@opentrons/shared-data 0.0.0-alpha.2

package/protocol/types/schemaV7/index.ts

@@ -0,0 +1,98 @@
+import { LoadedPipette, LoadedLabware, LoadedModule, Liquid } from '../../../js'
+import type { CreateCommand, RunTimeCommand } from './command'
+import type { LabwareDefinition2, RobotType } from '../../../js/types'
+
+export * from './command'
+
+// NOTE: must be kept in sync with '../schemas/7.json'
+export interface ProtocolFile<DesignerApplicationData = {}> {
+  $otSharedSchema: '#/protocol/schemas/7'
+  schemaVersion: 7
+  metadata: {
+    protocolName?: string
+    author?: string
+    description?: string | null | undefined
+    created?: number
+    lastModified?: number | null | undefined
+    category?: string | null | undefined
+    subcategory?: string | null | undefined
+    tags?: string[]
+  }
+  designerApplication?: {
+    name?: string
+    version?: string
+    data?: DesignerApplicationData
+  }
+  robot: {
+    model: 'OT-2 Standard' | 'OT-3 Standard'
+    deckId: 'ot2_standard' | 'ot2_short_trash' | 'ot3_standard'
+  }
+  labwareDefinitions: {
+    [definitionId: string]: LabwareDefinition2
+  }
+  liquids: {
+    [liquidId: string]: {
+      displayName: string
+      description: string
+      displayColor?: string
+    }
+  }
+  commands: CreateCommand[]
+  commandAnnotations?: {
+    commandIds: string[]
+    annotationType: string
+    params?: { [key: string]: any }
+  }
+}
+
+/**
+ * This type should not be used, any time you want a function/hook/component to take in
+ * a protocol file with run time commands, split your function signature to take in each param
+ * separately, and import the RunTimeCommand type separately. RunTimeCommand is a server concept
+ * and should not be mixed with our Protocol types
+ * @deprecated Use {@link ProtocolFile}
+ */
+export interface ProtocolAnalysisFile<DesignerApplicationData = {}>
+  extends Omit<ProtocolFile<DesignerApplicationData>, 'commands'> {
+  commands: RunTimeCommand[]
+}
+
+/**
+ * This type interface is represents the output of the opentrons analyze cli tool
+ * which contains the protocol analysis engine
+ * TODO: reconcile this type with that of the analysis returned from
+ * the protocols record endpoints on the robot-server
+ */
+export interface ProtocolAnalysisOutput {
+  createdAt: string
+  files: AnalysisSourceFile[]
+  config: JsonConfig | PythonConfig
+  metadata: { [key: string]: any }
+  commands: RunTimeCommand[]
+  labware: LoadedLabware[]
+  pipettes: LoadedPipette[]
+  modules: LoadedModule[]
+  liquids: Liquid[]
+  errors: AnalysisError[]
+  robotType?: RobotType
+}
+
+interface AnalysisSourceFile {
+  name: string
+  role: 'main' | 'labware'
+}
+export interface JsonConfig {
+  protocolType: 'json'
+  schemaVersion: number
+}
+export interface PythonConfig {
+  protocolType: 'python'
+  apiVersion: [major: number, minor: number]
+}
+
+interface AnalysisError {
+  id: string
+  errorType: string
+  createdAt: string
+  detail: string
+}

