playground/DEVELOPMENT.md

In tbenavi1/sibling_kmers:

STANDARDS

• spaces around operators
• snake_case for variables and functions
• camelCase for classes and methods
• verbose naming is more important than a detailed documentation
• R code is tested using testthat and python code in dev branch using unittest

versioning

• we try to keep master branch clean (i.e. production ready code).
• dev branch should be also a working code, however here mistakes are permitted. Most of the development is done in subbranches of dev branch, once a feature is implemented, it should be merged to dev. I like to use --no-ff to keep a record, what was developed where (this might be a bad practice and if you know why, let me know).
• One rule I would like to keep is this. There must be at least 72 hours incubation period between commits merged into dev and merging dev into master. The reason is simple, if there are any mistakes that were not spotted, there is a change to catch them. Also it takes while to run all the tests and stuff (the travis.ci testing is not working yet, but I hope it will quite soon).

language

The future is python3, and potentially in a low level language if we will ever need a speed-up.

R will be abolished as some point. It's just that some of the R libraries (for kernel smoothing) seems to work way faster than the pythonic ones and I have not really figured why. The pythonic smudgpelot is not there yet (although a lot of code is already written, check dev branch).

tbenavi1/sibling_kmers documentation built on Jan. 28, 2024, 11:12 a.m.