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Improve testing in dedicated conda env #411

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Improve testing in dedicated conda env

Improve testing in dedicated conda env #411

Workflow file for this run

.github/workflows/build.yaml at 0728060
name: Test and Deploy bioimageio.core
on:
push:
branches: [main]
pull_request:
branches: ['**']
defaults:
run:
shell: bash -el {0}
jobs:
populate-cache:
runs-on: ubuntu-latest
outputs:
cache-key: ${{steps.cache-key.outputs.cache-key}}-0
steps:
- name: Get Date
id: get-date
run: |
echo "date=$(date +'%Y-%b')"
echo "date=$(date +'%Y-%b')" >> $GITHUB_OUTPUT
- id: cache-key
run: echo "cache-key=test-${{steps.get-date.outputs.date}}" >> $GITHUB_OUTPUT
- uses: actions/cache/restore@v4
id: look-up
with:
path: bioimageio_cache
key: ${{steps.cache-key.outputs.cache-key}}
lookup-only: true
- uses: actions/checkout@v4
if: steps.look-up.outputs.cache-hit != 'true'
- uses: actions/cache@v4
if: steps.look-up.outputs.cache-hit != 'true'
with:
path: bioimageio_cache
key: ${{steps.cache-key.outputs.cache-key}}
- uses: actions/setup-python@v6
if: steps.look-up.outputs.cache-hit != 'true'
with:
python-version: '3.12'
cache: 'pip'
- name: Install dependencies
if: steps.look-up.outputs.cache-hit != 'true'
run: |
pip install -e .[dev]
- run: pytest --disable-pytest-warnings tests/test_bioimageio_collection.py::test_rdf_format_to_populate_cache
if: steps.look-up.outputs.cache-hit != 'true'
env:
BIOIMAGEIO_POPULATE_CACHE: '1'
BIOIMAGEIO_CACHE_PATH: bioimageio_cache
test:
needs: populate-cache
runs-on: ubuntu-latest
strategy:
matrix:
include:
- python-version: '3.9'
numpy-version: 1
- python-version: '3.9'
numpy-version: 2
- python-version: '3.10'
run-expensive-tests: true
report-coverage: true
save-cache: true
numpy-version: 1
- python-version: '3.11'
numpy-version: 2
- python-version: '3.12'
numpy-version: 1
# - python-version: '3.13'
# numpy-version: 2
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v6
with:
python-version: ${{matrix.python-version}}
cache: 'pip'
- name: Install dependencies
run: |
pip install --upgrade pip
pip install -e .[dev,partners] numpy==${{matrix.numpy-version}}.*
- name: Pyright
if: matrix.run-expensive-tests # pyright is not expensive, but we only want to run it once due to otherwise inconsistent typing
run: |
pyright --version
pyright -p pyproject.toml --pythonversion ${{ matrix.python-version }}
- name: Restore bioimageio cache ${{needs.populate-cache.outputs.cache-key}}
uses: actions/cache/restore@v4
with:
path: bioimageio_cache
key: ${{needs.populate-cache.outputs.cache-key}}
- name: pytest
run: pytest --cov bioimageio.core --cov-append --capture no --disable-pytest-warnings
env:
BIOIMAGEIO_CACHE_PATH: bioimageio_cache
RUN_EXPENSIVE_TESTS: ${{ matrix.run-expensive-tests && 'true' || 'false' }}
- name: Save bioimageio cache ${{needs.populate-cache.outputs.cache-key}}
if: matrix.save-cache
uses: actions/cache/save@v4
with:
path: bioimageio_cache
key: ${{needs.populate-cache.outputs.cache-key}}
- run: cp .coverage .coverage.${{matrix.python-version}}-${{matrix.numpy-version}}
- uses: actions/upload-artifact@v4
with:
name: .coverage.${{matrix.python-version}}-${{matrix.numpy-version}}
retention-days: 1
path: .coverage.${{matrix.python-version}}-${{matrix.numpy-version}}
include-hidden-files: true
coverage:
needs: [test]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v6
- run: |
pip install coverage
- uses: actions/download-artifact@v4
with:
pattern: .coverage.*
merge-multiple: true
- run: |
ls -la .coverage*
coverage combine
