@opentrons/shared-data 0.1.7-alpha.0 → 0.2.0-alpha.0

package/.coveragerc

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

package/.flake8

@@ -0,0 +1,31 @@
+[flake8]
+
+extend-exclude = venv .venv
+
+# 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
+
+per-file-ignores =
+    python/opentrons_shared_data/load.py:D
+    python/opentrons_shared_data/deck/*:D
+    python/opentrons_shared_data/labware/*:D
+    python/opentrons_shared_data/module/*:D
+    python/opentrons_shared_data/pipette/*:D
+    python/opentrons_shared_data/protocol/*:D
+    python_tests/*:ANN,D

package/Config.in

@@ -0,0 +1,11 @@
+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
+  select BR2_PACKAGE_PYTHON_NUMPY # runtime
+
+  help
+    Opentrons data sources. Used on an OT-2 robot.
+
+    https://opentrons.com

package/LICENSE

@@ -0,0 +1,202 @@
+
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package/Makefile

@@ -65,51 +65,51 @@ lint-js-prettier:
 
 .PHONY: setup-py
 setup-py:
-	$(MAKE) -C python setup-py
+	$(MAKE) -f Makefile-python.mk setup-py
 
 .PHONY: dist-py
 dist-py:
-	$(MAKE) -C python sdist wheel
+	$(MAKE) -f Makefile-python.mk sdist wheel
 
 .PHONY: clean-py
 clean-py:
-	$(MAKE) -C python clean
+	$(MAKE) -f Makefile-python.mk clean
 
 .PHONY: teardown-py
 teardown-py:
-	$(MAKE) -C python teardown
+	$(MAKE) -f Makefile-python.mk teardown
 
 .PHONY: lint-py
 lint-py:
-	$(MAKE) -C python lint
+	$(MAKE) -f Makefile-python.mk lint
 
 .PHONY: format-py
 format-py:
-	$(MAKE) -C python format
+	$(MAKE) -f Makefile-python.mk format
 
 .PHONY: push-no-restart
 push-no-restart:
-	$(MAKE) -C python push-no-restart
+	$(MAKE) -f Makefile-python.mk push-no-restart
 
 .PHONY: push
 push:
-	$(MAKE) -C python push
+	$(MAKE) -f Makefile-python.mk push
 
 .PHONY: push-no-restart-ot3
 push-no-restart-ot3:
-	$(MAKE) -C python push-no-restart-ot3
+	$(MAKE) -f Makefile-python.mk push-no-restart-ot3
 
 .PHONY: push-ot3
 push-ot3:
-	$(MAKE) -C python push-ot3
+	$(MAKE) -f Makefile-python.mk push-ot3
 
 .PHONY: deploy-py
 deploy-py:
-	$(MAKE) -C python deploy
+	$(MAKE) -f Makefile-python.mk deploy
 
 .PHONY: test-py
 test-py:
-	$(MAKE) -C python test
+	$(MAKE) -f Makefile-python.mk test
 
 .PHONY: test
 test:
@@ -117,5 +117,4 @@ test:
 
 .PHONY: test-cov
 test-cov:
-	make -C .. test-js-shared-data tests=$(tests) test_opts="$(test_opts)" cov_opts="$(cov_opts)"
-
+	$(MAKE) -C .. test-js-shared-data tests=$(tests) test_opts="$(test_opts)" cov_opts="$(cov_opts)"

