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celloracle_weekly_build_and_test #94

celloracle_weekly_build_and_test

celloracle_weekly_build_and_test #94

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