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kkapplerkkappler
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split tests into notebooks and regular
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‎.github/workflows/test_notebooks.yaml‎

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# Notebook Testing Workflow
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#
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# This workflow tests Jupyter notebooks and runs by default on:
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# - Pull requests targeting the 'main' branch
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#
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# To manually trigger this workflow on any branch:
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# 1. Go to Actions tab in GitHub
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# 2. Select "Test Notebooks" workflow
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# 3. Click "Run workflow" dropdown
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# 4. Select your branch and click "Run workflow"
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name: Test Notebooks
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on:
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pull_request:
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branches:
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- main
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# Allow manual triggering from the Actions tab
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workflow_dispatch:
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jobs:
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test-notebooks:
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name: Notebooks (${{ matrix.python-version }}, ${{ matrix.os }})
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runs-on: ${{ matrix.os }}
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defaults:
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run:
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shell: bash
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strategy:
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fail-fast: true
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matrix:
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os: ["ubuntu-latest"]
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python-version: ["3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4
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- name: Install uv
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uses: astral-sh/setup-uv@v3
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with:
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version: "latest"
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- name: Set up Python ${{ matrix.python-version }}
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run: uv python install ${{ matrix.python-version }}
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- name: Cache MTH5 test files
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uses: actions/cache@v4
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with:
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path: ~/.cache/aurora
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key: mth5-test-files-${{ runner.os }}-${{ hashFiles('tests/conftest.py') }}
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restore-keys: |
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mth5-test-files-${{ runner.os }}-
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- name: Create virtual environment and install dependencies
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run: |
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uv venv --python ${{ matrix.python-version }}
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source .venv/bin/activate
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uv pip install --upgrade pip
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uv pip install 'setuptools<68'
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uv pip install -e ".[dev,test]"
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uv pip install mt_metadata[obspy]
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uv pip install "mt_metadata[obspy]"
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uv pip install mth5
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uv pip install git+https://github.com/kujaku11/mth5_test_data.git
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# Explicitly include nbconvert & ipykernel
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uv pip install jupyter nbconvert nbformat ipykernel
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python -m ipykernel install --user --name "python3"
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- name: Install system dependencies
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run: |
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sudo apt-get update
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sudo apt-get install -y pandoc
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- name: Execute Jupyter Notebooks
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run: |
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source .venv/bin/activate
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# debugging: print locations of key packages
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python -c "import pkg_resources; print('pkg_resources location:', pkg_resources.__file__)"
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python -c "import setuptools; print('setuptools location:', setuptools.__file__)"
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python << 'EOF'
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import nbformat
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import subprocess
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import sys
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notebooks = [
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"docs/examples/dataset_definition.ipynb",
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"docs/examples/operate_aurora.ipynb",
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"docs/tutorials/pkd_units_check.ipynb",
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"docs/tutorials/pole_zero_fitting/lemi_pole_zero_fitting_example.ipynb",
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"docs/tutorials/processing_configuration.ipynb",
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"docs/tutorials/process_cas04_multiple_station.ipynb",
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"docs/tutorials/synthetic_data_processing.ipynb"
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]
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failures = []
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for nb_path in notebooks:
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# Update kernel spec
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print(f"Updating kernel in {nb_path}")
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try:
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with open(nb_path, "r", encoding="utf-8") as f:
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nb = nbformat.read(f, as_version=4)
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nb["metadata"]["kernelspec"]["name"] = "python3"
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nb["metadata"]["kernelspec"]["display_name"] = "Python (python3)"
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with open(nb_path, "w", encoding="utf-8") as f:
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nbformat.write(nb, f)
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print(f"✓ Updated kernel in {nb_path}")
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except Exception as e:
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print(f"✗ Failed to update kernel in {nb_path}: {e}")
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failures.append(nb_path)
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continue
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# Execute notebook
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print(f"Executing {nb_path}")
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result = subprocess.run(
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["jupyter", "nbconvert", "--to", "notebook", "--execute", nb_path],
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capture_output=True,
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text=True
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)
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if result.returncode != 0:
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print(f"✗ Failed to execute {nb_path}")
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print(result.stderr)
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failures.append(nb_path)
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else:
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print(f"✓ Successfully executed {nb_path}")
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if failures:
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print("\n======= Summary =======")
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print(f"Failed notebooks: {failures}")
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sys.exit(1)
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else:
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print("\n✓ All notebooks executed successfully!")
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EOF

‎.github/workflows/tests.yaml‎

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uv pip install jupyter nbconvert nbformat ipykernel pytest pytest-cov pytest-timeout codecov
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python -m ipykernel install --user --name "python3"
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- name: Install system dependencies
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run: |
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sudo apt-get update
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sudo apt-get install -y pandoc
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- name: Set kernel and execute Jupyter Notebooks
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run: |
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source .venv/bin/activate
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# debugging: print locations of key packages
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python -c "import pkg_resources; print('pkg_resources location:', pkg_resources.__file__)"
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python -c "import setuptools; print('setuptools location:', setuptools.__file__)"
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python << 'EOF'
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import nbformat
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import subprocess
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import sys
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notebooks = [
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"docs/examples/dataset_definition.ipynb",
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"docs/examples/operate_aurora.ipynb",
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"docs/tutorials/pkd_units_check.ipynb",
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"docs/tutorials/pole_zero_fitting/lemi_pole_zero_fitting_example.ipynb",
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"docs/tutorials/processing_configuration.ipynb",
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"docs/tutorials/process_cas04_multiple_station.ipynb",
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"docs/tutorials/synthetic_data_processing.ipynb"
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]
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failures = []
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for nb_path in notebooks:
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# Update kernel spec
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print(f"Updating kernel in {nb_path}")
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try:
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with open(nb_path, "r", encoding="utf-8") as f:
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nb = nbformat.read(f, as_version=4)
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nb["metadata"]["kernelspec"]["name"] = "python3"
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nb["metadata"]["kernelspec"]["display_name"] = "Python (python3)"
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with open(nb_path, "w", encoding="utf-8") as f:
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nbformat.write(nb, f)
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print(f"✓ Updated kernel in {nb_path}")
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except Exception as e:
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print(f"✗ Failed to update kernel in {nb_path}: {e}")
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failures.append(nb_path)
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continue
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# Execute notebook
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print(f"Executing {nb_path}")
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result = subprocess.run(
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["jupyter", "nbconvert", "--to", "notebook", "--execute", nb_path],
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capture_output=True,
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text=True
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)
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if result.returncode != 0:
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print(f"✗ Failed to execute {nb_path}")
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print(result.stderr)
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failures.append(nb_path)
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else:
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print(f"✓ Successfully executed {nb_path}")
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if failures:
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print("\n======= Summary =======")
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print(f"Failed notebooks: {failures}")
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sys.exit(1)
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else:
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print("\n✓ All notebooks executed successfully!")
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EOF
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- name: Run Tests
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run: |
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source .venv/bin/activate

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