Research Tips and Tricks

Color Brewer

Color Brewer is a fantastic site for generating a colour scheme for a paper, and making sure it's colourblind and printer friendly.

Scalene

Scalene is a fast, accurate insanely useful profiler for Python. This video goes over why it's so good.

Overleaf Vim Mode

Want to vim-ify your life (why wouldn't you)?

Overleaf has a vim mode, just go to Menu (top left), then change keybindings from None to vim. You can also change it to emacs... if you must.

Overleaf Bibliography Workflow

I found myself getting annoyed by having to search for bibtex citations for papers I cited previously in other papers

I have a project in Overleaf called "Preamble" which contains:

• preamble.tex: All the custom commands, packages, and options I like to have by default.

• biblio.bib: An ever expanding bibliography containing every paper I ever cited (currently 6700 lines long). I make sure to name each citation FirstAuthorSecondAuthorDate so I avoid duplicate entries.

Now whenever I start a new project I simply need to these files From Another Project and then \input{preamble} after documentclass and include \bibliography{biblio.bib} before \end{document}.

Useful ssh config options

If you find yourself ssh-ing into servers a lot, there are a number of ssh config commands you might consider. In ~/.ssh/config, the general syntax is:

Host hostname
    HostName host.name.com
    User username

Allowing you to simply ssh hostname as a proxy for ssh username@host.name.com

In addition there are a number of options I impose on all ssh hosts:

Host * # Apply these options to all hosts
    ControlMaster auto
    ControlPersist 4800
    ControlPath ~/.ssh/control/%r.%h.%p.sock

This creates a file in ~/.ssh/control/ which contains my connection information. As long as I don't lose network connection, this allows me to keep whatever login authentication I used valid. This means that I login to the server once, this file is created, and then I don't need to login in again (at least until I restart my computer).

Doi2Bib

Doi2Bib lets you insert the doi of a paper and get its bibtex citation.

Interactive Echo

In my .bashrc files on servers I like to have echo commands to state various bits of info, however that makes non-interactive commands like scp and sshfs quite angry, so I usually include the following:

alias interactive_echo='[[ $- == *i* ]] && echo'

Which first checks if the session is interactive, and only then echoes.

You can use a similar syntax to speed up non-interactive ssh commands if the ~/.bashrc file on the server you're connecting to does a lot of work (aliasing, setting up environments, etc...)

# Test if interactive shell
if [[ $- == *i* ]]; then
    # Do all your work
    source ...
    conda activate ...
    module load ...
fi

Python For Loop / List Comprehension Easy Parallisation

If you have a for loop like:

result_list = []
for value in list:
    do
    stuff
    to
    value
    result_list.append(value)

Or a list comprehension like:

result_list = [do_stuff(value) for value in list]

Then you can easily parallise this via:

import multiprocessing
from joblib import Parallel, delayed

num_cores = multiprocessing.cpu_count()
def do_stuff(val):
    do
    stuff

result_list = Parallel(n_jobs=num_cores)(delayed(do_stuff)(value) for value in list)

You can even wrap list in tqdm to get a parallel friendly progress bar!

Force your latex tables to fit

I'm sure anyone who's written a scientific paper in latex has come across the issue that your tables just don't fit!

If your table is too wide, then \resizebox from graphicx can help you out:

\usepackage{graphicx}
\begin{document}

\begin{table}
\centering
\resizebox{\textwidth}{!}{
\begin{tabular}{c|c}
Holy moly, this is a very, very, very, very & very, very, very, very wide table!
\end{tabular}}
\caption{}
\label{}
\end{table}

\end{document}

If instead your table is too long, you can have it cross multiple pages via the longtable package:

\usepackage{longtable}
\begin{document}

\begin{longtable}{c|c}
Holy & moly \\
this & is \\
a & very \\
very & very \\
very & very \\
very & very \\
very & very \\
long & table!
\end{longtable}

\end{document}

Unfortunately, longtables require one column layout, so won't work in a two column environemnt, unless you first swap back to one column, create the longtable, then swap back to two column.