Formatting convention

Formatting convention

Define a formatting convention and clean up the code according to the new guidelines.

The formatting convention is defined in the Wiki.

To define:

• rule structure template/guidelines
• Python:
  • PEP8
  • 4 spaces instead of tabs
  • double or single quotes?
  • comments: reStructered Text or NumPy/SciPy?
• settings access
  • either only global variables or config
  • if global variables, then these should be defined in one place

To try:

• code quality checker (linter): snakemake --lint
  • highlights issues to be solved to follow best practices
  • highly recommended before publishing workflows
• automatic formatter: Snakefmt, based on Black

References:

• Python docstring formats

Code "cleaning"

• changes w.r.t. formatting conventions mentioned above
  • Python code
  • snakemake rules
  • (other scripts)
• add comments where possible
• one place for all helper functions
  • no variables/functions inside rule files
• use os.path utils when working with paths
• replace code duplication with custom functions
• consistent indentation
• Q: can we simplify the structure in workflow/rules/ ???