Modernize Makefile.

Replace tox-based lint target with direct uv run commands. Add E704
to flake8 ignores (black requires single-line overload stubs). Fix
import ordering in normalized models.

Include schema salad and schema-salad-plus-pydantic doc building in linting.

Update Makefile for testing and mypy also.

Author: jmchilton

.github/workflows/publishdocs.yml

@@ -21,7 +21,7 @@ jobs:
         python -m pip install -r requirements.txt -r dev-requirements.txt
     - name: Build docs
       run: |
-        SKIP_JAVA=1 SKIP_TYPESCRIPT=1 bash build_schema.sh
+        USE_VENV=0 SKIP_JAVA=1 SKIP_TYPESCRIPT=1 bash build_schema.sh
     - name: Deploy Docs
       if: github.event_name == 'push' && github.ref == 'refs/heads/main' && github.repository_owner == 'galaxyproject'
       uses: JamesIves/github-pages-deploy-action@releases/v4

Makefile

@@ -59,18 +59,19 @@ setup-git-hook-lint: ## setup precommit hook for linting project
 setup-git-hook-lint-and-test: ## setup precommit hook for linting and testing project
 	cp $(BUILD_SCRIPTS_DIR)/pre-commit-lint-and-test .git/hooks/pre-commit
 
-flake8: ## check style using flake8 for current Python (faster than lint)
-	$(IN_VENV) flake8 --max-complexity 11 $(SOURCE_DIR)  $(TEST_DIR)
-
-lint: ## check style using tox and flake8 for Python 2 and Python 3
-	$(IN_VENV) tox -e py36-lint && tox -e py39-lint
+lint: ## check style with ruff, flake8, black, and mypy
+	uv run --group lint ruff check
+	uv run --group lint flake8
+	uv run --group lint black --check --diff .
+	uv run --group mypy mypy gxformat2
+	SKIP_JAVA=1 SKIP_TYPESCRIPT=1 GXFORMAT2_SCHEMA_BUILD_DRY_RUN=1 bash build_schema.sh
 
 lint-docs: ready-docs
 	$(IN_VENV) $(MAKE) -C $(DOCS_DIR) clean
 	$(IN_VENV) $(MAKE) -C $(DOCS_DIR) html 2>&1 | python $(BUILD_SCRIPTS_DIR)/lint_sphinx_output.py
 
 test: ## run tests with the default Python (faster than tox)
-	$(IN_VENV) nosetests $(NOSE_TESTS)
+	uv run --group test pytest tests/
 
 tox: ## run tests with tox in the specified ENV
 	$(IN_VENV) tox -e $(ENV) -- $(ARGS)
@@ -127,4 +128,4 @@ format:
 	uv run --group lint black .
 
 mypy:
-	MYPYPATH=mypy-stubs mypy gxformat2
+	uv run --group mypy mypy gxformat2

build_schema.sh

@@ -4,6 +4,23 @@ set -x
 set -e
 
 PROJECT_DIRECTORY="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+USE_VENV=${USE_VENV:-"1"}
+if [ "$USE_VENV" != "0" ]; then
+    if [ -f "${PROJECT_DIRECTORY}/.venv/bin/activate" ]; then
+        source "${PROJECT_DIRECTORY}/.venv/bin/activate"
+    else
+        echo "ERROR: USE_VENV=${USE_VENV} but ${PROJECT_DIRECTORY}/.venv/bin/activate not found" >&2
+        exit 1
+    fi
+fi
+
+GXFORMAT2_SCHEMA_BUILD_DRY_RUN=${GXFORMAT2_SCHEMA_BUILD_DRY_RUN:-"0"}
+SCHEME_SOURCE_DIRECTORY="${PROJECT_DIRECTORY}/gxformat2/schema"
+if [ "${GXFORMAT2_SCHEMA_BUILD_DRY_RUN}" = "1" ]; then
+    SCHEME_SOURCE_DIRECTORY="$(mktemp -d -t gxformat2-schema.XXXXXX)"
+    echo "GXFORMAT2_SCHEMA_BUILD_DRY_RUN=1; writing generated schemas to ${SCHEME_SOURCE_DIRECTORY}" >&2
+fi
+mkdir -p "${SCHEME_SOURCE_DIRECTORY}"
 SKIP_JAVA=${SKIP_JAVA:-0}
 SKIP_TYPESCRIPT=${SKIP_TYPESCRIPT:-0}
 DIST_DIRECTORY="${PROJECT_DIRECTORY}/dist/schema"
@@ -17,7 +34,7 @@ for schema in "v19_09";
 do
     cd schema/"$schema";
     python_schema_name=${schema//./_}
-    schema-salad-tool --codegen python workflow.yml > "${PROJECT_DIRECTORY}/gxformat2/schema/${python_schema_name}.py"
+    schema-salad-tool --codegen python workflow.yml > "${SCHEME_SOURCE_DIRECTORY}/${python_schema_name}.py"
 
     out="${DIST_DIRECTORY}/${schema}.html"
     schema-salad-doc \
@@ -58,7 +75,7 @@ done
 
