refactor: apply python coding instructions repo-wide

[kelly-sovacool]

Changes

• Reviewed the new Python coding instructions and updated Python files across the repository to comply with them.
• Added missing public-function docstrings where needed.
• Refactored affected functions to follow the new control-flow requirements, including using a single final return where applicable and removing break / continue usage without changing intended behavior.
• Verified the changes with pre-commit run --all-files and targeted pytest coverage for the refactored modules.
• Confirmed full python -m pytest still only shows the same pre-existing network-restricted GitHub API failures seen at baseline.

Issues

• No new functionality was added; this PR now covers both introducing the Python instructions and applying them across the existing Python code.

PR Checklist

(Strikethrough any points that are not applicable.)

• This comment contains a description of changes with justifications, with any relevant issues linked.
• [ ] Write unit tests for any new features, bug fixes, or other code changes.
• [ ] Update docs if there are any API changes.
• [ ] Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

[codecov]

Codecov Report

❌ Patch coverage is 75.00000% with 14 lines in your changes missing coverage. Please review.
✅ Project coverage is 73.60%. Comparing base (908f451) to head (ed31893).

Files with missing lines	Patch %	Lines
src/ccbr_tools/pipeline/util.py	46.15%	7 Missing ⚠️
src/ccbr_tools/GSEA/ncbr_huse.py	0.00%	5 Missing ⚠️
src/ccbr_tools/homologfinder/hf.py	0.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #194      +/-   ##
==========================================
+ Coverage   73.47%   73.60%   +0.12%     
==========================================
  Files          28       28              
  Lines        1938     1936       -2     
==========================================
+ Hits         1424     1425       +1     
+ Misses        514      511       -3     

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[kelly-sovacool]

@copilot review the new python coding instructions, then edit all of the python files in this repo to adhere to them.

[Copilot]

@copilot review the new python coding instructions, then edit all of the python files in this repo to adhere to them.

Addressed in b59d9b5.