Add safety check for masked loading of ROI tables to support ngio masked ROI tables #594
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| name: Manifest creation (external packages) | |
| on: | |
| push: | |
| branches: ["main"] | |
| pull_request: | |
| branches: ["main"] | |
| workflow_dispatch: | |
| schedule: | |
| - cron: "0 23 * * 2,3,4" | |
| jobs: | |
| test-manifest-creation: | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| fail-fast: false # Do not make the whole matrix fail if one element fails | |
| matrix: | |
| package: [skip] | |
| github_repo: [skip] | |
| github_branch: [skip] | |
| manifest_path: [skip] | |
| cmd_install: [skip] | |
| cmd_create_manifest: [skip] | |
| custom_dependencies: [skip] | |
| include: | |
| - package: scMultipleX | |
| github_repo: fmi-basel/gliberal-scMultipleX | |
| github_branch: main | |
| manifest_path: src/scmultiplex/__FRACTAL_MANIFEST__.json | |
| cmd_install: 'python -m pip install -e .[fractal-tasks,spherical-harmonics]' | |
| cmd_create_manifest: 'python src/scmultiplex/dev/create_manifest.py' | |
| custom_dependencies: 'image_registration' | |
| # - package: APx_fractal_task_collection | |
| # github_repo: Apricot-Therapeutics/APx_fractal_task_collection | |
| # github_branch: main | |
| # manifest_path: src/apx_fractal_task_collection/__FRACTAL_MANIFEST__.json | |
| # cmd_install: 'python -m pip install -e .' | |
| # cmd_create_manifest: 'python src/apx_fractal_task_collection/dev/update_manifest.py' | |
| # custom_dependencies: '' | |
| exclude: | |
| - package: skip | |
| github_repo: skip | |
| github_branch: skip | |
| manifest_path: skip | |
| cmd_install: skip | |
| cmd_create_manifest: skip | |
| custom_dependencies: skip | |
| steps: | |
| - name: Print matrix-element information | |
| run: echo '${{ matrix.package }}, ${{ matrix.github_repo }}, ${{ matrix.cmd_install }}, ${{ matrix.cmd_create_manifest }}, ${{ matrix.manifest_path }}' | |
| - name: Get package source code | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: ${{ matrix.github_repo }} | |
| ref: ${{ matrix.github_branch }} | |
| persist-credentials: false | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| cache: 'pip' | |
| - name: Update pip | |
| run: python -m pip install --upgrade pip | |
| - name: Install package | |
| run: ${{ matrix.cmd_install }} | |
| - name: Get current branch of `fractal-tasks-core` | |
| uses: actions/checkout@v4 | |
| with: | |
| path: fractal-tasks-core | |
| persist-credentials: false | |
| - name: Install current fractal-tasks-core (this may fail) | |
| run: python -m pip install -e ./fractal-tasks-core | |
| - name: Install custom additional dependencies (see issue 803) | |
| if: ${{ matrix.custom_dependencies != '' }} | |
| run: python -m pip install ${{ matrix.custom_dependencies }} | |
| - name: Create manifest | |
| run: ${{ matrix.cmd_create_manifest }} | |
| - name: Setup friendly diff style | |
| run: echo "*.json diff=json" >> .gitattributes && git config diff.json.textconv "jq --sort-keys '.' \$1" | |
| - name: Run git diff for manifest | |
| run: git diff ${{ matrix.manifest_path }} | |
| - name: Clean up before checking repo status | |
| run: rm -rf fractal-tasks-core .gitattributes | |
| - name: Check repo status | |
| run: if [[ -z $(git status -s) ]]; then echo "Clean status"; else echo "Dirty status"; git status; exit 1; fi |