Bump version: 0.2.2 → 0.2.3 #760
Workflow file for this run
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# This workflow will install Python dependencies, run tests and lint with a single version of Python | |
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | |
name: CI | |
on: | |
push: | |
pull_request: | |
branches: [ "main" ] | |
permissions: | |
contents: read | |
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"] | |
os: [windows-latest, macOS-latest, ubuntu-latest] | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
submodules: "recursive" | |
- name: Set up Python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip | |
pip install oldest-supported-numpy==2023.10.25 | |
# --ignore-requires-python ensures docs deps don't break install on early python versions | |
if [ -f requirements.txt ]; then pip install --ignore-requires-python -r requirements.txt; fi | |
pip install -e . | |
- name: Lint with flake8 | |
run: | | |
# stop the build if there are Python syntax errors or undefined names | |
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
- name: Test with pytest | |
run: | | |
python -m pytest | |
coverage: | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
python-version: ["3.11"] | |
os: [ubuntu-latest] | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
submodules: "recursive" | |
- name: Set up Python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
# - name: Setup LCOV | |
# uses: hrishikesh-kadam/setup-lcov@v1 | |
- name: Install dependencies | |
run: | | |
sudo apt update -yy | |
sudo apt install -yy lcov | |
python -m pip install --upgrade pip | |
pip install wheel | |
pip install oldest-supported-numpy==2023.10.25 | |
# --ignore-requires-python ensures docs deps don't break install on early python versions | |
if [ -f requirements.txt ]; then pip install --ignore-requires-python -r requirements.txt; fi | |
rm -rf Empirical/.git | |
- name: Build phylotrackpy | |
run: | | |
make coverage | |
- name: Test with pytest | |
run: | | |
python -m pytest --cov=. --cov-report=lcov | |
lcov --output-file coverage.cpp --capture --directory . | |
lcov --output-file coverage.cpp --extract coverage.cpp "*" | |
- name: Upload coverage reports to Codecov | |
uses: codecov/codecov-action@v4 | |
with: | |
files: "coverage.cpp, coverage.lcov, Empirical/include/emp/Evolve/Systematics.hpp" | |
token: ${{ secrets.CODECOV_TOKEN }} | |
verbose: true | |
build_wheels: | |
name: Build wheels on ${{ matrix.os }} | |
needs: [] | |
# if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v') | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ubuntu-latest, windows-latest, macos-13, macos-14] | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
submodules: "recursive" | |
- name: Build wheels | |
uses: pypa/cibuildwheel@v2.21.3 | |
- uses: actions/upload-artifact@v4 | |
with: | |
name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }} | |
path: ./wheelhouse/*.whl | |
build_sdist: | |
name: Build source distribution | |
needs: [] | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
submodules: "recursive" | |
- name: Build sdist | |
run: pipx run build --sdist | |
- uses: actions/upload-artifact@v4 | |
with: | |
name: cibw-sdist | |
path: dist/*.tar.gz | |
# Regression test borrowed from https://github.com/mmore500/hstrat/blob/ba7b19d0f0561303b6bf789d5024a323aa5993fc/.github/workflows/ci.yaml#L201 | |
packaging-sdist: | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout | |
uses: actions/checkout@v4 | |
with: | |
submodules: "recursive" | |
- name: Build sdist | |
run: | | |
python3 -m venv env | |
source env/bin/activate | |
python3 -m pip install -r requirements.txt | |
python3 setup.py sdist | |
tree dist | |
deactivate | |
- name: Upgrade pip | |
run: python3 -m pip install pip --upgrade | |
- name: Install from sdist | |
run: python3 -m pip install dist/*.tar.gz | |
- name: Test install | |
run: | | |
find . -type f -name '*.py' -exec rm {} \; | |
python3 -c "import phylotrackpy; print(phylotrackpy.__version__)" | |
upload_pypi: | |
needs: [build_wheels, build_sdist, test] | |
runs-on: ubuntu-latest | |
environment: pypi | |
permissions: | |
id-token: write | |
# upload to PyPI on every tag starting with 'v' | |
if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v') | |
# alternatively, to publish when a GitHub Release is created, use the following rule: | |
# if: github.event_name == 'release' && github.event.action == 'published' | |
steps: | |
- uses: actions/download-artifact@v4 | |
with: | |
# unpacks default artifact into dist/ | |
# if `name: artifact` is omitted, the action will create extra parent dir | |
pattern: cibw-* | |
path: dist | |
merge-multiple: true | |
- uses: pypa/gh-action-pypi-publish@v1.8.12 | |
with: | |
user: __token__ | |
password: ${{ secrets.PYPI_API_TOKEN }} | |
paper: | |
runs-on: ubuntu-latest | |
name: Paper Draft | |
steps: | |
- name: Checkout | |
uses: actions/checkout@v4 | |
- name: Build draft PDF | |
uses: openjournals/openjournals-draft-action@master | |
with: | |
journal: joss | |
# This should be the path to the paper within your repo. | |
paper-path: joss/paper.md | |
- name: Upload | |
uses: actions/upload-artifact@v4 | |
with: | |
name: paper | |
# This is the output path where Pandoc will write the compiled | |
# PDF. Note, this should be the same directory as the input | |
# paper.md | |
path: joss/paper.pdf |