Release/v2 stable - #13

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EliHei2 wants to merge 31 commits into

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release/v2-stable

Commits on Feb 2, 2026

Add alignment loss integration and comprehensive test suite

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claude
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docs: add install tips and deps
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14d4733
feat: add spatialdata IO/export, datasets, and docs
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57925c0
fix: align prediction graph scale factor
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c69010d
docs: add release note and CLI params
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304762b
Add ME debug output and quiet warnings
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e674913
Wire ME params and silence predict warnings
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76e5439
Auto-normalize scRNA reference for ME genes
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b480bb4
Cache ME gene discovery results
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3e5cadb
Add ME discovery progress messages
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d06a355
Stabilize alignment loss with balancing and fixed weights
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139f2cd
Refine alignment loss with contrastive same-gene positives
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2e21a8c
Update alignment loss docs and comments
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aa3ea93
Subsample alignment positives to reduce imbalance
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dbb0c10
Adjust ME gene defaults for more pairs and stricter exclusivity
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1ae1102
Document ME discovery defaults
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49c805e

Commits on Feb 3, 2026

Commits on Feb 4, 2026

Speed up Delaunay boundaries and add parallel option
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1cb60bd
Improve Xenium Explorer export polygons and metadata
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6c5c714
Unify worker count across CLI steps
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b56441a

Commits on Feb 5, 2026

Update CLI help for format and export options
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312ad6f
Stop tracking CLAUDE.md
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210719f
Add spatialdata-io extra and enforce RAPIDS checks
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93f145d

Commits on Feb 12, 2026

chore: prepare v2 stable release updates
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77f2f52
Prepare v0.2.0 release updates
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2c92b43

Commits on Feb 13, 2026

docs: expand v0.2.0 release documentation
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1b862d8
docs: align v0.2.0 technical summary across markdown
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9ee0536