Testing pull requests

Here is one possible workflow for testing code updates in a pull request. It assumes you are starting in a terminal in a local clone of this repository. That is, you are in the ml4bio directory.

Activate the conda environment with the ml4bio dependencies.

conda activate ml4bio

Update remote branches from the GitHub repository.

git pull

Checkout the branch associated with the pull request you want to test. This examples uses the duplicate-name branch from #29.

git checkout duplicate-name

Reinstall the ml4bio package from source using the version of the code on this branch.

pip install -e .

Launch the ml4bio GUI and test the code updates.

ml4bio

If there are changes made in the pull request, you can pull those changes, re-install the software again, and continue testing.

git pull origin duplicate-name
pip install -e .
ml4bio

When you are done testing the pull request code, you can re-install the latest ml4bio release.

pip install --upgrade --no-deps --force-reinstall ml4bio