scverse/scvi-tools issues and pull requests

#2874 - ci: add git email for release

Pull Request - State: closed - Opened by martinkim0 2 days ago

#2873 - Backport PR #2872 on branch 1.1.x (release: add date for 1.1.4)

Pull Request - State: closed - Opened by martinkim0 2 days ago

#2872 - release: add date for 1.1.4

Pull Request - State: closed - Opened by martinkim0 2 days ago - 1 comment
Labels: on-merge: backport to 1.1.x

#2871 - Backport PR #2870 on branch 1.1.x (feat(external): add return_logits to solo predict for reproducibility)

Pull Request - State: closed - Opened by martinkim0 2 days ago

#2870 - feat(external): add return_logits to solo predict for reproducibility

Pull Request - State: closed - Opened by martinkim0 2 days ago - 2 comments
Labels: on-merge: backport to 1.1.x

#2869 - solo.predict() should take an argument to return Non-softmax transformed values, and return logits like previous iterations to allow for non-breaking change that was implemented in 1.1.3

Issue - State: closed - Opened by barstuart 2 days ago - 2 comments
Labels: enhancement

#2868 - style: add initial tensor shape typing to vae

Pull Request - State: open - Opened by martinkim0 4 days ago - 2 comments

#2867 - fix(module): address shape mismatch for scanvae loss n_samples

Pull Request - State: open - Opened by martinkim0 4 days ago

#2866 - How to modify scANVI to handle continuous cell labels?

Issue - State: open - Opened by patricks-lab 5 days ago - 1 comment
Labels: enhancement

#2865 - docs: add faq

Pull Request - State: closed - Opened by martinkim0 5 days ago - 1 comment

#2864 - Backport PR #2863 on branch 1.1.x (docs: add release entry for 1.1.4)

Pull Request - State: closed - Opened by martinkim0 6 days ago

#2863 - docs: add release entry for 1.1.4

Pull Request - State: closed - Opened by martinkim0 6 days ago - 1 comment
Labels: on-merge: backport to 1.1.x

#2862 - Backport PR #2861 on branch 1.1.x (release: bump version to 1.1.4)

Pull Request - State: closed - Opened by meeseeksmachine 6 days ago
Labels: on-merge: backport to 1.1.x

#2861 - release: bump version to 1.1.4

Pull Request - State: closed - Opened by martinkim0 6 days ago
Labels: on-merge: backport to 1.1.x

#2860 - ci: update release workflow

Pull Request - State: closed - Opened by martinkim0 6 days ago - 1 comment

#2859 - ci: add initial release workflow overhaul

Pull Request - State: closed - Opened by martinkim0 6 days ago

#2858 - docs: update developer docs

Pull Request - State: closed - Opened by martinkim0 6 days ago - 1 comment

#2857 - refactor: remove jax usage in data utils

Pull Request - State: closed - Opened by martinkim0 6 days ago

#2856 - build: specify all direct dependencies in pyproject

Pull Request - State: closed - Opened by martinkim0 6 days ago

#2855 - Backport PR #2854 on branch 1.1.x (feat: add support for scipy 1.14.0)

Pull Request - State: closed - Opened by meeseeksmachine 6 days ago
Labels: on-merge: backport to 1.1.x

#2854 - feat: add support for scipy 1.14.0

Pull Request - State: closed - Opened by martinkim0 6 days ago
Labels: on-merge: backport to 1.1.x

#2853 - Backport PR #2852 on branch 1.1.x (release: update tutorials and 1.1.3 release date)

Pull Request - State: closed - Opened by martinkim0 6 days ago

#2852 - release: update tutorials and 1.1.3 release date

Pull Request - State: closed - Opened by martinkim0 6 days ago - 1 comment
Labels: on-merge: backport to 1.1.x

#2851 - AttributeError: module 'numpy' has no attribute 'str'.

Issue - State: closed - Opened by klshen8386 7 days ago - 4 comments
Labels: bug

#2850 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 8 days ago - 1 comment

#2849 - Error in py_call_impl(callable, call_args$unnamed, call_args$named)

Issue - State: closed - Opened by liuzhuoliang123 9 days ago - 2 comments
Labels: bug

#2848 - refactor(autotune): change search space keys spec

Pull Request - State: closed - Opened by martinkim0 14 days ago - 1 comment

#2847 - refactor(data): remove jax usage for data check

Pull Request - State: closed - Opened by martinkim0 14 days ago

#2846 - Backport PR #2841 on branch 1.2.x ([pre-commit.ci] pre-commit autoupdate)

Pull Request - State: closed - Opened by martinkim0 15 days ago - 1 comment

#2845 - Backport PR #2843 on branch 1.1.x (build: upper bound numpy 2.0)

