Merge branch 'chore_release-8.0.0' into 8.0.0-alpha.0-mergeback

api-client/src/dataFiles/getCsvFile.ts

@@ -0,0 +1,12 @@
+import { GET, request } from '../request'
+
+import type { CsvFileDataResponse } from './types'
+import type { ResponsePromise } from '../request'
+import type { HostConfig } from '../types'
+
+export function getCsvFile(
+  config: HostConfig,
+  fileId: string
+): ResponsePromise<CsvFileDataResponse> {
+  return request<CsvFileDataResponse>(GET, `/dataFiles/${fileId}`, null, config)
+}

api-client/src/dataFiles/index.ts

@@ -1,3 +1,4 @@
+export { getCsvFile } from './getCsvFile'
 export { getCsvFileRaw } from './getCsvFileRaw'
 export { uploadCsvFile } from './uploadCsvFile'
 

api-client/src/dataFiles/types.ts

@@ -13,10 +13,12 @@ export interface CsvFileData {
   name: string
 }
 
-export interface UploadedCsvFileResponse {
+export interface CsvFileDataResponse {
   data: CsvFileData
 }
 
+export type UploadedCsvFileResponse = CsvFileDataResponse
+
 export interface UploadedCsvFilesResponse {
   data: CsvFileData[]
 }

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

@@ -0,0 +1,19 @@
+import { GET, request } from '../../request'
+
+import type { ResponsePromise } from '../../request'
+import type { HostConfig } from '../../types'
+import type { GetCommandsParams, RunCommandErrors } from '../types'
+
+export function getRunCommandErrors(
+  config: HostConfig,
+  runId: string,
+  params: GetCommandsParams
+): ResponsePromise<RunCommandErrors> {
+  return request<RunCommandErrors>(
+    GET,
+    `/runs/${runId}/commandErrors`,
+    null,
+    config,
+    params
+  )
+}

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

@@ -1,10 +1,15 @@
-import type { RunTimeCommand } from '@opentrons/shared-data'
+import type { RunTimeCommand, RunCommandError } from '@opentrons/shared-data'
 
 export interface GetCommandsParams {
   cursor: number | null // the index of the command at the center of the window
   pageLength: number // the number of items to include
 }
 
+export interface RunCommandErrors {
+  data: RunCommandError[]
+  meta: GetCommandsParams & { totalLength: number }
+}
+
 // NOTE: this incantation allows us to omit a key from each item in a union distributively
 // this means we can, for example, maintain the associated commandType and params after the Omit is applied
 type DistributiveOmit<T, K extends keyof T> = T extends any ? Omit<T, K> : never

api-client/src/runs/index.ts

@@ -9,6 +9,7 @@ export { getCommand } from './commands/getCommand'
 export { getCommands } from './commands/getCommands'
 export { getCommandsAsPreSerializedList } from './commands/getCommandsAsPreSerializedList'
 export { createRunAction } from './createRunAction'
+export { getRunCommandErrors } from './commands/getRunCommandErrors'
 export * from './createLabwareOffset'
 export * from './createLabwareDefinition'
 export * from './constants'

api/docs/v2/versioning.rst

@@ -132,6 +132,11 @@ This table lists the correspondence between Protocol API versions and robot soft
 Changes in API Versions
 =======================
 
+Version 2.20
+------------
+
+- You can now call :py:obj:`.ProtocolContext.define_liquid()` without supplying a ``description`` or ``display_color``.
+
 Version 2.19
 ------------
 

api/release-notes.md

@@ -4,6 +4,26 @@ log][]. For a list of currently known issues, please see the [Opentrons issue tr
 [technical change log]: https://github.com/Opentrons/opentrons/releases
 [opentrons issue tracker]: https://github.com/Opentrons/opentrons/issues?q=is%3Aopen+is%3Aissue+label%3Abug
 
