Retile demo site #36
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Retile demo site | |
| on: | |
| workflow_dispatch: {} | |
| permissions: | |
| contents: read | |
| env: | |
| LD_LIBRARY_PATH: "${{ github.workspace }}/install/lib" | |
| PYTHONPATH: "${{ github.workspace }}/install/python" | |
| PYTHONUNBUFFERED: 1 | |
| RUNTIME_DEPS: "python3 python3-boto3 python3-pillow python3-requests \ | |
| zlib libpng libjpeg-turbo libtiff openjpeg2 gdk-pixbuf2 \ | |
| gdk-pixbuf2-modules libxml2 sqlite cairo glib2" | |
| jobs: | |
| build: | |
| name: Build releases | |
| runs-on: ubuntu-latest | |
| container: registry.fedoraproject.org/fedora:latest | |
| steps: | |
| - name: Install dependencies | |
| run: | | |
| dnf install -y \ | |
| jq xz \ | |
| python3 python3-devel python3-pip python3-pillow \ | |
| gcc meson pkg-config \ | |
| zlib-devel \ | |
| libpng-devel \ | |
| libjpeg-turbo-devel \ | |
| libtiff-devel \ | |
| openjpeg2-devel \ | |
| gdk-pixbuf2-devel \ | |
| libxml2-devel \ | |
| sqlite-devel \ | |
| cairo-devel \ | |
| glib2-devel \ | |
| git-core | |
| - name: Download releases | |
| run: | | |
| set -euxo pipefail | |
| get_release() { | |
| # Query GitHub for latest release | |
| curl -s -H "Accept: application/vnd.github.v3+json" \ | |
| "https://api.github.com/repos/openslide/$1/releases/latest" \ | |
| > "$1-release.json" | |
| local env_var=$(echo "$1" | tr a-z- A-Z_)_VERSION | |
| local version=$(jq -r .tag_name < "$1-release.json" | sed s/^v//) | |
| echo "${env_var}=${version}" >> ${GITHUB_ENV} | |
| # Download release | |
| local url=$(jq -r '.assets | map(select(.content_type == "application/x-xz")) | .[0].browser_download_url' < "$1-release.json") | |
| curl -LO "${url}" | |
| # Unpack | |
| tar xf "$1-${version}.tar.xz" | |
| } | |
| git clone https://github.com/openslide/openslide | |
| git clone https://github.com/bgilbert/openslide-python -b icc | |
| #get_release openslide | |
| #get_release openslide-python | |
| - name: Build OpenSlide | |
| working-directory: openslide | |
| run: | | |
| meson setup builddir --prefix=${GITHUB_WORKSPACE}/install | |
| meson compile -C builddir | |
| meson install -C builddir | |
| - name: Build OpenSlide Python | |
| working-directory: openslide-python | |
| run: | | |
| pip install -t ${GITHUB_WORKSPACE}/install/python . | |
| - name: Upload build | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: build | |
| path: install | |
| setup: | |
| name: Set up tiling | |
| needs: build | |
| runs-on: ubuntu-latest | |
| container: registry.fedoraproject.org/fedora:latest | |
| steps: | |
| - name: Check out repo | |
| uses: actions/checkout@v3 | |
| with: | |
| path: website | |
| - name: Install dependencies | |
| run: dnf install -y ${RUNTIME_DEPS} | |
| - name: Download build | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: build | |
| path: install | |
| - name: Set up tiling | |
| id: start-tiling | |
| working-directory: website/demo | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ secrets.DEMO_TILER_AWS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.DEMO_TILER_AWS_SECRET_KEY }} | |
| run: | | |
| ./_synctiles.py start \ | |
| ${GITHUB_WORKSPACE}/context \ | |
| matrix | |
| echo "slide-matrix=$(cat matrix)" >> $GITHUB_OUTPUT | |
| - name: Upload context | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: context | |
| path: context | |
| outputs: | |
| slide-matrix: ${{ steps.start-tiling.outputs.slide-matrix }} | |
| tile: | |
| name: Tile | |
| needs: setup | |
| runs-on: ubuntu-latest | |
| container: registry.fedoraproject.org/fedora:latest | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJson(needs.setup.outputs.slide-matrix) }} | |
| steps: | |
| - name: Check out repo | |
| uses: actions/checkout@v3 | |
| with: | |
| path: website | |
| - name: Install dependencies | |
| run: dnf install -y ${RUNTIME_DEPS} | |
| - name: Download build | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: build | |
| path: install | |
| - name: Download context | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: context | |
| - name: Tile slide | |
| working-directory: website/demo | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ secrets.DEMO_TILER_AWS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.DEMO_TILER_AWS_SECRET_KEY }} | |
| run: | | |
| ./_synctiles.py tile \ | |
| ${GITHUB_WORKSPACE}/context \ | |
| "${{ matrix.slide }}" \ | |
| ${GITHUB_WORKSPACE}/summary | |
| - name: Upload summary | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: summary | |
| path: summary | |
| finish: | |
| name: Finish tiling | |
| needs: tile | |
| runs-on: ubuntu-latest | |
| container: registry.fedoraproject.org/fedora:latest | |
| steps: | |
| - name: Check out repo | |
| uses: actions/checkout@v3 | |
| with: | |
| path: website | |
| - name: Install dependencies | |
| run: dnf install -y ${RUNTIME_DEPS} | |
| - name: Download build | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: build | |
| path: install | |
| - name: Download context | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: context | |
| - name: Download summaries | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: summary | |
| path: summary | |
| - name: Finish tiling | |
| working-directory: website/demo | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ secrets.DEMO_TILER_AWS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.DEMO_TILER_AWS_SECRET_KEY }} | |
| run: | | |
| ./_synctiles.py finish \ | |
| ${GITHUB_WORKSPACE}/context \ | |
| ${GITHUB_WORKSPACE}/summary |