Merge branch 'main' into 17054-custom-name

Author: mr-c

Makefile

@@ -66,15 +66,19 @@ dev: install-dep
 ## dist        : create a module package for distribution
 dist: dist/${MODULE}-$(VERSION).tar.gz
 
-dist/${MODULE}-$(VERSION).tar.gz: $(SOURCES)
+check-python3:
+# Check that the default python version is python 3
+	python --version 2>&1 | grep "Python 3"
+
+dist/${MODULE}-$(VERSION).tar.gz: check-python3 $(SOURCES)
 	python setup.py sdist bdist_wheel
 
 ## docs	       : make the docs
 docs: FORCE
 	cd docs && $(MAKE) html
 
 ## clean       : clean up all temporary / machine-generated files
-clean: FORCE
+clean: check-python3 FORCE
 	rm -f ${MODILE}/*.pyc tests/*.pyc
 	python setup.py clean --all || true
 	rm -Rf .coverage
@@ -142,11 +146,11 @@ diff-cover.html: coverage.xml
 	diff-cover --compare-branch=main $^ --html-report $@
 
 ## test        : run the ${MODULE} test suite
-test: $(PYSOURCES)
+test: check-python3 $(PYSOURCES)
 	python -m pytest ${PYTEST_EXTRA}
 
 ## testcov     : run the ${MODULE} test suite and collect coverage
-testcov: $(PYSOURCES)
+testcov: check-python3 $(PYSOURCES)
 	python -m pytest --cov --cov-config=.coveragerc --cov-report= ${PYTEST_EXTRA}
 
 sloccount.sc: $(PYSOURCES) Makefile
@@ -162,10 +166,10 @@ list-author-emails:
 
 mypy3: mypy
 mypy: $(filter-out setup.py gittagger.py,$(PYSOURCES))
-	if ! test -f $(shell python3 -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))')/py.typed ; \
+	if ! test -f $(shell python -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))')/py.typed ; \
 	then \
 		rm -Rf typeshed/ruamel/yaml ; \
-		ln -s $(shell python3 -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))') \
+		ln -s $(shell python -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))') \
 			typeshed/ruamel/ ; \
 	fi  # if minimally required ruamel.yaml version is 0.15.99 or greater, than the above can be removed
 	MYPYPATH=$$MYPYPATH:typeshed mypy $^
@@ -181,7 +185,7 @@ shellcheck: FORCE
 pyupgrade: $(PYSOURCES)
 	pyupgrade --exit-zero-even-if-changed --py36-plus $^
 
-release-test: FORCE
+release-test: check-python3 FORCE
 	git diff-index --quiet HEAD -- || ( echo You have uncommited changes, please commit them and try again; false )
 	./release-test.sh
 

cwltool/process.py

@@ -357,28 +357,19 @@ def _relocate(src: str, dst: str) -> None:
             return
 
         # If the source is not contained in source_directories we're not allowed to delete it
-        real_src = fs_access.realpath(src)
+        src = fs_access.realpath(src)
         src_can_deleted = any(
-            os.path.commonprefix([p, real_src]) == p for p in source_directories
+            os.path.commonprefix([p, src]) == p for p in source_directories
         )
 
         _action = "move" if action == "move" and src_can_deleted else "copy"
 
         if _action == "move":
             _logger.debug("Moving %s to %s", src, dst)
-            if fs_access.isdir(src):
-                if fs_access.isdir(dst):
-                    if len(fs_access.listdir(dst)) > 0:
-                        # merge directories
-                        for dir_entry in scandir(src):
-                            _relocate(
-                                dir_entry.path, fs_access.join(dst, dir_entry.name)
-                            )
-                    else:
-                        os.rmdir(dst)
-                        shutil.move(src, dst)
-                else:
-                    shutil.move(src, dst)
+            if fs_access.isdir(src) and fs_access.isdir(dst):
+                # merge directories
+                for dir_entry in scandir(src):
+                    _relocate(dir_entry.path, fs_access.join(dst, dir_entry.name))
             else:
                 shutil.move(src, dst)
 

release-test.sh

@@ -19,7 +19,7 @@ fi
 test_prefix=""
 run_tests() {
 	local mod_loc
-	mod_loc=$(pip show ${package} | 
+	mod_loc=$(pip show ${package} |
 		grep ^Location | awk '{print $2}')/${module}
 	"${test_prefix}"bin/py.test "--ignore=${mod_loc}/schemas/" \
 		--pyargs -x ${module} -n auto --dist=loadfile
@@ -42,6 +42,7 @@ then
 		&& pip install --force-reinstall -U pip==${pipver} \
 		&& pip install setuptools==${setuptoolsver} wheel
 	pip install -rtest-requirements.txt
+	pip install -e .
 	make test
 	pip uninstall -y ${package} || true; pip uninstall -y ${package} || true; make install
 	mkdir testenv1/not-${module}

tests/symlinks.cwl

@@ -6,7 +6,10 @@
 
 from .util import get_data, needs_docker
 
-from io import StringIO
+if sys.version_info[0] < 3:
+    from StringIO import StringIO
+else:
+    from io import StringIO
 
 
 @needs_docker
@@ -15,21 +18,6 @@ def test_for_910() -> None:
     assert main([get_data("tests/wf/910.cwl")]) == 0
 
 
-def test_symlinks_with_absolute_paths(tmp_path: Path) -> None:
-    """Confirm that absolute paths in Directory types don't cause problems."""
-    assert (
-        main(
-            [
-                "--debug",
-                f"--outdir={tmp_path}/result",
-                f"--tmpdir-prefix={tmp_path}/tmp",
-                get_data("tests/symlinks.cwl"),
-            ]
-        )
-        == 0
-    )
-
-
 @needs_docker
 def test_for_conflict_file_names(tmp_path: Path) -> None:
     stream = StringIO()