+By installing and using Opentrons software, you agree to the Opentrons End-User License Agreement (EULA). You can view the EULA at [opentrons.com/eula](https://opentrons.com/eula).
+
+---
+
+## Opentrons Robot Software Changes in 8.0.0
+
+Welcome to the v8.0.0 release of the Opentrons robot software!
+
+### New Features
+
+- Create, store, and run quick transfers on Flex.
+- Define and use CSV runtime parameters in Python protocols.
+- Detect the presence or absence of liquid in a well (Flex pipettes only), and continue or pause the protocol based on the result.
+- Automatically pause Flex protocol runs when detecting overpressure, allowing for error recovery and run resumption.
+
+### Improved Features
+
+- Provides more partial tip pickup configurations. All multi-channel pipettes now support single and partial column pickup, and the Flex 96-channel pipette now supports row pickup.
+- Improves homing behavior when a Flex protocol completes or is canceled with liquid-filled tips attached to the pipette.
+
 ---
 
 ## Opentrons Robot Software Changes in 7.5.0

api/src/opentrons/cli/analyze.py

@@ -248,7 +248,7 @@ async def _do_analyze(protocol_source: ProtocolSource) -> RunResult:
             protocol_source=protocol_source,
             parse_mode=ParseMode.NORMAL,
             run_time_param_values=None,
-            run_time_param_files=None,
+            run_time_param_paths=None,
         )
     except Exception as error:
         err_id = "analysis-setup-error"

api/src/opentrons/execute.py

@@ -142,23 +142,23 @@ def get_protocol_api(
     When this function is called, modules and instruments will be recached.
 
     :param version: The API version to use. This must be lower than
-                    ``opentrons.protocol_api.MAX_SUPPORTED_VERSION``.
-                    It may be specified either as a string (``'2.0'``) or
-                    as a ``protocols.types.APIVersion``
-                    (``APIVersion(2, 0)``).
+        ``opentrons.protocol_api.MAX_SUPPORTED_VERSION``.
+        It may be specified either as a string (``'2.0'``) or
+        as a ``protocols.types.APIVersion``
+        (``APIVersion(2, 0)``).
     :param bundled_labware: If specified, a mapping from labware names to
-                            labware definitions for labware to consider in the
-                            protocol. Note that if you specify this, _only_
-                            labware in this argument will be allowed in the
-                            protocol. This is preparation for a beta feature
-                            and is best not used.
+        labware definitions for labware to consider in the
+        protocol. Note that if you specify this, *only*
+        labware in this argument will be allowed in the
+        protocol. This is preparation for a beta feature
+        and is best not used.
     :param bundled_data: If specified, a mapping from filenames to contents
-                         for data to be available in the protocol from
-                         :py:obj:`opentrons.protocol_api.ProtocolContext.bundled_data`.
+        for data to be available in the protocol from
+        :py:obj:`opentrons.protocol_api.ProtocolContext.bundled_data`.
     :param extra_labware: A mapping from labware load names to custom labware definitions.
-                          If this is ``None`` (the default), and this function is called on a robot,
-                          it will look for labware in the ``labware`` subdirectory of the Jupyter
-                          data directory.
+        If this is ``None`` (the default), and this function is called on a robot,
+        it will look for labware in the ``labware`` subdirectory of the Jupyter
+        data directory.
     :return: The protocol context.
     """
     if isinstance(version, str):
@@ -313,18 +313,18 @@ def execute(
 
     :param protocol_file: The protocol file to execute
     :param protocol_name: The name of the protocol file. This is required
-                          internally, but it may not be a thing we can get
-                          from the protocol_file argument.
+        internally, but it may not be a thing we can get
+        from the ``protocol_file`` argument.
     :param propagate_logs: Whether this function should allow logs from the
-                           Opentrons stack to propagate up to the root handler.
-                           This can be useful if you're integrating this
-                           function in a larger application, but most logs that
-                           occur during protocol simulation are best associated
-                           with the actions in the protocol that cause them.
-                           Default: ``False``
+        Opentrons stack to propagate up to the root handler.
+        This can be useful if you're integrating this
+        function in a larger application, but most logs that
+        occur during protocol simulation are best associated
+        with the actions in the protocol that cause them.
+        Default: ``False``
     :param log_level: The level of logs to emit on the command line:
-                      ``"debug"``, ``"info"``, ``"warning"``, or ``"error"``.
-                      Defaults to ``"warning"``.
+        ``"debug"``, ``"info"``, ``"warning"``, or ``"error"``.
+        Defaults to ``"warning"``.
     :param emit_runlog: A callback for printing the run log. If specified, this
         will be called whenever a command adds an entry to the
         run log, which can be used for display and progress
@@ -353,17 +353,17 @@ def execute(
           ``KeyError``.
 
