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FynnBeFynnBe
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merge conda and main test jobs
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‎.github/workflows/build.yaml

Lines changed: 42 additions & 91 deletions
Original file line numberDiff line numberDiff line change
@@ -22,35 +22,49 @@ jobs:
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jupyter: true
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version: "24.3"
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test-spec-conda:
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test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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include:
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- python-version: '3.8'
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conda-env: py38
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spec: conda
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- python-version: '3.8'
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conda-env: py38
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spec: main
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- python-version: '3.9'
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conda-env: wo-python
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spec: conda
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- python-version: '3.9'
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conda-env: tf
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spec: main
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- python-version: '3.10'
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conda-env: wo-python
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spec: conda
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- python-version: '3.11'
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conda-env: full
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spec: main
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run-expensive-tests: true
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report-coverage: true
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- python-version: '3.12'
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conda-env: wo-python
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spec: conda
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- python-version: '3.12'
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conda-env: tf
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spec: conda
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- python-version: '3.13'
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conda-env: wo-python
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spec: main
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steps:
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- uses: actions/checkout@v4
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- id: setup
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run: |
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echo "env-name=conda-${{ matrix.conda-env }}-${{ matrix.python-version }}"
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echo "env-name=conda-${{ matrix.conda-env }}-${{ matrix.python-version }}" >> $GITHUB_OUTPUT
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echo "env-name=${{ matrix.spec }}-${{ matrix.conda-env }}-${{ matrix.python-version }}"
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echo "env-name=${{ matrix.spec }}-${{ matrix.conda-env }}-${{ matrix.python-version }}" >> $GITHUB_OUTPUT
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echo "env-file=dev/env-${{ matrix.conda-env }}.yaml"
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echo "env-file=dev/env-${{ matrix.conda-env }}.yaml" >> $GITHUB_OUTPUT
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[ ! -f dev/env-${{ matrix.conda-env }}.yaml ] && exit 1
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- uses: actions/checkout@v4
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- uses: conda-incubator/setup-miniconda@v3
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with:
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auto-update-conda: true
@@ -78,102 +92,39 @@ jobs:
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CACHE_NUMBER: 0
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id: cache
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- name: Update env
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run: conda env update --name=${{steps.setup.outputs.env-name}} --file=${{steps.setup.output.env-file}} python=${{matrix.python-version}}
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run: conda env update --name=${{steps.setup.outputs.env-name}} --file=${{steps.setup.outputs.env-file}} python=${{matrix.python-version}}
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if: steps.cache.outputs.cache-hit != 'true'
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- run: |
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pyright --version
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pyright
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- uses: actions/cache@v4
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with:
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path: bioimageio_cache
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key: "test-spec-conda-${{ steps.get-date.outputs.date }}"
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- name: pytest-spec-conda
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key: "test-${{matrix.spec}}-${{ steps.get-date.outputs.date }}"
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- name: pytest
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run: pytest --disable-pytest-warnings
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env:
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BIOIMAGEIO_CACHE_PATH: bioimageio_cache
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RUN_EXPENSIVE_TESTS: ${{ matrix.run-expensive-tests && 'true' || 'false' }}
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93-
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test-spec-main:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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include:
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- python-version: '3.8'
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conda-env: py3.8
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- python-version: '3.9'
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conda-env: tf
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- python-version: '3.11'
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conda-env: full
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report-coverage: true
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run-expensive-tests: true
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- python-version: '3.12'
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conda-env: tf
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steps:
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- id: setup
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run: |
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echo "env-name=main-${{ matrix.conda-env }}-${{ matrix.python-version }}"
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echo "env-name=main-${{ matrix.conda-env }}-${{ matrix.python-version }}" >> $GITHUB_OUTPUT
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- uses: actions/checkout@v4
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- uses: conda-incubator/setup-miniconda@v3
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with:
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auto-update-conda: true
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auto-activate-base: true
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activate-environment: ${{steps.setup.outputs.env-name}}
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channel-priority: strict
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miniforge-version: latest
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- name: Get Date
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id: get-date
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run: |
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echo "date=$(date +'%Y-week%U')"
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echo "date=$(date +'%Y-week%U')" >> $GITHUB_OUTPUT
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echo "today=$(date -u '+%Y%m%d')"
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echo "today=$(date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
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- name: Cache env
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uses: actions/cache@v4
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with:
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path: ${{ env.CONDA }}/envs/${{steps.setup.outputs.env-name}}
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key: >-
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conda-${{ runner.os }}-${{ runner.arch }}
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-${{steps.get-date.outputs.today }}
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-${{ hashFiles(matrix.conda-env) }}
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-${{env.CACHE_NUMBER }}
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env:
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CACHE_NUMBER: 0
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id: cache
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- name: Update env
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run: |
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conda env update --name=${{steps.setup.outputs.env-name}} --file=dev/env-${{matrix.conda-env}}.yaml python=${{matrix.python-version}}
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conda remove --yes --force bioimageio.spec
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if: steps.cache.outputs.cache-hit != 'true'
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- name: Install spec from main branch
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run: pip install --no-deps git+https://github.com/bioimage-io/spec-bioimage-io
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- uses: actions/cache@v4
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with:
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path: bioimageio_cache
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key: "test-spec-main-${{ steps.get-date.outputs.date }}"
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- name: pytest-spec-main
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run: pytest --disable-pytest-warnings
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env:
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BIOIMAGEIO_CACHE_PATH: bioimageio_cache
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RUN_EXPENSIVE_TESTS: ${{ matrix.run-expensive-tests && 'true' || 'false' }}
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- if: matrix.report-coverage && github.event_name == 'pull_request'
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uses: orgoro/[email protected]
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with:
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coverageFile: coverage.xml
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token: ${{ secrets.GITHUB_TOKEN }}
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- if: matrix.report-coverage && github.ref == 'refs/heads/main'
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run: |
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pip install genbadge[coverage]
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genbadge coverage --input-file coverage.xml --output-file ./dist/coverage/coverage-badge.svg
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coverage html -d dist/coverage
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- if: matrix.report-coverage && github.ref == 'refs/heads/main'
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uses: actions/upload-artifact@v4
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with:
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name: coverage
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retention-days: 1
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path: dist
109+
- if: matrix.report-coverage && github.event_name == 'pull_request'
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uses: orgoro/[email protected]
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with:
112+
coverageFile: coverage.xml
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token: ${{ secrets.GITHUB_TOKEN }}
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- if: matrix.report-coverage && github.ref == 'refs/heads/main'
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run: |
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pip install genbadge[coverage]
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genbadge coverage --input-file coverage.xml --output-file ./dist/coverage/coverage-badge.svg
118+
coverage html -d dist/coverage
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- if: matrix.report-coverage && github.ref == 'refs/heads/main'
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uses: actions/upload-artifact@v4
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with:
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name: coverage
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retention-days: 1
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path: dist
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conda-build:
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needs: test-spec-conda
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needs: test
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
@@ -202,7 +153,7 @@ jobs:
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conda-build -c conda-forge conda-recipe --no-test --output-folder ./pkgs
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docs:
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needs: [test-spec-main]
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needs: test
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if: github.ref == 'refs/heads/main'
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runs-on: ubuntu-latest
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steps:

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