coverage xml -o coverage.xml
- uses: orgoro/[email protected]
with:
coverageFile: coverage.xml
token: ${{ secrets.GITHUB_TOKEN }}
thresholdAll: 0.7
thresholdNew: 0.9
thresholdModified: 0.6
- name: generate coverage badge and html report
run: |
pip install genbadge[coverage]
genbadge coverage --input-file coverage.xml --output-file ./dist/coverage/coverage-badge.svg
coverage html -d dist/coverage
- uses: actions/upload-artifact@v4
with:
name: coverage-summary
retention-days: 1
path: dist
conda-build:
needs: test # only so we run tests even if the pinned bioimageio.spec version is not yet published on conda-forge yet
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
- uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
auto-activate-base: true
activate-environment: ''
channel-priority: strict
miniforge-version: latest
conda-solver: libmamba
- name: install common conda dependencies
run: conda install -n base -c conda-forge conda-build -y
- uses: actions/cache@v4
with:
path: |
pkgs/noarch
pkgs/channeldata.json
key: ${{ github.sha }}-packages
- name: linux conda build test
shell: bash -l {0}
run: |
mkdir -p ./pkgs/noarch
conda-build -c conda-forge conda-recipe --output-folder ./pkgs
docs:
needs: test
if: github.ref == 'refs/heads/main'
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/download-artifact@v4
with:
name: coverage-summary
path: dist
- uses: actions/setup-python@v6
with:
python-version: '3.12'
cache: 'pip'
- run: pip install -e .[dev,partners]
- name: Generate developer docs
run: ./scripts/pdoc/run.sh
- run: cp README.md ./dist/README.md
- name: copy rendered presentations
run: |
mkdir ./dist/presentations
cp -r ./presentations/*.html ./dist/presentations/
- name: Deploy to gh-pages 🚀
uses: JamesIves/github-pages-deploy-action@v4
with:
branch: gh-pages
folder: dist
build:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v6
with:
python-version: '3.10'
cache: 'pip'
- name: Install dependencies
run: pip install --upgrade build
- name: Build package
run: python -m build
- uses: actions/upload-artifact@v4
with:
path: dist/
name: dist
publish:
needs: [test, build, conda-build, docs]
runs-on: ubuntu-latest
environment:
name: release
url: https://pypi.org/project/bioimageio.core/
permissions:
contents: write # required for tag creation
id-token: write # required for pypi publish action
steps:
- name: Check out the repository
uses: actions/checkout@v4
with:
fetch-depth: 2
- name: Check if there is a parent commit
id: check-parent-commit
run: |
echo "sha=$(git rev-parse --verify --quiet HEAD^)" >> $GITHUB_OUTPUT
- name: Detect new version
id: tag-version
if: github.ref == 'refs/heads/main' && steps.check-parent-commit.outputs.sha
uses: salsify/[email protected]
with:
create-tag: true
version-command: |
python -c "from pathlib import Path;import json;print(p_src.read_text().split('__version__ = \"')[1].split('\"')[0] if (p_src:=Path('src/bioimageio/core/__init__.py')).exists() else json.loads(Path('bioimageio/core/VERSION').read_text())['version'])"
- uses: actions/download-artifact@v4
if: github.ref == 'refs/heads/main' && steps.tag-version.outputs.tag
with:
name: dist
path: dist
- name: Publish package on PyPI
if: github.ref == 'refs/heads/main' && steps.tag-version.outputs.tag
uses: pypa/gh-action-pypi-publish@release/v1
with:
packages-dir: dist/
- name: Publish the release notes
if: github.ref == 'refs/heads/main'
uses: release-drafter/[email protected]
with:
publish: "${{ steps.tag-version.outputs.tag != '' }}"
tag: '${{ steps.tag-version.outputs.tag }}'
env:
GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'