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update deploy workflow to run tests and serve them as docs
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‎.github/workflows/deploy.yml‎

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branches: [ main ]
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jobs:
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# Run all the test jobs first
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arithmetic:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Conda config
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run: echo -e "channels:\n - conda-forge\n" > .condarc
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- uses: conda-incubator/setup-miniconda@v3
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with:
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python-version: "3.12"
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miniforge-version: latest
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condarc-file: .condarc
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environment-file: binder/environment.yml
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- name: Installation and setup
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shell: bash -l {0}
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run: |
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pip install --no-deps --no-build-isolation -e .
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conda install -c conda-forge jupyter papermill
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verdi presto --profile-name pwd
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- name: Tests
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shell: bash -l {0}
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run: |
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cd example_workflows/arithmetic
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papermill aiida.ipynb aiida_out.ipynb -k "python3"
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papermill cwl.ipynb cwl_out.ipynb -k "python3"
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papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
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papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
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papermill pyiron_workflow.ipynb pyiron_workflow_out.ipynb -k "python3"
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papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"
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- name: Upload executed notebooks
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uses: actions/upload-artifact@v4
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with:
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name: arithmetic-notebooks
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path: example_workflows/arithmetic/*_out.ipynb
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retention-days: 1
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quantumespresso:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Setup environment
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shell: bash -l {0}
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run: |
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echo -e "channels:\n - conda-forge\n" > .condarc
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tail --lines=+4 example_workflows/quantum_espresso/environment.yml >> binder/environment.yml
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- uses: conda-incubator/setup-miniconda@v3
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with:
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python-version: "3.12"
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miniforge-version: latest
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condarc-file: .condarc
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environment-file: binder/environment.yml
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- name: Installation and setup
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shell: bash -l {0}
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run: |
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pip install --no-deps --no-build-isolation -e example_workflows/quantum_espresso/qe_xml_parser
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pip install --no-deps --no-build-isolation -e .
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conda install -c conda-forge jupyter papermill
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verdi presto --profile-name pwd
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- name: Tests
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shell: bash -l {0}
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run: |
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export ESPRESSO_PSEUDO=$(pwd)/espresso/pseudo
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cp -r example_workflows/quantum_espresso/espresso .
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cd example_workflows/quantum_espresso
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papermill aiida.ipynb aiida_out.ipynb -k "python3"
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papermill cwl.ipynb cwl_out.ipynb -k "python3"
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papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
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papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
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papermill pyiron_workflow.ipynb pyiron_workflow_out.ipynb -k "python3"
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papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"
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- name: Upload executed notebooks
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uses: actions/upload-artifact@v4
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with:
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name: quantumespresso-notebooks
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path: example_workflows/quantum_espresso/*_out.ipynb
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retention-days: 1
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nfdi4ing:
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runs-on: ubuntu-22.04
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steps:
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- uses: actions/checkout@v4
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- name: Conda config
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run: echo -e "channels:\n - conda-forge\n" > .condarc
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- uses: conda-incubator/setup-miniconda@v3
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with:
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python-version: "3.12"
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miniforge-version: latest
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condarc-file: .condarc
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environment-file: binder/environment.yml
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- name: Installation and setup
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shell: bash -l {0}
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run: |
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pip install --no-deps --no-build-isolation -e .
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conda install -c conda-forge jupyter papermill
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verdi presto --profile-name pwd
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sudo apt-get install -y $(cat binder/apt.txt)
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- name: Create Additional Conda Environments
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shell: bash -l {0}
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run: |
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conda env create -n preprocessing -f example_workflows/nfdi/source/envs/preprocessing.yaml -y
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conda env create -n processing -f example_workflows/nfdi/source/envs/processing.yaml -y
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conda env create -n postprocessing -f example_workflows/nfdi/source/envs/postprocessing.yaml -y
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- name: Tests
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shell: bash -l {0}
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run: |
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cd example_workflows/nfdi/
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papermill aiida.ipynb aiida_out.ipynb -k "python3"
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papermill cwl.ipynb cwl_out.ipynb -k "python3"
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papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
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papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
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papermill pyiron_workflow.ipynb pyiron_workflow_out.ipynb -k "python3"
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papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"
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- name: Upload executed notebooks
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uses: actions/upload-artifact@v4
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with:
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name: nfdi-notebooks
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path: example_workflows/nfdi/*_out.ipynb
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retention-days: 1
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documentation:
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runs-on: ubuntu-latest
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needs: [arithmetic, quantumespresso, nfdi4ing]
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steps:
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- uses: actions/checkout@v4
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- name: Conda config
@@ -17,7 +137,21 @@ jobs:
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miniforge-version: latest
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condarc-file: .condarc
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environment-file: documentation/environment.yml
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- name: Install Jupyterbook
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- name: Download executed notebooks
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uses: actions/download-artifact@v4
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with:
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path: executed-notebooks
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- name: Copy executed notebooks to their locations
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run: |
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# Copy arithmetic notebooks
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cp executed-notebooks/arithmetic-notebooks/*.ipynb example_workflows/arithmetic/
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# Copy quantum espresso notebooks
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cp executed-notebooks/quantumespresso-notebooks/*.ipynb example_workflows/quantum_espresso/
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# Copy nfdi notebooks
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cp executed-notebooks/nfdi-notebooks/*.ipynb example_workflows/nfdi/
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- name: Build Jupyterbook
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shell: bash -l {0}
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run: |
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cp documentation/_config.yml .
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uses: JamesIves/github-pages-deploy-action@3.7.1
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with:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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BRANCH: gh-pages # The branch the action should deploy to.
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FOLDER: public_html # The folder the action should deploy.
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CLEAN: true
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BRANCH: gh-pages
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FOLDER: public_html
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CLEAN: true

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