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I-diagram matrix: connected hollow/filled dots and Jurgens atom labels - #16

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Autoplectic merged 2 commits into
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idiagram-hollow-dots
Oct 6, 2026
Merged

Autoplectic merged 2 commits into
mainfrom
idiagram-hollow-dots

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@Autoplectic Autoplectic commented Oct 6, 2026 •

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Summary

  • In the UpSet dot matrix of plot_information_diagram, every atom column now has a single connecting line spanning all variable rows, instead of a line spanning only the included variables.
  • Included variables are drawn as filled dots in the atom's colour; excluded variables are hollow dots (white face, atom-coloured edge) so the line doesn't show through them.
  • Each dot chain is labelled underneath with the atom's taxonomy name from Jurgens & Crutchfield (2026) Table II (t.rμ, p.r⁺μ, …, qμ, σμ) via IDiagramAtom.jurgens_label. The seven cancelling-partner atoms not in Table II keep their existing † labels, and always-zero atoms (only shown with atoms="all") fall back to the set-builder label.
  • Default figure height grows from 5.6 to 6.4 in, with a fixed ~0.85 in bottom strip for the rotated labels.

The 14 Table II labels in JURGENS_LABELS were checked against both the Taxonomy of Prediction and Information Machines manuscripts; they agree.

Test plan

  • uv run pytest tests/test_information_diagram.py (45 passed)
  • Rendered nemo with default and atoms="all" and checked the matrix and labels visually

Ryan James and others added 2 commits October 6, 2026 10:47
…w excluded ones

Co-authored-by: Cursor <cursoragent@cursor.com>
…nomy name

Co-authored-by: Cursor <cursoragent@cursor.com>
@Autoplectic Autoplectic changed the title I-diagram matrix: connect all dots, hollow markers for excluded variables I-diagram matrix: connected hollow/filled dots and Jurgens atom labels Oct 6, 2026
@Autoplectic
Autoplectic merged commit 3dd4496 into main Oct 6, 2026
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