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RaphaelBajonRaphaelBajon
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Merge pull request #8 from RaphaelBajon/feature/deployment
update docs for xarray accessor and deployment
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‎.github/workflows/deploy.yml‎

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workflow_dispatch:
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jobs:
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test-deploy:
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# ---------------------------------------------------------------------------
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# 1. Run the full test suite before attempting any deployment
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# ---------------------------------------------------------------------------
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test:
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name: Run tests (Python ${{ matrix.python-version }})
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runs-on: ubuntu-latest
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strategy:
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fail-fast: true
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matrix:
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python-version: ["3.9", "3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install pytest
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pip install -r requirements.txt
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- name: Run pytest
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run: pytest --tb=short
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# ---------------------------------------------------------------------------
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# 2. Build the distribution once — all deploy jobs reuse the same artifact
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# ---------------------------------------------------------------------------
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build:
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name: Build distribution
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runs-on: ubuntu-latest
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needs: test
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: "3.x"
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- name: Clean build cache
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run: |
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rm -rf build dist .eggs
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find . -name "*.pyc" -delete
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find . -name "__pycache__" -delete
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- name: Install build tools
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run: pip install --upgrade pip build tomli
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- name: Read version from pyproject.toml
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id: version
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run: |
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VERSION=$(python -c "import tomli; print(tomli.load(open('pyproject.toml', 'rb'))['project']['version'])")
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echo "version=$VERSION" >> $GITHUB_OUTPUT
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echo "Building version $VERSION"
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- name: Build sdist and wheel
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run: python -m build
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- name: Upload distribution artifact
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uses: actions/upload-artifact@v4
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with:
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name: dist-${{ steps.version.outputs.version }}
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path: dist/
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retention-days: 7
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outputs:
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version: ${{ steps.version.outputs.version }}
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# ---------------------------------------------------------------------------
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# 3. Deploy to TestPyPI and run a smoke test
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# ---------------------------------------------------------------------------
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deploy-test:
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name: Deploy to TestPyPI
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runs-on: ubuntu-latest
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needs: build
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environment: testpypi
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permissions:
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id-token: write
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contents: read
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.x"
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- name: Clean build cache
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run: |
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rm -rf build dist .eggs
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find . -name "*.pyc" -delete
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find . -name "__pycache__" -delete
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build twine tomli
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- name: Install dependencies requirements
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run: |
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if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
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- name: Debug directory content
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run: |
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pwd
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ls -la
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- name: Build package
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run: python -m build
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- name: Check version on TestPyPI and Upload if new
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env:
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TWINE_USERNAME: __token__
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TWINE_PASSWORD: ${{ secrets.TEST_PYPI_TOKEN }}
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TWINE_REPOSITORY_URL: https://test.pypi.org/legacy/
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continue-on-error: true
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run: |
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# Get current version from pyproject.toml
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VERSION=$(python -c "import tomli; print(tomli.load(open('pyproject.toml', 'rb'))['project']['version'])")
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echo "Package version: $VERSION"
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# Try to install current version from TestPyPI
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if pip install --index-url https://test.pypi.org/simple/ --no-deps canyonbpy==$VERSION 2>/dev/null; then
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echo "Version $VERSION already exists on TestPyPI"
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else
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echo "Version $VERSION not found on TestPyPI, uploading..."
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python -m twine upload --verbose dist/*
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fi
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- name: Wait for TestPyPI to process upload
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run: sleep 60
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- name: Test installation from TestPyPI
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run: |
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python -m pip install --index-url https://test.pypi.org/simple/ --no-deps canyonbpy
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python -c "from canyonbpy import canyonb"
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: "3.x"
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- name: Download distribution artifact
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uses: actions/download-artifact@v4
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with:
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name: dist-${{ needs.build.outputs.version }}
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path: dist/
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- name: Check if version already exists on TestPyPI
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id: testpypi-check
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run: |
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VERSION=${{ needs.build.outputs.version }}
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STATUS=$(curl -s -o /dev/null -w "%{http_code}" \
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https://test.pypi.org/pypi/canyonbpy/$VERSION/json)
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if [ "$STATUS" = "200" ]; then
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echo "exists=true" >> $GITHUB_OUTPUT
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echo "Version $VERSION already on TestPyPI — skipping upload."
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else
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echo "exists=false" >> $GITHUB_OUTPUT
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echo "Version $VERSION not found on TestPyPI — will upload."
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fi
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- name: Upload to TestPyPI
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if: steps.testpypi-check.outputs.exists == 'false'
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env:
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TWINE_USERNAME: __token__
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TWINE_PASSWORD: ${{ secrets.TEST_PYPI_TOKEN }}
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TWINE_REPOSITORY_URL: https://test.pypi.org/legacy/
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run: |
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pip install twine
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twine upload --verbose dist/*
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- name: Wait for TestPyPI to index the release
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if: steps.testpypi-check.outputs.exists == 'false'
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run: sleep 60
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- name: Install from TestPyPI
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run: |
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pip install -r requirements.txt
