Pointers

Johann Brehmer ([email protected]), 2020

This is a list of tools, techniques, and tips that made me feel more productive. In all of these areas I have much to learn, if you think "X is stupid, you should do Y instead", please let me know.

Project organization

• Claudio Jolowicz wrote a great guide on how to set up a Python project.
• My own repositories are far from these best practices, but worked well for me for testing out ideas fast. I included an example of my repository structure in example_repo.

Coding

• Black (but with -l 120, unless you're Gutenberg) is neat.
• My most visited website of 2019 and 2020 is probably this StackOverflow question on how to add conda environments to Jupyter Lab.

Machine learning

• Some advice on optimizing PyTorch code at this tweet.
• For config management, I have used sacred and hydra, preferring the latter.
• MLFlow is my favourite tool for experiment tracking so far.
• For hyperparameter tuning, I like Optuna.

Visualization

(I have too strong opinions on this, but here you go...)

• Colors, line styles etc should be chosen with semantics, accessability, and consistency in mind. Lots of good points on choosing discrete color palettes can be found in Lisa Charlotte Rost's guide. Color maps should be perceptually uniform, this matplotlib doc is a good starting point.
• To pick colors (and check for greyscale representations and accessibility issues), I like coolors.co. Palettable is fun.
• Figures should have consistent font sizes, roughly matching the paper text size. Authors that use small figures with tiny tiny captions are terrible people and eat kittens.
• Figures should also have consistent margins. Don't choose margins automatically through plt.tight_layout(), but set them consciously. I am partial to square panels inside square canvasses. I've been using some (rather ugly) helper functions to achieve that, you can find them in setup_figures.py, I'm sure there is a prettier way though.

Writing

• The best citation manager I found so far are BibDesk (local, free, only MacOS) and Paperpile (cloud-based, good for sharing folders). Mendeley frustrated me because of its poor BibTeX export, JabRef with its performance issues on Mac.

Acknowledgements

Thanks to Alexander Held, Kyle Cranmer, and Siddharth Mishra-Sharma for teaching me many of these things.