[main] Integration/peerlab#38
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Feature/pixi and conda installation
Support binary datatype of the columns
…sertions for gene corr reference" This reverts commit f5e8c2a8b3fb4227ae87b0f2d6c6df5c97502f7a. :wq :wq
… missing from the reference
…imisation [integration/peerlab] Optimisation/quadtree memory optimisation
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Segger still keeps 2 copies of |
[integration/peerlab] Bugfix/tiling issue
[integration/peerlab] Bugfix/writing anndata
Squash of four commits from bugfix/torch_array_overlow: - Refactor segger logs (--debug is now enough; SEGGER_LOG_LEVEL fallback) - Log full-graph edge counts in setup_heterodata - Improve debugging (additional debug-time artifacts + log lines) - Fix logging (misc message/level corrections) Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
[integration/peerlab] Bugfix/torch array overlow
andrewmoorman
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The squash-merge of #38 dropped co-author trailers. This empty commit credits them so their contributions are reflected in the repo's contributor graph. Co-authored-by: Ananya Nandula <225912921+ananya-nandula@users.noreply.github.com> Co-authored-by: Mostafa Shahhosseini <33085339+mossishahi@users.noreply.github.com> Co-authored-by: Sam Rose <4626152+srose89@users.noreply.github.com>
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Major: CUDA/Xenium install #21: CUDA 12.1 support; Xenium v1 + binary column datatype support; pixi/conda install updates Reference gene correlation #32: Add custom reference gene correlation support via `--gene-corr-reference-path` Memory optimisations #36: GPU/memory optimisations for large datasets; chunked subgraphing fallback Large dataset fixes #44: Fix torch array overflow and related scaling issues Tiling fixes #42: Fix tiling/bincount errors and transcript thresholding Minor: Logging improvements #31: Improve debug logging; support `SEGGER_LOG_LEVEL` Margin handling #34: Warn instead of fail when tiling margins are too large Misc cleanup: Refactors; assertions/debugging; remove unused code and comments --------- Co-authored-by: Nandula Co-authored-by: Kalfus
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Overview of changes introduced in this PR:
Major:
--save-anndata(thanks @mossishahi)--gene-corr-reference-path(thanks @ananya-nandula )condaandpixi. UpdateREADME.mdaccordingly.bincount only supports 1-d non-negative integral inputs.error.Minor:
--debug#31: Specify seggers log level withSEGGER_LOG_LEVELTotal PR size: +598 | -150 (remaining is
pixi.lock)