.github/workflows/generate_data.yaml #1396
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| on: | |
| schedule: | |
| - cron: "0 0 * * *" # daily | |
| push: | |
| branches: | |
| - master # Set a branch to deploy | |
| - develop # Note has logic around deployment | |
| - fix-pipeline | |
| name: build | |
| jobs: | |
| production: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GH_OPENPHARMA }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.9 # Specify the right version of python | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: "3.9" | |
| - name: Snakemake # python3 -m pip install --upgrade networkx pygraphvis | |
| run: | | |
| python3 -m pip install --upgrade pip | |
| python3 -m pip install pulp==2.7.0 | |
| python3 -m pip install snakemake==7.32.4 | |
| python3 -m pip install numpy==1.26.4 | |
| python3 -m pip install pandas==1.4.2 | |
| python3 -m pip install boto3==1.24.9 | |
| python3 -m pip install requests==2.28 | |
| python3 -m pip install PyYAML | |
| python3 -m pip install scikit-learn==1.1.1 | |
| python3 -m pip install pyarrow | |
| - name: Install system libs | |
| run: | | |
| sudo apt-get install libcurl4-openssl-dev | |
| sudo apt-get install libharfbuzz-dev libfribidi-dev | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: '4.1.0' | |
| - uses: r-lib/actions/setup-renv@v2 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| # IF develop | |
| - name: Build dev | |
| if: ${{ github.ref == 'refs/heads/develop' }} | |
| env: | |
| OPENPHARMA_AWS_ACCESS_KEY_ID: ${{ secrets.OPENPHARMA_AWS_ACCESS_KEY_ID }} | |
| OPENPHARMA_AWS_SECRET_ACCESS_KEY: ${{ secrets.OPENPHARMA_AWS_SECRET_ACCESS_KEY }} | |
| OPENPHARMA_AWS_DEFAULT_REGION: ${{ secrets.OPENPHARMA_AWS_DEFAULT_REGION }} | |
| OPENPHARMA_PAT: ${{ secrets.OPENPHARMA_PAT }} | |
| run: | | |
| snakemake -j2 -F python_icon_readme | |
| # IF main | |
| - name: Build prod | |
| if: ${{ github.ref == 'refs/heads/master' || github.ref == 'refs/heads/fix-pipeline' }} | |
| env: | |
| OPENPHARMA_AWS_ACCESS_KEY_ID: ${{ secrets.OPENPHARMA_AWS_ACCESS_KEY_ID }} | |
| OPENPHARMA_AWS_SECRET_ACCESS_KEY: ${{ secrets.OPENPHARMA_AWS_SECRET_ACCESS_KEY }} | |
| OPENPHARMA_AWS_DEFAULT_REGION: ${{ secrets.OPENPHARMA_AWS_DEFAULT_REGION }} | |
| OPENPHARMA_PAT: ${{ secrets.OPENPHARMA_PAT }} | |
| run: | | |
| snakemake -j4 -F all | |
| mkdir build | |
| cp index.html ./build | |
| cp os-health.html ./build | |
| - name: Deploy site 🚀 | |
| uses: JamesIves/[email protected] | |
| if: ${{ github.ref == 'refs/heads/master' }} | |
| with: | |
| branch: gh-pages # The branch the action should deploy to. | |
| folder: build # The folder the action should deploy. |