opentrons 8.0.0a2__tar.gz → 8.0.0a4__tar.gz

{opentrons-8.0.0a2 → opentrons-8.0.0a4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: opentrons
-Version: 8.0.0a2
+Version: 8.0.0a4
 Summary: The Opentrons API is a simple framework designed to make writing automated biology lab protocols easy.
 Author: Opentrons
 Author-email: engineering@opentrons.com
@@ -21,7 +21,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Topic :: Scientific/Engineering
 Requires-Python: >=3.10
 License-File: ../LICENSE
-Requires-Dist: opentrons-shared-data==8.0.0a2
+Requires-Dist: opentrons-shared-data==8.0.0a4
 Requires-Dist: aionotify==0.3.1
 Requires-Dist: anyio<4.0.0,>=3.6.1
 Requires-Dist: jsonschema<4.18.0,>=3.0.1
@@ -33,9 +33,9 @@ Requires-Dist: click<9,>=8.0.0
 Requires-Dist: importlib-metadata>=1.0; python_version < "3.8"
 Requires-Dist: packaging>=21.0
 Provides-Extra: ot2-hardware
-Requires-Dist: opentrons-hardware==8.0.0a2; extra == "ot2-hardware"
+Requires-Dist: opentrons-hardware==8.0.0a4; extra == "ot2-hardware"
 Provides-Extra: flex-hardware
-Requires-Dist: opentrons-hardware[FLEX]==8.0.0a2; extra == "flex-hardware"
+Requires-Dist: opentrons-hardware[FLEX]==8.0.0a4; extra == "flex-hardware"
 
 .. _Full API Documentation: http://docs.opentrons.com
 

{opentrons-8.0.0a2 → opentrons-8.0.0a4}/src/opentrons/protocol_api/core/engine/deck_conflict.py

@@ -416,23 +416,48 @@ def _is_within_pipette_extents(
     pipette_bounding_box_at_loc: Tuple[Point, Point, Point, Point],
 ) -> bool:
     """Whether a given point is within the extents of a configured pipette on the specified robot."""
-    mount = engine_state.pipettes.get_mount(pipette_id)
-    robot_extent_per_mount = engine_state.geometry.absolute_deck_extents
-    pip_back_left_bound, pip_front_right_bound, _, _ = pipette_bounding_box_at_loc
-    pipette_bounds_offsets = engine_state.pipettes.get_pipette_bounding_box(pipette_id)
-    from_back_right = (
-        robot_extent_per_mount.back_right[mount]
-        + pipette_bounds_offsets.back_right_corner
-    )
-    from_front_left = (
-        robot_extent_per_mount.front_left[mount]
-        + pipette_bounds_offsets.front_left_corner
-    )
+    channels = engine_state.pipettes.get_channels(pipette_id)
+    robot_extents = engine_state.geometry.absolute_deck_extents
+    (
+        pip_back_left_bound,
+        pip_front_right_bound,
+        pip_back_right_bound,
+        pip_front_left_bound,
+    ) = pipette_bounding_box_at_loc
+
+    # Given the padding values accounted for against the deck extents,
+    # a pipette is within extents when all of the following are true:
+
+    # Each corner slot full pickup case:
+    # A1: Front right nozzle is within the rear and left-side padding limits
+    # D1: Back right nozzle is within the front and left-side padding limits
+    # A3 Front left nozzle is within the rear and right-side padding limits
+    # D3: Back left nozzle is within the front and right-side padding limits
+    # Thermocycler Column A2: Front right nozzle is within padding limits
+
+    if channels == 96:
+        return (
+            pip_front_right_bound.y
+            <= robot_extents.deck_extents.y + robot_extents.padding_rear
+            and pip_front_right_bound.x >= robot_extents.padding_left_side
+            and pip_back_right_bound.y >= robot_extents.padding_front
+            and pip_back_right_bound.x >= robot_extents.padding_left_side
+            and pip_front_left_bound.y
+            <= robot_extents.deck_extents.y + robot_extents.padding_rear
+            and pip_front_left_bound.x
+            <= robot_extents.deck_extents.x + robot_extents.padding_right_side
+            and pip_back_left_bound.y >= robot_extents.padding_front
+            and pip_back_left_bound.x
+            <= robot_extents.deck_extents.x + robot_extents.padding_right_side
+        )
+    # For 8ch pipettes we only check the rear and front extents
     return (
-        from_back_right.x >= pip_back_left_bound.x >= from_front_left.x
-        and from_back_right.y >= pip_back_left_bound.y >= from_front_left.y
-        and from_back_right.x >= pip_front_right_bound.x >= from_front_left.x
-        and from_back_right.y >= pip_front_right_bound.y >= from_front_left.y
+        pip_front_right_bound.y
+        <= robot_extents.deck_extents.y + robot_extents.padding_rear
+        and pip_back_right_bound.y >= robot_extents.padding_front
+        and pip_front_left_bound.y
+        <= robot_extents.deck_extents.y + robot_extents.padding_rear
+        and pip_back_left_bound.y >= robot_extents.padding_front
     )
 
