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[v2]: Acceptance Testing for Numpy v2.0 #483

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[v2]: Acceptance Testing for Numpy v2.0

[v2]: Acceptance Testing for Numpy v2.0 #483

Workflow file for this run

.github/workflows/ci.yml at 40d9e4a
# ci.yml
#
# Continuous Integration for Chemprop - checks build, code formatting, and runs tests for all
# proposed changes and on a regular schedule
#
# Note: this file contains extensive inline documentation to aid with knowledge transfer.
name: Continuous Integration
on:
# run on pushes/pull requests to/against main
push:
branches: [main]
pull_request:
branches: [main]
# run this in the morning on weekdays to catch dependency issues
schedule:
- cron: "0 8 * * 1-5"
# allow manual runs
workflow_dispatch:
# cancel previously running tests if new commits are made
# https://docs.github.com/en/actions/examples/using-concurrency-expressions-and-a-test-matrix
concurrency:
group: actions-id-${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
cancel-in-progress: true
jobs:
build:
name: Check Build
runs-on: ubuntu-latest
steps:
# clone the repo, attempt to build
- uses: actions/checkout@v4
- run: python -m pip install build
- run: python -m build .
lint:
name: Check Formatting
needs: build
runs-on: ubuntu-latest
steps:
# clone the repo, run black and flake8 on it
- uses: actions/checkout@v4
- run: python -m pip install black==23.* flake8
- run: black --check .
- run: flake8 .
test:
name: Execute Tests
needs: lint
runs-on: ${{ matrix.os }}
defaults:
run:
# run with a login shell (so that the conda environment is activated)
# and echo the commands we run as we do them (for debugging purposes)
shell: bash -el {0}
strategy:
# if one platform/python version fails, continue testing the others
fail-fast: false
matrix:
# test on all platforms with both supported versions of Python
os: [ubuntu-latest, macos-13, windows-latest]
python-version: [3.11, 3.12]
steps:
- uses: actions/checkout@v4
# use a version of the conda virtual environment manager to set up an
# isolated environment with the Python version we want
- uses: mamba-org/setup-micromamba@main
with:
environment-name: temp
condarc: |
channels:
- defaults
- conda-forge
channel_priority: flexible
create-args: |
python=${{ matrix.python-version }}
- name: Install dependencies
shell: bash -l {0}
run: |
python -m pip install nbmake
python -m pip install ".[dev,docs,test]"
- name: Install hyperopt optional dependencies (Python 3.11 only)
if: ${{ matrix.python-version == '3.11' }}
run: |
python -m pip install ".[hpopt]"
- name: Test with pytest
shell: bash -l {0}
run: |
# specifically disable running on GPU, otherwise Lightning will attempt to use the Apple GPU
# that the GitHub actions runners still have but are not allowed to actually use
pytest -v tests
- name: Test notebooks
shell: bash -l {0}
run: |
pytest --nbmake examples/training.ipynb
pytest --nbmake examples/predicting.ipynb
pytest --nbmake examples/convert_v1_to_v2.ipynb
pytest --nbmake examples/training_regression_multicomponent.ipynb
pytest --nbmake examples/predicting_regression_multicomponent.ipynb
conda-test:
name: Execute Tests with Conda-based Install
needs: lint
runs-on: ubuntu-latest
defaults:
run:
# run with a login shell (so that the conda environment is activated)
# and echo the commands we run as we do them (for debugging purposes)
shell: bash -el {0}
strategy:
# if one platform/python version fails, continue testing the others
fail-fast: false
matrix:
python-version: [3.11, 3.12]
steps:
- uses: actions/checkout@v4
# use a version of the conda virtual environment manager to set up an
# isolated environment with the Python version we want
- uses: mamba-org/setup-micromamba@main
with:
environment-file: environment.yml
condarc: |
channels:
- defaults
- conda-forge
- pytorch
channel_priority: flexible
create-args: |
python=${{ matrix.python-version }}
- name: Install Testing Dependencies
run: conda install -c conda-forge pytest>=6.2 pytest-cov
- name: Install Chemprop
run: python -m pip install . --no-deps
- name: Test with pytest
shell: bash -l {0}
run: |
pytest -v tests
pypi:
name: Build and publish Python 🐍 distributions 📦 to PyPI
runs-on: ubuntu-latest
# only run if the tests pass
needs: [test, conda-test]
# run only on pushes to main on chemprop
if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' && github.repository == 'chemprop/chemprop'}}
steps:
- uses: actions/checkout@master
- name: Set up Python 3.12
uses: actions/setup-python@v3
with:
python-version: "3.11"
- name: Install pypa/build
run: >-
python -m
pip install
build
--user
- name: Build a binary wheel and a source tarball
run: >-
python -m
build
--sdist
--wheel
--outdir dist/
.
- name: Publish distribution 📦 to PyPI
uses: pypa/gh-action-pypi-publish@release/v1
with:
password: ${{ secrets.PYPI_API_TOKEN }}
skip-existing: true
verbose: true
build-and-push-docker:
# shamelessly copied from:
# https://github.com/ReactionMechanismGenerator/RMG-Py/blob/bfaee1cad9909a17103a8e6ef9a22569c475964c/.github/workflows/CI.yml#L359C1-L386C54
# which is also shamelessly copied from somewhere
runs-on: ubuntu-latest
# only run if the tests pass
needs: [test, conda-test]
# run only on pushes to main on chemprop
if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' && github.repository == 'chemprop/chemprop'}}
steps:
- name: Set up QEMU
uses: docker/setup-qemu-action@v2
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
- name: Login to Docker Hub
uses: docker/login-action@v2
with:
# repository secretes managed by the maintainers
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
- name: Build and Push
uses: docker/build-push-action@v4
with:
push: true
tags: chemprop/chemprop:latest