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contributing.md

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Contributing

Thank you for contributing to the development of INITATOR_SET, this is a quick guide just to let you know how to navigate this project.

Project structure

INITIATOR_SET is divided into submodules, these are;

  • Genetic Data Inputs
  • eORFs
  • Gene names
  • UTR & CDS
  • Ribosome Profiling predicted genes
  • Mutations
  • Edits
  • Map new AICs
  • FASTA
  • Protein Targeting & Localisation
  • Annotation Matcher
  • Functional Comparison Between Predicted Proteins
  • Kozak Calculator
  • Leaky Scanning Detector
  • GC Count
  • IRES or hairpin loop predictor
  • uORF Proximity
  • Ribosomal Assembly Checker

Most of these have yet to be coded, any submodules pending creation will be raised as a milestone, with a corresponding branch raised in the format feature/[submodule].

Bugs and features

If any bugs are found, general bugs may be raised to Python issue backlog milestone and may be resolved in the bugs/backlog branch. If multiple related bugs are found it a be worth raising a milestone and related branch with the format bugs/[milestone]. In general;

  • Milestone = Branch

Any new features simiarly should also have a milestone raised and a branch with the format feature/[milestone], similarly to the above as all submodules are features.

When creating a feature try and break it down into component parts (don't get too crazy) and raise a task under that milestone, an example would be;

* [Milestone] Fasta submodule 
---- [Task] Parse FASTA file
---- [Task] Generate FASTA file

The aim is to track back any code to the specification in order to make future maintainance easier.

Code quality

Once you are ready to merge in your changes, a MR will be raised and we will review and check your code, we're not overtly strict but try and follow these rules;

  • Variable and function names should be distinctive and descriptive; try to avoid too many similarly named values.
  • Functions should be short and snappy, following the advice of Uncle Bob if a function is above 20 lines, look at refactoring functionality out.
  • Indentation - this is mainly occurs with nested if and for, try and seperate out iteration into other functions or use iteration methods, early returns are your friend;
# This!
def divide(a, b):
   if(b == 0):
   	return "Not a number"
   return a / b
   
# Not this.
def divide(a, b):
   if(b != 0):
   	return a / b
   else:
   	return "Not a number"
  • Seperating your concerns, use multiple source files, don't put everying in a single 1000+ line file, this is very hard to navigate, in general you should look to refactor if your file starts exceeding 250 lines.