python-app.yml

name: CellBin Main Test

on:
  push:
    branches:
      - main

jobs:
  build:
    runs-on: self-hosted
    defaults:
      run:
        shell: bash -l {0}
    steps:
    - name: Checkout repository
      uses: actions/checkout@v2

    - name: Demo test
      run: |
        echo $CONDA_PREFIX/bin >> $GITHUB_PATH
        conda init bash
        source ~/.bashrc
        if conda info --envs | grep -q "myenv"; then
          echo "Environment 'myenv' already exists. Skipping creation."
        else
          echo "Environment 'myenv' does not exist. Creating."
          conda create --name myenv python=3.8 -y
        fi
        conda activate myenv
        which python
        python -c "print('Hello, World!')"
        pip install pytest
        pip install pytest-html
        pytest test/test_cellbin_pipeline.py --html=/media/Data1/user/dengzhonghan/data/cellbin2/auto_test_report/${GITHUB_SHA}.html --self-contained-html
        python /media/Data1/user/dengzhonghan/code/email_send/send_email.py \
        -s 'CellBin Research Group' \
        -t 'GitHub Auto Test Report' \
        -r dengzhonghan@genomics.cn \
        -a /media/Data1/user/dengzhonghan/data/cellbin2/auto_test_report/${GITHUB_SHA}.html \
        -m 'CellBin report'