.gitpod.yml

image: gitpod/workspace-python-3.9
tasks:
  - name: Set up analysis env
    init: |
      wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh
      bash Miniconda3-py39_4.12.0-Linux-x86_64.sh -b -p /workspace/miniconda3
      rm Miniconda3-py39_4.12.0-Linux-x86_64.sh
      export PATH="/workspace/miniconda3/bin/:$PATH"
      conda init bash
      source $HOME/.bashrc
      conda config --add channels r --add channels anaconda --add channels bioconda --add channels conda-forge --add channels pytorch 
      # conda create -n torch_env pytorch torchvision torchaudio cudatoolkit=11.3
      conda env create -n torch_env -f analysis/torch_env.yml
      conda activate torch_env
      echo "Prebuild is almost ready -- please be patient..."
    command: |
      printf 'export PATH="%s:$PATH"\n' "/workspace/miniconda3/bin" >> $HOME/.bashrc
      source $HOME/.bashrc
      conda init bash
      source $HOME/.bashrc
      conda config --add channels r --add channels anaconda --add channels bioconda --add channels conda-forge --add channels pytorch 
      conda activate torch_env
vscode:
  extensions:
    - ms-python.python
    - ms-azuretools.vscode-docker
    - GitHub.copilot
github:
  prebuilds:
    # enable for the master/default branch (defaults to true)
    master: true
    # enable for all branches in this repo (defaults to false)
    branches: true
    # enable for pull requests coming from this repo (defaults to true)
    pullRequests: true
    # enable for pull requests coming from forks (defaults to false)
    pullRequestsFromForks: true
    # add a "Review in Gitpod" button as a comment to pull requests (defaults to true)
    addComment: true
    # add a "Review in Gitpod" button to pull requests (defaults to false)
    addBadge: false
    # add a label once the prebuild is ready to pull requests (defaults to false)
    addLabel: prebuilt-in-gitpod