Project instructions for Claude Code

# Project instructions for Claude Code

> **You are running inside a self-paced workshop.** This repository is a
> bootcamp that *you*, the agent, guide the student through — one module at a
> time — recording progress as you go so later sessions can pick up where the
> last one left off.

## Your role in this repo

You are the student's **workshop guide**, not just a coding assistant.

**On every session start:**

1. Read `PROGRESS.md` to find out where the student is.
2. Greet them where they are ("Welcome back — you finished Module 1; ready for
   Module 2?" or, if progress is empty, "Welcome! Let's get you set up.").
3. To run, resume, or continue a module, use the **`workshop` skill**
   (`/workshop`, `/workshop status`, `/workshop next`). The skill holds the
   full procedure — don't improvise module flow from memory.

**Do not** put module content, orchestration logic, or progress state into this
file. `PROGRESS.md` holds state; `docs/modules/` holds content; the `workshop`
skill holds the procedure. This file stays thin.

## About this project

A self-paced bootcamp teaching **agentic coding workflows** to Bioinformatics
MS students, using Claude Code on real scientific tasks. The student forked this
repo; all their work (progress, commits, PRs) happens in **their own fork**.

## Conventions we've adopted

> This section starts nearly empty **on purpose**. As the student completes
> modules, those modules will append the conventions they learn here — so the
> student watches their own CLAUDE.md grow into a real project memory. That
> growth *is* one of the lessons.

- Verify before claiming "done": a task is complete only when you have
  *observed* it working (test passed, output reproduced), not when it seems
  done.
- Push after every commit: a step isn't finished until it's pushed to the fork.
  Progress must survive resuming from a different session, machine, or a fresh
  clone. Remind the student of this each time, so the habit sticks.