Fix dev CI #466
Workflow file for this run
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name: GH Actions CI | |
on: | |
push: | |
branches: | |
- main | |
pull_request: | |
branches: | |
- main | |
schedule: | |
# weekly tests, Sundays at midnight | |
- 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} | |
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: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [macOS-12, ubuntu-latest] | |
python-version: ["3.10", "3.11", "3.12"] | |
pydantic-version: ["1", "2"] | |
include-rdkit: [false, true] | |
include-openeye: [false, true] | |
include-dgl: [false, true] | |
exclude: | |
- include-rdkit: false | |
include-openeye: false | |
# Can't support 3.12 on Mac yet | |
- python-version: "3.12" | |
os: "macOS-latest" | |
# no openeye for 3.12 yet | |
- include-openeye: true | |
python-version: "3.12" | |
# no builds? | |
- include-dgl: true | |
python-version: "3.12" | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Build information | |
run: | | |
uname -a | |
df -h | |
ulimit -a | |
- name: Install environment | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-file: devtools/conda-envs/test_env_dgl_${{ matrix.include-dgl }}.yaml | |
create-args: >- | |
python=${{ matrix.python-version }} | |
pydantic=${{ matrix.pydantic-version }} | |
- name: Install package | |
run: | | |
python -m pip install . --no-deps | |
- uses: ./.github/actions/include-openeye | |
if: matrix.include-openeye == true | |
with: | |
openeye-license-text: ${{ secrets.OE_LICENSE }} | |
openeye-license-file: ${{ env.OE_LICENSE }} | |
- name: Uninstall OpenEye | |
if: matrix.include-openeye == false | |
run: conda remove --force openeye --yes || echo "openeye not installed" | |
- name: Uninstall RDKit | |
if: matrix.include-rdkit == false | |
run: conda remove --force rdkit --yes || echo "rdkit not installed" | |
# See https:/openforcefield/openff-nagl/issues/103 | |
- name: Rewrite DGL config | |
if: matrix.include-dgl == true | |
run: | | |
mkdir -p ~/.dgl | |
echo '{"backend": "pytorch"}' > ~/.dgl/config.json | |
- name: Python information | |
run: | | |
which python | |
conda info | |
conda list | |
- name: Check toolkit installations | |
shell: bash -l -c "python -u {0}" | |
run: | | |
from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE, RDKIT_AVAILABLE | |
assert str(OPENEYE_AVAILABLE).lower() == '${{ 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${{ matrix.python-version }} | |
pylint_check: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Set up Python | |
uses: actions/setup-python@v3 | |
with: | |
python-version: "3.10" | |
- name: Install Pylint | |
run: | | |
which pip | |
which python | |
pip install pylint | |
- name: Run Pylint | |
env: | |
PYLINTRC: .pylintrc | |
run: | | |
pylint openff-nagl | |
pypi_check: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Set up Python | |
uses: actions/setup-python@v3 | |
with: | |
python-version: "3.10" | |
- name: Install dependencies | |
run: | | |
pip install setuptools twine | |
- name: Build package | |
run: | | |
python setup.py sdist | |
- name: Check package build | |
run: | | |
DISTRIBUTION=$(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: ["3.10", "3.11", "3.12"] | |
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/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__)" |