Add PathCellObjects class and add_cell method #285
Workflow file for this run
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name: paquo ci | |
on: | |
push: | |
branches: | |
- main | |
tags: v[0-9]+.[0-9]+.[0-9]+ | |
pull_request: {} | |
env: | |
QUPATH_VERSION: 0.5.0 | |
jobs: | |
# RUN PYTEST ON PAQUO SOURCE | |
tests: | |
name: pytest ${{ matrix.os }}::py${{ matrix.python-version }} | |
runs-on: ${{ matrix.os }} | |
strategy: | |
max-parallel: 8 | |
fail-fast: false | |
matrix: | |
os: [ubuntu-latest, macos-latest, windows-latest] | |
python-version: ["3.12"] | |
include: | |
# we'll test the python support on ubuntu | |
- os: ubuntu-latest | |
python-version: '3.11' | |
- os: ubuntu-latest | |
python-version: '3.12' | |
- os: ubuntu-latest | |
python-version: '3.9' | |
- os: ubuntu-latest | |
python-version: '3.8' | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 | |
- name: Setup Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Install paquo | |
run: | | |
python -m pip install --upgrade pip | |
pip install -e .[dev] | |
- name: Restore qupath cache | |
uses: actions/cache@v3 | |
env: | |
CACHE_NUMBER: 0 | |
with: | |
path: ./qupath/download | |
key: ${{ runner.os }}-qupath-v${{ env.CACHE_NUMBER }} | |
- name: Install qupath and set PAQUO_QUPATH_DIR | |
shell: bash | |
run: | | |
python -c "import os; os.makedirs('qupath/download', exist_ok=True)" | |
python -c "import os; os.makedirs('qupath/apps', exist_ok=True)" | |
python -m paquo get_qupath --install-path ./qupath/apps --download-path ./qupath/download ${{ env.QUPATH_VERSION }} | grep -v "^#" | sed "s/^/PAQUO_QUPATH_DIR=/" >> $GITHUB_ENV | |
- name: Test with pytest | |
run: | | |
pytest --cov=./paquo --cov-report=xml | |
- name: Upload coverage to Codecov | |
uses: codecov/codecov-action@v3 | |
with: | |
name: paquo | |
# RUN MYPY STATIC TYPE ANALYSIS ON PAQUO SOURCE | |
typing: | |
name: mypy type analysis | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: 3.8 | |
- name: Install dependencies | |
shell: bash | |
run: | | |
python -m pip install --upgrade pip | |
pip install -e .[dev] | |
pip install ome_types || true | |
- name: Run mypy | |
run: | | |
mypy paquo | |
# DEPLOY PAQUO TO TEST.PYPI ON SUCCESS | |
testdeploy: | |
needs: [tests, typing] | |
name: deploy to test.pypi | |
runs-on: ubuntu-latest | |
if: github.event_name == 'push' && github.ref == 'refs/heads/main' | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: 3.8 | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip | |
- name: Install pep517 | |
run: >- | |
python -m | |
pip install | |
pep517 | |
--user | |
# we'll have to remove local_scheme for pushes to test.pypi pep440 | |
- name: Get version without local_scheme | |
id: non_local_version | |
run: | | |
python setup.py --version | awk -F+ '{print "::set-output name=version::"$1}' | |
- name: Build a binary wheel and a source tarball | |
env: | |
SETUPTOOLS_SCM_PRETEND_VERSION: ${{ steps.non_local_version.outputs.version }} | |
run: >- | |
python -m | |
pep517.build | |
--source | |
--binary | |
--out-dir dist/ | |
. | |
# push all versions on master to test.pypi.org | |
- name: Publish package to TestPyPI | |
continue-on-error: true | |
uses: pypa/gh-action-pypi-publish@master | |
with: | |
user: __token__ | |
password: ${{ secrets.test_pypi_password }} | |
repository_url: https://test.pypi.org/legacy/ | |
# DEPLOY PAQUO TO PYPI ON SUCCESS | |
deploy: | |
needs: [tests, typing] | |
name: deploy to pypi | |
runs-on: ubuntu-latest | |
if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: 3.8 | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip | |
- name: Install pep517 | |
run: >- | |
python -m | |
pip install | |
pep517 | |
--user | |
- name: Build a binary wheel and a source tarball | |
run: >- | |
python -m | |
pep517.build | |
--source | |
--binary | |
--out-dir dist/ | |
. | |
# push all tagged versions to pypi.org | |
- name: Publish package to PyPI | |
uses: pypa/gh-action-pypi-publish@master | |
with: | |
user: __token__ | |
password: ${{ secrets.pypi_password }} |