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pip install \
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--index-url https://test.pypi.org/simple/ \
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--extra-index-url https://pypi.org/simple/ \
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canyonbpy==${{ needs.build.outputs.version }}
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- name: Smoke test — verify imports, version and accessor
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run: |
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python - <<'EOF'
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import canyonbpy
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from canyonbpy import canyonb, DatasetToNumpy
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assert canyonbpy.__version__ == "${{ needs.build.outputs.version }}", \
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f"Version mismatch: {canyonbpy.__version__}"
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import xarray as xr
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import numpy as np
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ds = xr.Dataset({"pressure": ("x", [100.0])})
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assert hasattr(ds, "canyonb"), "ds.canyonb accessor not registered"
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print(f"OK canyonbpy {canyonbpy.__version__} smoke test passed")
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EOF
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# ---------------------------------------------------------------------------
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# 4. Deploy to PyPI — only runs after TestPyPI smoke test passes
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# ---------------------------------------------------------------------------
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deploy-prod:
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name: Deploy to PyPI
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needs: test-deploy
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runs-on: ubuntu-latest
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if: success()
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needs: [build, deploy-test]
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environment: pypi
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permissions:
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id-token: write
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contents: read
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steps:
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- uses: actions/setup-python@v5
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with:
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python-version: "3.x"
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- name: Download distribution artifact
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uses: actions/download-artifact@v4
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with:
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name: dist-${{ needs.build.outputs.version }}
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path: dist/
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- name: Check if version already exists on PyPI
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id: pypi-check
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run: |
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VERSION=${{ needs.build.outputs.version }}
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STATUS=$(curl -s -o /dev/null -w "%{http_code}" \
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https://pypi.org/pypi/canyonbpy/$VERSION/json)
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if [ "$STATUS" = "200" ]; then
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echo "exists=true" >> $GITHUB_OUTPUT
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echo "Version $VERSION already on PyPI — skipping upload."
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else
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echo "exists=false" >> $GITHUB_OUTPUT
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echo "Version $VERSION not found on PyPI — will upload."
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fi
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- name: Upload to PyPI
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if: steps.pypi-check.outputs.exists == 'false'
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env:
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TWINE_USERNAME: __token__
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TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
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run: |
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pip install twine
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twine upload --verbose dist/*
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# ---------------------------------------------------------------------------
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# 5. Attach the wheel and sdist to the GitHub Release
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# This also triggers Zenodo archiving (Zenodo watches release events)
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# ---------------------------------------------------------------------------
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attach-release-assets:
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name: Attach dist to GitHub Release
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runs-on: ubuntu-latest
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needs: [build, deploy-prod]
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# Only run when triggered by an actual published release, not workflow_dispatch
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if: github.event_name == 'release'
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.x"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build twine tomli
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- name: Build package
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run: python -m build
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- name: Check version on PyPI and Upload if new
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env:
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TWINE_USERNAME: __token__
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TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
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run: |
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# Get current version from pyproject.toml
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VERSION=$(python -c "import tomli; print(tomli.load(open('pyproject.toml', 'rb'))['project']['version'])")
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echo "Package version: $VERSION"
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# Try to install current version from PyPI
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if pip install canyonbpy==$VERSION 2>/dev/null; then
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echo "Version $VERSION already exists on PyPI"
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else
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echo "Version $VERSION not found on PyPI, uploading..."
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python -m twine upload --verbose dist/*
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fi
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- name: Download distribution artifact
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uses: actions/download-artifact@v4
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with:
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name: dist-${{ needs.build.outputs.version }}
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path: dist/
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- name: Upload wheel and sdist to GitHub Release
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uses: softprops/action-gh-release@v2
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with:
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files: dist/*

‎.zenodo.json‎

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{
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"title": "canyonbpy: A Python implementation of CANYON-B",
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"description": "canyonbpy is a Python package implementing the CANYON-B neural network for predicting ocean biogeochemical parameters (Total Alkalinity, Dissolved Inorganic Carbon, pH, pCO2, NO3, PO4, SiOH4) from temperature, salinity and dissolved oxygen. Based on Bittig et al. (2018).",
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"creators": [
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{
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"name": "Bajon, Raphaël",
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"affiliation": "UH Manoa, SOEST",
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"orcid": "0000-0003-1984-0539"
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}
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],
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"keywords": [
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"oceanography",
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"biogeochemistry",
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"neural network",
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"CANYON-B",
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"carbon cycle",
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"Argo",
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"xarray",
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"python"
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],
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"license": "MIT",
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"upload_type": "software",
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"access_right": "open",
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"related_identifiers": [
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{
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"identifier": "10.3389/fmars.2018.00328",
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"relation": "isDerivedFrom",
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"scheme": "doi",
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"resource_type": "publication-article"
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},
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{
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"identifier": "https://github.com/HCBScienceProducts/CANYON-B",
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"relation": "isDerivedFrom",
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"scheme": "url"
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}
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],
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"language": "eng"
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}

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