switch to hatch from setuptools

Author: mr-c

.github/workflows/ci-tests.yml

@@ -45,7 +45,6 @@ jobs:
           python-version: ${{ env.py-semver }}
           cache: pip
           cache-dependency-path: |
-            requirements.txt
             tox.ini
 
       - name: install dev libraries
@@ -137,7 +136,6 @@ jobs:
           python-version: 3.12
           cache: pip
           cache-dependency-path: |
-            requirements.txt
             test-requirements.txt
 
       - name: Install packages

Makefile

@@ -52,7 +52,7 @@ cleanup: sort_imports format flake8 pydocstyle
 install-dep: install-dependencies
 
 install-dependencies:
-	pip install -U pip setuptools wheel
+	pip install -U pip wheel
 	pip install --upgrade $(DEVPKGS)
 
 ## install-deb-dep        : install many of the dev dependencies via apt-get
@@ -65,14 +65,14 @@ install: FORCE
 
 ## dev                    : install the cwl-utils package in dev mode
 dev: install-dep
-	pip install -U pip setuptools wheel
+	pip install -U pip wheel
 	pip install -e .$(EXTRAS)
 
 ## dist                   : create a module package for distribution
 dist: dist/${MODULE}-$(VERSION).tar.gz
 
 dist/${MODULE}-$(VERSION).tar.gz: $(SOURCES)
-	python -m build
+	python3 -m build
 
 ## docs                   : make the docs
 docs: FORCE
@@ -86,36 +86,36 @@ clean: FORCE
 
 # Linting and code style related targets
 ## sort_import            : sorting imports using isort: https://github.com/timothycrosley/isort
-sort_imports: $(PYSOURCES)
-	isort $^
+sort_imports: FORCE
+	isort $(PYSOURCES)
 
-remove_unused_imports: $(PYSOURCES)
-	autoflake --in-place --remove-all-unused-imports $^
+remove_unused_imports: FORCE
+	autoflake --in-place --remove-all-unused-imports $(PYSOURCES)
 
 pep257: pydocstyle
 ## pydocstyle             : check Python docstring style
-pydocstyle: $(PYSOURCES)
-	ruff check $^
+pydocstyle: FORCE
+	ruff check $(PYSOURCES)
 
 ## codespell              : check for common misspellings
-codespell:
+codespell: FORCE
 	codespell -w $(shell git ls-files | grep -v mypy-stubs)
 
 ## format                 : check/fix all code indentation and formatting (runs black)
-format: $(PYSOURCES) FORCE
+format: FORCE
 	black $(PYSOURCES)
 
-format-check: $(PYSOURCES)
-	black --diff --check $^
+format-check: FORCE
+	black --diff --check $(PYSOURCES)
 
 ## pylint                 : run static code analysis on Python code
-pylint: $(PYSOURCES)
+pylint: FORCE
 	pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
-                $^ -j0|| true
+                $(PYSOURCES) -j0|| true
 
-pylint_report.txt: $(PYSOURCES)
+pylint_report.txt: FORCE
 	pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
-		$^ -j0> $@ || true
+		$(PYSOURCES) -j0> $@ || true
 
 diff_pylint_report: pylint_report.txt
 	diff-quality --compare-branch=main --violations=pylint pylint_report.txt
@@ -144,34 +144,37 @@ diff-cover.html: coverage.xml
 	diff-cover --compare-branch=main $^ --html-report $@
 
 ## test                   : run the cwl-utils test suite
-test: $(PYSOURCES)
-	python -m pytest ${PYTEST_EXTRA}
+test: FORCE
+	python3 -m pytest ${PYTEST_EXTRA}
 
 ## testcov                : run the cwl-utils test suite and collect coverage
-testcov: $(PYSOURCES)
-	python -m pytest --cov ${PYTEST_EXTRA}
+testcov: FORCE
+	python3 -m pytest --cov ${PYTEST_EXTRA}
 
-sloccount.sc: $(PYSOURCES) Makefile
-	sloccount --duplicates --wide --details $^ > $@
+sloccount.sc: FORCE
+	sloccount --duplicates --wide --details $(PYSOURCES) Makefile > $@
 
 ## sloccount              : count lines of code
-sloccount: $(PYSOURCES) Makefile
-	sloccount $^
+sloccount: FORCE
+	sloccount $(PYSOURCES) Makefile
 
 list-author-emails:
 	@echo 'name, E-Mail Address'
 	@git log --format='%aN,%aE' | sort -u | grep -v 'root'
 
