Johann Brehmer (mail@johannbrehmer.de), 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.
- Claudio Jolowicz wrote a great guide on how to set up a Python project: Guide to hypermodern Python.
- My own repositories are far from these best practices. Nevertheless, they worked well for me for testing out ideas fast. I included an example of my repository structure in example_repo.
- PyCharm and VS Code are both good IDEs.
- As far as Python style goes, I try to follow PEP8 (of course) and the black code style, though I like to increase the line length to 120 characters.
- My most visited website of 2019 and 2020 is probably this StackOverflow question on how to add conda environments to Jupyter Lab.
- Some advice on optimizing PyTorch code at this tweet.
- For experiment management, I have lately been using sacred. See experiment.py. Alternatives I want to try include MLFlow, which seems to be more actively developed.
- Optuna is my personal favorite hyperparameter scan library.
- I'm not very knowledgable on this, but my workflow involved synching code between my laptop and the cluster through git and data with rsync.
- I like to submit jobs arrays a la
sbatch --array 0-99 run.sh, see run.sh.
(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.
- VS Code is great for LaTeX as well.
- The best citation manager I found so far is BibDesk. Unfortunately, it's only available for MacOS. Mendeley frustrated me because of its poor BibTeX export (so many issues with special characters), JabRef with its performance issues on Mac.
Thanks to Alexander Held, Kyle Cranmer, and Siddharth Mishra-Sharma for teaching me many of these things.