 # Native workflow format schema
 cd "${PROJECT_DIRECTORY}"/schema/native_v0_1
-schema-salad-tool --codegen python workflow.yml > "${PROJECT_DIRECTORY}/gxformat2/schema/native_v0_1.py"
+schema-salad-tool --codegen python workflow.yml > "${SCHEME_SOURCE_DIRECTORY}/native_v0_1.py"
 
 out="${DIST_DIRECTORY}/native_v0_1.html"
 schema-salad-doc \
@@ -76,10 +93,10 @@ schema-salad-doc \
 SKIP_PYDANTIC=${SKIP_PYDANTIC:-0}
 if [ $SKIP_PYDANTIC -eq 0 ]; then
     cd "${PROJECT_DIRECTORY}"
-    schema-salad-plus-pydantic generate schema/v19_09/workflow.yml -o gxformat2/schema/gxformat2.py
-    schema-salad-plus-pydantic generate schema/v19_09/workflow.yml --strict -o gxformat2/schema/gxformat2_strict.py
-    schema-salad-plus-pydantic generate schema/native_v0_1/workflow.yml -o gxformat2/schema/native.py
-    schema-salad-plus-pydantic generate schema/native_v0_1/workflow.yml --strict -o gxformat2/schema/native_strict.py
+    schema-salad-plus-pydantic generate schema/v19_09/workflow.yml -o "${SCHEME_SOURCE_DIRECTORY}/gxformat2.py"
+    schema-salad-plus-pydantic generate schema/v19_09/workflow.yml --strict -o "${SCHEME_SOURCE_DIRECTORY}/gxformat2_strict.py"
+    schema-salad-plus-pydantic generate schema/native_v0_1/workflow.yml -o "${SCHEME_SOURCE_DIRECTORY}/native.py"
+    schema-salad-plus-pydantic generate schema/native_v0_1/workflow.yml --strict -o "${SCHEME_SOURCE_DIRECTORY}/native_strict.py"
     schema-salad-plus-pydantic enhance-docs schema/native_v0_1/workflow.yml "${DIST_DIRECTORY}/native_v0_1.html"
 else
     # Fallback post-processing without schema-salad-plus-pydantic

gxformat2/normalized/_expanded.py

@@ -28,7 +28,9 @@
 class ExpandedWorkflowStep(NormalizedWorkflowStep):
     """Format2 step with run fully resolved — no ImportReference remaining."""
 
-    run: ExpandedFormat2 | GalaxyUserToolStub | None = Field(default=None, description="Resolved subworkflow, user tool, or absent.")
+    run: ExpandedFormat2 | GalaxyUserToolStub | None = Field(
+        default=None, description="Resolved subworkflow, user tool, or absent."
+    )
 
 
 class ExpandedFormat2(NormalizedFormat2):

gxformat2/normalized/_format2.py

@@ -12,9 +12,8 @@
 from pathlib import Path
 from typing import Any, Literal, Union
 
-from typing_extensions import TypeAlias
-
 from pydantic import BaseModel, ConfigDict, Field, field_validator
+from typing_extensions import TypeAlias
 
 from gxformat2.schema.gxformat2 import (
     CreatorOrganization,

gxformat2/normalized/_native.py

@@ -12,9 +12,8 @@
 from pathlib import Path
 from typing import Annotated, Any, Union
 
-from typing_extensions import TypeAlias
-
 from pydantic import BaseModel, ConfigDict, Discriminator, Field, Tag
+from typing_extensions import TypeAlias
 
 from gxformat2.native import load_native
 from gxformat2.schema.native import (

setup.cfg

@@ -14,7 +14,8 @@ logging-filter=gxformat2
 logging-level=INFO
 
 [flake8]
-ignore = E203,E501,W503
+# E704: black formats overload stubs as single-line `def foo(): ...`
+ignore = E203,E501,E704,W503
 max-complexity = 30
 import-order-style = smarkets
 application-import-names = gxformat2,tests