squashed more commits

Author: neo-jesse

.github/actions/python/install-uv/action.yaml

@@ -62,7 +62,7 @@ runs:
         python -m pip install --user virtualenv==20.30.0
     - name: Install UV
       if: steps.project-type.outputs.type == 'uv'
-      uses: ./.github/actions/python/install-uv
+      uses: astral-sh/setup-uv@v7
     - name: Cache UV packages
       if: steps.project-type.outputs.type == 'uv'
       uses: ./.github/actions/python/cache-uv
@@ -84,12 +84,8 @@ runs:
             DEV_EXTRA="--extra dev"
           fi
           if [ -f "${{ inputs.project }}/uv.lock" ]; then
-            # Use --frozen only if no extras are requested (extras may not be in lockfile)
-            if [ -z "$DEV_EXTRA" ]; then
-              cd ${{ inputs.project }} && uv sync --frozen
-            else
-              cd ${{ inputs.project }} && uv sync $DEV_EXTRA
-            fi
+            # Use --frozen to ensure exact versions from lockfile
+            cd ${{ inputs.project }} && uv sync --frozen $DEV_EXTRA
             # Verify dev dependencies are installed if dev extra was used
             if [ -n "$DEV_EXTRA" ]; then
               echo "::notice::Verifying dev dependencies are installed..."

.github/actions/python/setup/action.yaml

@@ -121,11 +121,7 @@ jobs:
         name: Test with opentrons_hardware
         run: make -C api test-cov
       - name: Ensure assets build
-        run: |
-          # Ensure uv is in PATH (should already be there from setup action via $GITHUB_PATH)
-          # On Windows, $HOME maps to the user profile, so this works cross-platform
-          export PATH="$HOME/.cargo/bin:$PATH"
-          make -C api sdist wheel
+        run: make -C api sdist wheel
       - name: Upload coverage report
         uses: 'codecov/codecov-action@v3'
         with:
@@ -147,7 +143,7 @@ jobs:
           git fetch -f origin ${{ github.ref }}:${{ github.ref }}
           git checkout ${{ github.ref }}
       - name: Install UV
-        uses: ./.github/actions/python/install-uv
+        uses: astral-sh/setup-uv@v7
       - uses: 'actions/setup-python@v4'
         with:
           python-version: '3.10'

.github/workflows/api-test-lint-deploy.yaml

@@ -102,16 +102,9 @@ jobs:
             const { buildComplexEnvVars, } = require(`${process.env.GITHUB_WORKSPACE}/.github/workflows/utils.js`)
             buildComplexEnvVars(core, context)
       - name: Test
-        run: |
-          # Ensure uv is in PATH (should already be there from setup action via $GITHUB_PATH)
-          # On Windows, $HOME maps to the user profile, so this works cross-platform
-          export PATH="$HOME/.cargo/bin:$PATH"
-          make -C shared-data test-py
+        run: make -C shared-data test-py
       - name: Ensure assets build
-        run: |
-          # Ensure uv is in PATH (should already be there from setup action via $GITHUB_PATH)
-          export PATH="$HOME/.cargo/bin:$PATH"
-          make -C shared-data dist-py
+        run: make -C shared-data dist-py
       - name: 'Upload coverage report'
         uses: codecov/codecov-action@v3
         with:

.github/workflows/shared-data-test-lint-deploy.yaml

@@ -61,41 +61,27 @@ clean_all_cmd = $(clean_cmd) dist
 
 plot_type ?=
 
+define uv_sync_dev
+	if [ -f uv.lock ]; then \
+		uv sync --frozen --extra dev; \
+	else \
+		uv sync --extra dev; \
+	fi
+endef
+
 .PHONY: all
 all: clean wheel
 
 .PHONY: setup
 setup:
-	@UNAME_S=$$(uname -s 2>/dev/null || echo ""); \
-	LINUX_EXTRA=""; \
-	if echo "$$UNAME_S" | grep -qi linux; then \
-		if [ -f pyproject.toml ] && grep -q '\[project.optional-dependencies\]' pyproject.toml 2>/dev/null && grep -A 10 '\[project.optional-dependencies\]' pyproject.toml 2>/dev/null | grep -q 'linux'; then \
-			LINUX_EXTRA="--extra linux"; \
-		fi; \
-	fi; \
-	if [ -f uv.lock ]; then \
-		uv sync --frozen --extra dev $$LINUX_EXTRA; \
-	else \
-		uv sync --extra dev $$LINUX_EXTRA; \
-	fi; \
-	uv pip list
+	@$(uv_sync_dev)
+	@uv pip list
 
