Code quality, documentation, and repo hygiene cleanup

[asifahamed11]

Summary

A behavior-preserving cleanup pass to make the codebase read like it was written and maintained by an experienced researcher. No algorithms, hyper-parameters, data handling, training logic, or generated output files were changed — only presentation and code quality.

This was verified by tokenizing every file before/after and comparing all non-comment, non-string tokens (NAME/OP/NUMBER/keywords). The only executable differences are black's formatting (trailing commas, redundant-paren removal, semicolon splitting), one internal variable rename (code8_out -> stage08_out), and the removal of a runtime changelog banner that only printed to the console.

What changed

• Formatting — standardized the whole src/ tree with black (line length 100). Consistent spacing, quotes, and line wrapping throughout.
• Comments & docstrings — rewrote comments/docstrings to describe what the code does and removed iteration/revision-history artifacts (CHANGE 1/2/3, FIX 1-7, v4.0, Supervisor Request, Code 8/9, decorative # ==== banners). Added a concise module docstring to every script.
• Console output — trimmed revision-tag prefixes (e.g. [FIX 7], [CHANGE 3]) from log messages and dropped a changelog banner that was printed at the start of the stage-08 run.
• Repo hygiene — added a .gitignore (data, outputs, caches, editor cruft; the data/README.md already referenced one) and added a pipeline-stage map to the README.

Deliberately left untouched

To guarantee byte-identical results, every string literal written to an output file (report text, feature_count_audit.csv notes, the best-params change column, figure titles / model_name labels) was preserved exactly as-is.

All files compile (py_compile) after the changes.

[Copilot]

Pull request overview

Behavior-preserving cleanup focused on readability and repository hygiene across the TF-DFE pipeline scripts, while keeping the data/training logic intact (aside from formatting and console-text tweaks).

Changes:

• Apply consistent formatting (Black) and remove legacy revision-history banners/comments across src/.
• Add/standardize module docstrings and tidy logging output text.
• Improve repo hygiene/documentation via a new .gitignore and a pipeline stage map in README.md.

Reviewed changes

Copilot reviewed 11 out of 13 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
src/config.py	Reformats output directory constants and expands the output-dir creation list for readability.
src/10_exploratory_data_analysis.py	Adds module docstring and applies formatting cleanup in EDA script.
src/09_reviewer_experiments.py	Rewrites module header docs and refactors formatting/log strings in reviewer experiments utilities.
src/08_tda_fuzzy_ensemble.py	Adds module docstring and performs extensive formatting/comment cleanup across the stage-08 pipeline.
src/07_dataset_balancing.py	Adds module docstring and applies formatting cleanup.
src/06_clean_and_finalize.py	Adds module docstring and applies formatting cleanup.
src/05_remove_leakage.py	Adds module docstring and applies formatting/structure cleanup for chunked column dropping.
src/04_feature_engineering.py	Adds module docstring and applies formatting cleanup in feature engineering pipeline.
src/03_remove_duplicates.py	Adds module docstring and cleans up formatting/quoting.
src/02_remove_missing_values.py	Adds module docstring and cleans up formatting for chunked NA filtering.
src/01_dbnsfp_processor.py	Adds module docstring and applies formatting cleanup in dbNSFP processing.
README.md	Adds a concise pipeline stage map describing the numbered scripts and their roles.
.gitignore	Adds standard ignores for data, outputs, caches, and editor/OS artifacts.

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