test BioImage.IO resources #1681
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: 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 |