python-workflow-definition/.github/workflows/deploy.yml at 159d6b6556d552445cc3bbd5e130ed4cd9bc2854 · pythonworkflow/python-workflow-definition · GitHub

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name: Deploy

on:
  push:
    branches: [ main ]

jobs:
  # Run all the test jobs first
  arithmetic:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - name: Conda config
      run: echo -e "channels:\n  - conda-forge\n" > .condarc
    - uses: conda-incubator/setup-miniconda@v3
      with:
        python-version: "3.12"
        miniforge-version: latest
        condarc-file: .condarc
        environment-file: binder/environment.yml
    - name: Installation and setup
      shell: bash -l {0}
      run: |
        pip install --no-deps --no-build-isolation -e .
        conda install -c conda-forge jupyter papermill
        verdi presto --profile-name pwd
    - name: Tests
      shell: bash -l {0}
      run: |
        cd example_workflows/arithmetic
        papermill aiida.ipynb aiida_out.ipynb -k "python3"
        papermill cwl.ipynb cwl_out.ipynb -k "python3"
        papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
        papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
        papermill pyiron_workflow.ipynb pyiron_workflow_out.ipynb -k "python3"
        papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"
    - name: Upload executed notebooks
      uses: actions/upload-artifact@v4
      with:
        name: arithmetic-notebooks
        path: example_workflows/arithmetic/*_out.ipynb
        retention-days: 1

  quantumespresso:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - name: Setup environment
      shell: bash -l {0}
      run: |
        echo -e "channels:\n  - conda-forge\n" > .condarc
        tail --lines=+4 example_workflows/quantum_espresso/environment.yml >> binder/environment.yml
    - uses: conda-incubator/setup-miniconda@v3
      with:
        python-version: "3.12"
        miniforge-version: latest
        condarc-file: .condarc
        environment-file: binder/environment.yml
    - name: Installation and setup
      shell: bash -l {0}
      run: |
        pip install --no-deps --no-build-isolation -e example_workflows/quantum_espresso/qe_xml_parser
        pip install --no-deps --no-build-isolation -e .
        conda install -c conda-forge jupyter papermill
        verdi presto --profile-name pwd
    - name: Tests
      shell: bash -l {0}
      run: |
        export ESPRESSO_PSEUDO=$(pwd)/espresso/pseudo
        cp -r example_workflows/quantum_espresso/espresso .
        cd example_workflows/quantum_espresso
        papermill aiida.ipynb aiida_out.ipynb -k "python3"
        papermill cwl.ipynb cwl_out.ipynb -k "python3"
        papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
        papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
        papermill pyiron_workflow.ipynb pyiron_workflow_out.ipynb -k "python3"
        papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"
    - name: Upload executed notebooks
      uses: actions/upload-artifact@v4
      with:
        name: quantumespresso-notebooks
        path: example_workflows/quantum_espresso/*_out.ipynb
        retention-days: 1

  nfdi4ing:
    runs-on: ubuntu-22.04
    steps:
    - uses: actions/checkout@v4
    - name: Conda config
      run: echo -e "channels:\n  - conda-forge\n" > .condarc
    - uses: conda-incubator/setup-miniconda@v3
      with:
        python-version: "3.12"
        miniforge-version: latest
        condarc-file: .condarc
        environment-file: binder/environment.yml
    - name: Installation and setup
      shell: bash -l {0}
      run: |
        pip install --no-deps --no-build-isolation -e .
        conda install -c conda-forge jupyter papermill
        verdi presto --profile-name pwd
        sudo apt-get install -y $(cat binder/apt.txt)
    - name: Create Additional Conda Environments
      shell: bash -l {0}
      run: |
        conda env create -n preprocessing -f example_workflows/nfdi/source/envs/preprocessing.yaml -y
        conda env create -n processing -f example_workflows/nfdi/source/envs/processing.yaml -y
        conda env create -n postprocessing -f example_workflows/nfdi/source/envs/postprocessing.yaml -y
    - name: Tests
      shell: bash -l {0}
      run: |
        cd example_workflows/nfdi/
        papermill aiida.ipynb aiida_out.ipynb -k "python3"
        papermill cwl.ipynb cwl_out.ipynb -k "python3"
        papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
        papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
        papermill pyiron_workflow.ipynb pyiron_workflow_out.ipynb -k "python3"
        papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"
    - name: Upload executed notebooks
      uses: actions/upload-artifact@v4
      with:
        name: nfdi-notebooks
        path: example_workflows/nfdi/*_out.ipynb
        retention-days: 1

  documentation:
    runs-on: ubuntu-latest
    needs: [arithmetic, quantumespresso, nfdi4ing]
    steps:
    - uses: actions/checkout@v4
    - name: Conda config
      run: echo -e "channels:\n  - conda-forge\n" > .condarc
    - uses: conda-incubator/setup-miniconda@v3
      with:
        python-version: "3.12"
        miniforge-version: latest
        condarc-file: .condarc
        environment-file: documentation/environment.yml
    - name: Download executed notebooks
      uses: actions/download-artifact@v4
      with:
        path: executed-notebooks
    - name: Copy executed notebooks to their locations
      run: |
        # Copy arithmetic notebooks
        cp executed-notebooks/arithmetic-notebooks/*.ipynb example_workflows/arithmetic/

        # Copy quantum espresso notebooks
        cp executed-notebooks/quantumespresso-notebooks/*.ipynb example_workflows/quantum_espresso/

        # Copy nfdi notebooks
        cp executed-notebooks/nfdi-notebooks/*.ipynb example_workflows/nfdi/
    - name: Build Jupyterbook
      shell: bash -l {0}
      run: |
        cp documentation/_config.yml .
        cp documentation/_toc.yml .
        cp documentation/*.md .
        jupyter-book build . --path-output public
        mv public/_build/html public_html
        touch public_html/.nojekyll
    - name: Deploy 🚀
      uses: JamesIves/github-pages-deploy-action@3.7.1
      with:
        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        BRANCH: gh-pages
        FOLDER: public_html
        CLEAN: true