 .PHONY: setup-ot2
 setup-ot2:
-	@UNAME_S=$$(uname -s 2>/dev/null || echo ""); \
-	LINUX_EXTRA=""; \
-	if echo "$$UNAME_S" | grep -qi linux; then \
-		if [ -f pyproject.toml ] && grep -q '\[project.optional-dependencies\]' pyproject.toml 2>/dev/null && grep -A 10 '\[project.optional-dependencies\]' pyproject.toml 2>/dev/null | grep -q 'linux'; then \
-			LINUX_EXTRA="--extra linux"; \
-		fi; \
-	fi; \
-	if [ -f uv.lock ]; then \
-		uv sync --frozen --extra dev $$LINUX_EXTRA; \
-	else \
-		uv sync --extra dev $$LINUX_EXTRA; \
-	fi; \
-	uv pip uninstall python-can -y; \
-	uv pip list
+	@$(uv_sync_dev)
+	@uv pip uninstall python-can
+	@uv pip list
 
 .PHONY: clean
 clean: docs-clean
@@ -104,7 +90,7 @@ clean: docs-clean
 
 .PHONY: teardown
 teardown:
-	rm -rf .venv
+	$(UV) venv --remove
 
 .PHONY: wheel
 wheel: export OPENTRONS_PROJECT=$(PROJECT)
@@ -147,7 +133,7 @@ test-ot2:
 	$(pytest) -m 'not ot3_only' $(tests) $(test_opts) --ot2-only --ignore-glob="**/*ot3*"
 
 .PHONY: lint
-lint:
+lint: setup
 	$(python) -m mypy src tests integration_testing
 	$(python) -m black --check src tests integration_testing docs/v2/example_protocols
 	$(python) -m flake8 src tests integration_testing
@@ -193,7 +179,7 @@ dev:
 
 .PHONY: local-shell
 local-shell:
-	uv run bash
+	$(UV) run $(SHELL)
 
 .PHONY: push-no-restart
 push-no-restart: wheel

abr-testing/Pipfile.lock

@@ -12,20 +12,4 @@ init_typed = True
 warn_required_dynamic_aliases = True
 warn_untyped_fields = True
 
-# Ignore optional/local packages that may not be installed
-[mypy-opentrons_hardware.*]
-ignore_missing_imports = True
-
-[mypy-performance_metrics.*]
-ignore_missing_imports = True
-
-# Test-only dependencies that may not have type stubs
-[mypy-pytest_lazy_fixtures.*]
-ignore_missing_imports = True
-
-[mypy-hypothesis]
-ignore_missing_imports = True
-
-[mypy-hypothesis.*]
-ignore_missing_imports = True
 

api/Makefile

@@ -19,27 +19,26 @@ description = "The Opentrons API is a simple framework designed to make writing
 
 dependencies = [
    "opentrons-shared-data==0.0.0",
-    "aionotify==0.3.1",
-    "anyio==4.9.0",
-    "jsonschema==4.21.1",
-    "numpy==1.22.3",
-    "pydantic==2.11.7",
-    "pydantic-settings==2.4.0",
+    "aionotify~=0.3.1",
+    "anyio~=4.9.0",
+    "jsonschema~=4.17.3",
+    "numpy~=1.22.3",
+    "pydantic~=2.11.7",
+    "pydantic-settings~=2.4.0",
     "pyserial>=3.5",
     "typing-extensions>=4.0.0,<5",
     "click>=8.0.0,<9",
-    "pyusb==1.2.1",
+    "pyusb~=1.2.1",
     'importlib-metadata >= 1.0 ; python_version < "3.8"',
-    "packaging==22.0",
-    "referencing==0.37.0",
+    "packaging~=22.0",
 ]
 
 dynamic = ['version', 'hatch-dependency-coversion']
 
