test BioImage.IO resources #1672
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| 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: ${{ steps.pending_empty.outputs.is_empty }} | |
| steps: | |
| - name: is pending matrix empty? | |
| id: pending_empty | |
| shell: python | |
| run: | | |
| import json | |
| pm = json.loads('${{ github.event.inputs.pending_matrix }}') | |
| print(f"::set-output is_empty={'no' if pm['include'] else 'yes'}") | |
| - 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 | |
| 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]) | |
| print(f"::set-output name=version_matrix::{version_matrix}") | |
| 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@v2 | |
| - uses: actions/checkout@v2 | |
| with: | |
| repository: bioimage-io/collection-bioimage-io | |
| ref: gh-pages | |
| path: bioimageio-gh-pages | |
| - name: Setup ilastik env | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| activate-environment: ilastik-env | |
| use-mamba: true | |
| - name: Cache ilastik env | |
| uses: actions/cache@v2 | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: conda-${{ runner.os }}--${{ runner.arch }}--${{ matrix.v }}-${{ env.CACHE_NUMBER }} | |
| env: | |
| # Increase this value to reset cache if etc/example-environment.yml has not changed | |
| CACHE_NUMBER: 0 | |
| id: cache | |
| - name: Download ilastik env | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: wget --output-document env.yaml ${{ matrix.env_url }} | |
| - run: pip install ruamel.yaml # not in the conda env | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| - run: which python | |
| - run: which python | |
| shell: bash -l {0} | |
| - name: ignore unrelated packages | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| shell: python # not the conda env | |
| run: | | |
| from pathlib import Path | |
| from ruamel.yaml import YAML | |
| yaml = YAML(typ="safe") | |
| with Path("env.yaml").open() as f: | |
| env = yaml.load(f) | |
| ignore_deps = ["multi-hypotheses-tracking-with-gurobi", "gurobi-symlink"] | |
| ignored = [] | |
| remaining = [] | |
| for d in env["dependencies"]: | |
| if d.split("=")[0] in ignore_deps: | |
| ignored.append(d) | |
| else: | |
| remaining.append(d) | |
| print("ignored", ignored) | |
| env["dependencies"] = remaining | |
| with Path("env.yaml").open("w") as f: | |
| yaml.dump(env, f) | |
| - name: Update environment | |
| shell: bash -l {0} | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: mamba env update -n ilastik-env -f env.yaml | |
| - 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/[email protected] | |
| with: | |
| clean: false | |
| branch: gh-pages | |
| folder: dist |