GHA fix (#204)

* if tests pass, GHA passes
* if tests fail, GHA fails

.github/workflows/kb_sdk_test.yaml

@@ -54,4 +54,8 @@ jobs:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       run: |
         sh $GITHUB_WORKSPACE/kb_sdk_actions/bin/kb-sdk test
-        bash <(curl -s https://codecov.io/bash)
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        fail_ci_if_error: true

Makefile

@@ -51,7 +51,6 @@ build-test-script:
 	echo 'export PYTHONPATH=$$script_dir/../$(LIB_DIR):$$PATH:$$PYTHONPATH' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
 	echo 'cd $$script_dir/../$(TEST_DIR)' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
 	echo 'python -m nose --with-coverage --cover-package=$(SERVICE_CAPS) --cover-html --cover-html-dir=/kb/module/work/test_coverage --cover-xml --cover-xml-file=/kb/module/work/test_coverage/coverage.xml --nocapture  --nologcapture .' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
-	echo 'cp /kb/module/.coveragerc .' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
 	echo 'cp .coverage /kb/module/work/' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
 	echo 'mkdir -p /kb/module/work/kb/module/lib/' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
 	echo 'cp -R /kb/module/lib/$(SERVICE_CAPS)/ /kb/module/work/kb/module/lib/' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)

scripts/run_tests_within_container.sh

@@ -9,7 +9,8 @@ export TEST_PATH=.
 
 cd $script_dir/../test
 python -m nose --with-coverage --cover-package=GenomeFileUtil --cover-html --cover-html-dir=/kb/module/work/test_coverage --cover-xml --cover-xml-file=/kb/module/work/test_coverage/coverage.xml --nocapture --nologcapture $TEST_PATH
-cp /kb/module/.coveragerc .
+returncode=$?
+if [ $returncode != 0 ]; then exit $returncode; fi
 cp .coverage /kb/module/work/
 mkdir -p /kb/module/work/kb/module/lib/
 cp -R /kb/module/lib/GenomeFileUtil/ /kb/module/work/kb/module/lib/P