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dpeerlab / segger Public

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Release/v2 stable#13

Open

EliHei2 wants to merge 31 commits intomaindpeerlab/segger:mainfrom

release/v2-stabledpeerlab/segger:release/v2-stableCopy head branch name to clipboard

Conversation Commits31 (31)Checks Files changed

Open

Release/v2 stable#13
EliHei2 wants to merge 31 commits intomainfrom
release/v2-stable

Commits

Commits on Feb 2, 2026

Add alignment loss integration and comprehensive test suite

EliHei2
and
claude
committed
docs: add install tips and deps
EliHei2
committed
feat: add spatialdata IO/export, datasets, and docs
EliHei2
committed
fix: align prediction graph scale factor
EliHei2
committed
docs: add release note and CLI params
EliHei2
committed
Add ME debug output and quiet warnings
EliHei2
committed
Wire ME params and silence predict warnings
EliHei2
committed
Auto-normalize scRNA reference for ME genes
EliHei2
committed
Cache ME gene discovery results
EliHei2
committed
Add ME discovery progress messages
EliHei2
committed
Stabilize alignment loss with balancing and fixed weights
EliHei2
committed
Refine alignment loss with contrastive same-gene positives
EliHei2
committed
Update alignment loss docs and comments
EliHei2
committed
Subsample alignment positives to reduce imbalance
EliHei2
committed
Adjust ME gene defaults for more pairs and stricter exclusivity
EliHei2
committed
Document ME discovery defaults
EliHei2
committed

Commits on Feb 3, 2026

Subsample scRNA cells per type for faster ME discovery
EliHei2
committed
Lazy-load data utils to reduce import overhead
EliHei2
committed
Match main branch import strategy for data utils
EliHei2
committed
Lazy-load optional modules and update docs
EliHei2
committed
Add AnnData output and embed table in SpatialData
EliHei2
committed

Commits on Feb 4, 2026

Speed up Delaunay boundaries and add parallel option
EliHei2
committed
Improve Xenium Explorer export polygons and metadata
EliHei2
committed
Unify worker count across CLI steps
EliHei2
committed

Commits on Feb 5, 2026

Update CLI help for format and export options
EliHei2
committed
Stop tracking CLAUDE.md
EliHei2
committed
Add spatialdata-io extra and enforce RAPIDS checks
EliHei2
committed

Commits on Feb 12, 2026

chore: prepare v2 stable release updates
EliHei2
committed
Prepare v0.2.0 release updates
EliHei2
committed

Commits on Feb 13, 2026

docs: expand v0.2.0 release documentation
EliHei2
committed
docs: align v0.2.0 technical summary across markdown
EliHei2
committed

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