GitHub Usage

Owner: Jeff

Getting Access

Create a GitHub account, then send your username to Jeff (jeffrey.maurer@pennmedicine.upenn.edu) for contributor access to the relevant repo(s).

We prefer that as few hands as possible touch the main branch directly — use a branch + pull request for anything beyond a trivial fix.

Everyday Workflow

git clone <repo-url>
git status
git diff
git add <file>
git commit -m "short description of the change"
git push

For a new piece of work, branch first:

git checkout -b <your-name>/<short-description>
# make changes, commit, push
git push -u origin <your-name>/<short-description>

Then open a pull request on GitHub for review before merging to main.

Project Repos vs. This Manual

Project code/scripts belong in their own project repo (see Project Management → Dry Lab), not in lab-manual. lab-manual is only for onboarding/SOP content like this page.

.gitignore Conventions

For projects with test data, exclude files matching *_small* and *_toy* patterns in .gitignore.

Virtual Environments

The lab maintains a shared software directory for reproducible environments across projects. Check that directory’s README for the specific setup instructions for your project.