check compatibility ilastik #171
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| name: check compatibility ilastik | |
| concurrency: ilastik | |
| on: | |
| push: | |
| branches: | |
| - main | |
| paths: | |
| - .github/workflows/check_compatibility_ilastik.yaml | |
| - scripts/check_compatibility_ilastik.py | |
| - scripts/upload_reports.py | |
| workflow_dispatch: | |
| schedule: | |
| - cron: 0 1 * * * | |
| jobs: | |
| setup: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| version_matrix: ${{ steps.cvm.outputs.version_matrix }} | |
| steps: | |
| - name: download version list | |
| run: wget https://files.ilastik.org/ilastik-versions-bmz.json | |
| - name: create version matrix | |
| id: cvm | |
| shell: python | |
| run: | | |
| import json | |
| import os | |
| with open("ilastik-versions-bmz.json") as f: | |
| vs = json.load(f) | |
| version_matrix = dict(include=[dict(v=v, env_url=f"https://files.ilastik.org/ilastik-{v}-Linux.yml") for v in vs]) | |
| with open(os.environ["GITHUB_OUTPUT"], "a") as fh: | |
| print(f"version_matrix={version_matrix}", file=fh) | |
| generate-reports: | |
| runs-on: ubuntu-latest | |
| needs: setup | |
| environment: 'production' | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJson(needs.setup.outputs.version_matrix) }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - run: wget https://${{vars.S3_HOST}}/${{vars.S3_BUCKET}}/${{vars.S3_FOLDER}}/all_versions_draft.json | |
| - run: wget https://${{vars.S3_HOST}}/${{vars.S3_BUCKET}}/${{vars.S3_FOLDER}}/all_versions.json | |
| - name: Download ilastik env | |
| run: wget --output-document env.yaml ${{ matrix.env_url }} | |
| - name: ignore unrelated packages | |
| run: sed -i '/multi-hypotheses-tracking-with-gurobi/d; /gurobi-symlink/d' env.yaml | |
| - name: Setup ilastik env | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| generate-run-shell: false | |
| environment-file: env.yaml | |
| cache-downloads: true | |
| cache-environment: false # gets stuck for 6h? | |
| - name: test drafts with ilastik ${{ matrix.v }} | |
| shell: bash -l {0} | |
| run: python scripts/check_compatibility_ilastik.py ${{ matrix.v }} all_versions_draft.json generated-reports | |
| - name: test published versions with ilastik ${{ matrix.v }} | |
| shell: bash -l {0} | |
| run: python scripts/check_compatibility_ilastik.py ${{ matrix.v }} all_versions.json generated-reports | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: generated-reports-${{ matrix.v }} | |
| path: generated-reports | |
| upload-reports: | |
| needs: generate-reports | |
| environment: 'production' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| cache: "pip" # caching pip dependencies | |
| - run: pip install . | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| merge-multiple: true | |
| path: generated-reports | |
| - run: python scripts/upload_reports.py generated-reports | |
| env: | |
| S3_HOST: ${{vars.S3_HOST}} | |
| S3_BUCKET: ${{vars.S3_BUCKET}} | |
| S3_FOLDER: ${{vars.S3_FOLDER}} | |
| S3_ACCESS_KEY_ID: ${{secrets.S3_ACCESS_KEY_ID}} | |
| S3_SECRET_ACCESS_KEY: ${{secrets.S3_SECRET_ACCESS_KEY}} | |
| RUN_URL: ${{github.server_url}}/${{github.repository}}/actions/runs/${{github.run_id}} | |