add notebook to test substructures in data #593
Workflow file for this run
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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: ["3.9", "3.10"] | |
os: [ubuntu-latest, macOS-latest, windows-latest] | |
steps: | |
- name: Checkout git repo | |
uses: actions/checkout@v3 | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v3 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip | |
pip install pytest numpy scipy numba pandas==1.4.* scikit-learn==1.1.* | |
- 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 |