Setting up your computer

Most Isom Lab tools are desktop apps you start by double-clicking. Before the first one will run, your computer needs one or two free pieces of software. You do this once, not once per tool.

You do not need to know how to code. Apart from checking that an installer worked, you will not need to type anything.

Mac and Windows are equally supported — every step below covers both. Each tool’s own guide says which of these steps it actually needs, and if it contradicts this page, follow the tool: it knows about anything unusual it requires.

1. Miniforge

Most lab tools need conda, which gives each tool a private copy of Python and everything it depends on, without disturbing anything else on your computer. Miniforge is the free installer that provides it.

A few tools need none of this. Their guides say so, and send you to Tools that don’t need conda instead.

Mac

Go to conda-forge.org/download.
Download the macOS .pkg installer for your Mac: Apple Silicon (arm64) for any Mac from about 2020 onwards, Intel (x86_64) for older ones. Not sure which you have? Apple menu → About This Mac; a “Chip” line reading M1, M2, M3 or M4 means Apple Silicon.
Double-click the .pkg and click through, accepting the defaults.
Check it worked: quit Terminal if it’s open, then open a fresh one (⌘-Space, type Terminal, Enter). You should see (base) at the start of the line. Close it again.

Windows

Go to conda-forge.org/download.
Under Windows, download Miniforge3-Windows-x86_64.exe — the right choice for every normal PC, including new ones.
Double-click it. If Windows says “Windows protected your PC”, that is SmartScreen reacting to a freshly downloaded program, not a sign of trouble: click More info ▸ Run anyway.
Click through, accepting the defaults. Two screens are worth a glance:
- Install for: Just Me (recommended) — leave it. It installs into your own user folder and needs no administrator password, which is what makes this possible on a shared or locked-down instrument PC.
- The checkboxes near the end, about PATH and the default Python — leave them alone. The lab’s launchers find conda by themselves.
Check it worked: open the Start menu, type Miniforge, and open Miniforge Prompt. A window appears with (base) at the start of the line. That is all it is for — close it again.

2. GitHub Desktop (optional)

Every tool lives in a repository on GitHub. You can always download one as a ZIP straight from its page, and each tool’s guide shows you how. GitHub Desktop does the same job with buttons, and updates the tool later the same way.

Go to desktop.github.com, download, install.
Open it. You only need to sign in for the private tools described below.

On Windows there is one extra advantage: files GitHub Desktop downloads are never “blocked”, so you will not meet SmartScreen again.

You do not need Git. Git is a separate command-line tool. None of the lab’s apps ask you to use it, and GitHub Desktop already includes what it needs.

Private tools

Most lab tools are public — anyone can download them, no account required. A few are private, and those need a free GitHub account that has been given access.

Go to github.com and click Sign up. Enter your email, a password, and a username — keep that handy. Finish signing up and verify your email.
Send your GitHub username to Dan at disom@miami.edu. He adds you to the repository, and you get an email titled “[isomlab] invited you to collaborate”. Open it and click Accept invitation.

You cannot download a private tool until that invitation is accepted.

Tools that don’t need conda

A few lab tools are written in nothing but Python’s own standard library. They have no environment to build; they just need a Python 3 on the computer.

Mac: you already have one. Nothing to do.
Windows: install Python from python.org/downloads and tick “Add Python to PATH” on the first screen of the installer.

Both of those include Tk, the toolkit these tools use to open their windows, so there is nothing further to install. If you installed Miniforge for another tool, its Python includes Tk as well.

You’re set up

That is the shared groundwork. Next comes the same short routine for whichever tool you want to run — download its folder, double-click the launcher inside, and let it build its own private environment the first time:

Getting started with a lab tool

Every lab tool is listed on the Isom Lab on GitHub main page.

Trouble?

After installing Miniforge you don’t see (base) — close the window and open a brand-new one; the installer only affects windows opened afterwards. On Mac, if it still doesn’t appear, run source ~/miniforge3/bin/activate once. On Windows, make sure you opened Miniforge Prompt from the Start menu, and not the ordinary Command Prompt or PowerShell — those don’t know about conda.
The Miniforge installer asks for an administrator password (Windows) — you chose “All Users” rather than Just Me. Go back and pick Just Me; it needs no password and works exactly the same.
“Windows protected your PC” — SmartScreen, on anything downloaded from the internet. More info ▸ Run anyway. To avoid it on a downloaded ZIP, right-click the ZIP → Properties → tick Unblock → OK before extracting.
A launcher window flashes open and shuts (Windows) — something failed too fast to read. Right-click the launcher → Copy as path, open Miniforge Prompt, paste, press Enter. The same thing runs, but the message stays on screen. Send what it says to Dan at disom@miami.edu.
You already have Anaconda or Miniconda — that works too; you don’t need Miniforge as well.
Didn’t get the invitation email — check spam, and confirm Dan used the exact username you signed up with. Pending invitations also appear at github.com/notifications.

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