# Command-line or notebook?

Once you've decided on the language, you next have to decide on your
programming environment: the command line as in {ref}`the basics`, or the
notebook as in {ref}`the notebook server`.

## In favor of notebooks

-   They facilitate rapid code development. You fiddle inside a cell,
    hit SHIFT-ENTER to execute it, get it to do what you want. Then you
    move to the next cell.

<p />

-   Documentation is easy, as shown {ref}`here <markdown-cells>`.

<p />

-   Notebooks are easy to share. For example, a colleague of yours can
    copy one of your notebooks to their own area to look at it:

        %cp ~jsmith/energy-calibration/myanalysis.ipynb jsmith-analysis.ipynb

<p />

-   The interface to a notebook is through a web browser. You don't need
    ssh or an X-Windows emulator.

## Against notebooks

-   They're relatively new in software development. It's possible your
    supervisor has never heard of them. If you say you've got a .png
    plot in a Jupyter notebook, they'll reply "You've got a what in a
    where?"

<p />

-   The `%jsroot on` magic command does not enable every X-Window
    feature available from within the ROOT command line. There's no
    `TBrowser`, `Treeviewer`, or `FitPanel`. You can't add new elements to a
    plot and then save the ROOT commands so you can examine how to use
    them in a .C file.[^f64]

<p />

-   As you saw {ref}`before <first-notebook>`, your canvases are not
    automatically drawn or updated for you. You must explicitly issue
    `Draw()` commands for your canvases.

## Issues with the Nevis notebook server

Most of these points involve technical sysadmin issues. You may want to
skip them, and come back later if you have a notebook problem.

-   The Nevis particle-physics JupyterHub notebook server is not
    something you find at most institutions, at least not for now. Only
    the REU students and the particle-physics groups have access to it.
    Your astrophysics or RARAF colleagues won't be able to view your
    notebooks. You can install Jupyter on your laptop, but that won't
    help anyone else see your work.

<p />

-   You can develop software in notebooks, but you can't run multi-hour
    jobs with them on our notebook server.[^f65]

<p />

-   Some physics software is a "chimera", a blend of software compiled
    in two languages. For example, the Neutrino Deep Learning group uses
    Python to call pre-compiled C++ routines. Our notebook server may
    not be able to run software that's been compiled on another
    machine.[^f66]

<p />

-   As you get more familiar with the UNIX shell, you may start making
    changes to your standard shell setup. You do this by editing special
    shell initialization files such as `.profile`.[^f67] If you add new
    variables to your environment, these variables are available in our
    notebook server as well.[^f68]

    However, if you modify certain variables such as
    `$LD_LIBRARY_PATH` or run environment-customization scripts (such
    as `conda activate /usr/nevis/conda/root`) in your default
    initialization, it can affect the execution of the notebook
    server. The typical symptoms are a notebook kernel that refuses to
    start or you get library load errors.

You can get around many of these issues by [running
Jupyter](https://twiki.nevis.columbia.edu/twiki/bin/view/Main/IPython)
on your Nevis workgroup server.

[^f64]: See {ref}`magic-command` for a minor exception to this.

[^f65]: The way to handle such tasks is with {ref}`batch-systems`.

[^f66]: I doubt this will be important to your work this summer, but so
    you can look it up if necessary: As of 2024, most of the
    Nevis particle-physics systems are running [AlmaLinux 9](https://almalinux.org/).

[^f67]: Here's a list of [shell initialization
    files](https://twiki.nevis.columbia.edu/twiki/bin/view/Main/Shell), at
    least for the systems at Nevis.

    A UNIX survival tip: Never let a well-meaning friend start editing
    your shell initialization scripts for you. I can't count the number
    of times I've looked at someone's shell init scripts and saw they
    were last edited in the 1990s. A user had either forgotten or never
    knew that their friend had put any such commands there, and so never
    kept them updated in the years since. These init scripts were copied
    from user to user for decades.

    If you edit your scripts yourself, at least you have a chance to
    maintain them.

[^f68]: For reference:

    If you define a variable in a shell, e.g.,

        export mywork=~/analysis_work_directory

    then you can access the variable within your program in ROOT C++:

        TString my_location = gSystem->Getenv("mywork");

    In Python:

        import os
        my_location = os.environ["mywork"]

:::{figure-md} mac_pc-fig
:align: center

<img src="https://imgs.xkcd.com/comics/mac_pc.png" alt="xkcd mac_pc" width="30%">

<https://xkcd.com/934/> by Randall Munroe
:::