package/protocol/types/schemaV8/index.ts

@@ -0,0 +1,160 @@
+import type { CreateCommand } from '../../../command/types'
+import type {
+  LoadedPipette,
+  LoadedLabware,
+  LoadedModule,
+  Liquid,
+} from '../../../js'
+import type { CommandAnnotation } from '../../../commandAnnotation/types'
+import type { LabwareDefinition2, RobotType } from '../../../js/types'
+import type { RunTimeCommand } from '../schemaV8'
+
+export * from '../../../command/types'
+
+export interface CommandsStructure {
+  commandSchemaId: string
+  commands: any[]
+}
+
+export interface CommandV8Mixin {
+  commandSchemaId: 'opentronsCommandSchemaV8'
+  commands: CreateCommand[]
+}
+
+export interface CommandAnnotationsStructure {
+  commandAnnotationSchemaId: string
+  commandAnnotations: any[]
+}
+
+export interface CommandAnnotationV1Mixin {
+  commandAnnotationSchemaId: 'opentronsCommandAnnotationSchemaV1'
+  commandAnnotations: CommandAnnotation[]
+}
+
+export interface LabwareStructure {
+  labwareDefinitionSchemaId: string
+  labwareDefinitions: {
+    [definitionId: string]: any
+  }
+}
+
+export interface LabwareV2Mixin {
+  labwareDefinitionSchemaId: 'opentronsLabwareSchemaV2'
+  labwareDefinitions: {
+    [definitionId: string]: LabwareDefinition2
+  }
+}
+
+export interface LiquidStructure {
+  liquidSchemaId: string
+  liquids: {
+    [liquidId: string]: any
+  }
+}
+
+export interface LiquidV1Mixin {
+  liquidSchemaId: 'opentronsLiquidSchemaV1'
+  liquids: {
+    [liquidId: string]: {
+      displayName: string
+      description: string
+      displayColor?: string
+    }
+  }
+}
+
+export interface RobotStructure {
+  model: string
+  deckId: string
+}
+
+export interface OT2RobotMixin {
+  robot: {
+    model: 'OT-2 Standard'
+    deckId: 'ot2_standard' | 'ot2_short_trash'
+  }
+}
+
+export interface OT3RobotMixin {
+  robot: {
+    model: 'OT-3 Standard'
+    deckId: 'ot3_standard'
+  }
+}
+
+export interface ProtocolBase<DesignerApplicationData> {
+  $otSharedSchema: '#/protocol/schemas/8'
+  schemaVersion: 8
+  metadata: {
+    protocolName?: string
+    author?: string
+    description?: string | null | undefined
+    created?: number
+    lastModified?: number | null | undefined
+    category?: string | null | undefined
+    subcategory?: string | null | undefined
+    tags?: string[]
+  }
+  designerApplication?: {
+    name?: string
+    version?: string
+    data?: DesignerApplicationData
+  }
+}
+
+// NOTE: must be kept in sync with '../schemas/8.json'
+export type ProtocolFile<
+  DesignerApplicationData = {}
+> = ProtocolBase<DesignerApplicationData> &
+  (OT2RobotMixin | OT3RobotMixin) &
+  LabwareV2Mixin &
+  LiquidV1Mixin &
+  CommandV8Mixin &
+  CommandAnnotationV1Mixin
+
+export type ProtocolStructure = ProtocolBase<{}> &
+  RobotStructure &
+  LabwareStructure &
+  LiquidStructure &
+  CommandsStructure &
+  CommandAnnotationsStructure
+
+/**
+ * This type interface is represents the output of the opentrons analyze cli tool
+ * which contains the protocol analysis engine
+ * TODO: reconcile this type with that of the analysis returned from
+ * the protocols record endpoints on the robot-server
+ */
+export interface ProtocolAnalysisOutput {
+  createdAt: string
+  files: AnalysisSourceFile[]
+  config: JsonConfig | PythonConfig
+  metadata: { [key: string]: any }
+  commands: RunTimeCommand[]
+  labware: LoadedLabware[]
+  pipettes: LoadedPipette[]
+  modules: LoadedModule[]
+  liquids: Liquid[]
+  errors: AnalysisError[]
+  robotType?: RobotType
+}
+
+interface AnalysisSourceFile {
+  name: string
+  role: 'main' | 'labware'
+}
+export interface JsonConfig {
+  protocolType: 'json'
+  schemaVersion: number
+}
+export interface PythonConfig {
+  protocolType: 'python'
+  apiVersion: [major: number, minor: number]
+}
+
+interface AnalysisError {
+  id: string
+  errorType: string
+  createdAt: string
+  detail: string
+}

package/python/.coveragerc

@@ -0,0 +1,4 @@
+[report]
+exclude_lines =
+    @overload
+    if TYPE_CHECKING:

