setuptools: silence package discovery warnings

Makefile

@@ -72,22 +72,18 @@ dev: install-dep
 ## dist                   : create a module package for distribution
 dist: dist/${MODULE}-$(VERSION).tar.gz
 
-check-python3:
-# Check that the default python version is python 3
-	python --version 2>&1 | grep "Python 3"
-
-dist/${MODULE}-$(VERSION).tar.gz: check-python3 $(SOURCES)
-	python -m build
+dist/${MODULE}-$(VERSION).tar.gz: $(SOURCES)
+	python3 -m build
 
 ## docs                   : make the docs
 docs: FORCE
 	cd docs && $(MAKE) html
 
 ## clean                  : clean up all temporary / machine-generated files
-clean: check-python3 FORCE
+clean: FORCE
 	rm -f ${MODULE}/*.pyc tests/*.pyc *.so ${MODULE}/*.so cwltool/cwlprov/*.so
 	rm -Rf ${MODULE}/__pycache__/
-	python setup.py clean --all || true
+	rm -Rf build
 	rm -Rf .coverage
 	rm -f diff-cover.html
 
@@ -163,12 +159,12 @@ diff-cover.html: coverage.xml
 	diff-cover --compare-branch=main $^ --html-report $@
 
 ## test                   : run the cwltool test suite
-test: check-python3 $(PYSOURCES)
-	python -m pytest -rs ${PYTEST_EXTRA}
+test: $(PYSOURCES)
+	python3 -m pytest -rs ${PYTEST_EXTRA}
 
 ## testcov                : run the cwltool test suite and collect coverage
-testcov: check-python3 $(PYSOURCES)
-	python -m pytest -rs --cov --cov-config=.coveragerc --cov-report= ${PYTEST_EXTRA}
+testcov: $(PYSOURCES)
+	python3 -m pytest -rs --cov --cov-config=.coveragerc --cov-report= ${PYTEST_EXTRA}
 
 sloccount.sc: $(PYSOURCES) Makefile
 	sloccount --duplicates --wide --details $^ > $@
@@ -197,7 +193,7 @@ pyupgrade: $(PYSOURCES)
 	pyupgrade --exit-zero-even-if-changed --py38-plus $^
 	auto-walrus $^
 
-release-test: check-python3 FORCE
+release-test: FORCE
 	git diff-index --quiet HEAD -- || ( echo You have uncommitted changes, please commit them and try again; false )
 	./release-test.sh
 
@@ -206,7 +202,7 @@ release:
 	./release-test.sh && \
 	. testenv2/bin/activate && \
 		pip install build && \
-		python -m build testenv2/src/${MODULE} && \
+		python3 -m build testenv2/src/${MODULE} && \
 		pip install twine && \
 		twine upload testenv2/src/${MODULE}/dist/* && \
 		git tag ${VERSION} && git push --tags

setup.py

@@ -95,7 +95,29 @@
     ext_modules=ext_modules,
     # platforms='',  # empty as is conveyed by the classifier below
     # license='',  # empty as is conveyed by the classifier below
-    packages=["cwltool", "cwltool.tests", "cwltool.cwlprov"],
+    packages=[
+        "cwltool",
+        "cwltool.cwlprov",
+        "cwltool.jshint",
+        "cwltool.rdfqueries",
+        "cwltool.schemas",
+        "cwltool.tests",
+        "cwltool.tests.checker_wf",
+        "cwltool.tests.input_deps",
+        "cwltool.tests.loop",
+        "cwltool.tests.override",
+        "cwltool.tests.reloc",
+        "cwltool.tests.subgraph",
+        "cwltool.tests.test_deps_env",
+        "cwltool.tests.test_deps_env.modulefiles",
+        "cwltool.tests.tmp1.tmp2.tmp3",
+        "cwltool.tests.tmp4.alpha",
+        "cwltool.tests.trs",
+        "cwltool.tests.wf",
+        "cwltool.tests.wf.generator",
+        "cwltool.tests.wf.indir",
+        "cwltool.tests.wf.operation",
+    ],
     package_dir={"cwltool.tests": "tests"},
     include_package_data=True,
     install_requires=[

tests/seqtk_seq.cwl

@@ -22,4 +22,4 @@ hints:
     packages:
     - package: seqtk
       version:
-      - r93
+      - "1.4"

tests/seqtk_seq_with_docker.cwl

@@ -22,6 +22,6 @@ hints:
     packages:
     - package: seqtk
       version:
-      - '1.2'
+      - '1.4'
   DockerRequirement:
-    dockerPull: quay.io/biocontainers/seqtk:1.2--0
+    dockerPull: quay.io/biocontainers/seqtk:1.4--he4a0461_1

tests/test_dependencies.py

@@ -53,7 +53,7 @@ def test_biocontainers_resolution(tmp_path: Path) -> None:
         get_container_from_software_requirements(
             True, tool, container_image_cache_path=str(tmp_path)
         )
-        == "quay.io/biocontainers/seqtk:r93--0"
+        == "quay.io/biocontainers/seqtk:1.4--he4a0461_1"
     )