Refactor structure

[ypriverol]

Summary by CodeRabbit

Release Notes

• Documentation

  • Updated research manuscript with comprehensive analysis covering 2021–2025 data period
  • Revised abstract, introduction, results, and discussion with updated findings and metrics
  • Enhanced figure typography and accessibility for improved readability

• New Features

  • Implemented dynamic data metrics computation from source datasets
  • Enhanced bibliography system with improved citation formatting

• Chores

  • Updated author information and affiliations
  • Added new references and standardized existing bibliography entries

[coderabbitai]

Caution

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📝 Walkthrough

Walkthrough

The pull request updates a research paper manuscript with a revised temporal scope (2021-2025 instead of 2020-2025), corrects author names, introduces new BibTeX style files, updates bibliography references with abbreviated journal names, and refactors analysis scripts to compute metrics dynamically from parquet data while improving figure typography and styling.

Changes

Cohort / File(s)	Summary
Paper manuscript and bibliography paper/main.tex, paper/supplementary.tex, paper/references.bib	Title and author name corrections; temporal scope updated from 2020-2025 to 2021-2025 throughout text, abstracts, and figure captions; bibliography style changed from unsrt-nat to proteomics; new BibTeX entries (Deutsch2026, WellcomeLMIC) added; journal names abbreviated across multiple reference entries (e.g., Nature Communications → Nat Commun).
BibTeX style definitions paper/WileyNJD-AMA.bst, paper/proteomics.bst	New comprehensive BibTeX style files implementing AMA/IEEE-like and RSC/Wiley-style citation formatting with entry type handlers, author/editor formatting, DOI/URL linking, crossref integration, and bibliography preamble/finalization logic.
Data processing and temporal filters scripts/run_full_analysis.py, scripts/generate_supp_figures.py	SQL queries updated to restrict analysis data from year ≥ 2021 instead of year ≥ 2020 across temporal, protocol, and hourly pattern analyses.
Figure generation and visualization scripts/generate_figures.py, scripts/generate_pride_overview.py	Font sizes, axis labels, legend fonts, DPI, and typography enhanced across multiple figures; LMIC_COUNTRIES list revised; generate_pride_overview.py refactored to dynamically compute metrics from parquet data and PRIDE metadata via DuckDB instead of using hardcoded values; new helper functions (_duckdb_conn, _grep_count, compute_metrics, make_figure) introduced.

Sequence Diagram(s)

sequenceDiagram
    participant OldFlow as Old Flow (Hardcoded)
    participant NewFlow as New Flow (Dynamic)
    participant ParquetData as Parquet Data<br/>(2021-present)
    participant PrideMetadata as PRIDE Metadata<br/>(JSON)
    participant DuckDB as DuckDB
    participant FigureGen as Figure Generator

    Note over OldFlow: Static hardcoded values for<br/>downloads, files, projects, users

    NewFlow->>ParquetData: Load 2021-present records
    NewFlow->>PrideMetadata: Read project/file counts
    NewFlow->>DuckDB: Initialize connection
    DuckDB->>ParquetData: Query totals, year bounds,<br/>country counts, records
    DuckDB-->>NewFlow: Return computed metrics dict
    NewFlow->>FigureGen: Pass metrics dictionary
    FigureGen->>FigureGen: Build 6-panel figure with<br/>dynamic annotations
    FigureGen-->>NewFlow: Figure complete

    Note over NewFlow: All values computed from data<br/>with dynamic year range & scale

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Estimated code review effort

🎯 4 (Complex) | ⏱️ ~50 minutes

Possibly related PRs

• minor changes #16: Modifies paper/references.bib to add/update BibTeX entries, overlapping with reference bibliography changes in this PR.
• Refactor structure #10: Updates paper author blocks in paper/main.tex and paper/supplementary.tex, directly overlapping with author name corrections in this PR.

Poem

🐰 From twenty-twenty's distant past,
We've trimmed the timeline, fresh and fast!
New styles for BibTeX now appear,
While metrics bloom from data clear. ✨
Typography grows bold and bright—
This manuscript shines ever right!

✨ Finishing Touches

• 📝 Generate docstrings

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch refactor-structure

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