.gitpod.yml

# Download & install dependencies, run build scripts, you name it - tasks Gitpod takes care of before you start a new development environment 
# so you don’t have to wait for any of that. With prebuilds enabled for your project, Gitpod runs the before, init and prebuild commands 
# in your `.gitpod.yml` file every time code is pushed to your repository. The resulting snapshot of the development environment is called a prebuilt workspace.
# When anyone starts a new workspace, all Gitpod needs to do is load the prebuilt workspace. 
# Since the heavy-lifting happened during the prebuild phase, the workspace starts up quickly, allowing you to start your work right away.

# Setup for GitHub.com -- Install the app here: https://github.com/apps/gitpod-io

github:
  prebuilds:
    # enable for the default branch (defaults to true)
    master: true
    # enable for all branches in this repo (defaults to false)
    branches: false
    # enable for pull requests coming from this repo (defaults to true)
    pullRequests: false
    # enable for pull requests coming from forks (defaults to false)
    pullRequestsFromForks: false
    # add a check to pull requests (defaults to true)
    addCheck: true
    # add a "Review in Gitpod" button as a comment to pull requests (defaults to false)
    addComment: true
    # add a "Review in Gitpod" button to the pull request's description (defaults to false)
    addBadge: true

# The prebuilds section in the `.gitpod.yml` file configures when prebuilds are run. 
# By default, prebuilds are run on push to the default branch and for each pull request coming from the same repository. 
# Additionally, you can enable prebuilds for all branches (branches) and for pull requests from forks (pullRequestsFromForks).

# List the start up tasks. Learn more https://www.gitpod.io/docs/config-start-tasks/

# Note: mamba is a drop-in replacement for conda which does faster package resolution

tasks:
  - name: setupconda
  - before: |
      curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh \
        --output /workspace/Mambaforge3-Linux-x86_64.sh
      bash /workspace/Mambaforge3-Linux-x86_64.sh -b -p /workspace/miniforge3
      echo "PATH="/workspace/miniforge3/bin:$PATH"" >> ${HOME}/.bashrc
      rm /workspace/Mambaforge3-Linux-x86_64.sh
      /workspace/miniforge3/bin/conda init bash
      source ~/.bashrc
      # conda deactivate
      conda config --set report_errors false
      conda env update --name=base --file=environment-mamba.yml 
      source activate base
      python -m ipykernel install --user --name=base
      conda -V && python -V
      python -m pip install planemo


# NOTE: Plan for now is just to work in the conda base environment - could use a one or two other
#       conda envs if warranted -- this disposable Gitpod.io infrastructure sort of takes care
#       of not getting too distracted with Docker / virtualenvs / conda envs.


# List the ports to expose. Learn more https://www.gitpod.io/docs/config-ports/

#ports:
#  - port: 8888
#    onOpen: notify

# VS Code extensions to install

vscode:
  extensions:
    - "gitpod.gitpod-desktop"
    - "eamodio.gitlens"
    - "ms-toolsai.jupyter"
    - "ms-toolsai.jupyter-keymap"
    - "ms-vscode-remote.remote-ssh"
    - "ms-vscode-remote.remote-ssh-edit"
    - "github.vscode-pull-request-github"
    - "ms-python.python"
    - "ms-python.vscode-pylance"
    - "redhat.vscode-yaml"
    - "dotjoshjohnson.xml"
#    - "ms-azuretools.vscode-docker"