-mypy3: mypy
-mypy: ${PYSOURCES}
-	MYPYPATH=$$MYPYPATH:mypy-stubs mypy $^
+mypy: FORCE
+	MYPYPATH=$$MYPYPATH:mypy-stubs mypy $(PYSOURCES)
+
+mypyc: FORCE
+	MYPYPATH=mypy-stubs HATCH_BUILD_HOOKS_ENABLE=1 pip install --verbose -e . \
+		 && pytest "${PYTEST_EXTRA}"
 
 shellcheck: FORCE
 	shellcheck release-test.sh
 
-pyupgrade: $(PYSOURCES)
-	pyupgrade --exit-zero-even-if-changed --py310-plus $^
-	auto-walrus $^
+pyupgrade: FORCE
+	pyupgrade --exit-zero-even-if-changed --py310-plus $(PYSOURCES)
+	auto-walrus $(PYSOURCES)
 
 release-test: FORCE
 	git diff-index --quiet HEAD -- || ( echo You have uncommitted changes, please commit them and try again; false )
@@ -180,13 +183,13 @@ release-test: FORCE
 release: release-test
 	. testenv2/bin/activate && \
 		pip install build && \
-		python -m build testenv2/src/${PACKAGE} && \
+		python3 -m build testenv2/src/${PACKAGE} && \
 		pip install twine && \
 		twine upload testenv2/src/${PACKAGE}/dist/* && \
 		git tag ${VERSION} && git push --tags
 
-flake8: $(PYSOURCES)
-	flake8 $^
+flake8: FORCE
+	flake8 $(PYSOURCES)
 
 cwl_utils/parser/cwl_v1_0.py: FORCE
 	schema-salad-tool --codegen python \

pyproject.toml

@@ -1,6 +1,6 @@
 [build-system]
-requires = ["setuptools>=61.2"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling>=1.27.0"]
+build-backend = "hatchling.build"
 
 [project]
 name = "cwl-utils"
@@ -30,7 +30,15 @@ classifiers = [
     "Typing :: Typed",
 ]
 requires-python = ">=3.10,<3.15"
-dynamic = ["version", "dependencies"]
+dynamic = ["version"]
+dependencies = [
+    "cwl-upgrader >= 1.2.3",
+    "packaging",
+    "rdflib",
+    "requests",
+    "schema-salad >= 8.8.20250205075315,<9",
+    "ruamel.yaml >= 0.17.6, < 0.19",
+]
 
 [project.urls]
 Documentation = "https://cwl-utils.readthedocs.io/"
@@ -44,7 +52,13 @@ Changelog = "https://github.com/common-workflow-language/cwl-utils/releases"
 pretty = ["cwlformat"]
 testing = [
     "pytest<10",
-    "pytest-mock",
+    "pytest-cov",
+    "pytest-xdist[psutil]",
+    "cwl-utils[pretty]",
+    "pytest-mock >= 1.10.0",
+    "jsonschema >= 4.21.1",
+    "udocker",
+    "cwltool",
 ]
 
 [project.scripts]
@@ -55,41 +69,109 @@ cwl-graph-split = "cwl_utils.graph_split:main"
 cwl-normalizer = "cwl_utils.normalizer:main"
 cwl-inputs-schema-gen = "cwl_utils.inputs_schema_gen:main"
 
-[tool.aliases]
-test = "pytest"
-
 [tool.pytest.ini_options]
 testpaths = ["tests"]
 addopts = "-rsx -n auto"
 
-[tool.setuptools]
-packages = [
-    "cwl_utils",
-    "cwl_utils.parser",
-    "cwl_utils.tests",
-    "cwl_utils.testdata",
-    "cwl_utils.testdata.checker_wf",
-    "cwl_utils.testdata.extensions",
-    "cwl_utils.testdata.types",
-    "cwl_utils.testdata.workflows",
+[tool.hatch.version]
+path = "cwl_utils/__meta__.py"
+
+[tool.hatch.build.targets.sdist]
+exclude = [
+  "/.github",
+  "**~",
+  "**.pyc",
+  "**.orig",
+]
+include = [
+"/README.rst",
+"/Makefile",
+"/LICENSE",
+"/*requirements.txt",
+"/create_cwl_from_objects.py",
+"/load_cwl_by_path.py",
+"/cwl_utils/**.py",
+"/cwl_utils/*.js",
+"/cwl_utils/templates/*",
+"/tests/**.py",
+"/testdata/*.cwl",
+"/testdata/*.yaml",
+"/testdata/*.yml",
+"/testdata/*.input",
+"/testdata/*.json",
+"/testdata/*.ttl",
+"/testdata/*.owl",
+"/testdata/*.js",
+"/testdata/remote-cwl/*.cwl",
+"/testdata/workflows/*.cwl",
+"/testdata/workflows/*.yaml",
+"/testdata/types/*.yml",
+"/testdata/checker_wf/*.cwl",
+"/testdata/extensions/*.cwl",
+"/cwl_utils/py.typed",
+"/docs/conf.py",
+"/docs/Makefile",
+"/docs/_static/favicon.ico",
+"/docs/requirements.txt",
+"/docs/*.rst",
+]
+
+[tool.hatch.build.targets.wheel]
+exclude = [
+  "/.github",
+  "**~",
+  "**.pyc",
+  "**.orig",
+]
+include = [
+"/README.rst",
+"/Makefile",
+"/LICENSE",
+"/load_cwl_by_path.py",
+"/cwl_utils/**.py",
+"/cwl_utils/*.js",
+"/cwl_utils/templates/*",
+"/tests/**.py",
+"/testdata/*.cwl",
+"/testdata/*.yaml",
+"/testdata/*.yml",
+"/testdata/*.input",
+"/testdata/*.json",
+"/testdata/*.ttl",
+"/testdata/*.owl",
+"/testdata/*.js",
+"/testdata/remote-cwl/*.cwl",
+"/testdata/workflows/*.cwl",
+"/testdata/workflows/*.yaml",
+"/testdata/types/*.yml",
+"/testdata/checker_wf/*.cwl",
+"/testdata/extensions/*.cwl",
+"/cwl_utils/py.typed",
 ]
-include-package-data = true
 
