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pirl-unc / tcrsift / 26640054702
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DEFAULT BRANCH: main
Ran 29 May 2026 01:30PM UTC
Jobs 4
Files 31
Run time 1min
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29 May 2026 01:28PM UTC coverage: 78.237% (+0.9%) from 77.296%
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2.0.2: fix #109 — plot label categories (closes #108 too) (#111)

Two related label issues affecting ~half of the ``tcrsift run``
output plots, filed together in #109. Both addressed here in one
PR; #108 (the Jaccard heatmap subset of category 1) closes as well.

## Category 1: sites that bypassed pretty_samples

Five plot sites previously rendered raw sample names like
``AIMpos-2``, ``CTYneg_tetpos-2`` instead of the Unicode
prettified forms ``AIM⁺``, ``tet⁺CTY⁻``:

  - ``qc_read_counts.png``: histogram legend
    (``label=sample`` → ``label=pretty_sample(sample)``)
  - ``qc_genes_detected.png``: violin x-tick labels
  - ``qc_mito_percent.png``: violin x-tick labels
  - ``phenotype_composition.png``: pandas stacked-bar tick labels
    (driven by the DataFrame's index; rename the index via
    ``pretty_samples`` post-``set_index('sample')``)
  - ``clonotype_sharing_heatmap.png``: seaborn heatmap x/y tick
    labels (covers #108). Also shortens the title from "Clone
    Sharing Between Samples" to "Sample Sharing", matching the
    section heading and avoiding the "samples" word twice in
    one figure.

The other heatmaps and rank-family panels already routed labels
through pretty_samples / pretty_methods; #109 brings the
stragglers into line. Tier labels, gene symbols, CDR3 strings,
species names, and bin numbers were correctly NOT being prettified
and stay untouched.

## Category 2: Unicode superscripts rendering as empty boxes

``pretty_sample`` uses U+207A SUPERSCRIPT PLUS SIGN and U+207B
SUPERSCRIPT MINUS for the ``AIM⁺`` / ``CTY⁻`` style. Arial — the
matplotlib default on the user's macOS environment — doesn't carry
either glyph, so the superscripts rendered as empty boxes on every
affected plot and ``Glyph 8314/8315 missing from font(s) Arial``
spammed the log on every render.

Fix: configure ``plt.rcParams['font.sans-serif']`` to lead with
``DejaVu Sans`` at module import time. DejaVu Sans is bundled with
matplotlib (no new dependency), carrie... (continued)

6647 of 8496 relevant lines covered (78.24%)

3.13 hits per line

Coverage Regressions

Lines Coverage ∆ File
218
69.15
6.3% plots.py
Jobs
ID Job ID Ran Files Coverage
1 python-3.11 - 26640054702.1 29 May 2026 01:30PM UTC 31
78.23
GitHub Action Run
2 python-3.10 - 26640054702.2 29 May 2026 01:30PM UTC 31
78.23
GitHub Action Run
3 python-3.12 - 26640054702.3 29 May 2026 01:30PM UTC 31
78.23
GitHub Action Run
4 python-3.9 - 26640054702.4 29 May 2026 01:31PM UTC 31
78.2
GitHub Action Run
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