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Merge pull request #114 from bgilbert/retile
Retiling simplifications
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‎.github/workflows/retile.yml‎

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@@ -7,189 +7,124 @@ permissions:
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contents: read
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env:
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LD_LIBRARY_PATH: "${{ github.workspace }}/install/lib64"
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PYTHONPATH: "${{ github.workspace }}/install/python"
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PIP_CACHE_KEY: retile-pip-${{ github.run_id }}
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PYTHONUNBUFFERED: 1
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RUNTIME_DEPS: "python3 python3-boto3 python3-pillow python3-requests \
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zlib libpng libjpeg-turbo libtiff openjpeg2 gdk-pixbuf2 \
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gdk-pixbuf2-modules-extra libxml2 sqlite cairo glib2"
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PYTHON_VER: "3.14t"
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PYTHON_DEPS: "boto3 openslide-bin openslide-python requests"
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jobs:
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build:
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name: Build releases
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runs-on: ubuntu-latest
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container: registry.fedoraproject.org/fedora:latest
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steps:
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- name: Install dependencies
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run: |
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dnf install -y \
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jq xz \
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python3 python3-devel python3-pip python3-pillow python3-wheel \
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gcc meson pkg-config \
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zlib-devel \
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libpng-devel \
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libjpeg-turbo-devel \
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libtiff-devel \
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openjpeg2-devel \
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gdk-pixbuf2-devel \
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gdk-pixbuf2-modules-extra \
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libxml2-devel \
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sqlite-devel \
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cairo-devel \
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glib2-devel
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- name: Download releases
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run: |
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set -euxo pipefail
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get_release() {
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# Query GitHub for latest release
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curl -s -H "Accept: application/vnd.github.v3+json" \
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"https://api.github.com/repos/openslide/$1/releases/latest" \
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> "$1-release.json"
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local env_var=$(echo "$1" | tr a-z- A-Z_)_VERSION
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local version=$(jq -r .tag_name < "$1-release.json" | sed s/^v//)
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echo "${env_var}=${version}" >> ${GITHUB_ENV}
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# Download release
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local url=$(jq -r '.assets | map(select(.content_type == "application/x-xz")) | .[0].browser_download_url' < "$1-release.json")
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curl -LO "${url}"
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# Unpack
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tar xf "$(echo "$1" | tr - _)-${version}.tar.xz"
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}
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get_release openslide
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get_release openslide-python
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- name: Build OpenSlide
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working-directory: openslide-${{ env.OPENSLIDE_VERSION }}
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run: |
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meson setup builddir --prefix=${GITHUB_WORKSPACE}/install
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meson compile -C builddir
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trap "cat builddir/meson-logs/testlog.txt" ERR
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meson test -C builddir
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trap - ERR
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meson install -C builddir
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- name: Build OpenSlide Python
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working-directory: openslide_python-${{ env.OPENSLIDE_PYTHON_VERSION }}
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run: |
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pip install -t ${GITHUB_WORKSPACE}/install/python .
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- name: Upload build
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uses: actions/upload-artifact@v5
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with:
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name: build
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path: install
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setup:
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name: Set up tiling
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environment: demo-site
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needs: build
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runs-on: ubuntu-latest
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container: registry.fedoraproject.org/fedora:latest
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steps:
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- name: Check out repo
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uses: actions/checkout@v5
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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path: website
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python-version: ${{ env.PYTHON_VER }}
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- name: Install dependencies
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run: dnf install -y ${RUNTIME_DEPS}
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- name: Download build
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uses: actions/download-artifact@v6
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run: pip install --break-system-packages ${PYTHON_DEPS}
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- name: Cache dependencies
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uses: actions/cache/save@v4
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with:
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name: build
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path: install
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key: ${{ env.PIP_CACHE_KEY }}
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path: /home/runner/.cache/pip
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- name: Set up tiling
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id: start-tiling
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working-directory: website/demo
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working-directory: demo
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env:
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AWS_ACCESS_KEY_ID: ${{ secrets.DEMO_TILER_AWS_KEY_ID }}
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AWS_SECRET_ACCESS_KEY: ${{ secrets.DEMO_TILER_AWS_SECRET_KEY }}
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run: |
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./_synctiles.py start \
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"${{ vars.DEMO_TILER_BUCKET }}" \
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${GITHUB_WORKSPACE}/context \
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matrix
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./_synctiles.py start "${{ vars.DEMO_TILER_BUCKET }}" context matrix
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echo "slide-matrix=$(cat matrix)" >> $GITHUB_OUTPUT
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- name: Upload context
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uses: actions/upload-artifact@v5
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with:
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name: context
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path: context
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path: demo/context
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outputs:
