VSCode for Scientists — Workshop

Hands-on, in-person workshop to get the lab using VSCode for daily work: Fortran (TM5), IDL, legacy Python, Jupyter notebooks, instrument calibration, and LaTeX paper writing.

If you've never used VSCode before, this workshop is for you. We assume you arrive with VSCode + the Remote-SSH extension installed (about 10 minutes of pre-arrival work — see pre-session.md, Part 1). The in-session hour is for the parts that actually need a live demo.

What is VSCode?

A free, open-source code editor from Microsoft. It runs on your laptop and looks like this:

• A file tree on the left.
• A main editor area in the center, where files open as tabs.
• A terminal at the bottom (toggle with Ctrl+`).
• A status bar at the very bottom — shows your Python interpreter, git branch, error count.
• A command palette searchable with Cmd+Shift+P — the "M-x" analog for emacs users.

What makes it relevant to a scientific lab:

1. It edits files on your HPC server as if they were local, via Remote-SSH. No more PuTTY + scp.
2. It understands your code: jump to a function's definition with F12, find every caller with Shift+F12, rename a variable across files with F2 — for Python, Fortran, and IDL.
3. It runs Jupyter notebooks inline, with a variable explorer that shows array shapes and dtypes at a glance.
4. It has tens of thousands of extensions — Fortran syntax, IDL syntax, LaTeX live preview, AI assistants, netCDF viewers — installable in one click.

What to bring

• Laptop with admin rights to install software.
• VSCode + Remote-SSH pre-installed. See pre-session.md, Part 1 — about 10 minutes. Required.
• Your SSH credentials for your HPC server (whatever you use today to log in from your terminal).
• Charger.

Repo layout

.
├── README.md                # this file — the session script
├── pre-session.md           # Part 1 (homework) + Part 2 (Block 0 walkthrough)
├── cheatsheet.md            # one-page shortcut reference (print this)
├── extensions.txt           # `code --install-extension`-able list
├── settings.example.json    # sensible defaults for User Settings JSON
├── setup/                   # SSH config examples, verify.sh, troubleshooting, OOD walkthrough
├── exercises/               # hands-on exercises done in the live session (in order)
│   ├── 01-ruff-magic/       # the "magic save" — ruff fixes on Cmd+S
│   ├── 02-navigation/       # F12 / Shift+F12 / F2 / multi-cursor
│   ├── 03-search-replace/   # Cmd+Shift+F across the workspace
│   ├── 04-scientific-data/  # netCDF / HDF5 / CSV / PNG viewers
│   └── 05-git/              # visual hunk staging
└── self-study/              # take-home exercises and reference docs
    ├── 01-debugging/        # breakpoints, variable inspection (Python)
    ├── 02-jupyter/          # notebooks with variable explorer
    ├── 03-fortran/          # navigation in Fortran
    ├── 04-idl/              # navigation in IDL
    ├── 05-latex/            # LaTeX live preview
    ├── adjacent-tools.md    # CLI tools worth knowing (ruff, uv, fzf, tmux…)
    ├── ai-assistants.md     # Gemini, Copilot, BYO-key in depth
    └── customization.md     # emacs keymap, profiles, settings sync

Session arc (70 minutes)

Time	Block	Exercise
0:00–0:15	Block 0 — Setup together — verify SSH from terminal, clone the workshop repo locally, run verify.sh, connect via Remote-SSH, clone the repo on the remote, confirm with hostname. Walk through pre-session.md Part 2 step-by-step on the projector. MSU users follow setup/msu-ood-walkthrough.md in parallel.	—
0:15–0:20	First contact — UI tour: file tree, editor, terminal (Ctrl+` — already on the remote you just connected to; ls shows your HPC home, hostname confirms it), status bar, command palette as the M-x analog. The "this is what replaces PuTTY" moment.	—
0:20–0:30	The magic save — open messy.py, hit Cmd+S, watch ruff clean up unsorted imports, deprecated numpy aliases, == None, whitespace, all at once. The "good defaults already exist" pitch made concrete.	01
0:30–0:45	Editor superpowers — F12, Shift+F12, F2, multi-cursor, Cmd+Shift+F across the workspace. The "navigation that respects your codebase" pitch.	02, 03
0:45–0:55	Scientific data — open a CSV with Rainbow CSV, open a netCDF with H5Web (graphical browser inside the editor), click on a PNG sitting on the HPC and watch it render in a tab — no scp needed. Replaces ncdump | less and the "copy plot to laptop to look at it" workflow.	04
0:55–1:05	Git — visual hunk staging, inline blame.	05
1:05–1:10	Wrap — cheatsheet, self-study pointers (debugger, notebooks, Fortran, IDL, LaTeX, AI), Q&A.	—

Self-study exercises all live under self-study/. Debugger (01) and notebooks (02) extend the live arc with Python-daily features that wouldn't fit in 70 minutes. Fortran (03), IDL (04), and LaTeX (05) are language- and format-specific re-runs of the navigation and preview exercises — anyone whose daily work involves those will want to do them on their own time. The mechanics are the same; only the languages and tools change.

The three-sentence pitch

1. You stop alt-tabbing. Editor and terminal in the same window, both on the remote, no PuTTY chaos.
2. Navigation that respects your codebase. F12 jumps to a definition across files; Shift+F12 finds all callers. Works on Fortran, IDL, Python, even Markdown links. Once you have this, you can't go back.
3. The good defaults already exist. Multi-cursor rename, visual hunk staging, format-on-save, integrated Jupyter, AI completion. You don't have to assemble or maintain it. (Exercise 10 demonstrates this in 30 seconds.)

The big counter-objection — "but my emacs muscle memory" — is solved by the Awesome Emacs Keymap extension. Keybindings carry over.

The one shortcut that matters

Cmd+Shift+P (Ctrl+Shift+P on Linux/Windows) opens the command palette — a searchable list of every action and setting in VSCode. The M-x analog.

Don't bother memorizing the rest of the shortcuts. Type the verb: "format", "rename", "compare", "git stash", "fold", "reload". If you can describe what you want, you can find it.

The cheatsheet has the dozen shortcuts that are worth learning anyway, but the command palette is the only one that's non-negotiable.

After the workshop

• Keep this repo as reference; every exercise is designed to be re-attempted.
• Work through the self-study exercises in self-study/ on your own as you encounter the relevant work: Python debugging (01), notebooks (02), Fortran (03), IDL (04), LaTeX (05).
• Read self-study/adjacent-tools.md for the CLI tools (ruff, uv, fzf, tmux, …) that pair with VSCode.
• Read self-study/ai-assistants.md for the AI story — what the lab pays for, what CIRES users get free, BYO-key options.
• Read self-study/customization.md for emacs keymaps, profiles, settings sync.
• Look at git log of this repo — it's a worked example of how a small project's history can read well.