package/python/.flake8

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+[flake8]
+
+# max cyclomatic complexity
+max-complexity = 9
+
+extend-ignore =
+    # defer formatting concerns to black
+    # E203: space around `:` operator
+    # E501: maximum line length
+    E203,
+    E501,
+    # do not require type annotations for self nor cls
+    ANN101,
+    ANN102
+
+# configure flake8-docstrings
+# https://pypi.org/project/flake8-docstrings/
+docstring-convention = google
+
+noqa-require-code = true
+
+# TODO(mc, 2021-04-12): this config ignores type annotation and doc
+# string lints in these modules; remove entries as they are fixed
+per-file-ignores =
+    setup.py:ANN,D
+    opentrons_shared_data/load.py:ANN,D
+    opentrons_shared_data/deck/*:ANN,D
+    opentrons_shared_data/labware/*:ANN,D
+    opentrons_shared_data/module/*:ANN,D
+    opentrons_shared_data/pipette/*:ANN,D
+    opentrons_shared_data/protocol/*:ANN,D
+    tests/*:ANN,D

package/python/Config.in

@@ -0,0 +1,10 @@
+config BR2_PACKAGE_PYTHON_OPENTRONS_SHARED_DATA
+  bool "python-opentrons-shared-data"
+  depends on BR2_PACKAGE_PYTHON3
+  select BR2_PACKAGE_PYTHON_JSONSCHEMA # runtime
+  select BR2_PACKAGE_PYTHON_TYPING_EXTENSIONS # runtime
+
+  help
+    Opentrons data sources. Used on an OT-2 robot.
+
+    https://opentrons.com

