add more tests #1521
Workflow file for this run
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name: Test and Deploy bioimageio.spec | |
on: | |
push: | |
branches: [main] | |
pull_request: | |
branches: ["**"] | |
jobs: | |
test: | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
python-version: ["3.8", "3.9", "3.10", "3.11","3.12", "3.13"] | |
include: | |
- python-version: "3.12" | |
is-dev-version: true | |
run_expensive_tests: true | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
cache: "pip" | |
- name: Install dependencies | |
run: | | |
pip install --upgrade pip | |
pip install -e .[dev] | |
- name: Get Date | |
id: get-date | |
run: | | |
echo "date=$(date +'%Y-%b')" | |
echo "date=$(date +'%Y-%b')" >> $GITHUB_OUTPUT | |
shell: bash | |
- uses: actions/cache/restore@v4 | |
with: | |
path: bioimageio_cache | |
key: "py${{ matrix.python-version }}-${{ steps.get-date.outputs.date }}" | |
- name: Check autogenerated imports | |
run: python scripts/generate_version_submodule_imports.py check | |
- run: black --check . | |
if: matrix.is-dev-version | |
- name: install additinal deps for a full pyright check | |
run: pip install json_schema_for_humans | |
if: matrix.is-dev-version | |
- run: ruff check **/*.py # ignore notebooks for now | |
if: matrix.is-dev-version | |
- run: pyright --version | |
if: matrix.is-dev-version | |
- run: pyright -p pyproject.toml --pythonversion ${{ matrix.python-version }} | |
if: matrix.is-dev-version | |
- run: pytest | |
env: | |
BIOIMAGEIO_CACHE_PATH: bioimageio_cache | |
SKIP_EXPENSIVE_TESTS: ${{ matrix.run_expensive_tests && 'false' || 'true' }} | |
- uses: actions/cache/save@v4 | |
# explicit restore/save instead of cache action to cache even if coverage fails | |
with: | |
path: bioimageio_cache | |
key: "py${{ matrix.python-version }}-${{ steps.get-date.outputs.date }}" | |
- if: matrix.is-dev-version && github.event_name == 'pull_request' | |
uses: orgoro/[email protected] | |
with: | |
coverageFile: coverage.xml | |
token: ${{ secrets.GITHUB_TOKEN }} | |
thresholdAll: 0.7 | |
thresholdNew: 0.9 | |
thresholdModified: 0.6 | |
- if: matrix.is-dev-version | |
run: | | |
pip install genbadge[coverage] | |
genbadge coverage --input-file coverage.xml --output-file ./dist/coverage/coverage-badge.svg | |
coverage html -d dist/coverage | |
- if: matrix.is-dev-version | |
uses: actions/upload-artifact@v4 | |
with: | |
name: coverage | |
retention-days: 1 | |
path: dist | |
deploy: | |
needs: [test] | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: actions/download-artifact@v4 | |
with: | |
name: coverage | |
path: dist | |
- uses: actions/setup-python@v5 | |
with: | |
python-version: "3.12" | |
cache: "pip" | |
- name: Install dependencies | |
run: | | |
pip install --upgrade pip | |
pip install -e .[dev] | |
- name: Generate spec docs | |
run: python scripts/generate_spec_documentation.py --dist dist/user_docs | |
- name: Generate interactive documentation | |
env: | |
PYTHONPATH: "./scripts" | |
run: python -m interactive_docs | |
- name: Generate JSON schemas | |
run: python scripts/generate_json_schemas.py | |
- run: pip install json_schema_for_humans | |
- name: Generate JSON schema documentation | |
run: python scripts/generate_json_schema_documentation.py | |
- name: Generate developer docs | |
run: ./scripts/pdoc/run.sh | |
- name: copy legacy file until BioImage.IO-packager is updated # TODO: remove if packager does not depend on it anymore | |
run: cp weight_formats_spec.json ./dist/weight_formats_spec.json | |
- name: Get branch name to deploy to | |
id: get_branch | |
shell: bash | |
run: | | |
if [[ -n '${{ github.event.pull_request.head.ref }}' ]]; then branch=gh-pages-${{ github.event.pull_request.head.ref }}; else branch=gh-pages; fi | |
echo "::set-output name=branch::$branch" | |
- name: Deploy to ${{ steps.get_branch.outputs.branch }} 🚀 | |
uses: JamesIves/github-pages-deploy-action@v4 | |
with: | |
branch: ${{ steps.get_branch.outputs.branch }} | |
folder: dist | |
mamba-build: | |
runs-on: ubuntu-latest | |
needs: test | |
steps: | |
- name: checkout | |
uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 | |
- name: Install Conda environment with Micromamba | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
cache-downloads: true | |
cache-environment: true | |
environment-name: build-env | |
condarc: | | |
channels: | |
- conda-forge | |
- nodefaults | |
create-args: >- | |
boa | |
- name: linux conda build | |
run: | | |
conda mambabuild -c conda-forge conda-recipe | |
shell: bash -l {0} | |
# rattler-build: | |
# name: Build package | |
# runs-on: ubuntu-latest | |
# steps: | |
# - uses: actions/checkout@v4 | |
# - name: Build conda package | |
# uses: prefix-dev/[email protected] | |
# with: | |
# recipe-path: conda-recipe/recipe.yaml |