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Checkout recursively #682

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Checkout recursively

Checkout recursively #682

Workflow file for this run

.github/workflows/ci.yml at f2e769b
# 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"]
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: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: [ubuntu-latest, windows-latest, macos-13, macos-14]
steps:
- uses: actions/checkout@v4
with:
submodules: "recursive"
- name: Build wheels
uses: pypa/[email protected]
- uses: actions/upload-artifact@v4
with:
name: cibw-wheels-${{ 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/[email protected]
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