Skip to content

add notebook to test substructures in data #593

add notebook to test substructures in data

add notebook to test substructures in data #593

Workflow file for this run

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