fix pybiolib url -> path #59
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| name: PPRCODE_Guideline Workflow | |
| on: | |
| push: | |
| paths: | |
| - 'docker/**' # Monitor the entire 'docker' directory | |
| - 'scripts/**' # Monitor the entire 'scripts' directory | |
| - '.github/workflows/pprcode-guideline.yml' # monitor the main workflow script. enable it again if in necessary maintainances. | |
| - '.biolib/config.yml' # Monitor the Biolib config file | |
| branches: | |
| - main | |
| jobs: | |
| build-and-push: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| # - name: Upload coverage reports to Codecov | |
| # uses: codecov/codecov-action@v3 | |
| # with: | |
| # token: ${{ secrets.CODECOV_TOKEN }} | |
| - name: Set environment variable with current date | |
| run: | | |
| echo "DATE=$(date +'%Y-%m-%d')" >> $GITHUB_ENV | |
| echo "DATE: ${{ env.DATE }}" | |
| - name: Set environment variable with current repo dir | |
| run: | | |
| echo "REPO=$PWD" >> $GITHUB_ENV | |
| echo "REPO: ${{ env.REPO }}" | |
| - name: Build Docker image | |
| run: docker build -f docker/Dockerfile -t pprcode . | |
| - name: Tag Docker image with date and latest | |
| run: | | |
| docker tag pprcode yaoyinying/pprcode:${{ env.DATE }} | |
| docker tag pprcode yaoyinying/pprcode:latest | |
| - name: Log in to Docker Hub | |
| run: echo "${{ secrets.DOCKER_GITHUB_REPO_SECRET }}" | docker login -u yaoyinying --password-stdin | |
| - name: Create Testing and Run it | |
| run: | | |
| python -m venv pprcode_test | |
| source pprcode_test/bin/activate | |
| pip install -r docker/requirements.txt | |
| python ${{ env.REPO }}/docker/run_docker.py --fasta ${{ env.REPO }}/ppr_example.fasta --save_dir ./save-psscan --plot_item=bar,score,edge,ppr,rna --debug | |
| python ${{ env.REPO }}/docker/run_docker.py --fasta ${{ env.REPO }}/ppr_example.fasta --save_dir ./save-pprfinder --plot_item=bar,score,edge,ppr,rna --program=pprfinder --debug | |
| deactivate | |
| - name: Push Docker image | |
| run: | | |
| cd ${{ env.REPO }} | |
| docker push yaoyinying/pprcode:${{ env.DATE }} | |
| docker push yaoyinying/pprcode:latest | |
| - name: Update Readme file for CI actions | |
| run: | | |
| awk '{if ($0 !~ "https://img.shields.io" && $0 !~ "https://tinyurl.com/pprcode-badge" && $0 !~ "badge.svg" ){print }}' README.md >README.ci.md | |
| cat README.ci.md | |
| - name: Install pybiolib package | |
| run: pip3 install -U pybiolib | |
| - name: Build and push biolib application | |
| run: BIOLIB_TOKEN=${{ secrets.BIOLIB_TOKEN }} biolib push YaoYinYing/pprcode | |
| - name: Delete temp Readme | |
| run: rm -f README.ci.md |