scverse/scvi-tools issues and pull requests

#2903 - ci: change cuda test to ghcr image

Pull Request - State: closed - Opened by martinkim0 3 months ago
Labels: cuda tests

#2902 - feat(dataloaders): add argument for custom data split indexes

Pull Request - State: closed - Opened by ori-kron-wis 3 months ago - 3 comments

#2901 - style: change to isinstance checks

Pull Request - State: closed - Opened by martinkim0 3 months ago - 1 comment

#2900 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 3 months ago - 1 comment

#2899 - build: fix ref check in image build

Pull Request - State: closed - Opened by martinkim0 3 months ago

#2898 - build: add image build for release branch

Pull Request - State: closed - Opened by martinkim0 3 months ago - 1 comment

#2897 - build: add release branches to image build

Pull Request - State: closed - Opened by martinkim0 3 months ago

#2896 - build: update dockerfile and workflows

Pull Request - State: closed - Opened by martinkim0 3 months ago

#2895 - Autotuning with Ray: DeprecationWarning: The `RunConfig(local_dir)` argument is deprecated. You should set the `RunConfig(storage_path)` instead.

Issue - State: closed - Opened by Rafael-Silva-Oliveira 3 months ago - 2 comments
Labels: bug

#2894 - build: fix docker cache ref

Pull Request - State: closed - Opened by martinkim0 3 months ago

#2890 - docs: automated update of tutorials

Pull Request - State: closed - Opened by github-actions[bot] 3 months ago

#2889 - scvi-tools 1.2.0

Issue - State: closed - Opened by martinkim0 3 months ago - 4 comments
Labels: releases

#2883 - refactor(model): refactor out common minified mode methods

Pull Request - State: open - Opened by martinkim0 3 months ago - 2 comments
Labels: cuda tests

#2882 - docs: update release workflow documentation

Pull Request - State: closed - Opened by martinkim0 3 months ago - 1 comment

#2881 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 3 months ago - 1 comment

#2879 - release: update template for link

Pull Request - State: closed - Opened by martinkim0 3 months ago - 1 comment

#2878 - Backport PR #2877 on branch 1.1.x (release: add 1.1.5 release)

Pull Request - State: closed - Opened by martinkim0 3 months ago - 1 comment

#2877 - release: add 1.1.5 release

Pull Request - State: closed - Opened by martinkim0 3 months ago - 2 comments
Labels: on-merge: backport to 1.1.x

#2876 - backport: add release note template for release

Pull Request - State: closed - Opened by martinkim0 3 months ago - 1 comment

#2875 - ci: update release workflow for correct ref

Pull Request - State: closed - Opened by martinkim0 3 months ago - 1 comment

#2874 - ci: add git email for release

Pull Request - State: closed - Opened by martinkim0 3 months ago - 1 comment

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

Pull Request - State: closed - Opened by martinkim0 3 months ago

#2872 - release: add date for 1.1.4

Pull Request - State: closed - Opened by martinkim0 3 months ago - 2 comments
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 3 months ago - 1 comment

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

Pull Request - State: closed - Opened by martinkim0 3 months 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 3 months ago - 2 comments
Labels: enhancement

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

Pull Request - State: open - Opened by martinkim0 3 months ago - 2 comments
Labels: on-merge: backport to 1.2.x

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

Pull Request - State: closed - Opened by martinkim0 3 months ago - 1 comment

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

Issue - State: closed - Opened by patricks-lab 3 months ago - 1 comment
Labels: enhancement

#2865 - docs: add faq

Pull Request - State: closed - Opened by martinkim0 3 months 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 3 months ago - 1 comment

#2863 - docs: add release entry for 1.1.4

Pull Request - State: closed - Opened by martinkim0 3 months ago - 2 comments
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 3 months ago - 1 comment
Labels: on-merge: backport to 1.1.x

#2861 - release: bump version to 1.1.4

Pull Request - State: closed - Opened by martinkim0 3 months ago - 1 comment
Labels: on-merge: backport to 1.1.x

#2860 - ci: update release workflow

Pull Request - State: closed - Opened by martinkim0 3 months ago - 1 comment

#2859 - ci: add initial release workflow overhaul

Pull Request - State: closed - Opened by martinkim0 3 months ago - 1 comment

#2858 - docs: update developer docs

Pull Request - State: closed - Opened by martinkim0 3 months ago - 1 comment

#2857 - refactor: remove jax usage in data utils

Pull Request - State: closed - Opened by martinkim0 3 months ago - 1 comment

#2856 - build: specify all direct dependencies in pyproject

Pull Request - State: closed - Opened by martinkim0 3 months ago - 1 comment

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

Pull Request - State: closed - Opened by meeseeksmachine 3 months ago - 1 comment
Labels: on-merge: backport to 1.1.x

#2854 - feat: add support for scipy 1.14.0

Pull Request - State: closed - Opened by martinkim0 3 months ago - 1 comment
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 3 months ago - 1 comment

#2852 - release: update tutorials and 1.1.3 release date

Pull Request - State: closed - Opened by martinkim0 3 months ago - 2 comments
Labels: on-merge: backport to 1.1.x

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

Issue - State: closed - Opened by klshen8386 3 months ago - 4 comments
Labels: bug

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 3 months ago - 1 comment

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

Issue - State: closed - Opened by liuzhuoliang123 3 months ago - 2 comments
Labels: bug

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

Pull Request - State: closed - Opened by martinkim0 4 months ago - 1 comment

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

Pull Request - State: closed - Opened by martinkim0 4 months ago

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

Pull Request - State: closed - Opened by martinkim0 4 months 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 4 months 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 4 months ago - 1 comment
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 4 months 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 4 months ago - 2 comments

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 4 months ago - 2 comments
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 4 months ago - 2 comments
Labels: enhancement

#2839 - Specifying cell types in the new MRVI tool

Issue - State: closed - Opened by jindalk 4 months ago - 1 comment
Labels: bug

#2838 - Question about the output of scVI and scANVI

Issue - State: closed - Opened by ngvananh2508 4 months ago - 2 comments

#2837 - CellAssign tensor size error

Issue - State: closed - Opened by andrewjkwok 4 months ago - 9 comments
Labels: bug, P0

#2836 - Trying to run PeakVI model returns mpi4py error

Issue - State: open - Opened by Sun-storm 4 months ago - 1 comment
Labels: bug

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 4 months ago - 1 comment

#2834 - feat(external): implement METHLYVI for scBS-seq data

Pull Request - State: open - Opened by ethanweinberger 4 months ago - 9 comments
Labels: cuda tests

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

Issue - State: closed - Opened by Rafael-Silva-Oliveira 4 months 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 4 months ago - 1 comment
Labels: on-merge: backport to 1.2.x

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

Pull Request - State: closed - Opened by martinkim0 4 months 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: closed - Opened by Rafael-Silva-Oliveira 4 months ago - 10 comments
Labels: bug, P0

GitHub / scverse/scvi-tools issues and pull requests