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gh-ci.yaml
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name: GH Actions CI
on:
push:
branches:
- main
pull_request:
branches:
- main
schedule:
# Weekly tests at midnight on Sundays run on main by default:
# Scheduled workflows run on the latest commit on the default or base branch.
# (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
- cron: "0 0 * * 0"
concurrency:
# Specific group naming so CI is only cancelled
# within same PR or on merge to main
group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
cancel-in-progress: true
defaults:
run:
shell: bash -l {0}
jobs:
main-tests:
if: "github.repository == 'MDAnalysis/mdaencore'"
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
# macos-13 is x86_64 and macos-14 is arm64
os: [ubuntu-latest, windows-latest, macos-14, macos-13]
python-version: ["3.10", "3.11", "3.12"]
mdanalysis-version: ["latest", "develop"]
# Manually exclude any combinations of the test matrix that can't be run
exclude:
# The latest release of MDAnalysis only supports up to Python 3.11
# so we exclude 3.12 from the test matrix (issue #68)
- python-version: "3.12"
mdanalysis-version: "latest"
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
- name: Build information
run: |
uname -a
df -h
ulimit -a
# More info on options: https://github.com/conda-incubator/setup-miniconda
- name: Install conda dependencies
uses: conda-incubator/setup-miniconda@v3
with:
python-version: ${{ matrix.python-version }}
environment-file: devtools/conda-envs/test_env.yaml
add-pip-as-python-dependency: true
architecture: x64
miniforge-variant: Mambaforge
use-mamba: true
channels: conda-forge, defaults
activate-environment: mdaencore-test
auto-update-conda: true
auto-activate-base: false
show-channel-urls: true
- name: Install MDAnalysis version
uses: MDAnalysis/install-mdanalysis@main
with:
version: ${{ matrix.mdanalysis-version }}
install-tests: true
installer: mamba
shell: bash -l {0}
- name: Install package
run: |
python --version
python -m pip install -e . --no-deps
- name: Python information
run: |
which python
which pip
pip list
conda info
conda list
- name: Test imports
run: |
python -Ic "import mdaencore; print(mdaencore.__version__)"
- name: Run tests
run: |
pytest -n auto -v --cov=mdaencore --cov-report=xml --color=yes --pyargs mdaencore
- name: codecov
if: github.repository == 'MDAnalysis/mdaencore' && github.event_name != 'schedule'
uses: codecov/codecov-action@v4
with:
file: coverage.xml
name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
token: ${{ secrets.CODECOV_TOKEN }}
verbose: True
fail_ci_if_error: True
pylint_check:
if: "github.repository == 'MDAnalysis/mdaencore'"
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: "3.11"
- name: Install Pylint
run: |
which pip
which python
pip install pylint mdanalysis
- name: Run Pylint
env:
PYLINTRC: .pylintrc
run: |
pylint mdaencore
pypi_check:
if: "github.repository == 'MDAnalysis/mdaencore'"
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: "3.11"
- name: Install dependencies
run: |
pip install setuptools cython numpy twine
- name: Build package
run: |
python setup.py sdist
- name: Check package build
run: |
DISTRIBUTION=$(ls -t1 dist/mdaencore-*.tar.gz | head -n 1)
test -n "${DISTRIBUTION}" || { echo "no distribution dist/mdaencore-*.tar.gz found"; exit 1; }
echo "twine check $DISTRIBUTION"
twine check $DISTRIBUTION