package/python/Makefile

@@ -0,0 +1,134 @@
+# shared-data/python makefile
+
+include ../../scripts/python.mk
+include ../../scripts/push.mk
+
+# Host key location for robot
+ssh_key ?= $(default_ssh_key)
+# Other SSH args for robot
+ssh_opts ?= $(default_ssh_opts)
+
+# using bash instead of /bin/bash in SHELL prevents macOS optimizing away our PATH update
+SHELL := bash
+
+# add node_modules/.bin to PATH
+PATH := $(shell cd ../.. && yarn bin):$(PATH)
+
+# This may be set as an environment variable (and is by CI tasks that upload
+# to test pypi) to add a .dev extension to the python package versions. If
+# empty, no .dev extension is appended, so this definition is here only as
+# documentation
+BUILD_NUMBER ?=
+
+ot_project := $(OPENTRONS_PROJECT)
+project_rs_default = $(if $(ot_project),$(ot_project),robot-stack)
+project_ot3_default = $(if $(ot_project),$(ot_project),ot3)
+
+# this may be set as an environment variable to select the version of
+# python to run if pyenv is not available. it should always be set to
+# point to a python3.6.
+OT_PYTHON ?= python
+
+BUILD_DIR := dist
+
+
+wheel_file = $(BUILD_DIR)/$(call python_get_wheelname,shared-data,$(project_rs_default),opentrons_shared_data,$(BUILD_NUMBER),../../scripts/python_build_utils.py)
+sdist_file = $(BUILD_DIR)/$(call python_get_sdistname,shared-data,$(project_ot3_default),opentrons_shared_data,,../../scripts/python_build_utils.py)
+
+py_sources = $(filter %.py,$(shell $(SHX) find opentrons_shared_data)) opentrons_shared_data/py.typed
+deck_sources = $(wildcard ../deck/definitions/*/*.json) $(wildcard ../deck/schemas/*.json)
+labware_sources = $(wildcard ../labware/definitions/*/*.json) $(wildcard ../labware/schemas/*.json)
+module_sources = $(wildcard ../module/definitions/*.json) $(wildcard ../module/definitions/*/*.json) $(wildcard ../module/schemas/*.json)
+pipette_sources = $(wildcard ../pipette/definitions/*.json) $(wildcard ../pipette/schemas/*.json)
+protocol_sources = $(wildcard ../protocol/schemas/*.json)
+gripper_sources = $(wildcard ../gripper/definitions/*.json) $(wildcard ../gripper/schemas/*.json)
+
+json_sources = $(deck_sources) $(labware_sources) $(module_sources) $(pipette_sources) $(protocol_sources) $(gripper_sources)
+
+tests ?= tests
+
+twine_auth_args := --username $(pypi_username) --password $(pypi_password)
+twine_repository_url ?= $(pypi_test_upload_url)
+
+clean_cmd = $(SHX) rm -rf build $(BUILD_DIR) .coverage coverage.xml '*.egg-info' ' **/__pycache__' '**/*.pyc' 'opentrons_shared_data/**/.mypy_cache'
+
+.PHONY: all
+all: clean sdist wheel
+
+.PHONY: setup
+setup: setup-py
+
+.PHONY: setup-py
+setup-py:
+	$(pipenv) sync $(pipenv_opts)
+	$(pipenv) run pip freeze
+
+.PHONY: teardown
+teardown: teardown-py
+
+.PHONY: teardown-py
+teardown-py:
+	$(pipenv) --rm
+
+
+.PHONY: clean
+clean:
+	$(clean_cmd)
+
+.PHONY: wheel
+wheel: export OPENTRONS_PROJECT=$(project_rs_default)
+wheel: setup.py $(py_sources) $(json_sources)
+	$(SHX) mkdir -p build
+	$(python) setup.py $(wheel_opts) bdist_wheel
+	$(SHX) ls $(BUILD_DIR)
+
+
+.PHONY: sdist
+sdist: export OPENTRONS_PROJECT=$(project_ot3_default)
+sdist: setup.py $(py_sources) $(json_sources)
+	$(SHX) mkdir -p build
+	$(python) setup.py sdist
+	$(SHX) ls $(BUILD_DIR)
+
+
+.PHONY: lint
+lint: $(py_sources)
+	$(python) -m mypy opentrons_shared_data tests
+	$(python) -m black --check opentrons_shared_data tests setup.py
+	$(python) -m flake8 opentrons_shared_data tests setup.py
+
+.PHONY: format
+format:
+	$(python) -m black opentrons_shared_data tests setup.py
+
+.PHONY: push-no-restart
+push-no-restart: wheel
+	$(call push-python-package,$(host),$(ssh_key),$(ssh_opts),$(wheel_file))
+
+.PHONY: push
+push: push-no-restart
+	$(call restart-service,$(host),$(ssh_key),$(ssh_opts),opentrons-robot-server)
+
+.PHONY: push-no-restart-ot3
+push-no-restart-ot3: sdist
+	$(call push-python-sdist,$(host),$(ssh_key),$(ssh_opts),$(sdist_file),/opt/opentrons-robot-server,opentrons_shared_data)
+
+.PHONY: push-ot3
+push-ot3: push-no-restart-ot3
+	$(call restart-server,$(host),$(ssh_key),$(ssh_opts),opentrons-robot-server)
+
+.PHONY: deploy
+deploy: wheel
+	$(call python_upload_package,$(twine_auth_args),$(twine_repository_url),$(wheel_file))
+
+.PHONY: test
+test:
+	$(python) -m pytest --cov=opentrons_shared_data --cov-report xml:coverage.xml $(tests) $(test_opts)
+
+
+.PHONY: generate-schema
+generate-schema:
+	$(python) -c "from opentrons_shared_data.$(target) import generate_schema; print(generate_schema())" > ../${target}/schemas/${version}.json
+
+%-schema:
+	$(MAKE) generate-schema target=$*

package/python/Pipfile

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+[[source]]
+url = "https://pypi.python.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[dev-packages]
+mypy = "==0.800"
+flake8 = "~=3.9.0"
+flake8-annotations = "~=2.6.2"
+flake8-docstrings = "~=1.6.0"
+flake8-noqa = "~=1.2.1"
+twine = "==2.0.0"
+wheel = "==0.30.0"
+pytest = "==7.0.1"
+pytest-cov = "==2.10.1"
+pytest-xdist = "~=2.2.1 "
+typeguard = "~=2.13"
+# specify typing-extensions explicitly to force lockfile inclusion on Python >= 3.8
+typing-extensions = ">=4.0.0,<5"
+# pytest dependencies on windows, spec'd here to force lockfile inclusion
+# https://github.com/pypa/pipenv/issues/4408#issuecomment-668324177
+atomicwrites = { version = "==1.4.0", sys_platform = "== 'win32'" }
+colorama = { version = "==0.4.4", sys_platform = "== 'win32'" }
+black = "==22.3.0"
+pytest-clarity = "~=1.0.0"
+
+[packages]
+opentrons-shared-data = { editable = true, path = "." }