package/Makefile-python.mk

@@ -0,0 +1,134 @@
+# shared-data python code 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 ?=
+
+# 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,$(PROJECT),opentrons_shared_data,$(BUILD_NUMBER),../scripts/python_build_utils.py)
+sdist_file = $(BUILD_DIR)/$(call python_get_sdistname,shared-data,$(PROJECT),opentrons_shared_data,,../scripts/python_build_utils.py)
+
+py_sources = $(filter %.py,$(shell $(SHX) find python/opentrons_shared_data)) python/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 ?= python_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'
+clean_cache_cmd	 = $(SHX) rm -rf '**/__pycache__' '**/*.pyc' '**/.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)
+	$(clean_cache_cmd)
+
+.PHONY: wheel
+wheel: export OPENTRONS_PROJECT=$(PROJECT)
+wheel: export HATCH_VCS_TUNABLE_TAG_PATTERN=$(call git_tag_regex_for_project,$(PROJECT))
+wheel: export HATCH_VCS_TUNABLE_RAW_OPTIONS=$(call hatch_raw_options_for_project,$(PROJECT))
+wheel: $(py_sources) $(json_sources)
+	$(python) -m build --wheel $(build_wheel_opts) .
+	$(SHX) ls $(BUILD_DIR)
+
+
+.PHONY: sdist
+sdist: export OPENTRONS_PROJECT=$(PROJECT)
+sdist: export HATCH_VCS_TUNABLE_TAG_PATTERN=$(call git_tag_regex_for_project,$(PROJECT))
+sdist: export HATCH_VCS_TUNABLE_RAW_OPTIONS=$(call hatch_raw_options_for_project,$(PROJECT))
+sdist: $(py_sources) $(json_sources)
+	$(python) -m build --sdist .
+	$(SHX) ls $(BUILD_DIR)
+
+
+.PHONY: lint
+lint: $(py_sources)
+	$(python) -m mypy python/opentrons_shared_data python_tests
+	$(python) -m black --check python/opentrons_shared_data python_tests
+	$(python) -m flake8 python/opentrons_shared_data python_tests
+
+.PHONY: format
+format:
+	$(python) -m black python/opentrons_shared_data python_tests
+
+.PHONY: push-no-restart
+push-no-restart: wheel
+	$(call push-python,$(host),$(ssh_key),$(ssh_opts),$(wheel_file),/usr/lib/python3.10/site-packages/)
+
+.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: wheel
+	$(call push-python,$(host),$(ssh_key),$(ssh_opts),$(wheel_file),/opt/opentrons-robot-server/)
+
+.PHONY: push-ot3
+push-ot3: push-no-restart-ot3
+	$(call restart-service,$(host),$(ssh_key),$(ssh_opts),"opentrons-robot-server")
+
+.PHONY: deploy
+deploy: wheel sdist
+	$(call python_upload_package,$(twine_auth_args),$(twine_repository_url),$(wheel_file),$(sdist_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/buildroot.mk

@@ -0,0 +1,35 @@
+################################################################################
+#
+# python-opentrons-shared-data
+#
+################################################################################
+include $(BR2_EXTERNAL_OPENTRONS_MONOREPO_PATH)/scripts/python.mk
+
+define OTSHAREDDATA_CALL_PBU
+	$(shell python $(BR2_EXTERNAL_OPENTRONS_MONOREPO_PATH)/scripts/python_build_utils.py shared-data $(or $(OPENTRONS_PROJECT),robot-stack) $(1))
+endef
+
+PYTHON_OPENTRONS_SHARED_DATA_VERSION = $(call OTSHAREDDATA_CALL_PBU,get_version)
+PYTHON_OPENTRONS_SHARED_DATA_LICENSE = Apache-2
+PYTHON_OPENTRONS_SHARED_DATA_LICENSE_FILES = $(BR2_EXTERNAL_OPENTRONS_MONOREPO_PATH)/LICENSE
+PYTHON_OPENTRONS_SHARED_DATA_SETUP_TYPE = hatch
+PYTHON_OPENTRONS_SHARED_DATA_SITE_METHOD = local
+PYTHON_OPENTRONS_SHARED_DATA_SITE = $(BR2_EXTERNAL_OPENTRONS_MONOREPO_PATH)
+PYTHON_OPENTRONS_SHARED_DATA_DEPENDENCIES = host-python-hatch-vcs host-python-hatch-vcs-tunable
+PYTHON_OPENTRONS_SHARED_DATA_SUBDIR = shared-data
+PYTHON_OPENTRONS_SHARED_DATA_ENV = \
+  HATCH_VCS_TUNABLE_TAG_PATTERN="$(call git_tag_regex_for_project,$(PROJECT))" \
+  HATCH_VCS_TUNABLE_RAW_OPTIONS="$(call hatch_raw_options_for_project,$(PROJECT));root=$(shell realpath --relative-to=$(PYTHON_OPENTRONS_SHARED_DATA_BUILDDIR) $(BR2_EXTERNAL_OPENTRONS_MONOREPO_PATH))"
+
+define PYTHON_OPENTRONS_SHARED_DATA_INSTALL_VERSION
+	echo '$(call OTSHAREDDATA_CALL_PBU,dump_br_version)' > $(BINARIES_DIR)/opentrons-shared-data-version.json
+endef
+
+ot_sd_name := python-opentrons-shared-data
+
+export OPENTRONS_GIT_DIR=$(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
+# having the directory name be the package name
+$(eval $(call inner-python-package,$(ot_sd_name),$(call UPPERCASE,$(ot_sd_name)),$(call UPPERCASE,$(ot_sd_name)),target))

package/command/index.ts

@@ -2,7 +2,21 @@ import commandSchemaV7 from './schemas/7.json'
 import commandSchemaV8 from './schemas/8.json'
 import commandSchemaV9 from './schemas/9.json'
 import commandSchemaV10 from './schemas/10.json'
+import commandSchemaV11 from './schemas/11.json'
+import commandSchemaV12 from './schemas/12.json'
+import commandSchemaV13 from './schemas/13.json'
+import commandSchemaV14 from './schemas/14.json'
+
 export * from './types/index'
-export const commandSchemaLatest = commandSchemaV10
+export const commandSchemaLatest = commandSchemaV14
 
