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fix: linting

fix: linting #525

Workflow file for this run

name: tests
on:
push:
branches:
- "*"
pull_request:
branches:
- master
workflow_dispatch:
defaults:
run:
shell: bash -l {0}
concurrency:
group: "${{ github.ref }}-${{ github.head_ref }}"
cancel-in-progress: true
jobs:
build:
name: Build
# only run once if internal PR
if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
uses: ./.github/workflows/_build-package.yml
with:
check-prerelease: ${{ github.event_name == 'workflow_dispatch' }}
cache-package: true
upload-package: true
test-files: true
test-imports: true
unit-tests:
name: Test ${{ matrix.label }}
runs-on: ${{ matrix.os }}
# only run once if internal PR
if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
strategy:
matrix:
include:
- label: earliest
os: ubuntu-latest
python-version: 3.9
mamba-deps: "rdkit==2022.09.1"
coverage: false
- label: baseline
os: ubuntu-latest
python-version: "3.10"
mamba-deps: "rdkit~=2023.03.1"
coverage: true
- label: latest
os: ubuntu-latest
python-version: "3.12"
# remove numpy<2 when MDAnalysis 2.8.0 is released
mamba-deps: "rdkit 'numpy<2'"
coverage: false
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Setup Conda
uses: conda-incubator/setup-miniconda@v3
with:
python-version: ${{ matrix.python-version }}
auto-update-conda: true
use-mamba: true
miniforge-variant: Mambaforge
- name: Check conda and pip
run: |
which python
python --version
pip --version
conda --version
mamba --version
- name: Install conda dependencies
run: |
mamba install uv ${{ matrix.mamba-deps }}
mamba list
- name: Install package through pip
run: |
uv pip install .[dev]
uv pip list
- name: Run tests
run: |
pytest --color=yes --disable-pytest-warnings --cov=prolif --cov-report=xml tests/
- name: Measure tests coverage
if: matrix.coverage
uses: codecov/codecov-action@v3
with:
files: ./coverage.xml
fail_ci_if_error: true
verbose: true
token: ${{ secrets.CODECOV_TOKEN }}