check compatibility ilastik #29
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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 | |
| workflow_dispatch: | |
| schedule: | |
| - cron: 0 1 * * * # update compatibility once a day | |
| 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) | |
| run: | |
| runs-on: ubuntu-latest | |
| needs: setup | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJson(needs.setup.outputs.version_matrix) }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/checkout@v3 | |
| with: | |
| repository: bioimage-io/collection-bioimage-io | |
| ref: gh-pages | |
| path: bioimageio-gh-pages | |
| - 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: | |
| environment-file: env.yaml | |
| cache-downloads: true | |
| cache-environment: true | |
| - name: install backoffice | |
| shell: bash -l {0} | |
| run: pip install . | |
| - name: test with ilastik ${{ matrix.v }} | |
| shell: bash -l {0} | |
| run: python scripts/check_compatibility_ilastik.py ${{ matrix.v }} |