     :param custom_labware_paths: A list of directories to search for custom labware.
-                                 Loads valid labware from these paths and makes them available
-                                 to the protocol context. If this is ``None`` (the default), and
-                                 this function is called on a robot, it will look in the ``labware``
-                                 subdirectory of the Jupyter data directory.
+        Loads valid labware from these paths and makes them available
+        to the protocol context. If this is ``None`` (the default), and
+        this function is called on a robot, it will look in the ``labware``
+        subdirectory of the Jupyter data directory.
     :param custom_data_paths: A list of directories or files to load custom
-                              data files from. Ignored if the apiv2 feature
-                              flag if not set. Entries may be either files or
-                              directories. Specified files and the
-                              non-recursive contents of specified directories
-                              are presented by the protocol context in
-                              ``ProtocolContext.bundled_data``.
+        data files from. Ignored if the apiv2 feature
+        flag if not set. Entries may be either files or
+        directories. Specified files and the
+        non-recursive contents of specified directories
+        are presented by the protocol context in
+        ``ProtocolContext.bundled_data``.
     """
     stack_logger = logging.getLogger("opentrons")
     stack_logger.propagate = propagate_logs
@@ -457,10 +457,10 @@ def main() -> int:
     """Handler for command line invocation to run a protocol.
 
     :param argv: The arguments the program was invoked with; this is usually
-                 :py:obj:`sys.argv` but if you want to override that you can.
+        :py:obj:`sys.argv` but if you want to override that you can.
     :returns int: A success or failure value suitable for use as a shell
-                  return code passed to :py:obj:`sys.exit` (0 means success,
-                  anything else is a kind of failure).
+        return code passed to :py:obj:`sys.exit` (0 means success,
+        anything else is a kind of failure).
     """
     parser = argparse.ArgumentParser(
         prog="opentrons_execute", description="Run an OT-2 protocol"

api/src/opentrons/protocol_api/__init__.py

@@ -12,6 +12,7 @@
 from opentrons.protocols.parameters.exceptions import (
     RuntimeParameterRequired as RuntimeParameterRequiredError,
 )
+from opentrons.protocols.parameters.csv_parameter_interface import CSVParameter
 
 from .protocol_context import ProtocolContext
 from .deck import Deck
@@ -74,6 +75,7 @@
     "ALL",
     "OFF_DECK",
     "RuntimeParameterRequiredError",
+    "CSVParameter",
     # For internal Opentrons use only:
     "create_protocol_context",
     "ProtocolEngineCoreRequiredError",

api/src/opentrons/protocol_api/_parameter_context.py

@@ -1,8 +1,8 @@
 """Parameter context for python protocols."""
-
 from typing import List, Optional, Union, Dict
 
 from opentrons.protocols.api_support.types import APIVersion
+from opentrons.protocols.api_support.util import requires_version
 from opentrons.protocols.parameters import (
     parameter_definition,
     csv_parameter_definition,
@@ -19,7 +19,7 @@
 from opentrons.protocol_engine.types import (
     RunTimeParameter,
     PrimitiveRunTimeParamValuesType,
-    CSVRunTimeParamFilesType,
+    CSVRuntimeParamPaths,
     FileInfo,
 )
 
@@ -169,6 +169,7 @@ def add_str(
         )
         self._parameters[parameter.variable_name] = parameter
 
+    @requires_version(2, 20)
     def add_csv_file(
         self,
         display_name: str,
@@ -218,15 +219,15 @@ def set_parameters(
                 parameter.value = validated_value
 
     def initialize_csv_files(
-        self, run_time_param_file_overrides: CSVRunTimeParamFilesType
+        self, run_time_param_file_overrides: CSVRuntimeParamPaths
     ) -> None:
         """Initializes the files for CSV parameters.
 