 

{opentrons-8.0.0a2 → opentrons-8.0.0a4}/src/opentrons/protocol_api/instrument_context.py

@@ -268,7 +268,6 @@ class InstrumentContext(publisher.CommandPublisher):
             and self._96_tip_config_valid()
         ):
             self.require_liquid_presence(well=well)
-            self.prepare_to_aspirate()
 
         with publisher.publish_context(
             broker=self.broker,
@@ -2064,6 +2063,8 @@ class InstrumentContext(publisher.CommandPublisher):
             NozzleLayout.QUADRANT,
         ]
         if style in disabled_layouts:
+            # todo(mm, 2024-08-20): UnsupportedAPIError boils down to an API_REMOVED
+            # error code, which is not correct here.
             raise UnsupportedAPIError(
                 message=f"Nozzle layout configuration of style {style.value} is currently unsupported."
             )
@@ -2074,7 +2075,11 @@ class InstrumentContext(publisher.CommandPublisher):
             < _PARTIAL_NOZZLE_CONFIGURATION_SINGLE_ROW_PARTIAL_COLUMN_ADDED_IN
         ) and (style not in original_enabled_layouts):
             raise APIVersionError(
-                f"Nozzle layout configuration of style {style.value} is unsupported in API Versions lower than {_PARTIAL_NOZZLE_CONFIGURATION_SINGLE_ROW_PARTIAL_COLUMN_ADDED_IN}."
+                api_element=f"Nozzle layout configuration of style {style.value}",
+                until_version=str(
+                    _PARTIAL_NOZZLE_CONFIGURATION_SINGLE_ROW_PARTIAL_COLUMN_ADDED_IN
+                ),
+                current_version=str(self._api_version),
             )
 
         front_right_resolved = front_right

{opentrons-8.0.0a2 → opentrons-8.0.0a4}/src/opentrons/protocol_api/labware.py

@@ -581,7 +581,7 @@ class Labware:
                 api_element="Labware.set_calibration()",
                 since_version=f"{ENGINE_CORE_API_VERSION}",
                 current_version=f"{self._api_version}",
-                message=" Try using the Opentrons App's Labware Position Check.",
+                extra_message="Try using the Opentrons App's Labware Position Check.",
             )
         self._core.set_calibration(delta)
 
@@ -632,7 +632,7 @@ class Labware:
                 api_element="Labware.set_offset()",
                 until_version=f"{SET_OFFSET_RESTORED_API_VERSION}",
                 current_version=f"{self._api_version}",
-                message=" This feature not available in versions 2.14 thorugh 2.17. You can also use the Opentrons App's Labware Position Check.",
+                extra_message="This feature not available in versions 2.14 thorugh 2.17. You can also use the Opentrons App's Labware Position Check.",
             )
         else:
             self._core.set_calibration(Point(x=x, y=y, z=z))
@@ -974,7 +974,7 @@ class Labware:
                 api_element="Labware.use_tips",
                 since_version=f"{ENGINE_CORE_API_VERSION}",
                 current_version=f"{self._api_version}",
-                message=" To modify tip state, use Labware.reset.",
+                extra_message="To modify tip state, use Labware.reset.",
             )
 
         assert num_channels > 0, "Bad call to use_tips: num_channels<=0"
@@ -1064,7 +1064,7 @@ class Labware:
                 api_element="Labware.return_tips()",
                 since_version=f"{ENGINE_CORE_API_VERSION}",
                 current_version=f"{self._api_version}",
-                message=" Use Labware.reset() instead.",
+                extra_message="Use Labware.reset() instead.",
             )
 
