the specified liquid. Standard three-value, four-value, six-value, and eight-value syntax are all acceptable.
+
+        :return: A :py:class:`~opentrons.protocol_api.Liquid` object representing the specified liquid.
         """
         return self._core.define_liquid(
             name=name,

api/src/opentrons/protocol_engine/errors/exceptions.py

@@ -94,6 +94,9 @@ class PipetteNotLoadedError(ProtocolEngineError):
 class ModuleNotLoadedError(ProtocolEngineError):
     """Raised when referencing a module that has not been loaded."""
 
+    def __init__(self, *, module_id: str) -> None:
+        super().__init__(f"Module {module_id} not found.")
+
 
 class ModuleNotOnDeckError(ProtocolEngineError):
     """Raised when trying to use a module that is loaded off the deck."""
@@ -207,3 +210,7 @@ class FirmwareUpdateRequired(ProtocolEngineError):
 
 class PipetteNotReadyToAspirateError(ProtocolEngineError):
     """Raised when the pipette is not ready to aspirate."""
+
+
+class InvalidPipettingVolumeError(ProtocolEngineError):
+    """Raised when pipetting a volume larger than the pipette volume."""