test_bioimageio_resources.yaml

name: test BioImage.IO resources  # for compatibility with ilastik

concurrency: test-resources

on:
  workflow_dispatch:
    inputs:
      pending_matrix:
        description: 'json encoded gh matrix of pending validations for new or updated resources (default: test on all resources)'
        required: true
        default: '{"include": [{"resource_id": "**", "version_id": "**"}]}'
        type: string

env:
  BIOIMAGEIO_COUNT_RDF_DOWNLOADS: 'false'

jobs:
  setup:
    runs-on: ubuntu-latest
    outputs:
      version_matrix: ${{ steps.cvm.outputs.version_matrix }}
      pending_empty: ${{ steps.pending_empty.outputs.is_empty }}
    steps:
    - name: is pending matrix empty?
      id: pending_empty
      shell: python
      run: |
        import json
        import os
        pm = json.loads('${{ github.event.inputs.pending_matrix }}')
        with open(os.environ['GITHUB_OUTPUT'], 'a') as fh:
            print(f"is_empty={'no' if pm['include'] else 'yes'}", file=fh)
    - name: download version list
      if: steps.pending_empty.outputs.is_empty == 'no'
      run: wget https://files.ilastik.org/ilastik-versions-bmz.json
    - name: create version matrix
      if: steps.pending_empty.outputs.is_empty == 'no'
      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
    if: needs.setup.outputs.pending_empty == 'no'
    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: test with ilastik ${{ matrix.v }}
      shell: bash -l {0}
      run: python scripts/test_many_with_ilastik.py dist '${{ github.event.inputs.pending_matrix }}' --postfix ${{ matrix.v }}
    - name: Upload test summaries
      uses: actions/upload-artifact@v3
      with:
        name: ${{ matrix.v }}
        path: dist
        retention-days: 1

  deploy:
    needs: [run, setup]
    if: needs.setup.outputs.pending_empty == 'no'
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v3
    - uses: actions/download-artifact@v3
      with:
        path: artifacts
    - name: merge ilastik test summaries  # (they differ by postfix)
      run: |
        mkdir dist
        cp -r artifacts/*/* dist
    - name: Deploy test summaries to gh-pages 🚀
      uses: JamesIves/github-pages-deploy-action@v4.2.3
      with:
        clean: false
        branch: gh-pages
        folder: dist