         # This logic is the inverse of :py:meth:`use_tips`

{opentrons-8.0.0a2 → opentrons-8.0.0a4}/src/opentrons/protocol_api/module_contexts.py

@@ -103,7 +103,7 @@ class ModuleContext(CommandPublisher):
             raise UnsupportedAPIError(
                 api_element="`ModuleContext.load_labware_object`",
                 since_version="2.14",
-                message=" Use `ModuleContext.load_labware` or `load_labware_by_definition` instead.",
+                extra_message="Use `ModuleContext.load_labware` or `load_labware_by_definition` instead.",
             )
 
         _log.warning(
@@ -305,7 +305,7 @@ class ModuleContext(CommandPublisher):
         raise UnsupportedAPIError(
             api_element="`ModuleContext.geometry`",
             since_version="2.14",
-            message=" Use properties of the `ModuleContext` itself.",
+            extra_message="Use properties of the `ModuleContext` itself.",
         )
 
     def __repr__(self) -> str:
@@ -482,7 +482,7 @@ class MagneticModuleContext(ModuleContext):
                     api_element="The height parameter of MagneticModuleContext.engage()",
                     since_version=f"{_MAGNETIC_MODULE_HEIGHT_PARAM_REMOVED_IN}",
                     current_version=f"{self._api_version}",
-                    message=" Use offset or height_from_base.",
+                    extra_message="Use offset or height_from_base.",
                 )
             self._core.engage(height_from_home=height)
 

{opentrons-8.0.0a2 → opentrons-8.0.0a4}/src/opentrons/protocol_api/protocol_context.py

@@ -279,7 +279,7 @@ class ProtocolContext(CommandPublisher):
                 api_element="ProtocolContext.max_speeds",
                 since_version=f"{ENGINE_CORE_API_VERSION}",
                 current_version=f"{self._api_version}",
-                message=" Set speeds using InstrumentContext.default_speed or the per-method 'speed' argument.",
+                extra_message="Set speeds using InstrumentContext.default_speed or the per-method 'speed' argument.",
             )
 
         return self._core.get_max_speeds()
@@ -915,6 +915,7 @@ class ProtocolContext(CommandPublisher):
                              from the Opentrons App or touchscreen.
         :param bool liquid_presence_detection: If ``True``, enable automatic
             :ref:`liquid presence detection <lpd>` for Flex 1-, 8-, or 96-channel pipettes.
+
             .. versionadded:: 2.20
         """
         instrument_name = validation.ensure_lowercase_name(instrument_name)
@@ -1048,7 +1049,7 @@ class ProtocolContext(CommandPublisher):
                 api_element="A Python Protocol safely resuming itself after a pause",
                 since_version=f"{ENGINE_CORE_API_VERSION}",
                 current_version=f"{self._api_version}",
-                message=" To wait automatically for a period of time, use ProtocolContext.delay().",
+                extra_message="To wait automatically for a period of time, use ProtocolContext.delay().",
             )
 
         # TODO(mc, 2023-02-13): this assert should be enough for mypy
@@ -1169,7 +1170,7 @@ class ProtocolContext(CommandPublisher):
                     api_element="Fixed Trash",
                     since_version="2.16",
                     current_version=f"{self._api_version}",
-                    message=" Fixed trash is no longer supported on Flex protocols.",
+                    extra_message="Fixed trash is no longer supported on Flex protocols.",
                 )
             disposal_locations = self._core.get_disposal_locations()
             if len(disposal_locations) == 0:
@@ -1242,7 +1243,7 @@ class ProtocolContext(CommandPublisher):
                     api_element="Calling `define_liquid()` without a `description`",
                     current_version=str(self._api_version),
                     until_version=str(desc_and_display_color_omittable_since),
-                    message="Use a newer API version or explicitly supply `description=None`.",
+                    extra_message="Use a newer API version or explicitly supply `description=None`.",
                 )
             else:
                 description = None
@@ -1252,7 +1253,7 @@ class ProtocolContext(CommandPublisher):
                     api_element="Calling `define_liquid()` without a `display_color`",
                     current_version=str(self._api_version),
                     until_version=str(desc_and_display_color_omittable_since),
-                    message="Use a newer API version or explicitly supply `display_color=None`.",
+                    extra_message="Use a newer API version or explicitly supply `display_color=None`.",
                 )
             else:
                 display_color = None

