major changes to the report style

[ypriverol]

Summary by CodeRabbit

• New Features

  • New CLI flag to control two-sided QC plot layout.
  • Standalone "Sample Completeness" and "Missing Frequency" visualizations.

• Improvements

  • Restructured QC report: updated completeness metrics, revised plot titles, and simplified summary table logic.
  • Missing-data block now shown only when LOD information is absent; some QC summary rows simplified.

• Tests

  • Updated HTML test expectations to reflect renamed summary fields.

[coderabbitai]

Caution

Review failed

The pull request is closed.

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: eb44e732-cf70-4825-9d04-b17d592aa6b7

📥 Commits

Reviewing files that changed from the base of the PR and between 97a5b89 and 0e77a23.

📒 Files selected for processing (1)

• tests/test_qc_pipeline.py

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📝 Walkthrough

Walkthrough

Adds a CLI flag --two-sides/--no-two-sides and threads it into report generation; introduces two standalone QC visualizers (sample completeness and missing-frequency); updates labels and rewires split-report generation to optionally produce deferred side-by-side HTML pages and adjust summary table content.

Changes

Cohort / File(s)	Summary
CLI Option Threading src/pyprideap/cli.py	Added --two-sides/--no-two-sides option (default on) and two_sides: bool = True parameter to _generate_report/report, passed to qc_report_split.
Data Label Update src/pyprideap/viz/qc/compute.py	Changed DataCompletenessData.title default from "Data Completeness" to "Sample Completeness".
New Renderers src/pyprideap/viz/qc/render.py	Added render_sample_completeness() and render_missing_frequency(); adjusted subplot titles in existing render_data_completeness().
Report Split & Summary Logic src/pyprideap/viz/qc/report.py	Added two_sides: bool = True to qc_report_split; introduced _DATA_KEY_MAP, replaced data_completeness with two new sections, deferred side-by-side plot generation when two_sides set, simplified summary table rows/logic.
Tests tests/test_qc_pipeline.py	Updated assertions to expect "Features (assays)" in dataset summary table instead of "Detection rate".

Sequence Diagram(s)

sequenceDiagram
    participant User as CLI User
    participant CLI as cli.py
    participant Gen as _generate_report()
    participant Split as qc_report_split()
    participant Render as Plot Renderer
    participant HTML as HTML Output

    User->>CLI: run `report --two-sides` (or default)
    CLI->>Gen: call with two_sides=True
    Gen->>Split: qc_report_split(..., two_sides=True)
    
    rect rgba(100,150,200,0.5)
    Split->>Render: render plots (sample_completeness, missing_frequency, other QC plots)
    end
    
    alt two_sides=True
        Split->>HTML: defer complementary plots and compose side-by-side pages
    else two_sides=False
        Split->>HTML: emit individual plot pages/fragments
    end

    HTML-->>User: deliver report (layout varies by two_sides)

Loading

Estimated code review effort

🎯 4 (Complex) | ⏱️ ~45 minutes

Possibly related PRs

• Minor changes splitting reports, fix bug with CDN  #6: Modifies qc_report_split and split-report assembly—strong overlap on split/report output logic.
• Minor changes in Summary table #16: Threads a new boolean CLI flag through cli.py and viz/qc/report.py, similar wiring changes here.
• Fix QC/LOD report and summaries #14: Overlaps on QC reporting and data-completeness rendering changes used by the split-report flow.

Suggested reviewers

• selvaebi
• chakrabandla

Poem

🐰 Two-sided plots hop into view,
Bars stack high on samples true,
Missing beats in histogram light,
Reports split neat — a bunny's delight! ✨

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Title check	❓ Inconclusive	The title 'major changes to the report style' is vague and generic, using non-descriptive language that doesn't convey the specific nature of the changes.	Consider a more specific title that highlights key changes, such as 'Add two-sides layout option for QC reports and refactor data completeness visualizations' or 'Restructure QC report rendering with sample completeness charts and configurable layout'.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Docstring Coverage	✅ Passed	Docstring coverage is 88.89% which is sufficient. The required threshold is 80.00%.

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