# This workflow will install Python dependencies, run tests, and report the coverage with a variety of Python versions and OSs.

# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: test

on:

push:

branches: [main]

pull_request:

branches: [main]

schedule:

# * is a special character in YAML, so you have to quote this string

- cron: "0 0 * * *" # every midnight

jobs:

test:

name: Test (${{ matrix.os }}, python version ${{ matrix.python-version }})

runs-on: ${{ matrix.os }}

strategy:

matrix:

# os: [ubuntu-latest, windows-latest]

os: [ubuntu-latest]

python-version: ["3.10", "3.11", "3.12"] # list of Python versions to test

# exclude:

# - os: windows-latest

# python-version: "3.10"

include:

- os: ubuntu-latest

path: ~/.cache/pip

# - os: windows-latest

# path: ~\AppData\Local\pip\Cache

steps:

- uses: actions/checkout@v4

- name: Set up Python using Miniconda

uses: conda-incubator/setup-miniconda@v3

with:

auto-update-conda: true

python-version: ${{ matrix.python-version }}

miniconda-version: latest

- name: Cache pip dependencies

id: cache_pip

uses: actions/cache@v4

with:

path: ${{ matrix.path }}

key: ${{ runner.os }}-python${{ matrix.python-version }}-pip-20250302-${{ hashFiles('**/setup.py') }}

restore-keys: |

${{ runner.os }}-python${{ matrix.python-version }}-pip-20250302-

# We have used a softer matching strategy for the full hash of setup.py, as recommended by GitHub.

# See: https://github.com/davronaliyev/Cache-dependencies-in-GitHub-Actions/blob/main/examples.md#python---pip

# This restores the cache first and then downloads any changed packages to avoid updating the cache with

# every change to the setup.py file, thus reducing the storage requirements of GitHub Action.

# We set a date tag to the cache key to show the updated date of the cache. We can update this date tag to

# generate new cache after every major changes in setup.py.

- name: Install PyTorch + PyG

run: |

pip install rdkit

pip install gdown

pip install pyparsing==3.2.0

pip install numpy>=2.0.0

pip install torch==2.6.0 torchvision==0.21.0 torchaudio==2.6.0 --index-url https://download.pytorch.org/whl/cpu

pip install torch_scatter==2.1.2 -f https://data.pyg.org/whl/torch-2.6.0+cpu.html

pip install torch_sparse==0.6.18 -f https://data.pyg.org/whl/torch-2.6.0+cpu.html

pip install torch_cluster==1.6.3 -f https://data.pyg.org/whl/torch-2.6.0+cpu.html

pip install torch_spline_conv==1.2.2 -f https://data.pyg.org/whl/torch-2.6.0+cpu.html

pip install torch_geometric==2.6.0

shell: bash -l {0}

- name: Install project and dev dependencies

run: |

pip install --no-build-isolation -e .[dev]

shell: bash -l {0}

- name: Cache downloaded test data

id: cache_data

uses: actions/cache@v4

with:

path: tests/test_data

key: ${{ runner.os }}-python${{ matrix.python-version }}-data-${{ hashFiles('tests/download_test_data.py') }}

restore-keys: |

${{ runner.os }}-python${{ matrix.python-version }}-data-${{ hashFiles('tests/download_test_data.py') }}

# Use strict matching for the hash of download_test_data.py, as we want to update the cache whenever the file changes.

- name: Download test data

if: steps.cache_data.outputs.cache-hit != 'true'

run: |

python tests/download_test_data.py

shell: bash -l {0}

- name: Run tests with thread limits

id: run_tests

run: |

export OMP_NUM_THREADS=1

export MKL_NUM_THREADS=1

export NUMEXPR_NUM_THREADS=1

pytest --nbmake --nbmake-timeout=3000 --cov=kale

shell: bash -l {0}

- name: Determine coverage

run: |

coverage xml

shell: bash -l {0}

- name: Report coverage

uses: codecov/codecov-action@v4

with:

token: ${{ secrets.CODECOV_TOKEN }}