Creating GitHub Repositories — Mindfully

A guide for the Radiation Medicine & Applied Sciences team: how to take work that lives on your laptop or a network share and put it on GitHub without ever letting patient data (PHI) leave the building.

Why this exists

Every project's code belongs in a repository — that's a team rule, because our project catalog links to repos and a catalog that points at nothing is a liability. But our work sits next to DICOM files, ARIA exports, and spreadsheets full of MRNs. GitHub is not a HIPAA-covered environment. PHI in a repo — even a private repo — is a reportable incident. The single most important idea in this guide:

Scan and ignore first. Commit second. Push last.

Once a file is committed, it lives in git history forever unless the history is rewritten. Once it's pushed, it has left UCSD. Everything here is designed to catch problems before the first commit, when fixing them costs nothing.

Contents

File	What it's for
docs/creating-a-repo.md	Step-by-step: existing folder → GitHub repo (GitHub Desktop and command-line paths)
docs/mindful-gitignore.md	How to think about a .gitignore, not just copy one
docs/pr-workflow.md	Giving the scan teeth: branch → PR → merge, with main protected by the phi-scan check
docs/phi-scanner-options.md	Analysis: GitHub Action vs. C# tool vs. Claude prompt — and what we built
csharp/	PHI Scan desktop app (recommended) — the scanner as a point-and-click tool; no Python or terminal needed
tools/phi_scan.py	The same scanner as a Python script (terminal users, pre-commit hook, CI). Run it on any folder before git init.
templates/medical-project.gitignore	Ready-to-copy .gitignore for our typical projects
templates/pre-commit	Git hook that runs the scanner on every commit
templates/phi-scan-workflow.yml	GitHub Action tripwire (copy into .github/workflows/)
prompts/phi-review-prompt.md	A prompt for Claude to review borderline files the scanner flags

The 60-second version (recommended: the desktop app)

Most people should use the PHI Scan desktop app — no Python, no terminal:

1. Download PhiScanGui.exe from the Releases page. No installation — just double-click it. (Windows SmartScreen may warn the first time because the exe is unsigned; choose "More info → Run anyway".)
2. Click Browse…, pick your project folder, click Scan.
3. Work the findings top-down: red (HIGH) rows are almost certainly patient data — use Open in Explorer and move those files out of the folder entirely. Yellow (MEDIUM) rows need your judgment; blue (REVIEW) rows are files the scanner can't read (Excel, PDFs) — open them yourself. Rows marked ✓ ignored are already covered by your .gitignore — nothing to do.
4. For anything that must stay in the folder but should never be committed, leave its box checked and click Add checked items to .gitignore. The app shows you exactly what it will write before it writes it.
5. Then publish the folder with GitHub Desktop (no command line) — the step-by-step "Path A" instructions in docs/creating-a-repo.md pick up from here: add the folder, review the file list, commit, and publish private.

Second option: the Python script (for terminal users)

If you already live in a terminal, the same scanner is a Python script — handy for scripting, the pre-commit hook, and CI:

# 0. You need: git, Python 3.8+, and a GitHub account. Nothing else.

# 1. BEFORE creating any repo, scan the folder:
python phi_scan.py "C:\path\to\my\project"

# 2. Fix what it finds (move data out, or let it write your .gitignore):
python phi_scan.py "C:\path\to\my\project" --update-gitignore

# 3. Only then: create the repo (PRIVATE), review `git status`, commit, push.

Both routes run the exact same detection rules, so they give the same protection — pick whichever you're comfortable with. Full walkthrough in docs/creating-a-repo.md; more on the app in csharp/README.md.

The non-negotiables

1. Private by default. Public requires a deliberate decision and a second set of eyes.
2. No PHI, ever, in any repo — private does not mean HIPAA-compliant.
3. Scan before the first commit. A .gitignore added after the fact does not un-commit anything.
4. Data lives outside the code folder (or in one data/ folder that is ignored wholesale). Code and patient data should never be interleaved.
5. If PHI gets committed: stop. Don't push. If it was already pushed, treat it as an incident (see the last section of the repo guide) — deleting the file in a new commit does not remove it from history.