-[tool.setuptools.package-dir]
-"cwl_utils.parser" = "cwl_utils/parser"
-"cwl_utils.tests" = "tests"
-"cwl_utils.testdata" = "testdata"
-"cwl_utils.testdata.checker_wf" = "testdata/checker_wf"
-"cwl_utils.testdata.extensions" = "testdata/extensions"
-"cwl_utils.testdata.types" = "testdata/types"
-"cwl_utils.testdata.workflows" = "testdata/workflows"
+[tool.hatch.build.targets.wheel.sources]
+"tests" = "cwl_utils/tests" 
+"testdata" = "cwl_utils/testdata"
+"testdata/checker_wf" = "cwl_utils/testdata/checker_wf"
+"testdata/extensions" = "cwl_utils/testdata/extensions"
+"testdata/types" = "cwl_utils/testdata/types"
+"testdata/workflows" = "cwl_utils/testdata/workflows"
+
+[tool.hatch.build.targets.wheel.hooks.mypyc]
+enable-by-default = false
+dependencies = [
+    "hatch-mypyc>=0.16.0",
+    "mypy==1.19.0",
+]
+require-runtime-dependencies = true
+exclude = [
+"/create_cwl_from_objects.py",
+"/load_cwl_by_path.py",
+]
 
-[tool.setuptools.package-data]
-"cwl_utils" = ["templates/*.json"]
 
-[tool.setuptools.dynamic]
-version = {attr = "cwl_utils.__meta__.__version__"}
-dependencies = {file = ["requirements.txt"]}
+[tool.hatch.envs.test]
+features = ["testing"]
 
 [tool.isort]
 profile = "black"

release-test.sh

@@ -19,7 +19,6 @@ else
 fi
 run_tests="bin/py.test --pyargs ${module}"
 pipver=23.1  # minimum required version of pip for Python 3.12
-setuptoolsver=67.6.1  # required for Python 3.12
 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
 
 rm -Rf testenv? || /bin/true
@@ -31,10 +30,7 @@ then
 	# First we test the head
 	# shellcheck source=/dev/null
 	source testenv1/bin/activate
-	rm -Rf testenv1/local
-	rm -f testenv1/lib/python-wheels/setuptools* \
-		&& pip install --force-reinstall -U pip==${pipver} \
-		&& pip install setuptools==${setuptoolsver} wheel
+	pip install --force-reinstall -U pip==${pipver} build
 	pip install -rtest-requirements.txt ".${extras}"
 	make test
 	pip uninstall -y ${package} || true; pip uninstall -y ${package} || true; make install
@@ -57,9 +53,8 @@ rm -Rf testenv[2345]/local
 pushd testenv2
 # shellcheck source=/dev/null
 source bin/activate
-rm -f lib/python-wheels/setuptools* \
-	&& pip install --force-reinstall -U pip==${pipver} \
-        && pip install setuptools==${setuptoolsver} wheel
+pip install --force-reinstall -U pip==${pipver} \
+        && pip install build wheel
 # The following can fail if you haven't pushed your commits to ${repo}
 pip install -e "git+${repo}@${HEAD}#egg=${package}${extras}"
 pushd src/${package}
@@ -80,9 +75,8 @@ popd
 pushd testenv3/
 # shellcheck source=/dev/null
 source bin/activate
-rm -f lib/python-wheels/setuptools* \
-	&& pip install --force-reinstall -U pip==${pipver} \
-        && pip install setuptools==${setuptoolsver} wheel
+pip install --force-reinstall -U pip==${pipver} \
+        && pip install build wheel
 package_tar=$(find . -name "${module}*tar.gz")
 pip install "-r${DIR}/test-requirements.txt" build
 pip install "${package_tar}${extras}"
@@ -103,10 +97,9 @@ popd
 
 pushd testenv4/
 # shellcheck source=/dev/null
-source bin/activate
-rm -f lib/python-wheels/setuptools* \
+source bin/activate \
 	&& pip install --force-reinstall -U pip==${pipver} \
-        && pip install setuptools==${setuptoolsver} wheel
+        && pip install build wheel
 pip install "$(ls ${module}*.whl)${extras}"
 pip install "-r${DIR}/test-requirements.txt"
 mkdir not-${module}