GitHub Actions: Separate concurrency groups

.github/workflows/ci-tests.yml

@@ -88,8 +88,8 @@ jobs:
         step: [lintreadme, shellcheck, pydocstyle]
 
     env:
-      py-semver: 3.9
-      TOXENV: ${{ format('py39-{0}', matrix.step) }}
+      py-semver: "3.10"
+      TOXENV: ${{ format('py310-{0}', matrix.step) }}
 
     steps:
       - uses: actions/checkout@v2
@@ -171,7 +171,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.9
+          python-version: "3.10"  # quoted, otherwise that turns into the number 3.1
 
       - name: Give the test runner user a name to make provenance happy.
         run: sudo usermod -c 'CI Runner' $(whoami)

.github/workflows/codeql-analysis.yml

@@ -9,7 +9,7 @@ on:
     - cron: '0 10 * * 2'
 
 concurrency:
-  group: build-${{ github.event.pull_request.number || github.ref }}
+  group: codeql-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
 jobs:

Makefile

@@ -27,7 +27,7 @@ MODULE=cwltool
 PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py) setup.py
 DEVPKGS=diff_cover black pylint pep257 pydocstyle flake8 tox tox-pyenv \
 	isort wheel autoflake flake8-bugbear pyupgrade bandit \
-	-rtest-requirements.txt -rmypy_requirements.txt
+	-rtest-requirements.txt -rmypy-requirements.txt
 DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pydocstyle sloccount \
 	   python-flake8 python-mock shellcheck
 

cwltool.Dockerfile

@@ -5,7 +5,7 @@ RUN apk add --no-cache git gcc python3-dev libxml2-dev libxslt-dev libc-dev linu
 WORKDIR /cwltool
 COPY . .
 
-RUN pip install toml -rmypy_requirements.txt "$(grep ruamel requirements.txt)" \
+RUN pip install toml -rmypy-requirements.txt "$(grep ruamel requirements.txt)" \
 	"$(grep schema.salad requirements.txt)"
 # schema-salad is needed to be installed (this time as pure Python) for
 # cwltool + mypyc

cwltool/provenance_profile.py

@@ -45,13 +45,7 @@
     WFPROV,
 )
 from .stdfsaccess import StdFsAccess
-from .utils import (
-    CWLObjectType,
-    JobsType,
-    get_listing,
-    posix_path,
-    versionstring,
-)
+from .utils import CWLObjectType, JobsType, get_listing, posix_path, versionstring
 from .workflow_job import WorkflowJob
 
 if TYPE_CHECKING:

release-test.sh

@@ -7,6 +7,7 @@ export LC_ALL=C
 
 package=cwltool
 module=cwltool
+extras="[deps]"
 
 if [ "$GITHUB_ACTIONS" = "true" ]; then
     # We are running as a GH Action
@@ -24,7 +25,7 @@ run_tests() {
 	"${test_prefix}"bin/py.test "--ignore=${mod_loc}/schemas/" \
 		--pyargs -x ${module} -n auto --dist=loadfile
 }
-pipver=20.3 # minimum required version of pip for Python 3.10
+pipver=20.3.3 # minimum required version of pip for Python 3.10
 setuptoolsver=50.0.0 # required for Python 3.10
 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
 
@@ -41,8 +42,7 @@ then
 	rm -f testenv1/lib/python-wheels/setuptools* \
 		&& pip install --force-reinstall -U pip==${pipver} \
 		&& pip install setuptools==${setuptoolsver} wheel
-	pip install -rtest-requirements.txt
-	pip install -e .
+	pip install -rtest-requirements.txt ".${extras}"
 	make test
 	pip uninstall -y ${package} || true; pip uninstall -y ${package} || true; make install
 	mkdir testenv1/not-${module}
@@ -67,7 +67,7 @@ rm -f lib/python-wheels/setuptools* \
 	&& pip install --force-reinstall -U pip==${pipver} \
         && pip install setuptools==${setuptoolsver} wheel
 # The following can fail if you haven't pushed your commits to ${repo}
-pip install -e "git+${repo}@${HEAD}#egg=${package}"
+pip install -e "git+${repo}@${HEAD}#egg=${package}${extras}"
 pushd src/${package}
 pip install -rtest-requirements.txt
 make dist
@@ -90,12 +90,14 @@ rm -f lib/python-wheels/setuptools* \
         && pip install setuptools==${setuptoolsver} wheel
 package_tar=$(find . -name "${package}*tar.gz")
 pip install "-r${DIR}/test-requirements.txt"
-pip install "${package_tar}"
+pip install "${package_tar}${extras}"
 mkdir out
 tar --extract --directory=out -z -f ${package}*.tar.gz
 pushd out/${package}*
 make dist
 make test
+pip install "-r${DIR}/mypy-requirements.txt"
+make mypy
 pip uninstall -y ${package} || true; pip uninstall -y ${package} || true; make install
 mkdir ../not-${module}
 pushd ../not-${module}

tests/test_trs.py

@@ -2,6 +2,7 @@
 from unittest import mock
 from unittest.mock import MagicMock
 
+from cwltool.loghandler import _logger
 from cwltool.main import main
 
 from .util import get_data
@@ -21,8 +22,7 @@ def json(self) -> Any:
         return self.json_data
 
 
-def mocked_requests_head(*args: Any) -> MockResponse1:
-
+def mocked_requests_head(*args: Any, **kwargs: Any) -> MockResponse1:
     return MockResponse1(None, 200)
 
 
@@ -87,14 +87,18 @@ def mocked_requests_get(*args: Any, **kwargs: Any) -> MockResponse2:
             200,
         )
 
-    print("A mocked call to TRS missed, target was %s", args[0])
+    _logger.debug("A mocked call to TRS missed, target was %s", args[0])
     return MockResponse2(None, 404)
 
 
 @mock.patch("requests.Session.head", side_effect=mocked_requests_head)
 @mock.patch("requests.Session.get", side_effect=mocked_requests_get)
 def test_tool_trs_template(mock_head: MagicMock, mock_get: MagicMock) -> None:
-    params = ["--make-template", r"quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4"]
+    params = [
+        "--debug",
+        "--make-template",
+        r"quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4",
+    ]
     return_value = main(params)
     mock_head.assert_called()
     mock_get.assert_called()
@@ -105,6 +109,7 @@ def test_tool_trs_template(mock_head: MagicMock, mock_get: MagicMock) -> None:
 @mock.patch("requests.Session.get", side_effect=mocked_requests_get)
 def test_workflow_trs_template(mock_head: MagicMock, mock_get: MagicMock) -> None:
     params = [
+        "--debug",
         "--make-template",
         r"#workflow/github.com/dockstore-testing/md5sum-checker:develop",
     ]

tox.ini

@@ -50,7 +50,7 @@ deps =
   py3{6,7,8,9,10}-lint: black
   py3{6,7,8,9,10}-bandit: bandit
   py3{6,7,8,9,10}-bandit: importlib_metadata != 4.8.0
-  py3{6,7,8,9,10}-mypy: -rmypy_requirements.txt
+  py3{6,7,8,9,10}-mypy: -rmypy-requirements.txt
   py39-pydocstyle: pydocstyle
   py39-pydocstyle: diff-cover
   py39-lintreadme: twine