         :meta private:
 
         This is intended for Opentrons internal use only and is not a guaranteed API.
         """
-        for variable_name, file_id in run_time_param_file_overrides.items():
+        for variable_name, file_path in run_time_param_file_overrides.items():
             try:
                 parameter = self._parameters[variable_name]
             except KeyError:
@@ -241,10 +242,12 @@ def initialize_csv_files(
                     f" but '{variable_name}' is not a CSV parameter."
                 )
 
-            parameter.file_info = FileInfo(id=file_id, name="")
-            # TODO (spp, 2024-07-16): set the file name and assign the file as parameter.value.
-            #  Most likely, we will be creating a temporary file copy of the original
-            #  to pass onto the protocol context
+            # The parent folder in the path will be the file ID, so we can use that to resolve that here
+            file_id = file_path.parent.name
+            file_name = file_path.name
+
+            parameter.file_info = FileInfo(id=file_id, name=file_name)
+            parameter.value = file_path
 
     def export_parameters_for_analysis(self) -> List[RunTimeParameter]:
         """Exports all parameters into a protocol engine models for reporting in analysis.
@@ -269,7 +272,7 @@ def export_parameters_for_protocol(self) -> Parameters:
         for parameter in self._parameters.values():
             value: UserFacingTypes
             if isinstance(parameter, csv_parameter_definition.CSVParameterDefinition):
-                value = parameter.as_csv_parameter_interface()
+                value = parameter.as_csv_parameter_interface(self._api_version)
             else:
                 value = parameter.value
             parameters_for_protocol[parameter.variable_name] = value

api/src/opentrons/protocol_api/protocol_context.py

@@ -87,6 +87,16 @@
 ]
 
 
+class _Unset:
+    """A sentinel value for when no value has been supplied for an argument,
+    when `None` is already taken for some other meaning.
+
+    User code should never use this explicitly.
+    """
+
+    pass
+
+
 class ProtocolContext(CommandPublisher):
     """A context for the state of a protocol.
 
@@ -1197,17 +1207,54 @@ def set_rail_lights(self, on: bool) -> None:
 
     @requires_version(2, 14)
     def define_liquid(
-        self, name: str, description: Optional[str], display_color: Optional[str]
+        self,
+        name: str,
+        description: Union[str, None, _Unset] = _Unset(),
+        display_color: Union[str, None, _Unset] = _Unset(),
     ) -> Liquid:
+        # This first line of the docstring overrides the method signature in our public
+        # docs, which would otherwise have the `_Unset()`s expanded to a bunch of junk.
         """
+        define_liquid(self, name: str, description: Optional[str] = None, display_color: Optional[str] = None)
+
         Define a liquid within a protocol.
 
         :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.
+        :param Optional[str] description: An optional description of the liquid.
+        :param Optional[str] display_color: An optional hex color code, with hash included,
+            to represent the specified liquid. For example, ``"#48B1FA"``.
+            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.
+
+        .. versionchanged:: 2.20
+            You can now omit the ``description`` and ``display_color`` arguments.
+            Formerly, when you didn't want to provide values, you had to supply
+            ``description=None`` and ``display_color=None`` explicitly.
         """
+        desc_and_display_color_omittable_since = APIVersion(2, 20)
+        if isinstance(description, _Unset):
+            if self._api_version < desc_and_display_color_omittable_since:
+                raise APIVersionError(
+                    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`.",
+                )
+            else:
+                description = None
+        if isinstance(display_color, _Unset):
+            if self._api_version < desc_and_display_color_omittable_since:
+                raise APIVersionError(
+                    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`.",
+                )
+            else:
+                display_color = None
+
         return self._core.define_liquid(
             name=name,
             description=description,