specify image for docker #39
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| name: bifrost sp ecoli workflow | |
| on: | |
| push: | |
| branches: ["main"] | |
| pull_request: | |
| branches: ["main"] | |
| repository_dispatch: # webhook event to trigger this action workflow upon push to the submodule ecoli_fbi | |
| types: | |
| - ecoli-fbi-webhook | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.11"] | |
| steps: | |
| # Step 1: Checkout repository | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: 'true' #Initialize and update submodules -> git submodule init && git submodule update | |
| # Step 2: Update submodule to the latest commit | |
| - name: Update submodule | |
| run: | | |
| cd bifrost_sp_ecoli/ecoli_fbi | |
| # Show the current commit hash before updating | |
| CURRENT_COMMIT=$(git rev-parse HEAD) | |
| echo "Current commit hash of ecoli_fbi before update: $CURRENT_COMMIT" | |
| echo "Fetching latest changes from origin" | |
| git fetch origin --tags | |
| echo "Switching to the main branch and pulling latest updates" | |
| git checkout main # or the specific branch you want to track | |
| git pull origin main --tags # pull the latest changes | |
| # Show the new commit hash after the update | |
| LATEST_COMMIT=$(git rev-parse HEAD) | |
| echo "Updated commit hash of ecoli_fbi after update: $LATEST_COMMIT" | |
| # print the latest tag of ecoli_fbi | |
| LATEST_TAG_COMMIT=$(git tag --sort=-creatordate --format '%(objectname)'|head -1) | |
| LATEST_TAG=$(git tag --sort=-creatordate|head -1) | |
| echo "Checking commit hash for the latest tag of ecoli_fbi: $LATEST_TAG_COMMIT" | |
| echo "Checking the lastest tag of ecoli_fbi: $LATEST_TAG" | |
| git checkout $LATEST_TAG_COMMIT | |
| # Step 4: Extract version from __init__.py and set ENV_NAME | |
| - name: Set ENV_NAME | |
| run: | | |
| VERSION=$(grep "__version__" bifrost_sp_ecoli/__init__.py | cut -d "'" -f 2) | |
| REPO_NAME=$(basename "${{ github.workspace }}") | |
| ENV_NAME="${REPO_NAME}_v${VERSION}" | |
| # Echo the ENV_NAME to the log for debugging | |
| echo "Setting ENV_NAME to: $ENV_NAME" | |
| echo "ENV_NAME=$ENV_NAME" >> $GITHUB_ENV | |
| # Step 5: Build Docker image | |
| - name: Build docker image | |
| run: | | |
| docker build --build-arg CONDA_ENV_NAME="${{ env.ENV_NAME }}" -t bifrost_sp_ecoli_image . | |
| - name: Get_tests_data | |
| run: > | |
| git clone https://github.com/ssi-dk/bifrost_test_data.git; | |
| cd bifrost_test_data/samples; | |
| bash download_S1.sh | |
| - name: Run_tests | |
| run: > | |
| docker run | |
| --env BIFROST_DB_KEY=${{ secrets.MONGODB_ATLAS_CONNECTION }}/bifrost_test \ | |
| --env CONDA_ENV_NAME="${{ env.ENV_NAME }}" \ | |
| -w /bifrost/components/${{ github.event.repository.name }} \ | |
| -v /home/runner/work/${{ github.event.repository.name }}/${{ github.event.repository.name }}/bifrost_test_data:/bifrost/test_data \ | |
| bifrost_sp_ecoli_image \ | |
| -m pytest |