Pull Request - State: closed - Opened by martinkim0 15 days ago - 1 comment

#2844 - Backport PR #2843 on branch 1.2.x (build: upper bound numpy 2.0)

Pull Request - State: closed - Opened by meeseeksmachine 15 days ago
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x

#2843 - build: upper bound numpy 2.0

Pull Request - State: closed - Opened by martinkim0 15 days ago - 2 comments
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x

#2842 - feat: support numpy 2.0

Pull Request - State: open - Opened by martinkim0 15 days ago - 2 comments
Labels: on-merge: backport to 1.1.x

#2841 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 15 days ago - 1 comment
Labels: on-merge: backport to 1.2.x

#2840 - Discussion thread: New DestVI model that supports Visium HD (single-cell spatial transcriptomics) data - Timeline, releases and alternatives

Issue - State: closed - Opened by Rafael-Silva-Oliveira 15 days ago - 2 comments
Labels: enhancement

#2839 - Specifying cell types in the new MRVI tool

Issue - State: closed - Opened by jindalk 19 days ago - 1 comment
Labels: bug

#2838 - Question about the output of scVI and scANVI

Issue - State: closed - Opened by ngvananh2508 21 days ago - 2 comments

#2837 - CellAssign tensor size error

Issue - State: open - Opened by andrewjkwok 21 days ago
Labels: bug

#2836 - Trying to run PeakVI model returns mpi4py error

Issue - State: open - Opened by Sun-storm 22 days ago - 1 comment
Labels: bug

#2835 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 22 days ago - 1 comment

#2834 - Implement methylVI

Pull Request - State: open - Opened by ethanweinberger 22 days ago - 1 comment

#2833 - Exception has occurred: ImportError cannot import name 'REGISTRY_KEYS' from 'scvi'

Issue - State: closed - Opened by Rafael-Silva-Oliveira 22 days ago - 3 comments
Labels: bug

#2832 - Backport PR #2831 on branch 1.2.x (feat(autotune): add support for ray 2.24)

Pull Request - State: closed - Opened by meeseeksmachine 23 days ago
Labels: on-merge: backport to 1.2.x

#2831 - feat(autotune): add support for ray 2.24

Pull Request - State: closed - Opened by martinkim0 23 days ago - 1 comment
Labels: on-merge: backport to 1.2.x

#2830 - Expected value argument (Parameter of shape (7150,)) to be within the support (Real()) of the distribution Normal(loc: torch.Size([7150]), scale: torch.Size([7150])), but found invalid values: Parameter containing: tensor([nan, nan, nan, ..

Issue - State: open - Opened by Rafael-Silva-Oliveira 26 days ago - 9 comments
Labels: bug

#2829 - Backport PR #2828 on branch 1.2.x (fix(external): add save load mrvi tests and fix pickling)

Pull Request - State: closed - Opened by meeseeksmachine 27 days ago
Labels: on-merge: backport to 1.2.x

#2828 - fix(external): add save load mrvi tests and fix pickling

Pull Request - State: closed - Opened by martinkim0 27 days ago - 1 comment
Labels: on-merge: backport to 1.2.x

#2827 - Backport PR #2578 on branch 1.2.x (Reference mapping with MuData-based models)

Pull Request - State: closed - Opened by meeseeksmachine 29 days ago
Labels: on-merge: backport to 1.2.x

#2826 - compute DE+ and DE- separately

Pull Request - State: open - Opened by LevyNat 29 days ago - 3 comments

#2825 - Backport PR #2824 on branch 1.2.x (docs: remove left nav icons)

Pull Request - State: closed - Opened by meeseeksmachine 29 days ago
Labels: on-merge: backport to 1.2.x

#2824 - docs: remove left nav icons

Pull Request - State: closed - Opened by martinkim0 29 days ago - 1 comment
Labels: on-merge: backport to 1.2.x

#2823 - Backport PR #2822 on branch 1.2.x (refactor: remove unused file)

Pull Request - State: closed - Opened by meeseeksmachine 29 days ago
Labels: on-merge: backport to 1.2.x

#2822 - refactor: remove unused file

Pull Request - State: closed - Opened by martinkim0 29 days ago
Labels: on-merge: backport to 1.2.x

#2821 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 29 days ago - 1 comment

#2820 - Error computing posterior predictive check `calibration_error`

Issue - State: closed - Opened by jpintar 29 days ago - 1 comment
Labels: bug

#2819 - Release 1.1.3

Issue - State: closed - Opened by martinkim0 about 1 month ago
Labels: releases

#2818 - Backport PR #2816 on branch 1.1.x (fix(dataloaders): sample without replacement for unlabeled obs)

