# Using Git And Github

> Git and GitHub for research work — commits, branches, what to track, big-file pushback, PRs; on the Yale SOM HPC cluster also module load git and SSH agent forwarding. TRIGGER when running git/gh, committing, deciding what to track or ignore, or opening PRs.

- **Type:** Skill
- **Install:** `agentstack add skill-yale-som-hpc-claude-code-marketplace-using-git-and-github`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [yale-som-hpc](https://agentstack.voostack.com/s/yale-som-hpc)
- **Installs:** 0
- **Category:** [Developer Tools](https://agentstack.voostack.com/c/developer-tools)
- **Latest version:** 0.1.0
- **License:** Unlicense
- **Upstream author:** [yale-som-hpc](https://github.com/yale-som-hpc)
- **Source:** https://github.com/yale-som-hpc/claude-code-marketplace/tree/main/plugins/hpc/skills/using-git-and-github

## Install

```sh
agentstack add skill-yale-som-hpc-claude-code-marketplace-using-git-and-github
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# Using Git and GitHub

For agents helping researchers get version-control benefits without becoming git experts.

## Rules

- Track code, config, metadata, docs, lockfiles, small examples.
- Do not track raw data, secrets, env dirs, package libraries, large generated outputs.
- Commit logical checkpoints.
- Prefer simple history. No force-push on shared branches unless explicitly approved.
- Explain git decisions plainly.

## Git on HPC

Git may require a module:

```bash
module load git
git --version
```

Use `module load git` in setup notes/scripts that need git on HPC.

## Auth and pushing

Laptop: HTTPS with `gh auth login` or normal SSH keys are fine.

HPC: prefer SSH agent forwarding so private keys stay on the laptop:

```bash
ssh -A hpc
module load git
ssh -T git@github.com
git push
```

If `SSH_AUTH_SOCK` is stale, fix the socket pointer. Do **not** copy private keys to the cluster. See [connecting securely](../connecting-securely/SKILL.md).

HTTPS / `gh` token auth is also fine if already configured:

```bash
module load git
gh auth status
git push
```

Never copy `~/.ssh/id_*` private keys onto the cluster. Public keys (`*.pub`) are safe; private keys are not.

## Agent behavior

- Run `git status --short` before and after edits.
- Do not silently stage ambiguous untracked files. Report and propose track/ignore/refuse.
- Commit when asked, or when a coherent requested task is complete and repo norms expect commits. If uncertain, ask once.
- Use imperative messages: `Add panel construction script`, `Fix Slurm memory request`.
- Report hash + summary.

## Track / ignore

Track:

- source, scripts, Slurm scripts,
- README/docs,
- `pyproject.toml`, `uv.lock`, `renv.lock`, `.Rprofile`,
- small metadata/codebooks/config,
- tiny synthetic fixtures,
- Makefiles/justfiles.

Ignore:

```gitignore
# Data and outputs
data/raw/
data/derived/
output/
outputs/
results/
logs/
*.parquet
*.rds
*.RDS
*.dta
*.sas7bdat
*.feather
*.h5
*.h5ad

# Python
.venv/
__pycache__/
*.pyc
.pytest_cache/
.ruff_cache/

# R
.Rhistory
.RData
.Rproj.user/
renv/library/
renv/local/
renv/staging/

# Secrets / local config
.env
.env.local
*.pem
*.key

# OS/editor
.DS_Store
Thumbs.db
```

Adjust per project. Final manuscript figures may belong in `paper/figures/`; rebuildable `results/` usually does not.

## Big files

Before committing:

```bash
git diff --cached --name-only | while read -r f; do
  test -f "$f" && wc -c "$f"
done | sort -n
```

Rules:

- >5 MB: warn and ask.
- >50 MB: refuse unless strong reason and repo policy allow it.
- Do not suggest Git LFS reflexively. Prefer documented filesystem path, DOI, or object store.

Track a pointer file instead:

```yaml
- name: crsp_panel.parquet
  location: /gpfs/project/myproject/data/derived/crsp_panel.parquet
  size_bytes: 1234567890
  description: Rebuildable panel from scripts/build_panel.py
```

## Branches

Default for solo/small research repos: commit on `main`.

Use a branch when multiple people are active, the change is experimental, the user asks, or review matters.

Never force-push a shared branch. Prefer revert commits.

## GitHub CLI

```bash
gh auth status
gh repo view --web
gh pr create --fill
```

If `gh` is missing on HPC, do not block. Use git + web UI.

## Checklist

- [ ] `module load git` used on HPC if needed
- [ ] `git status --short` reviewed
- [ ] No raw data, secrets, env dirs, or large outputs staged
- [ ] Lockfiles updated if deps changed
- [ ] Smoke test/check run if practical
- [ ] Plain specific commit message
- [ ] No private SSH keys copied to HPC

## Further reading

- [Pro Git](https://git-scm.com/book/en/v2)
- [GitHub CLI manual](https://cli.github.com/manual/)

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [yale-som-hpc](https://github.com/yale-som-hpc)
- **Source:** [yale-som-hpc/claude-code-marketplace](https://github.com/yale-som-hpc/claude-code-marketplace)
- **License:** Unlicense

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** yes
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-yale-som-hpc-claude-code-marketplace-using-git-and-github
- Seller: https://agentstack.voostack.com/s/yale-som-hpc
- Browse the marketplace: https://agentstack.voostack.com/browse

---
Listed on AgentStack — the marketplace for AI agent skills and MCP servers. Every listing is security-reviewed. Creators keep 70%.