reimplemented calculation of angles and dihedrals in cython. Speed up… #670
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name: Test code and publish package | |
on: [push] | |
jobs: | |
test: | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: ["ubuntu-latest", "macos-latest", "windows-latest"] | |
python-version: ["3.8", "3.9", "3.10"] | |
defaults: # Needed for conda | |
run: | |
shell: bash -l {0} | |
steps: | |
- uses: actions/checkout@v2 | |
with: | |
lfs: true | |
submodules: true | |
- uses: conda-incubator/setup-miniconda@v2 | |
with: | |
auto-update-conda: true | |
python-version: ${{ matrix.python-version }} | |
uses-mamba: true | |
miniforge-variant: Mambaforge | |
channels: acellera,conda-forge,defaults | |
- name: Lint with flake8 | |
run: | | |
pip install flake8 coverage pytest-cov pytest pytest-subtests | |
# stop the build if there are Python syntax errors or undefined names | |
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
- name: Install moleculekit conda deps. rdkit version is just set high for tests to pass | |
run: | | |
mamba install -y -q --file extra_requirements.txt python=${{ matrix.python-version }} -c acellera -c conda-forge | |
mamba install -y -q rdkit=2023.03.3 -c conda-forge | |
# scikit-learn, joblib, biopython are only used for rarely-used functions in smallmol | |
mamba install -y -q scikit-learn joblib biopython -c conda-forge | |
- name: Install moleculekit | |
run: | | |
pip install "numpy>=1.18.5" "Cython>=0.29.21" | |
pip install . | |
pip install "versioneer==0.28" | |
python setup.py build_ext --inplace | |
- name: Test | |
run: | | |
pytest ./moleculekit | |
env: | |
GITHUB_ACTIONS: 1 | |
# - name: Upload coverage to Codecov | |
# uses: codecov/codecov-action@v3 | |
deploypypi: | |
if: startsWith(github.event.ref, 'refs/tags/') | |
needs: test | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: ["ubuntu-latest"] | |
python-version: ["3.9"] | |
steps: | |
- uses: actions/checkout@v1 | |
- uses: conda-incubator/setup-miniconda@v2 | |
with: | |
activate-environment: deploy | |
python-version: ${{ matrix.python-version }} | |
- name: Build PyPI 📦 | |
run: | | |
pip install numpy>=1.18.5 Cython>=0.29.21 build | |
python -m build --sdist --outdir dist/ . | |
- name: Publish distribution 📦 to PyPI | |
uses: pypa/gh-action-pypi-publish@master | |
with: | |
password: ${{ secrets.PUBLIC_PYPI_API_TOKEN }} | |
skip_existing: true | |
deploy_linux: | |
if: startsWith(github.event.ref, 'refs/tags/') | |
needs: test | |
runs-on: ${{ matrix.os }} | |
container: ${{ matrix.container }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: ["ubuntu-latest"] | |
python-version: ["3.8", "3.9", "3.10"] | |
container: ["quay.io/pypa/manylinux2014_x86_64"] | |
steps: | |
- uses: actions/checkout@v1 | |
- uses: conda-incubator/setup-miniconda@v2 | |
with: | |
miniconda-version: "latest" | |
activate-environment: ../deploy-env | |
python-version: ${{ matrix.python-version }} | |
- name: Build moleculekit package | |
shell: bash -l {0} | |
run: | | |
git config --global --add safe.directory '*' | |
conda install anaconda-client conda-build python=${{ matrix.python-version }} toml | |
pip install versioneer==0.28 | |
python package/moleculekit/insert_placeholder_values.py | |
conda build --python ${{ matrix.python-version }} package/moleculekit/ --output-folder ./pkg/ --no-include-recipe --no-anaconda-upload -c acellera -c conda-forge | |
- name: Upload to conda | |
shell: bash -l {0} | |
run: | | |
anaconda -t ${{ secrets.ANACONDA_TOKEN_BASIC }} upload -u acellera ./pkg/*/moleculekit-*.tar.bz2 | |
deploy_osx_win: | |
if: startsWith(github.event.ref, 'refs/tags/') | |
needs: test | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: ["macos-latest", "windows-latest"] | |
python-version: ["3.8", "3.9", "3.10"] | |
steps: | |
- uses: actions/checkout@v1 | |
- uses: conda-incubator/setup-miniconda@v2 | |
with: | |
miniconda-version: "latest" | |
activate-environment: ../deploy-env | |
python-version: ${{ matrix.python-version }} | |
- name: Build moleculekit package | |
shell: bash -l {0} | |
run: | | |
git config --global --add safe.directory '*' | |
conda install anaconda-client conda-build python=${{ matrix.python-version }} toml | |
pip install versioneer==0.28 | |
python package/moleculekit/insert_placeholder_values.py | |
conda build --python ${{ matrix.python-version }} package/moleculekit/ --output-folder ./pkg/ --no-include-recipe --no-anaconda-upload -c acellera -c conda-forge | |
- name: Upload to conda | |
shell: bash -l {0} | |
run: | | |
anaconda -t ${{ secrets.ANACONDA_TOKEN_BASIC }} upload -u acellera ./pkg/*/moleculekit-*.tar.bz2 |