Pull Request - State: closed - Opened by martinkim0 about 1 month ago

#2817 - Backport PR #2816 on branch 1.2.x (fix(dataloaders): sample without replacement for unlabeled obs)

Pull Request - State: closed - Opened by meeseeksmachine about 1 month ago
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x

#2816 - fix(dataloaders): sample without replacement for unlabeled obs

Pull Request - State: closed - Opened by martinkim0 about 1 month ago - 2 comments
Labels: Still Needs Manual Backport, on-merge: backport to 1.1.x, on-merge: backport to 1.2.x

#2815 - Issues in Load Dataset with SeuratData and convert to adata

Issue - State: closed - Opened by GischD about 1 month ago - 2 comments
Labels: bug

#2814 - ImportError: cannot import name 'packaging' from 'pkg_resources' for Model Tuning using Ray

Issue - State: closed - Opened by shahrozeabbas about 1 month ago - 4 comments
Labels: bug

#2813 - Error saving MrVI model

Issue - State: closed - Opened by lior-ness about 1 month ago - 2 comments
Labels: bug

#2812 - Backport PR #2809 on branch 1.2.x (docs: add census tutorial to index)

Pull Request - State: closed - Opened by meeseeksmachine about 1 month ago - 1 comment
Labels: on-merge: backport to 1.2.x

#2811 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 month ago - 1 comment

#2810 - bug for custom classifier in adversarial training plan

Issue - State: open - Opened by SabrinaRichter about 1 month ago - 1 comment
Labels: bug

#2809 - docs: add census tutorial to index

Pull Request - State: closed - Opened by martinkim0 about 1 month ago - 1 comment
Labels: on-merge: backport to 1.2.x

#2808 - Backport PR #2807 on branch 1.2.x (build: remove torchmetrics upperbound)

Pull Request - State: closed - Opened by meeseeksmachine about 1 month ago
Labels: on-merge: backport to 1.2.x

#2807 - build: remove torchmetrics upperbound

Pull Request - State: closed - Opened by martinkim0 about 1 month ago - 1 comment
Labels: on-merge: backport to 1.2.x

#2806 - cannot import name 'MRVI' from 'scvi.external'

Issue - State: closed - Opened by zy-fang about 1 month ago - 2 comments
Labels: bug

#2805 - Fix for get_normalized_expression

Pull Request - State: open - Opened by lauradmartens about 2 months ago - 1 comment

#2804 - different hidden unit in each layer

Issue - State: closed - Opened by verao-amy about 2 months ago - 1 comment
Labels: enhancement

#2803 - Support the latest version of torchmetrics

Issue - State: closed - Opened by martinkim0 about 2 months ago

#2802 - Mmd noamgal

Pull Request - State: closed - Opened by noamgal about 2 months ago - 2 comments

#2801 - Backport PR #2780 on branch 1.2.x (feat(model): add normal distribution support for scvi)

Pull Request - State: closed - Opened by meeseeksmachine about 2 months ago
Labels: on-merge: backport to 1.2.x

#2800 - Issues installing recommended packages

Issue - State: closed - Opened by bykovam about 2 months ago - 4 comments
Labels: bug

#2799 - Backport PR #2798 on branch 1.2.x (ci: add pytest-pretty plugin, register custom marks)

Pull Request - State: closed - Opened by meeseeksmachine about 2 months ago - 1 comment
Labels: on-merge: backport to 1.2.x

#2798 - ci: add pytest-pretty plugin, register custom marks

Pull Request - State: closed - Opened by martinkim0 about 2 months ago
Labels: on-merge: backport to 1.2.x

#2797 - Backport PR #2796 on branch 1.2.x (ci: mark mrvi tests as optional)

Pull Request - State: closed - Opened by meeseeksmachine about 2 months ago
Labels: on-merge: backport to 1.2.x

#2796 - ci: mark mrvi tests as optional

Pull Request - State: closed - Opened by martinkim0 about 2 months ago
Labels: on-merge: backport to 1.2.x

#2795 - Backport PR #2787 on branch 1.2.x (feat(module): change base module to support jax device removal)

Pull Request - State: closed - Opened by meeseeksmachine about 2 months ago
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x

#2794 - Backport PR #2787 on branch 1.1.x (feat(module): change base module to support jax device removal)

Pull Request - State: closed - Opened by meeseeksmachine about 2 months ago - 1 comment
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x

#2793 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 2 months ago

#2792 - The scrna_raw_counts_properties method has an error in the calculation method of the raw_normalized_mean2 field, causing the raw_normalized_mean2 indicator to be invalid.

Issue - State: closed - Opened by raozuming about 2 months ago - 4 comments
Labels: enhancement

GitHub / scverse/scvi-tools issues and pull requests