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Add nbstripout via pre commit and apply it #140

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f645f45
add .pre-commit-config.yaml
GeigerJ2 Oct 23, 2025
53e5325
apply nbstripout on all files
GeigerJ2 Oct 23, 2025
159d6b6
update deploy workflow to run tests and serve them as docs
GeigerJ2 Oct 23, 2025
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142 changes: 138 additions & 4 deletions .github/workflows/deploy.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,128 @@ on:
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
Expand All @@ -17,7 +137,21 @@ jobs:
miniforge-version: latest
condarc-file: .condarc
environment-file: documentation/environment.yml
- name: Install Jupyterbook
- 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 .
Expand All @@ -30,6 +164,6 @@ jobs:
uses: JamesIves/github-pages-deploy-action@3.7.1
with:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
BRANCH: gh-pages # The branch the action should deploy to.
FOLDER: public_html # The folder the action should deploy.
CLEAN: true
BRANCH: gh-pages
FOLDER: public_html
CLEAN: true
9 changes: 9 additions & 0 deletions .pre-commit-config.yaml
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@@ -0,0 +1,9 @@
repos:
- repo: https://github.com/kynan/nbstripout
rev: 0.7.1
hooks:
- id: nbstripout
name: nbstripout - Strip outputs from notebooks
args:
- --extra-keys
- "metadata.kernelspec metadata.language_info"
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