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install_doctest_lint_typecheck.yml
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name: linting-typechecking-doctests
# Source: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#using-multiple-python-versions
on: [pull_request, workflow_dispatch]
jobs:
install_and_test:
runs-on: ubuntu-latest
strategy:
# You can use PyPy versions in python-version.
# For example, pypy2.7 and pypy3.9
matrix:
python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
steps:
- uses: actions/checkout@v3
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install
run: pip install .
- name: Install add-ons
run: pip install pyrle pybigwig bamread pyfaidx fisher
- run: pip install pytest
- name: doctests
env:
GITHUB_ACTIONS: true
run: |
shopt -s globstar # allow recursive globs
python -m doctest pyranges/**.py
- name: unittests
env:
GITHUB_ACTIONS: true
run: |
pytest tests/unit
isort:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python environment
uses: actions/setup-python@v4
with:
python-version: "3.11"
- run: pip install isort
- run: isort --profile black -l 120 --check --diff .
black:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python environment
uses: actions/setup-python@v4
with:
python-version: "3.11.0"
max-line-length: "120"
- run: pip install black
- run: black -l 120 --check --diff pyranges tests
flake8:
runs-on: ubuntu-latest
name: Lint
steps:
- name: Check out source repository
uses: actions/checkout@v3
- name: Set up Python environment
uses: actions/setup-python@v4
- name: flake8 Lint install
run: pip install flake8
- name: flake8 Lint
run: flake8 --max-line-length=120 --ignore E203,E501,W503 pyranges
mypy:
runs-on: ubuntu-latest
name: Mypy
steps:
- name: Check out source repository
uses: actions/checkout@v3
- name: Set up Python environment
uses: actions/setup-python@v4
with:
python-version: "3.11"
- name: Install mypy
run: pip install mypy
- name: mypy
run: |
pip install numpy # for the typing stubs
python -m pip install pandas-stubs types-setuptools types-tabulate
mypy pyranges