-export { commandSchemaV7, commandSchemaV8, commandSchemaV9, commandSchemaV10 }
+export {
+  commandSchemaV7,
+  commandSchemaV8,
+  commandSchemaV9,
+  commandSchemaV10,
+  commandSchemaV11,
+  commandSchemaV12,
+  commandSchemaV13,
+  commandSchemaV14,
+}

package/command/schemas/12.json

@@ -5755,6 +5755,67 @@
       "title": "UnsafeEngageAxesParams",
       "type": "object"
     },
+    "UnsafeManualRetrieveCreate": {
+      "description": "A request to execute a Flex Stacker manual retrieve command.",
+      "properties": {
+        "commandType": {
+          "const": "unsafe/manualRetrieve",
+          "default": "unsafe/manualRetrieve",
+          "enum": ["unsafe/manualRetrieve"],
+          "title": "Commandtype",
+          "type": "string"
+        },
+        "intent": {
+          "$ref": "#/$defs/CommandIntent",
+          "description": "The reason the command was added. If not specified or `protocol`, the command will be treated as part of the protocol run itself, and added to the end of the existing command queue.\n\nIf `setup`, the command will be treated as part of run setup. A setup command may only be enqueued if the run has not started.\n\nUse setup commands for activities like pre-run calibration checks and module setup, like pre-heating.",
+          "title": "Intent"
+        },
+        "key": {
+          "description": "A key value, unique in this run, that can be used to track the same logical command across multiple runs of the same protocol. If a value is not provided, one will be generated.",
+          "title": "Key",
+          "type": "string"
+        },
+        "params": {
+          "$ref": "#/$defs/UnsafeManualRetrieveParams"
+        }
+      },
+      "required": ["params"],
+      "title": "UnsafeManualRetrieveCreate",
+      "type": "object"
+    },
+    "UnsafeManualRetrieveParams": {
+      "description": "Input parameters for a labware retrieval command.",
+      "properties": {
+        "adapterId": {
+          "description": "An optional ID to assign to an adapter. If None, an ID will be generated.",
+          "title": "Adapterid",
+          "type": "string"
+        },
+        "displayName": {
+          "description": "An optional user-specified display name or label for this labware.",
+          "title": "Displayname",
+          "type": "string"
+        },
+        "labwareId": {
+          "description": "An optional ID to assign to this labware. If None, an ID will be generated.",
+          "title": "Labwareid",
+          "type": "string"
+        },
+        "lidId": {
+          "description": "An optional ID to assign to a lid. If None, an ID will be generated.",
+          "title": "Lidid",
+          "type": "string"
+        },
+        "moduleId": {
+          "description": "Unique ID of the Flex Stacker.",
+          "title": "Moduleid",
+          "type": "string"
+        }
+      },
+      "required": ["moduleId"],
+      "title": "UnsafeManualRetrieveParams",
+      "type": "object"
+    },
     "UnsafePlaceLabwareCreate": {
       "description": "UnsafePlaceLabware command request model.",
       "properties": {
@@ -6749,6 +6810,7 @@
       "unsafe/blowOutInPlace": "#/$defs/UnsafeBlowOutInPlaceCreate",
       "unsafe/dropTipInPlace": "#/$defs/UnsafeDropTipInPlaceCreate",
       "unsafe/engageAxes": "#/$defs/UnsafeEngageAxesCreate",
+      "unsafe/manualRetrieve": "#/$defs/UnsafeManualRetrieveCreate",
       "unsafe/placeLabware": "#/$defs/UnsafePlaceLabwareCreate",
       "unsafe/ungripLabware": "#/$defs/UnsafeUngripLabwareCreate",
       "unsafe/updatePositionEstimators": "#/$defs/UpdatePositionEstimatorsCreate",
@@ -7033,6 +7095,9 @@
     {
       "$ref": "#/$defs/UnsafePlaceLabwareCreate"
     },
+    {
+      "$ref": "#/$defs/UnsafeManualRetrieveCreate"
+    },
     {
       "$ref": "#/$defs/MoveAxesRelativeCreate"
     },