.github/workflows/generate_data.yaml #1391
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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. |