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ci.yml
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name: CI
on:
push:
branches:
- master
pull_request:
branches:
- "*"
workflow_dispatch:
defaults:
run:
shell: bash -l {0}
concurrency:
group: ${{ github.ref }}-${{ github.head_ref }}"
cancel-in-progress: true
jobs:
tests:
name: ${{ matrix.label }}
runs-on: ${{ matrix.os }}
strategy:
matrix:
include:
- label: CI-old
os: ubuntu-latest
python-version: 3.8
extra_dependencies: "rdkit==2020.03.1 boost-cpp=1.72.0=h359cf19_6"
- label: CI-edge
os: ubuntu-latest
python-version: "3.10"
extra_dependencies: "rdkit"
- label: CI-py3.8-rdkit2022
os: ubuntu-latest
python-version: 3.8
extra_dependencies: "rdkit==2022.03.1"
steps:
- uses: actions/checkout@v3
- name: Install node
uses: actions/setup-node@v3
with:
node-version: "12.x"
cache: "npm"
- name: Install Firefox
uses: browser-actions/setup-firefox@latest
- run: firefox --version
- name: Prepare Selenium
uses: browser-actions/setup-geckodriver@latest
with:
geckodriver-version: "0.32.0"
- run: geckodriver --version
- name: Cache conda
uses: actions/cache@v3
env:
CACHE_NUMBER: 0
with:
path: ~/conda_pkgs_dir
key:
conda-${{ hashFiles('environment.yml') }}-${{ matrix.label }}-${{ env.CACHE_NUMBER }}
- name: Cache pip
uses: actions/cache@v3
with:
path: ~/.cache/pip
key: pip-${{ hashFiles('setup.cfg') }}
restore-keys: pip-
- name: Setup Conda
uses: conda-incubator/setup-miniconda@v2
with:
python-version: ${{ matrix.python-version }}
environment-file: environment.yml
use-only-tar-bz2: true
miniforge-variant: Mambaforge
miniforge-version: latest
use-mamba: true
- name: Check conda and pip
run: |
which python
python --version
pip --version
conda --version
mamba --version
- name: Install remaining conda dependencies
run: |
mamba install ${{ matrix.extra_dependencies }}
mamba list
- name: Install package through pip
run: |
pip install .[tests,build]
pip list
- name: Run tests
run: |
pytest --color=yes --disable-pytest-warnings \
--cov=mols2grid --cov-report=xml \
tests/ -m "not webdriver"
- name: Run webdriver tests
uses: nick-fields/retry@v2
with:
timeout_seconds: 340
max_attempts: 5
retry_on: timeout
shell: bash
command: |
source /usr/share/miniconda/etc/profile.d/conda.sh
conda activate /usr/share/miniconda3/envs/test
pytest --color=yes --disable-pytest-warnings \
--cov=mols2grid --cov-report=xml --cov-append \
tests/ -m "webdriver"
- name: Measure tests coverage
uses: codecov/codecov-action@v3
with:
files: ./coverage.xml
fail_ci_if_error: true
verbose: true
- name: Prepare for build
run: |
pip uninstall -y mols2grid
python -m build .
echo "$SCRIPT" > test_install.py
cat test_install.py
env:
SCRIPT: |
import mols2grid as mg
from rdkit import RDConfig
sdf = f"{RDConfig.RDDocsDir}/Book/data/solubility.test.sdf"
mg.save(sdf, output="/dev/null")
- name: Test tar.gz build
run: |
pip install dist/mols2grid-*.tar.gz
python test_install.py
pip uninstall -y mols2grid
- name: Test wheel build
run: |
pip install dist/mols2grid-*.whl
python test_install.py