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pytest.yaml
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name: tests
on:
push:
pull_request:
types: [opened, reopened]
env:
# Increase this value to reset cache if environment.yml has not changed.
PY_CACHE_NUMBER: 2
PY_ENV: ccc_gene_expr
jobs:
ccc_pytest:
name: Python tests for CCC
runs-on: ${{ matrix.os }}
strategy:
max-parallel: 4
fail-fast: false
matrix:
python-version: ["3.10", "3.11"]
os: [ubuntu-latest, macOS-latest, windows-latest]
steps:
- name: Checkout git repo
uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install pytest "numpy<2.0" scipy numba pandas scikit-learn
- name: Test CCC with pytest
env:
PYTHONPATH: libs/
run: |
pytest tests/test_coef.py tests/test_pytorch_core.py tests/test_scipy_stats.py tests/test_sklearn_metrics.py
# pytest:
# name: Python tests for analyses
# runs-on: ${{ matrix.os }}
# strategy:
# max-parallel: 4
# fail-fast: false
# matrix:
# python-version: ["3.9"]
# os: [ubuntu-latest, macOS-latest, windows-latest]
# steps:
# - name: Checkout git repo
# uses: actions/checkout@v3
# - name: Cache conda
# id: cache
# uses: actions/cache@v3
# with:
# path: "${{ env.PY_ENV }}.tar.gz"
# key: ${{ runner.os }}-${{ env.PY_CACHE_NUMBER }}-${{ hashFiles('environment/environment.yml', 'environment/scripts/install_r_packages.r', 'environment/scripts/install_other_packages.sh') }}
# - name: Setup Miniconda
# if: steps.cache.outputs.cache-hit != 'true'
# uses: conda-incubator/setup-miniconda@v2
# with:
# activate-environment: ${{ env.PY_ENV }}
# environment-file: environment/environment.yml
# auto-activate-base: false
# miniforge-variant: Mambaforge
# miniforge-version: 'latest'
# use-mamba: true
# - name: Install other packages and Conda-Pack environment
# if: steps.cache.outputs.cache-hit != 'true'
# shell: bash -l {0}
# run: |
# # other packages (R packages mainly)
# bash environment/scripts/install_other_packages.sh
#
# # install conda-pack, and pack environment
# conda install --yes -c conda-forge conda-pack coverage
# conda pack -f -n ${{ env.PY_ENV }} -o "${{ env.PY_ENV }}.tar.gz"
# - name: Unpack environment
# shell: bash -l {0}
# run: |
# mkdir -p "${{ env.PY_ENV }}"
# tar -xzf "${{ env.PY_ENV }}.tar.gz" -C "${{ env.PY_ENV }}"
# - name: Setup data and run pytest (Windows systems)
# if: runner.os == 'Windows'
# env:
# PYTHONPATH: libs/
# shell: cmd
# run: |
# echo on
# cd ${{ env.PY_ENV }}
# call .\Scripts\activate.bat
# .\Scripts\conda-unpack.exe
# cd ..
# set R_HOME=%CONDA_PREFIX%\Lib\R
# python environment\scripts\setup_data.py --mode testing
# pytest -v -rs tests
# - name: Setup data and run pytest (non-Windows systems)
# if: runner.os != 'Windows'
# shell: bash
# env:
# PYTHONPATH: libs/
# run: |
# source ${{ env.PY_ENV }}/bin/activate
# conda-unpack
#
# python environment/scripts/setup_data.py --mode testing
#
# if [ "$RUNNER_OS" == "Linux" ]; then
# # for linux/ubuntu, run the tests once: with numba jit activated
# # (which is the expected implementation) and with the jit
# # deactivated (otherwise coverage does not work).
#
# # numba jit activated
# pytest -v -rs tests
#
# # numba jit deactivated + code coverage
# export NUMBA_DISABLE_JIT=1
# coverage run --source=libs/ -m pytest -v -rs tests
# coverage xml -o coverage.xml
# else
# pytest -v -rs tests
# fi
# - name: Codecov upload
# if: runner.os == 'Linux'
# uses: codecov/codecov-action@v2
# with:
# files: ./coverage.xml
# name: codecov-${{ matrix.os }}-python${{ matrix.python-version }}
# fail_ci_if_error: true
# verbose: true