[User Story] Refactoring

[ivadym]

Need

As a Balsamic developer, I want to improve the codebase by refactoring existing code to enhance maintainability, readability, and performance, ensuring the long-term sustainability of the pipeline.

Suggested approach

Use static code analysis tools and manual review to identify code smells, duplicated code, and areas with high complexity. Prioritise sections of code that are prone to bugs, difficult to understand, or hinder future development.

Considered alternatives

No response

Deviation

No response

System requirements assessed

• [x] Yes, I have reviewed the system requirements

Requirements affected by this story

No response

Risk assessment needed

• [ ] Needed
• [x] Not needed

Risk assessment

No response

SOUPs

No response

Can be closed when

• [ ] Python design and style

  • [ ] Refactor to PEP 585 – Type Hinting Generics In Standard Collections
  • [ ] Refactor to PEP 604 – Allow writing union types as X | Y
  • [ ] Refactor to PEP 498 – Literal String Interpolation (f-strings)
  • [ ] Refactor to PEP 428 – The pathlib module – object-oriented filesystem paths

• [ ] Codebase

  • [ ] Reduced complexity of pydantic models (both structure and validators).
  • [ ] Unified config case implementation across workflows.
  • [ ] Added variant calling parameters to constants.
  • [ ] Replaced hardcoded values with constants.
  • [ ] Remove unused references (e.g. ascat_chr_y_loci).
  • [ ] Remove --disable-variant-callers since it has been not supported by our latest changes.
  • [ ] Refactored deliver.py
  • [ ] Refactored scheduler.py script (https://github.com/Clinical-Genomics/BALSAMIC/pull/1372)
  • [ ] Refactored rule.py
  • [ ] Refactored gender to sex
  • [ ] Remove -r flag and make use of --dry-run exclusively
  • [ ] Format rules and smk with snakefmt (consider adding a specific GitHub Actions)
  • [ ] Update fixture names (remove fixture prefix and stop using name=fixture_)
  • [ ] Create a hierarchical structure directory for fixtures (pytest_plugins)

• [ ] Snakemake

  • [ ] ConfigModel is used across rules to access the config case JSON file.
  • [ ] Simplified *.smk, which should only contain the rule all
  • [ ] Centralised the definition of rules_to_include, removing the need for appends in smk

• [ ] Sonarcloud issues

  • [ ] WORKDIR instruction should be used instead of cd command (Dockerfiles)

Blockers

No response

Anything else?

No response

[ivadym]

Closing. Not relevant anymore.