Running marimo notebooks on your own computer

If you are having trouble logging in to molab or opening the notebooks there, you can run the class notebooks on your own computer instead. These instructions work on Windows, macOS, and Linux.

You will use a free tool called pixi that installs Python, marimo, and everything else the notebooks need, exactly as I have them set up on my computer. You only need to type a few short commands.

The setup has three parts, and you only need to do them once:

Install pixi
Download the class files
Start marimo

After that, getting back into your notebooks takes two commands.

Before you start

You will need an internet connection and about 1 GB of free disk space.
The first time you start marimo, it will take a few minutes to download and install everything. After that, it starts in a few seconds.
Below, choose the tab for your computer’s operating system (Windows, macOS, or Linux). Picking a tab once will switch all the tabs on this page.

Install pixi

Download the pixi installer by clicking this link: pixi installer for Windows
Open your Downloads folder and double-click the file you just downloaded (pixi-x86_64-pc-windows-msvc.msi). Follow the prompts to install pixi, accepting the default options.

If Windows shows a blue “Windows protected your PC” window, click “More info” and then “Run anyway.”

The installer didn’t work. Is there another way?

Yes. Open the Terminal app (see Open a terminal below), copy the command below, paste it into the terminal, and press Enter:

powershell -ExecutionPolicy Bypass -c "irm -useb https://pixi.sh/install.ps1 | iex"

Open the Terminal app. The easiest way to find it is to press Command (⌘) + Space, type Terminal, and press Enter.
Copy the command below, paste it into the Terminal window (Command (⌘) + V), and press Enter:
```
curl -fsSL https://pixi.sh/install.sh | sh
```
You will see some messages about pixi being downloaded and installed. When the command is done, you will get a new prompt.

Open a terminal.
Copy the command below, paste it into the terminal, and press Enter:
```
curl -fsSL https://pixi.sh/install.sh | sh
```
If you get a message that curl is not found, use this instead:
```
wget -qO- https://pixi.sh/install.sh | sh
```

Close your terminal and open a new one

After installing pixi, close any terminal windows you have open. Your terminal only learns about newly installed programs when it starts, so pixi will not work in a terminal that was already open.

Check that pixi is installed

Open a new terminal (see Open a terminal below if you are not sure how), type the following command, and press Enter:

pixi --version

You should see something like pixi 0.81.0 (your version number may be different). If you see an error that pixi is “not recognized” or “command not found,” close the terminal, open a new one, and try again. If you still get the error, see Troubleshooting.

Download the class files

Go to the class GitHub repository.
Click the green “Code” button, and then click “Download ZIP” at the bottom of the menu that pops up. This will download a file named intro-to-comp-bio-main.zip.
Unzip the file:
Open your Downloads folder, right-click intro-to-comp-bio-main.zip, choose “Extract All…”, and then click “Extract.”

Do not just double-click the ZIP file and work from inside it. That only lets you peek at the files; it does not unzip them.

Open your Downloads folder and double-click intro-to-comp-bio-main.zip. A folder named intro-to-comp-bio-main will appear next to it.

Use your file manager to extract intro-to-comp-bio-main.zip, or run unzip intro-to-comp-bio-main.zip from your Downloads folder.
Open the unzipped folder until you see a folder named notebooks and a file named pixi.toml. The folder that holds notebooks and pixi.toml is your class folder and you want to rename it as comp-bio. On Windows, you may need to open a second intro-to-comp-bio-main folder inside the first one to find notebooks and pixi.toml, and pixi.toml may show up as just pixi. Just make sure you rename the folder that contains notebooks and pixi.toml as comb-bio.
Move your class folder that you renamed as comp-bio into your home folder:
Your home folder is the folder with your username, such as C:\Users\YourName. To open it, open File Explorer, click in the address bar at the top, type %USERPROFILE%, and press Enter. Then drag your comp-bio folder into it.

Your home folder is the folder with your username (it has a house icon). To open it, click on the desktop or a Finder window, and then in the Finder menu at the top of the screen choose Go → Home. Then drag your comp-bio folder into it.

Move the folder to your home directory (~/comp-bio).

