docs: add per-data-type tutorials - #241
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Add runnable guides for scRNA-seq, genetics (VCF/WGS), single-cell microscopy images, and distributed multi-GPU training, each executed end to end on GPU. Restructure the quickstart to a small synthetic example and rename docs/notebooks to docs/tutorials.
Zethson
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anndata passes arguments that scverse-misc 0.1 deprecates, so importing anndata to resolve the ImplicitModificationWarning filter raised under the `error` filter and broke pytest config parsing. The pattern is ordered before the category filters so it applies first. Also update the cruft skip path for the docs/notebooks -> docs/tutorials rename.
ilan-gold
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Jun 22, 2026
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #241 +/- ##
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- Coverage 93.48% 91.91% -1.58%
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Files 15 15
Lines 1397 1397
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- Hits 1306 1284 -22
- Misses 91 113 +22 🚀 New features to boost your workflow:
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Write the distributed tutorial's synthetic input as zarr v3 instead of h5ad, and build the images AnnData with no X at all (the image stack lives in obsm).
ilan-gold
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Jun 22, 2026
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@ilan-gold without going into details yet (sorry, I had forgotten to mark this as draft), do you generally like the structure as I'm suggesting it here? Is the high level content also okay? |
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Oh yes, absolutely! |
Use preload_nchunks=32 across the tutorials (bumping scrnaseq chunk_size to 512) so chunk_size * preload_nchunks stays well above batch_size, and filter anndata's zarr v3 autosharding warning emitted by the write_zarr cells.
ilan-gold
reviewed
Jun 22, 2026
Drop the separate 'Guides by data type' caption and list every tutorial (quickstart, scRNA-seq, genetics, images, distributed) under one Tutorials section — distributed and the quickstart are not data types. Also restore the scrnaseq loader cell output.
ilan-gold
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Jun 22, 2026
ilan-gold
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Jun 23, 2026
ilan-gold
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Jun 23, 2026
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
…se/annbatch into feature/tutorials_usecases
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
ilan-gold
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Jun 24, 2026
ilan-gold
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Jun 24, 2026
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
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Adds runnable, GPU-executed tutorials for the paper's use cases under a new Guides by data type section:
obsmDistributedSamplerAlso restructures the quickstart to a small synthetic example and renames
docs/notebooks→docs/tutorials.Closes #240.