celloracle_weekly_build_and_test #94
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name: celloracle_weekly_build_and_test | |
on: | |
schedule: | |
- cron: '0 9 * * 0' | |
workflow_dispatch: | |
jobs: | |
build_and_test: | |
runs-on: ubuntu-20.04 | |
timeout-minutes: 60 | |
steps: | |
- uses: actions/checkout@v2 | |
- name: Setup conda, install packages, and test celloracle | |
run: | | |
sudo apt-get update | |
sudo apt-get install -y bedtools | |
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh | |
bash miniconda.sh -b -p $HOME/miniconda | |
source "$HOME/miniconda/etc/profile.d/conda.sh" | |
hash -r | |
conda config --set always_yes yes --set changeps1 no | |
#conda update -q conda | |
# Useful for debugging any issues with conda | |
conda info -a | |
# Create env | |
conda create -q -n test-environment python=3.10 | |
# command to install dependencies | |
conda activate test-environment | |
conda install cython numpy pytest | |
conda list | |
ls /home/runner/miniconda | |
ls /home/runner/miniconda/bin | |
python --version | |
which pip | |
#Install fa2 for tutorial | |
#pip install fa2 | |
# Install CellOracle | |
git clone https://github.com/morris-lab/CellOracle.git | |
cd CellOracle | |
pip install . | |
# command to run tests | |
pytest -v | |