{opentrons-8.0.0a2 → opentrons-8.0.0a4}/src/opentrons/protocol_api/validation.py

@@ -208,7 +208,7 @@ def ensure_and_convert_deck_slot(
                 api_element=f"Specifying a deck slot like '{deck_slot}'",
                 until_version=f"{_COORDINATE_DECK_LABEL_VERSION_GATE}",
                 current_version=f"{api_version}",
-                message=f"Increase your protocol's apiLevel, or use slot '{alternative}' instead.",
+                extra_message=f"Increase your protocol's apiLevel, or use slot '{alternative}' instead.",
             )
 
         return parsed_slot.to_equivalent_for_robot_type(robot_type)

{opentrons-8.0.0a2 → opentrons-8.0.0a4}/src/opentrons/protocol_engine/state/addressable_areas.py

@@ -352,6 +352,20 @@ class AddressableAreaView(HasState[AddressableAreaState]):
             "right": Point(x=right_offset[0], y=right_offset[1], z=right_offset[2]),
         }
 
+    @cached_property
+    def padding_offsets(self) -> Dict[str, float]:
+        """The padding offsets to be applied to the deck extents of the robot."""
+        rear_offset = self.state.robot_definition["paddingOffsets"]["rear"]
+        front_offset = self.state.robot_definition["paddingOffsets"]["front"]
+        left_side_offset = self.state.robot_definition["paddingOffsets"]["leftSide"]
+        right_side_offset = self.state.robot_definition["paddingOffsets"]["rightSide"]
+        return {
+            "rear": rear_offset,
+            "front": front_offset,
+            "left_side": left_side_offset,
+            "right_side": right_side_offset,
+        }
+
     def get_addressable_area(self, addressable_area_name: str) -> AddressableArea:
         """Get addressable area."""
         if not self._state.use_simulated_deck_config:

{opentrons-8.0.0a2 → opentrons-8.0.0a4}/src/opentrons/protocol_engine/state/geometry.py

@@ -77,6 +77,11 @@ class _GripperMoveType(enum.Enum):
 class _AbsoluteRobotExtents:
     front_left: Dict[MountType, Point]
     back_right: Dict[MountType, Point]
+    deck_extents: Point
+    padding_rear: float
+    padding_front: float
+    padding_left_side: float
+    padding_right_side: float
 
 
 _LabwareLocation = TypeVar("_LabwareLocation", bound=LabwareLocation)
@@ -118,7 +123,13 @@ class GeometryView:
             MountType.RIGHT: self._addressable_areas.deck_extents + right_offset,
         }
         return _AbsoluteRobotExtents(
-            front_left=front_left_abs, back_right=back_right_abs
+            front_left=front_left_abs,
+            back_right=back_right_abs,
+            deck_extents=self._addressable_areas.deck_extents,
+            padding_rear=self._addressable_areas.padding_offsets["rear"],
+            padding_front=self._addressable_areas.padding_offsets["front"],
+            padding_left_side=self._addressable_areas.padding_offsets["left_side"],
+            padding_right_side=self._addressable_areas.padding_offsets["right_side"],
         )
 
     def get_labware_highest_z(self, labware_id: str) -> float:

{opentrons-8.0.0a2 → opentrons-8.0.0a4}/src/opentrons/protocol_engine/state/pipettes.py

@@ -845,8 +845,6 @@ class PipetteView(HasState[PipetteState]):
             - primary_nozzle_offset
             + pipette_bounds_offsets.front_right_corner
         )
-        # TODO (spp, 2024-02-27): remove back right & front left;
-        #  return only back left and front right points.
         pip_back_right_bound = Point(
             pip_front_right_bound.x, pip_back_left_bound.y, pip_front_right_bound.z
         )

{opentrons-8.0.0a2 → opentrons-8.0.0a4}/src/opentrons/protocols/parameters/csv_parameter_interface.py

@@ -16,7 +16,10 @@ class CSVParameter:
 
