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<code>use_observed_lib_size=False</code> fails with NaN for some datasets

bug

nan

P0

Status: Closed (completed).

#1903 In scverse/scvi-tools;

· by vitkl was closed on Aug 3, 2025

Enable checkpointing with autotune

good first issue

P1

Status: Closed (completed).

#2580 In scverse/scvi-tools;

· by martinkim0 was closed on Aug 4, 2025

dataloader which stratifies train-validation split by adata.obs columns

data

enhancement

good first issue

P0

Status: Closed (completed).

#1063 In scverse/scvi-tools;

· by vitkl was closed on Jul 25, 2024

Allow custom train/test/val splits

data

enhancement

good first issue

P0

Status: Closed (completed).

#1765 In scverse/scvi-tools;

· by adamgayoso was closed on Jul 25, 2024

ValueError with NaN tensors in gimVI training

bug

P0

Status: Closed (completed).

#2215 In scverse/scvi-tools;

· by sunericd was closed on Jan 5, 2025

MultiVI Tensor shape invalid values nan

bug

P0

Status: Closed (completed).

#2262 In scverse/scvi-tools;

· by bhhlee was closed on Sep 21, 2024

batch and max_kl_weight parameters ignored when mapping to scvi reference

bug

P0

Status: Closed (completed).

#2331 In scverse/scvi-tools;

· by LisaSikkema was closed on Sep 19, 2024

Unable to retrieve region factors for PoissonVI model

bug

good first issue

P1

Status: Closed (completed).

#2529 In scverse/scvi-tools;

· by duyguk was closed on Aug 19, 2024

multiVI fails with invalid tensor

bug

P0

Status: Closed (completed).

#2581 In scverse/scvi-tools;

· by bio-la was closed on Jul 26, 2024

Update typing in all files to match new format

backlog

enhancement

good first issue

Status: Closed (completed).

#2432 In scverse/scvi-tools;

· by martinkim0 was closed on Sep 21, 2024

<code>SCANVI.loss</code> fails when <code>n_samples&gt;1</code>

bug

P0

Status: Closed (completed).

#2429 In scverse/scvi-tools;

· by martinkim0 was closed on Jul 30, 2024

Enable custom splits in <code>DataSplitter</code>

enhancement

good first issue

P0

Status: Closed (completed).

#2547 In scverse/scvi-tools;

· by martinkim0 was closed on Jul 25, 2024

VeloVI uses np.argsort, does not work with sparse spliced/unspliced layers

bug

good first issue

P0

Status: Closed (completed).

#2687 In scverse/scvi-tools;

· by jberkh was closed on Jul 29, 2024

Support for weighted loss either per-batch or per-cell?

enhancement

P2

Status: Closed (completed).

#2785 In scverse/scvi-tools;

· by kamilkrukowski was closed on Jul 26, 2024

lightning dependency critical CVE - Update dependency list, especially for conda which is pinned below the CVE patch

bug

Status: Closed (completed).

#2941 In scverse/scvi-tools;

· by pranavmishra90 was closed on Sep 21, 2024

Drop python 3.9 and replace with python 3.12

bug

Status: Closed (completed).

#2966 In scverse/scvi-tools;

· by ori-kron-wis was closed on Sep 16, 2024

Backport PR #3173 on branch 1.2.x ([pre-commit.ci] pre-commit autoupdate)

Status: Merged (completed).

scverse/scvi-toolsnumber 3174

#3174 In scverse/scvi-tools;

· by meeseeksmachine was closed on Feb 3, 2025

[pre-commit.ci] pre-commit autoupdate

Status: Merged (completed).

scverse/scvi-toolsnumber 3173

#3173 In scverse/scvi-tools;

· by pre-commit-ci was closed on Feb 3, 2025

feat: support numpy 2.0

Status: Merged (completed).

scverse/scvi-toolsnumber 2842

#2842 In scverse/scvi-tools;

· by martinkim0 was closed on Dec 22, 2024

feat(external): implement METHLYVI for scBS-seq data

cuda testsRun test suite on CUDARun test suite on CUDA

Status: Merged (completed).

scverse/scvi-toolsnumber 2834

#2834 In scverse/scvi-tools;

· by ethanweinberger was closed on Oct 6, 2024

fix(module): address shape mismatch for scanvae loss n_samples

Status: Merged (completed).

scverse/scvi-toolsnumber 2867

#2867 In scverse/scvi-tools;

· by martinkim0 was closed on Jul 30, 2024

refactor(model): refactor out common minified mode methods

Status: Merged (completed).

scverse/scvi-toolsnumber 2883

#2883 In scverse/scvi-tools;

· by martinkim0 was closed on Nov 29, 2024

Backport PR #3085 on branch 1.2.x (misc: Address AnnData &gt;= 0.11 deprecation warnings)

Status: Merged (completed).

scverse/scvi-toolsnumber 3088

#3088 In scverse/scvi-tools;

· by meeseeksmachine was closed on Dec 11, 2024

Backport PR #3098 on branch 1.2.x ([pre-commit.ci] pre-commit autoupdate)

Status: Merged (completed).

scverse/scvi-toolsnumber 3099

#3099 In scverse/scvi-tools;

· by meeseeksmachine was closed on Dec 16, 2024

[pre-commit.ci] pre-commit autoupdate

Status: Merged (completed).

scverse/scvi-toolsnumber 3098

#3098 In scverse/scvi-tools;

· by pre-commit-ci was closed on Dec 16, 2024