🔐 try appending GH_PAT to repo url

.github/workflows/run-test.yaml

@@ -10,14 +10,6 @@ jobs:
     - name: Checkout code
       uses: actions/checkout@v2
 
-    - name: Configure credential helper to clone private repos
-      run: |
-        echo '#!/bin/bash' > ~/.git-credential-helper.sh
-        echo 'echo username=${{ secrets.GH_USERNAME }}' >> ~/.git-credential-helper.sh
-        echo 'echo password=${{ secrets.GH_PAT }}' >> ~/.git-credential-helper.sh
-        chmod +x ~/.git-credential-helper.sh
-        git config --global credential.helper "/bin/bash ~/.git-credential-helper.sh"
-
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
@@ -42,9 +34,11 @@ jobs:
 
     - name: Install dependencies
       run: pip install -r requirements.txt
-    
+
     - name: Run tests
       run: bash tests/test-with-compose.sh
+      env:
+        GH_PAT: ${{ secrets.GH_PAT }}
 
     - name: Upload coverage reports to Codecov with GitHub Action
       uses: codecov/[email protected]

tests/test-with-compose.sh

@@ -12,11 +12,12 @@ echo "API directory set to: $API_DIR"
 echo "CLI directory set to: $CLI_DIR"
 
 # get current isabl branch in case this test depends on a particular branch
-ISABL_BRANCH=${TRAVIS_PULL_REQUEST_BRANCH:-${TRAVIS_BRANCH:-master}}
-echo "ISABL_BRANCH set to $ISABL_BRANCH given travis branch: $TRAVIS_BRANCH $TRAVIS_PULL_REQUEST_BRANCH"
+GH_BRANCH=$(echo ${GITHUB_REF#refs/heads/})
+ISABL_BRANCH=${GH_BRANCH:-master}
+echo "ISABL_BRANCH set to $ISABL_BRANCH given Github branch: $GH_BRANCH"
 
 # clone api from github
-rm -rf $API_DIR && git clone https://github.com/papaemmelab/isabl_api.git $API_DIR
+rm -rf $API_DIR && git clone https://${GH_PAT}@github.com/papaemmelab/isabl_api.git $API_DIR
 cd $API_DIR && (git checkout $ISABL_BRANCH || true) && docker-compose build && docker-compose up -d
 
 # give some time to API to start and test Isabl CLI