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Preparing PolyPhy package #229

Preparing PolyPhy package

Preparing PolyPhy package #229

# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
name: Python package
on:
push:
branches: [ "main" ]
pull_request:
branches: [ "main" ]
jobs:
build:
runs-on: ubuntu-22.04
strategy:
fail-fast: false
matrix:
python-version: ["3.8", "3.9", "3.10"]
steps:
- uses: actions/checkout@v3
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v3
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
python -m pip install flake8 pytest
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
pip install . -U
- name: Lint with flake8
run: |
# stop the build if there are Python syntax errors or undefined names
flake8 ./src --count --select=E9,F63,F7,F82 --show-source --statistics
# exit-zero treats all errors as warnings. The GitHub editor is 90 chars wide
flake8 ./src --count --exit-zero --max-complexity=10 --max-line-length=90 --statistics
flake8 ./src --ignore=E501,W503,E402,F401,F403,E722,F841,W504 --max-line-length=90 2>&1
yapf -d --recursive ./src --style=.style.yapf 2>&1
isort ./src -c -v
- name: Test with pytest
run: |
pytest -v --cov=./src --cov-report=xml
- name: Upload coverage to Codecov
if: matrix.python-version == 3.8
uses: codecov/codecov-action@v1
with:
token: ${{ secrets.CODECOV_TOKEN }}