Remove warnings filter (#65) #303
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
name: GH Actions CI | |
on: | |
push: | |
branches: | |
- main | |
pull_request: | |
branches: | |
- main | |
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} | |
env: | |
OE_LICENSE: ${{ github.workspace }}/oe_license.txt | |
jobs: | |
main_tests: | |
name: CI (${{ matrix.os }}, py-${{ matrix.python-version }}, rdkit=${{ matrix.include-rdkit }}, openeye=${{ matrix.include-openeye }}, dgl=${{ matrix.include-dgl }}), pydantic=${{ matrix.pydantic-version }} | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [macOS-latest, ubuntu-latest] | |
python-version: ["3.9", "3.10"] | |
pydantic-version: ["1", "2"] | |
include-rdkit: [true, false] | |
include-openeye: [true, false] | |
include-dgl: [true, false] | |
exclude: | |
- include-rdkit: false | |
include-openeye: false | |
# broken OpenMM build for Mac on 3.10 | |
- os: "macOS-latest" | |
python-version: "3.10" | |
# - os: "macOS-latest" | |
# python-version: "3.9" | |
# include-dgl: false | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Build information | |
run: | | |
uname -a | |
df -h | |
ulimit -a | |
- name: Install environment | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-file: devtools/conda-envs/test_env.yaml | |
create-args: >- | |
python=${{ matrix.python-version }} | |
pydantic=${{ matrix.pydantic-version }} | |
- name: Install package | |
run: | | |
python -m pip install . --no-deps | |
- name: Python information | |
run: | | |
which python | |
conda info | |
conda list | |
- uses: ./.github/actions/include-openeye | |
if: matrix.include-openeye == true | |
with: | |
openeye-license-text: ${{ secrets.OE_LICENSE }} | |
openeye-license-file: ${{ env.OE_LICENSE }} | |
- name: Uninstall OpenEye | |
if: matrix.include-openeye == false | |
run: conda remove --force openeye --yes || echo "openeye not installed" | |
- name: Uninstall RDKit | |
if: matrix.include-rdkit == false | |
run: conda remove --force rdkit --yes || echo "rdkit not installed" | |
- name: Uninstall DGL | |
if: matrix.include-dgl == false | |
run: conda remove --force dgl --yes || echo "dgl not installed" | |
- name: Check toolkit installations | |
shell: bash -l -c "python -u {0}" | |
run: | | |
from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE, RDKIT_AVAILABLE | |
assert str(OPENEYE_AVAILABLE).lower() == '${{ matrix.include-openeye }}' | |
assert str(RDKIT_AVAILABLE).lower() == '${{ matrix.include-rdkit }}' | |
- name: Run tests | |
run: | | |
python -m pytest -n 4 -v --cov=openff/nagl --cov-config=setup.cfg --cov-append --cov-report=xml --color=yes openff/nagl/ | |
- name: codecov | |
uses: codecov/codecov-action@v3 | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
file: ./coverage.xml | |
verbose: True | |
# name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} | |
pylint_check: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Set up Python | |
uses: actions/setup-python@v3 | |
with: | |
python-version: 3.9 | |
- name: Install Pylint | |
run: | | |
which pip | |
which python | |
pip install pylint | |
- name: Run Pylint | |
env: | |
PYLINTRC: .pylintrc | |
run: | | |
pylint openff-nagl | |
pypi_check: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Set up Python | |
uses: actions/setup-python@v3 | |
with: | |
python-version: 3.9 | |
- name: Install dependencies | |
run: | | |
pip install setuptools twine | |
- name: Build package | |
run: | | |
python setup.py sdist | |
- name: Check package build | |
run: | | |
DISTRIBUTION=$(ls -t1 dist/openff-nagl-*.tar.gz | head -n 1) | |
test -n "${DISTRIBUTION}" || { echo "no distribution dist/openff-nagl-*.tar.gz found"; exit 1; } | |
echo "twine check $DISTRIBUTION" | |
twine check $DISTRIBUTION | |
install_from_source_conda: | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
python-version: ["3.9", "3.10"] | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Install conda | |
uses: conda-incubator/setup-miniconda@v2 | |
with: | |
python-version: ${{ matrix.python-version }} | |
add-pip-as-python-dependency: true | |
architecture: x64 | |
miniforge-variant: Mambaforge | |
use-mamba: true | |
auto-update-conda: true | |
show-channel-urls: true | |
channels: conda-forge, defaults | |
- name: Build from source | |
run: | | |
conda create --name openff-nagl | |
conda activate openff-nagl | |
conda list | |
mamba env update --name openff-nagl --file devtools/conda-envs/test_env.yaml | |
mamba env update --name openff-nagl --file devtools/conda-envs/docs_env.yaml | |
python --version | |
python -m pip install . --no-deps | |
conda list | |
- name: Check success | |
run: | | |
conda activate openff-nagl | |
python -c "import openff.nagl ; print(openff.nagl.__version__)" |