Fix integration test workflow (#124)

* Update integration test workflow

* add skip conditions

.github/workflows/integration_tests.yaml

@@ -74,33 +74,28 @@ jobs:
           # - name: Enable Step Debugging
           #   run: echo "ACTIONS_STEP_DEBUG=true >> $GITHUB_ENV"
 
-          # Checkout current branch of gen3-code-vigil if it is the repo under test
-          - name: Checkout integration test code from dev branch
-            if: ${{ github.event.repository.name == 'gen3-code-vigil' }}
-            uses: actions/checkout@v4
-
-          # Checkout master branch of gen3-code-vigil when another repo is under test
-          - name: Checkout integration test code from master branch
-            if: ${{ github.event.repository.name  != 'gen3-code-vigil' }}
-            uses: actions/checkout@v4
-            with:
-              repository: uc-cdis/gen3-code-vigil
-              ref: master
-
           # Skip integration tests when the following PR labels are present:
           # not-ready-for-ci / decommission-environment
           - name: Skip integration tests for specific PR labels
+            working-directory: ${{ github.workspace }}
             run: |
               if gh api repos/$REPO_FN/pulls/$PR_NUM --jq '.labels | map(.name) | .[] | select(. == "not-ready-for-ci" or . == "decommission-environment")' | grep -q .; then
                   echo "Skipping CI since one of the PR labels is present - not-ready-for-ci / decommission-environment"
                   echo "SKIP_TESTS=true" >> $GITHUB_ENV
               fi
 
+          # Checkout current repo
+          - name: Checkout current repo
+            if: ${{ env.SKIP_TESTS != 'true' }}
+            uses: actions/checkout@v4
+
           # Skip tests when there are only markdown files
           - name: Skip integration tests if PR contains only Markdown files
+            if: ${{ env.SKIP_TESTS != 'true' }}
+            working-directory: ${{ github.workspace }}
             run: |
               git fetch -q
-              FILE_TYPES=$(git show --name-only ${{ env.COMMIT_SHA }} | awk -F . '{print $NF}' | sort -u)
+              FILE_TYPES=$(git show --name-only ${{ env.COMMIT_SHA }} | grep -o '\S\+\.\S\+'  | grep -v '@' | awk -F . '{print $NF}' | sort -u)
               echo $FILE_TYPES
 
               # Check if the only file type is markdown
@@ -109,6 +104,14 @@ jobs:
                 echo "SKIP_TESTS=true" >> $GITHUB_ENV
               fi
 
+          # Checkout master branch of gen3-code-vigil when another repo is under test
+          - name: Checkout integration test code
+            if: ${{ env.SKIP_TESTS != 'true' && github.event.repository.name  != 'gen3-code-vigil' }}
+            uses: actions/checkout@v4
+            with:
+              repository: uc-cdis/gen3-code-vigil
+              ref: master
+
           # gen3-integration-tests run with python 3.9
           - name: Set up Python
             if: ${{ env.SKIP_TESTS != 'true' }}