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Test code and publish package

cleanup wrapping code to reduce warnings #821

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cleanup wrapping code to reduce warnings

cleanup wrapping code to reduce warnings #821

Workflow file for this run

.github/workflows/test_and_publish.yml at e611bc0
name: Test code and publish package
on: [push]
jobs:
# test:
# runs-on: ${{ matrix.os }}
# strategy:
# fail-fast: false
# matrix:
# os: ["ubuntu-latest", "macos-latest", "macos-13", "windows-2019"]
# python-version: ["3.9", "3.10", "3.11", "3.12"]
# defaults: # Needed for conda
# run:
# shell: bash -l {0}
# steps:
# - uses: actions/checkout@v4
# with:
# lfs: true
# submodules: true
# - uses: conda-incubator/setup-miniconda@v3
# with:
# python-version: ${{ matrix.python-version }}
# channels: acellera,conda-forge,defaults
# - name: Lint with flake8
# run: |
# pip install flake8 coverage pytest-cov pytest pytest-subtests
# # stop the build if there are Python syntax errors or undefined names
# flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
# # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
# flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
# - name: Install moleculekit conda deps
# run: |
# conda install -y -q --file extra_requirements.txt python=${{ matrix.python-version }} -c acellera -c conda-forge
# # scikit-learn, joblib, biopython are only used for rarely-used functions in smallmol
# conda install -y -q scikit-learn joblib biopython -c conda-forge
# # - name: Install cdpkit
# # # if: ${{ matrix.os == 'ubuntu-latest' }}
# # run: |
# # # for testing CDPKit SmallMol
# # pip install CDPKit
# - name: Install moleculekit
# run: |
# pip install "numpy>=1.23.5" "Cython>=0.29.21"
# pip install .
# pip install "versioneer==0.28"
# python setup.py build_ext --inplace
# - name: List conda environment
# run: conda list
# - 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: ["3.10"]
# steps:
# - uses: actions/checkout@v4
# - uses: conda-incubator/setup-miniconda@v3
# with:
# activate-environment: deploy
# python-version: ${{ matrix.python-version }}
# - name: Build PyPI 📦
# run: |
# pip install numpy>=1.23.5 Cython>=0.29.21 build
# python -m build --sdist --outdir dist/ .
# - name: Publish distribution 📦 to PyPI
# uses: pypa/gh-action-pypi-publish@release/v1
# 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: ["3.10"]
# container: ["quay.io/pypa/manylinux_2_28_x86_64"]
# steps:
# - uses: actions/checkout@v4
# - uses: conda-incubator/setup-miniconda@v2
# with:
# miniconda-version: "latest"
# activate-environment: ../deploy-env
# python-version: ${{ matrix.python-version }}
# - name: Install build deps
# shell: bash -l {0}
# run: |
# git config --global --add safe.directory '*'
# conda install anaconda-client rattler-build python=${{ matrix.python-version }} -c conda-forge
# pip install versioneer==0.28 toml pyyaml
# - name: Build conda package
# shell: bash -l {0}
# run: |
# python package/moleculekit/insert_placeholder_values.py
# rattler-build build --recipe ./package/moleculekit/recipe.yaml --output-dir ../pkg/ --no-include-recipe -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-*.conda
# deploy_osx_win:
# if: startsWith(github.event.ref, 'refs/tags/')
# needs: test
# runs-on: ${{ matrix.os }}
# strategy:
# fail-fast: false
# matrix:
# os: ["macos-latest", "macos-13", "windows-2019"]
# python-version: ["3.10"]
# steps:
# - uses: actions/checkout@v4
# - uses: ilammy/msvc-dev-cmd@v1
# - uses: conda-incubator/setup-miniconda@v3
# with:
# miniconda-version: "latest"
# activate-environment: ../deploy-env
# python-version: ${{ matrix.python-version }}
# - name: Install build deps
# shell: bash -l {0}
# run: |
# git config --global --add safe.directory '*'
# conda install anaconda-client rattler-build python=${{ matrix.python-version }} -c conda-forge
# pip install versioneer==0.28 toml pyyaml
# - name: Build conda package
# shell: bash -l {0}
# run: |
# python package/moleculekit/insert_placeholder_values.py
# rattler-build build --recipe ./package/moleculekit/recipe.yaml --output-dir ../pkg/ --no-include-recipe -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-*.conda
windows_build:
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: ["windows-2019"]
python-version: ["3.10"]
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
miniconda-version: "latest"
activate-environment: ../deploy-env
python-version: ${{ matrix.python-version }}
- name: Add compiler to PATH
run: |
echo "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Tools\MSVC\14.16.27023\bin\HostX64\x64\" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
- name: Install build deps
shell: bash -l {0}
run: |
git config --global --add safe.directory '*'
conda install anaconda-client rattler-build python=${{ matrix.python-version }} -c conda-forge
pip install versioneer==0.28 toml pyyaml
- name: Build conda package
shell: bash -l {0}
run: |
python package/moleculekit/insert_placeholder_values.py
rattler-build build --recipe ./package/moleculekit/recipe.yaml --output-dir ../pkg/ --no-include-recipe -c acellera -c conda-forge