     @property
     def file(self) -> TextIO:
-        """Returns the file handler for the CSV file."""
+        """Returns the file handler for the CSV file.
+
+        The file is treated as read-only, UTF-8-encoded text.
+        """
         if self._file is None:
             text = self.contents
             temporary_file = NamedTemporaryFile("r+")
@@ -30,7 +33,7 @@ class CSVParameter:
 
     @property
     def file_opened(self) -> bool:
-        """Return if a file handler has been opened for the CSV parameter."""
+        """Returns ``True`` if a file handler is open for the CSV parameter."""
         return self._file is not None
 
     @property
@@ -45,10 +48,22 @@ class CSVParameter:
     def parse_as_csv(
         self, detect_dialect: bool = True, **kwargs: Any
     ) -> List[List[str]]:
-        """Returns a list of rows with each row represented as a list of column elements.
+        """Parses the CSV data and returns a list of lists.
+
+        Each item in the parent list corresponds to a row in the CSV file.
+        If the CSV has a header, that will be the first row in the list: ``.parse_as_csv()[0]``.
+
+        Each item in the child lists corresponds to a single cell within its row.
+        The data for each cell is represented as a string. You may need to trim whitespace
+        or otherwise validate string contents before passing them as inputs to other API methods.
+        For numeric data, cast these strings to integers or floating point numbers,
+        as appropriate.
 
-        If there is a header for the CSV that will be the first row in the list (i.e. `.rows()[0]`).
-        All elements will be represented as strings, even if they are numeric in nature.
+        :param detect_dialect: If ``True``, examine the file and try to assign it a
+            :py:class:`csv.Dialect` to improve parsing behavior.
+        :param kwargs: For advanced CSV handling, you can pass any of the
+            `formatting parameters <https://docs.python.org/3/library/csv.html#csv-fmt-params>`_
+            accepted by :py:func:`csv.reader` from the Python standard library.
         """
         rows: List[List[str]] = []
         if detect_dialect:

{opentrons-8.0.0a2 → opentrons-8.0.0a4}/src/opentrons.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: opentrons
-Version: 8.0.0a2
+Version: 8.0.0a4
 Summary: The Opentrons API is a simple framework designed to make writing automated biology lab protocols easy.
 Author: Opentrons
 Author-email: engineering@opentrons.com
@@ -21,7 +21,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Topic :: Scientific/Engineering
 Requires-Python: >=3.10
 License-File: ../LICENSE
-Requires-Dist: opentrons-shared-data==8.0.0a2
+Requires-Dist: opentrons-shared-data==8.0.0a4
 Requires-Dist: aionotify==0.3.1
 Requires-Dist: anyio<4.0.0,>=3.6.1
 Requires-Dist: jsonschema<4.18.0,>=3.0.1
@@ -33,9 +33,9 @@ Requires-Dist: click<9,>=8.0.0
 Requires-Dist: importlib-metadata>=1.0; python_version < "3.8"
 Requires-Dist: packaging>=21.0
 Provides-Extra: ot2-hardware
-Requires-Dist: opentrons-hardware==8.0.0a2; extra == "ot2-hardware"
+Requires-Dist: opentrons-hardware==8.0.0a4; extra == "ot2-hardware"
 Provides-Extra: flex-hardware
-Requires-Dist: opentrons-hardware[FLEX]==8.0.0a2; extra == "flex-hardware"
+Requires-Dist: opentrons-hardware[FLEX]==8.0.0a4; extra == "flex-hardware"
 
 .. _Full API Documentation: http://docs.opentrons.com
 

{opentrons-8.0.0a2 → opentrons-8.0.0a4}/src/opentrons.egg-info/requires.txt

@@ -1,4 +1,4 @@
-opentrons-shared-data==8.0.0a2
+opentrons-shared-data==8.0.0a4
 aionotify==0.3.1
 anyio<4.0.0,>=3.6.1
 jsonschema<4.18.0,>=3.0.1
@@ -13,7 +13,7 @@ packaging>=21.0
 importlib-metadata>=1.0
 
 [flex-hardware]
-opentrons-hardware[FLEX]==8.0.0a2
+opentrons-hardware[FLEX]==8.0.0a4
 
 [ot2-hardware]
-opentrons-hardware==8.0.0a2
+opentrons-hardware==8.0.0a4