scverse/annbatch

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Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse

Stars: 68
Forks: 6
Open beginner issues: 0
Indexed issues: 26
Avg merge: 7h 24m
Merged PRs (30d): 6

Dominant language: Python
License: MIT
Last GitHub push: Sep 18, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

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26 open issues indexed

Some bugs I found while reviewing a PR Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/annbatch#278 · Opened Sep 19, 2026
`ClassSampler` undersamples longer runs and doesn't sample proportionally by run length Open

bug

scverse/annbatch#273 · 1 assignee · Opened Sep 17, 2026
`ClassSampler` only draws cat ~ Cats; batch ~ cat; exactly iff `batch_size % chunk_size == 0` Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/annbatch#271 · Opened Sep 9, 2026
Support for non-spatial multimodal data Open

enhancement

scverse/annbatch#266 · 1 comment · 2 assignees · Opened Aug 26, 2026
Possible overflow in np.diff usages with unsigned integers Open

scverse/annbatch#259 · 1 assignee · Opened Jul 23, 2026
Investigate Double Buffering Open

enhancement question

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/annbatch#220 · Opened Jun 3, 2026
Revisit shuffle-before-persist ordering in DatasetCollection writes Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/annbatch#194 · Opened Apr 16, 2026
Validate categorical consistency across all obs columns when building or extending DatasetCollection Open

scverse/annbatch#193 · 6 comments · 1 assignee · Opened Apr 16, 2026
Improve `Sampler` Parameter Documentation Open

enhancement

scverse/annbatch#178 · 1 assignee · Opened Mar 25, 2026
Multiple workers with replacement sampling Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/annbatch#173 · Opened Mar 25, 2026
`hdf5` support via `virtualizarr` Open

enhancement

scverse/annbatch#138 · 1 comment · 1 assignee · Opened Feb 5, 2026
Concatenating and other operations without dask Open

enhancement

scverse/annbatch#120 · 1 assignee · Opened Jan 22, 2026
Handling different var spaces in `Loader Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

scverse/annbatch#110 · Opened Jan 15, 2026
Use a buffer pools for reads from disk + in-memory shuffling Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/annbatch#105 · Opened Jan 6, 2026
Supporting multiple `layers`, `X`, `obsm` etc. Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

scverse/annbatch#91 · 3 comments · Opened Dec 4, 2025
Questions and deciding between scDataset and annbatch Open

question

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/annbatch#90 · 3 comments · Opened Dec 3, 2025
Making the output datasets of `add_to_collection` split-able Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/annbatch#88 · Opened Nov 20, 2025
Custom indexes Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 28/100

scverse/annbatch#87 · 3 comments · Opened Nov 20, 2025
Handle categoricals + `obs` better in preprocessing Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

scverse/annbatch#84 · Opened Nov 11, 2025
Outputting Data to Multiple GPUs Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/annbatch#56 · Opened Oct 7, 2025
`Loader` handling of var spaces Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/annbatch#33 · Opened Sep 12, 2025
Benchmark different compression settings Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

scverse/annbatch#8 · Opened Jun 24, 2025
Baseline Benchmarks Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/annbatch#5 · Opened Jun 20, 2025
Benchmark randomness vs performance tradeoff Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/annbatch#4 · Opened Jun 20, 2025
Improve the shuffling/preprocessing code Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/annbatch#3 · Opened Jun 20, 2025
Understand Sparse vs. Dense Tradeoff Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/annbatch#2 · Opened Jun 20, 2025

scverse/annbatch

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