record coverage while running the conformance tests

Author: mr-c

.coveragerc

@@ -1,6 +1,9 @@
 [run]
 branch = True
-source = cwlupgrader
+source_pkgs = cwlupgrader
+omit =
+    tests/*
+    */site-packages/cwlupgrader/tests/*
 
 [report]
 exclude_lines =

.github/workflows/ci-tests.yml

@@ -123,11 +123,16 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v6
         with:
-          python-version: 3.12
+          python-version: 3.14
           cache: pip
-
       - name: "Test upgrading CWL conformance tests & running them"
         run: ./conformance-test.sh
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
 
   release_test:
     name: cwl-upgrader release test
@@ -139,7 +144,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v6
         with:
-          python-version: 3.12
+          python-version: 3.14
           cache: pip
           cache-dependency-path: |
             requirements.txt

conformance-test.sh

@@ -84,21 +84,24 @@ fi
 
 CONFORMANCE_TEST1="${SCRIPT_DIRECTORY}/common-workflow-language-main/v1.0/conformance_test_v1_0_to_v1_1.yaml"
 CONFORMANCE_TEST2="${SCRIPT_DIRECTORY}/common-workflow-language-main/v1.0/conformance_test_v1_0_to_v1_2.yaml"
+COVBASE="coverage run --append --rcfile=${SCRIPT_DIRECTORY}/.coveragerc --data-file=${SCRIPT_DIRECTORY}/.coverage -m cwlupgrader"
 
 pushd "${SCRIPT_DIRECTORY}"/common-workflow-language-main/v1.0
 cp -r v1.0 v1.1
 cp -r v1.0 v1.2
 rm v1.1/*.cwl
 rm v1.2/*.cwl
 set +x
-pushd v1.0 ; cwl-upgrader --v1.1-only --dir ../v1.1 --always-write ./*.cwl; popd
-pushd v1.0 ; cwl-upgrader             --dir ../v1.2 --always-write ./*.cwl; popd
+pushd v1.0 ; $COVBASE --v1.1-only --dir ../v1.1 --always-write ./*.cwl; popd
+pushd v1.0 ; $COVBASE             --dir ../v1.2 --always-write ./*.cwl; popd
 set -x
 cp conformance_test_v1.0.yaml "${CONFORMANCE_TEST1}"
 cp conformance_test_v1.0.yaml "${CONFORMANCE_TEST2}"
 sed -i 's=v1.0/=v1.1/=g' "${CONFORMANCE_TEST1}"
 sed -i 's=v1.0/=v1.2/=g' "${CONFORMANCE_TEST2}"
 popd
+coverage report
+coverage xml
 
 cp "${CONFORMANCE_TEST1}" "${CONFORMANCE_TEST1%".yaml"}.cwltest.yaml"
 CONFORMANCE_TEST1="${CONFORMANCE_TEST1%".yaml"}.cwltest.yaml"
@@ -114,7 +117,7 @@ if [[ -n "${EXCLUDE}" ]] ; then
   EXCLUDE_COMMAND="--cwl-exclude=${EXCLUDE}"
 fi
 
-pushd $(dirname "${CONFORMANCE_TEST1}")
+pushd "$(dirname "${CONFORMANCE_TEST1}")"
 set +e
 python3 -m pytest "${CONFORMANCE_TEST1}" -n auto -rs --junit-xml="${SCRIPT_DIRECTORY}"/cwltool_v1.0_to_v1.1_"${CONTAINER}".xml -o junit_suite_name=cwltool_$(echo "${CWLTOOL_OPTIONS}" | tr "[:blank:]-" _) ${EXCLUDE_COMMAND} ; RETURN_CODE1=$?
 

cwlupgrader/__main__.py

@@ -0,0 +1,7 @@
+"""Default entry point for the cwl-upgrader module."""
+
+import sys
+
+from . import main
+
+sys.exit(main.main())