Don’t put your class folder in OneDrive or iCloud

On many computers, the Desktop and Documents folders are automatically backed up to OneDrive (Windows) or iCloud (macOS). pixi creates thousands of small files, and backing those up can make everything very slow or cause errors. Your home folder avoids this problem.

Start marimo

Open a terminal

Click the Start button, type Terminal, and open the Terminal app. On Windows 10, if Terminal doesn’t show up, type PowerShell and open Windows PowerShell instead.

Press Command (⌘) + Space, type Terminal, and press Enter.

Open your terminal app of choice.

Move into your class folder

A new terminal starts in your home folder, which is where you put your class folder. Type the following command and press Enter:

cd comp-bio

The cd command means “change directory” (a directory is another name for a folder).

I put my class folder somewhere else. How do I get there?

Type cd followed by a space (don’t press Enter yet). Then drag your class folder from File Explorer or Finder and drop it onto the terminal window. The folder’s location will be typed in for you. Now press Enter.

Run marimo

Type the following command and press Enter:

pixi run start

The first time you do this, pixi will download and install Python, marimo, and the other packages the notebooks need. This can take several minutes, and you will see a lot of messages scroll by. That is normal.

When it is done, marimo will open in your web browser, showing a list of the class notebooks. Click on a notebook to open it. If your browser doesn’t open by itself, look in the terminal for a line starting with http://localhost:2718 (the numbers may be different), and copy and paste that whole address into your web browser.

Keep the terminal open while you work

The terminal is running marimo for you. If you close the terminal window, your notebook will stop working. You can minimize the terminal, but don’t close it until you are done.

When you are done

Save your notebook by pressing Ctrl + S (Windows and Linux) or Command (⌘) + S (macOS). marimo also saves automatically, but it doesn’t hurt to make sure.
Close the browser tab.
Go back to the terminal and press Ctrl + C to stop marimo (this is Ctrl + C on macOS too, not ⌘ + C). If marimo asks whether you want to shut down, type y and press Enter.
Now you can close the terminal.

Your notebooks are saved in the notebooks folder inside your class folder.

Each time you work on a notebook

Once everything is set up, here is all you need to do:

Open a terminal.
Type cd comp-bio and press Enter.
Type pixi run start and press Enter.

Getting new notebooks

When I post a new notebook during the semester, you only need to download that one file. Please do not download the whole ZIP file again, because your new class folder would not contain the work you have already done.

Go to the notebooks folder on GitHub and click into the folder for the new notebook.
Click on the notebook file (it ends in .py).
Near the top right of the file, click the download button (the icon with a downward-pointing arrow, labeled “Download raw file”).
Find the downloaded file in your Downloads folder, and move it into the notebooks folder inside your class folder.

The next time you run pixi run start, the new notebook will show up in marimo’s list of notebooks.

Troubleshooting

“pixi is not recognized” or “pixi: command not found”

Your terminal doesn’t know about pixi yet. Close all of your terminal windows, open a new one, and try again. If that doesn’t work, restart your computer and try again. If you still get the error, try installing pixi again.

“could not find pixi.toml” or “could not find a pixi workspace”

The terminal is not in your class folder. Type the command below and press Enter to list what is in the folder your terminal is in:

ls

You should see notebooks and pixi.toml in the list. If you don’t, you are in the wrong folder. See the tip under Move into your class folder for an easy way to get to the right one. If you see another intro-to-comp-bio-main folder, your class folder is inside it, so go back to step 4 under Download the class files.

“cd: no such file or directory” or “Cannot find path”

Your class folder isn’t named comp-bio, or it isn’t in your home folder. Go back to step 5 under Download the class files, or use the drag-and-drop tip under Move into your class folder.

`pixi run start` takes a very long time or fails partway through

The first run downloads a lot of files, so make sure you have a good internet connection (campus Wi-Fi is usually fine). If it fails partway through, run pixi run start again; pixi will pick up where it left off. If it is extremely slow, make sure your class folder is not inside OneDrive or iCloud (see the warning under Download the class files).

A notebook says it “Failed to download file”

Some notebooks download small data files from GitHub the first time they run. Check that your computer is connected to the internet, and then re-run the notebook.

Still stuck?

Please come to office hours or send me a message. It helps a lot if you include a screenshot of your terminal window showing the error message.