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Merge pull request #393 from simpeg/patches
Patches
2 parents 6561482 + 386df6f commit 3d990c8

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‎.bumpversion.cfg‎

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‎.github/workflows/publish.yaml‎

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name: Publish on PR merge
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on:
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pull_request:
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types: [opened, synchronize, reopened, labeled, closed]
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branches:
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- main
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permissions:
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contents: write
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id-token: write
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pull-requests: write
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jobs:
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update-version-and-changelog:
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# Run only when a release label is added (not on every push)
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if: |
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github.event.action == 'labeled' &&
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github.event.pull_request.merged == false && (
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contains(github.event.pull_request.labels.*.name, 'release:major') ||
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contains(github.event.pull_request.labels.*.name, 'release:minor') ||
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contains(github.event.pull_request.labels.*.name, 'release:patch')
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)
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runs-on: ubuntu-latest
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steps:
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- name: Check out PR branch
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uses: actions/checkout@v4
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with:
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ref: ${{ github.head_ref }}
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fetch-depth: 0
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token: ${{ secrets.GITHUB_TOKEN }}
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.13"
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- name: Install tools
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run: |
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pip install bump-my-version build pandoc
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sudo apt-get update
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sudo apt-get install -y pandoc
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cargo install git-cliff
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- name: Set up Git user
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run: |
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git config --local user.email "github-actions[bot]@users.noreply.github.com"
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git config --local user.name "github-actions[bot]"
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- name: Determine version bump type
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id: bump
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run: |
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if [[ "${{ contains(github.event.pull_request.labels.*.name, 'release:major') }}" == "true" ]]; then
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echo "type=major" >> $GITHUB_OUTPUT
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elif [[ "${{ contains(github.event.pull_request.labels.*.name, 'release:minor') }}" == "true" ]]; then
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echo "type=minor" >> $GITHUB_OUTPUT
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else
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echo "type=patch" >> $GITHUB_OUTPUT
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fi
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- name: Bump version
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run: bump-my-version bump ${{ steps.bump.outputs.type }}
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env:
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BMV_ALLOW_DIRTY: "true"
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- name: Extract version
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id: version
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run: |
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VERSION=$(bump-my-version show current)
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echo "Extracted version: $VERSION"
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echo "version=$VERSION" >> $GITHUB_OUTPUT
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- name: Generate changelog
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run: |
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git cliff -o CHANGELOG.md
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echo "Generated changelog for version ${{ steps.version.outputs.version }}"
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- name: Commit and push changes to PR branch
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run: |
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git add .
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git commit -m "chore: bump version to ${{ steps.version.outputs.version }} and update changelog [skip ci]" || echo "No changes to commit"
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git push origin HEAD:${{ github.head_ref }}
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publish-after-merge:
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# Run only after PR is merged with release labels
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if: |
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github.event.pull_request.merged == true && (
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contains(github.event.pull_request.labels.*.name, 'release:major') ||
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contains(github.event.pull_request.labels.*.name, 'release:minor') ||
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contains(github.event.pull_request.labels.*.name, 'release:patch')
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)
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runs-on: ubuntu-latest
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steps:
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- name: Check out repository
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.12"
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- name: Install tools
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run: pip install bump-my-version build
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- name: Extract version
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id: version
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run: |
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VERSION=$(bump-my-version show current)
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echo "version=$VERSION" >> $GITHUB_OUTPUT
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- name: Create GitHub Release
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uses: softprops/action-gh-release@v2
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with:
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tag_name: v${{ steps.version.outputs.version }}
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name: v${{ steps.version.outputs.version }}
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body_path: CHANGELOG.md
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generate_release_notes: false
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- name: Build package
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run: python -m build
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- name: Publish to TestPyPI
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id: test-pypi
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uses: pypa/gh-action-pypi-publish@v1.13.0
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with:
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repository-url: https://test.pypi.org/legacy/
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skip-existing: true
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attestations: false
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- name: Publish to PyPI
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if: steps.test-pypi.outcome == 'success'
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uses: pypa/gh-action-pypi-publish@v1.13.0
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with:
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skip-existing: true

‎.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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run:
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shell: bash
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strategy:
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fail-fast: false
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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"]
@@ -46,10 +46,16 @@ jobs:
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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] @ git+https://github.com/kujaku11/mt_metadata.git@patches"
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uv pip install git+https://github.com/kujaku11/mth5.git@patches
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uv pip install mt_metadata[obspy]
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# uv pip install "mt_metadata[obspy] @ git+https://github.com/kujaku11/mt_metadata.git@patches"
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# uv pip install git+https://github.com/kujaku11/mth5.git@patches
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# uv pip install "mt_metadata[obspy] @ git+https://github.com/kujaku11/mt_metadata.git"
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# uv pip install git+https://github.com/kujaku11/mth5.git
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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 mth5
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uv pip install git+https://github.com/kujaku11/mth5_test_data.git
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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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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",
76-
"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"
81-
]
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failures = []
84-
85-
for nb_path in notebooks:
86-
# Update kernel spec
87-
print(f"Updating kernel in {nb_path}")
88-
try:
89-
with open(nb_path, "r", encoding="utf-8") as f:
90-
nb = nbformat.read(f, as_version=4)
91-
92-
nb["metadata"]["kernelspec"]["name"] = "python3"
93-
nb["metadata"]["kernelspec"]["display_name"] = "Python (python3)"
94-
95-
with open(nb_path, "w", encoding="utf-8") as f:
96-
nbformat.write(nb, f)
97-
print(f"✓ Updated kernel in {nb_path}")
98-
except Exception as e:
99-
print(f"✗ Failed to update kernel in {nb_path}: {e}")
100-
failures.append(nb_path)
101-
continue
102-
103-
# Execute notebook
104-
print(f"Executing {nb_path}")
105-
result = subprocess.run(
106-
["jupyter", "nbconvert", "--to", "notebook", "--execute", nb_path],
107-
capture_output=True,
108-
text=True
109-
)
110-
111-
if result.returncode != 0:
112-
print(f"✗ Failed to execute {nb_path}")
113-
print(result.stderr)
114-
failures.append(nb_path)
115-
else:
116-
print(f"✓ Successfully executed {nb_path}")
117-
118-
if failures:
119-
print("\n======= Summary =======")
120-
print(f"Failed notebooks: {failures}")
121-
sys.exit(1)
122-
else:
123-
print("\n✓ All notebooks executed successfully!")
124-
EOF
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- name: Run Tests
12772
run: |
12873
source .venv/bin/activate

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