 [project.optional-dependencies]
 # Robot dependencies - exact versions from Pipfile [packages] for robot deployment
 robot = [
-    "jsonschema==4.21.1",
+    "jsonschema==4.17.3",
     "pydantic==2.11.7",
     "pydantic-settings==2.4.0",
     "anyio==4.9.0",
@@ -83,6 +82,9 @@ dev = [
     "build~=1.2.0",
     # opentrons-hardware is needed for tests but not for package installation
     "opentrons-hardware[FLEX]==0.0.0",
+    # performance_metrics is needed for type checking (used in TYPE_CHECKING blocks)
+    # even though it's optional at runtime
+    "performance_metrics==0.0.0",
 ]
 "ot2-hardware" = ["opentrons-hardware==0.0.0"]
 "flex-hardware" = ["opentrons-hardware[FLEX]==0.0.0"]

api/mypy.ini

@@ -7,8 +7,6 @@
 from typing import Mapping, Optional, Union, List, Sequence, Literal
 
 import jsonschema  # type: ignore
-from referencing import Registry, Resource
-from referencing.jsonschema import DRAFT7
 
 from opentrons_shared_data import load_shared_data, get_shared_data_root
 from opentrons.protocols.api_support.util import ModifiedList
@@ -187,17 +185,7 @@ def verify_definition(  # noqa: C901
         raise NotALabwareError("bad-schema-id", [e]) from e
 
     try:
-        # Use referencing library for JSON pointer resolution
-        # Labware schemas contain JSON pointer references like #/definitions/vector
-        schema_id = schema.get("$id", "") if isinstance(schema, dict) else ""
-        registry = Registry()
-        if schema_id:
-            registry = registry.with_resource(
-                schema_id,
-                Resource.from_contents(schema, default_specification=DRAFT7),
-            )
-        validator = jsonschema.Draft7Validator(schema, registry=registry)
-        validator.validate(parsed_json)
+        jsonschema.validate(parsed_json, schema)
     except jsonschema.ValidationError as e:
         raise NotALabwareError("schema-mismatch", [e]) from e
 

api/pyproject.toml

@@ -15,8 +15,6 @@
 from typing import Any, Dict, Optional, Union, Tuple, TYPE_CHECKING
 
 import jsonschema  # type: ignore
-from referencing import Registry, Resource
-from referencing.jsonschema import DRAFT7
 
 from opentrons_shared_data.labware import load_schema as load_labware_schema
 from opentrons_shared_data.protocol import (
@@ -628,14 +626,7 @@ def validate_json(protocol_json: Dict[Any, Any]) -> Tuple[int, "JsonProtocolDef"
     # Check if this is actually a labware
     labware_schema_v2 = load_labware_schema()
     try:
-        # Use referencing library for JSON pointer resolution
-        # Labware schemas contain JSON pointer references like #/definitions/vector
-        labware_registry = Registry().with_resource(
-            labware_schema_v2.get("$id", "labware_schema"),
-            Resource.from_contents(labware_schema_v2, default_specification=DRAFT7),
-        )
-        validator = jsonschema.Draft7Validator(labware_schema_v2, registry=labware_registry)
-        validator.validate(protocol_json)
+        jsonschema.validate(protocol_json, labware_schema_v2)
     except jsonschema.ValidationError:
         pass
     else:
@@ -660,29 +651,16 @@ def validate_json(protocol_json: Dict[Any, Any]) -> Tuple[int, "JsonProtocolDef"
         raise JSONSchemaVersionTooNewError(attempted_schema_version=version_num)
     protocol_schema = _get_schema_for_protocol(version_num)
 
-    # Use referencing library for JSON pointer resolution
-    # Protocol schemas reference both same-document (#/definitions/slot) and
-    # cross-schema (opentronsLabwareSchemaV2) references.
-    # The referencing library handles both automatically when schemas are in the registry.
-    registry = Registry()
-    # Add labware schema for cross-schema references
-    labware_schema_id = labware_schema_v2.get("$id", "opentronsLabwareSchemaV2")
-    registry = registry.with_resource(
-        labware_schema_id,
-        Resource.from_contents(labware_schema_v2, default_specification=DRAFT7),
+    # instruct schema how to resolve all $ref's used in protocol schemas
+    resolver = jsonschema.RefResolver(
+        protocol_schema.get("$id", ""),
+        protocol_schema,
+        store={"opentronsLabwareSchemaV2": labware_schema_v2},
     )
-    # Add protocol schema to registry (needed for same-document and cross-schema refs)
-    protocol_schema_id = protocol_schema.get("$id", "")
-    if protocol_schema_id:
-        registry = registry.with_resource(
-            protocol_schema_id,
-            Resource.from_contents(protocol_schema, default_specification=DRAFT7),
-        )
 
-    # Validate using jsonschema with the referencing registry
+    # do the validation
     try:
-        validator = jsonschema.Draft7Validator(protocol_schema, registry=registry)
-        validator.validate(protocol_json)
+        jsonschema.validate(protocol_json, protocol_schema, resolver=resolver)
     except jsonschema.ValidationError:
         MODULE_LOG.exception("JSON protocol validation failed")
         raise RuntimeError(