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docs: preview modernized dj.Diagram style on the LC-MS pipeline - #3

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viz/diagram-restyle-1534
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docs: preview modernized dj.Diagram style on the LC-MS pipeline#3
dimitri-yatsenko wants to merge 5 commits into
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viz/diagram-restyle-1534

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Draft — for visual review only. Regenerates docs/pipeline.svg (the README diagram) using the restyled dj.Diagram from datajoint/datajoint-python#1534 (issue #1532), so the new diagram style can be seen against a real pipeline.

The regenerated diagram shows:

  • the modern tier palette (Manual green, Lookup gray rectangle, Imported/Computed ellipses, near-white part boxes),
  • master–part entity clustering with prefix-dropped part labels,
  • rounded nodes + schema cluster,
  • the corrected edge-weight = cardinality rule (thick = 1:1, thin = multi-valued),
  • Helvetica typography.

Rendered against datajoint/lcms-demo@main's schema with a pre-release build of dj from #1534. Not for merge until #1534 is released; opening as a draft so the README preview renders the new diagram for review.

Rendered with the restyled dj.Diagram (datajoint-python #1532 / PR #1534):
modern tier palette, rounded nodes, master-part entity clustering, corrected
edge-weight (cardinality) rule, and Helvetica typography. For visual review of
the new diagram style against the LC-MS pipeline.
…ma label

Re-rendered with the updated #1534 defaults: 'auto' color theme (single SVG that
adapts to the viewer's light/dark mode via prefers-color-scheme) and Helvetica
schema (cluster) labels.
Bump the README's 'DataJoint 2.1' mentions and the dependency floor
(datajoint[postgres]>=2.1.0 -> >=2.3.0) to the current 2.3 line.
Re-render against datajoint-python #1534 (fix/1532-diagram-restyle) so the
schema name sits in the top-right corner of each schema cluster.
#1534 is merged; regenerating also picks up the brand tier colors (#1544)
and the collapsed-edge style fix (#1545).
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Re-ran against datajoint/datajoint-python@master (2.3.3.dev16+g8e6ef316) now that #1534 has merged — docs/pipeline.svg regenerated in 58c9ed8.

Regenerating against master also picks up the two diagram changes that landed after #1534:

  • #1544 — the DataJoint brand tier colors in the diagram themes (visible here as green Manual, gray Lookup, blue Imported, orange Computed).
  • #1545 — collapsed-to-collapsed edges no longer carry per-foreign-key style.

Everything the original preview was opened to show still holds: master–part entity clustering with prefix-dropped part labels (Scan, Spectrum, Peak), rounded nodes, schema clusters with top-right labels, and edge weight encoding cardinality.

Still a draft: #1534 merged after v2.3.2, so the style is unreleased and pyproject.toml's datajoint[postgres]>=2.3.0 does not yet pin a version that produces this diagram. Ready to mark for merge once the release lands.

One rough edge worth a separate issue upstream: Diagram.save() on an .svg path imports IPython (via make_svg), so saving a diagram to a file fails in a plain non-notebook environment unless IPython is installed.

@dimitri-yatsenko
dimitri-yatsenko marked this pull request as ready for review August 20, 2026 15:05
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