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slide-matrix: ${{ steps.start-tiling.outputs.slide-matrix }}
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tile:
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name: Tile
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environment: demo-site
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needs: setup
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runs-on: ubuntu-latest
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container: registry.fedoraproject.org/fedora:latest
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strategy:
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fail-fast: false
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matrix: ${{ fromJson(needs.setup.outputs.slide-matrix) }}
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steps:
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- name: Check out repo
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uses: actions/checkout@v5
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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path: website
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- name: Install dependencies
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run: dnf install -y ${RUNTIME_DEPS}
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- name: Download build
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uses: actions/download-artifact@v6
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python-version: ${{ env.PYTHON_VER }}
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- name: Cache dependencies
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uses: actions/cache/restore@v4
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with:
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name: build
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path: install
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key: ${{ env.PIP_CACHE_KEY }}
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path: /home/runner/.cache/pip
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fail-on-cache-miss: true
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- name: Install dependencies
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run: pip install --break-system-packages ${PYTHON_DEPS}
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- name: Download context
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uses: actions/download-artifact@v6
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with:
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name: context
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path: demo
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- name: Tile slide
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working-directory: website/demo
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working-directory: demo
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env:
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AWS_ACCESS_KEY_ID: ${{ secrets.DEMO_TILER_AWS_KEY_ID }}
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AWS_SECRET_ACCESS_KEY: ${{ secrets.DEMO_TILER_AWS_SECRET_KEY }}
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run: |
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./_synctiles.py tile \
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${GITHUB_WORKSPACE}/context \
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"${{ matrix.slide }}" \
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${GITHUB_WORKSPACE}/summary
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./_synctiles.py tile context "${{ matrix.slide }}" summary
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echo "ARTIFACT_NAME=summary-$(echo "${{ matrix.slide }}" | tr -c "a-zA-Z0-9\n" _)" >> $GITHUB_ENV
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- name: Upload summary
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uses: actions/upload-artifact@v5
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with:
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name: ${{ env.ARTIFACT_NAME }}
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path: summary
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path: demo/summary
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finish:
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name: Finish tiling
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environment: demo-site
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needs: tile
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runs-on: ubuntu-latest
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container: registry.fedoraproject.org/fedora:latest
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steps:
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- name: Check out repo
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uses: actions/checkout@v5
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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path: website
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- name: Install dependencies
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run: dnf install -y ${RUNTIME_DEPS}
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- name: Download build
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uses: actions/download-artifact@v6
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python-version: ${{ env.PYTHON_VER }}
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- name: Cache dependencies
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uses: actions/cache/restore@v4
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with:
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name: build
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path: install
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key: ${{ env.PIP_CACHE_KEY }}
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path: /home/runner/.cache/pip
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fail-on-cache-miss: true
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- name: Install dependencies
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run: pip install --break-system-packages ${PYTHON_DEPS}
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- name: Download context
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uses: actions/download-artifact@v6
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with:
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name: context
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path: demo
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- name: Download summaries
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uses: actions/download-artifact@v6
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with:
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pattern: "summary-*"
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path: summary
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path: demo/summary
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merge-multiple: true
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- name: Finish tiling
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working-directory: website/demo
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working-directory: demo
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env:
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AWS_ACCESS_KEY_ID: ${{ secrets.DEMO_TILER_AWS_KEY_ID }}
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AWS_SECRET_ACCESS_KEY: ${{ secrets.DEMO_TILER_AWS_SECRET_KEY }}
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run: |
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./_synctiles.py finish \
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${GITHUB_WORKSPACE}/context \
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${GITHUB_WORKSPACE}/summary
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./_synctiles.py finish context summary

‎.pre-commit-config.yaml‎

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- id: trailing-whitespace
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- repo: https://github.com/asottile/pyupgrade
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rev: v3.21.0
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rev: v3.21.2
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hooks:
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- id: pyupgrade
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name: Modernize Python code
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name: Reorder Python imports with isort
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- repo: https://github.com/psf/black
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rev: 25.9.0
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rev: 25.11.0
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hooks:
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- id: black
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name: Format Python code with black
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additional_dependencies: [flake8-bugbear, Flake8-pyproject]
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- repo: https://github.com/pre-commit/mirrors-mypy
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rev: v1.18.2
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rev: v1.19.0
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hooks:
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- id: mypy
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name: Check Python types

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