Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / scverse/scvi-tools issues and pull requests
#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 5 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] 5 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 5 months ago
- 4 comments
Labels: enhancement
#2791 - Backport PR #2756 on branch 1.2.x (feat(external): add mrvi)
Pull Request -
State: closed - Opened by meeseeksmachine 5 months ago
Labels: cuda tests, on-merge: backport to 1.2.x
#2790 - Update MrVI reference
Pull Request -
State: closed - Opened by justjhong 5 months ago
#2789 - SCVI-MMD HW task
Pull Request -
State: closed - Opened by o869k 5 months ago
#2788 - poor integration effect cross species
Issue -
State: closed - Opened by GGboy-Zzz 5 months ago
- 2 comments
Labels: bug
#2787 - feat(module): change base module to support jax device removal
Pull Request -
State: closed - Opened by martinkim0 5 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x
#2786 - Backport PR #2783 on branch 1.2.x (build: upperbound on torchmetrics)
Pull Request -
State: closed - Opened by meeseeksmachine 5 months ago
Labels: on-merge: backport to 1.2.x
#2785 - Support for weighted loss either per-batch or per-cell?
Issue -
State: closed - Opened by kamilkrukowski 5 months ago
- 2 comments
Labels: enhancement, P2
#2784 - AttributeError: module 'scvi' has no attribute 'autotune'
Issue -
State: closed - Opened by itamarb-cgen 5 months ago
- 4 comments
Labels: bug
#2783 - build: upperbound on torchmetrics
Pull Request -
State: closed - Opened by martinkim0 5 months ago
Labels: on-merge: backport to 1.2.x
#2782 - flax: Trying to access a property that is accessing a non-existent attribute. - JaxBaseModuleClass
Issue -
State: closed - Opened by Zethson 5 months ago
- 2 comments
Labels: bug
#2781 - Scvi in R doesn't update to scvi-tools even after uninstalling and reinstalling (I think :)
Issue -
State: closed - Opened by Sun-storm 5 months ago
- 3 comments
Labels: bug
#2780 - feat(model): add normal distribution support for scvi
Pull Request -
State: closed - Opened by martinkim0 5 months ago
- 1 comment
Labels: on-merge: backport to 1.2.x
#2779 - Jax version of VAEMixin
Issue -
State: open - Opened by justjhong 5 months ago
Labels: enhancement, good first issue, jax, P1
#2778 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 5 months ago
#2777 - Backport PR #2776 on branch 1.2.x (docs: update tutorials head)
Pull Request -
State: closed - Opened by meeseeksmachine 5 months ago
Labels: on-merge: backport to 1.2.x
#2776 - docs: update tutorials head
Pull Request -
State: closed - Opened by martinkim0 5 months ago
Labels: on-merge: backport to 1.2.x
#2775 - Add normal distribution modelling of scVI for handling log-normalized data
Pull Request -
State: closed - Opened by HelloWorldLTY 5 months ago
- 4 comments
#2774 - Consider non-jitting MRVI tests/long tests pytest flag
Issue -
State: open - Opened by martinkim0 5 months ago
Labels: P2, backlog
#2773 - add mrvi tutorial to index
Pull Request -
State: closed - Opened by martinkim0 5 months ago
- 1 comment
#2772 - Remove unused continuous covs from MrVI
Pull Request -
State: closed - Opened by justjhong 5 months ago
- 1 comment
#2771 - Speed up MrVI tests
Pull Request -
State: closed - Opened by justjhong 5 months ago
- 1 comment
#2770 - Backport PR #2769 on branch 1.2.x (feat(model): save mudata var names per modality)
Pull Request -
State: closed - Opened by meeseeksmachine 5 months ago
- 1 comment
Labels: on-merge: backport to 1.2.x
#2769 - feat(model): save mudata var names per modality
Pull Request -
State: closed - Opened by martinkim0 5 months ago
- 2 comments
Labels: on-merge: backport to 1.2.x
#2768 - update module class names
Pull Request -
State: closed - Opened by martinkim0 5 months ago
#2767 - add mrvi to api docs
Pull Request -
State: closed - Opened by martinkim0 5 months ago
- 1 comment
#2766 - Backport PR #2765 on branch 1.2.x (docs: update contributing guide)
Pull Request -
State: closed - Opened by meeseeksmachine 5 months ago
Labels: on-merge: backport to 1.2.x
#2765 - docs: update contributing guide
Pull Request -
State: closed - Opened by martinkim0 5 months ago
- 1 comment
Labels: on-merge: backport to 1.2.x
#2764 - Address future warning in distances function
Pull Request -
State: closed - Opened by justjhong 5 months ago
- 1 comment
#2763 - rename mrvi class for consistent styling
Pull Request -
State: closed - Opened by martinkim0 5 months ago
- 1 comment
#2762 - replace statsmodels with scipy stats
Pull Request -
State: closed - Opened by martinkim0 5 months ago
- 4 comments
#2761 - docs: add mrvi user guide
Pull Request -
State: closed - Opened by martinkim0 5 months ago
- 1 comment
#2760 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 5 months ago
- 1 comment
#2759 - Backport PR #2758 on branch 1.2.x (ci: run tests on pr to any branch)
Pull Request -
State: closed - Opened by meeseeksmachine 5 months ago
Labels: on-merge: backport to 1.2.x
#2758 - ci: run tests on pr to any branch
Pull Request -
State: closed - Opened by martinkim0 5 months ago
Labels: on-merge: backport to 1.2.x
#2757 - docs(external): add typing and docstrings for mrvi, remove laplace scaling
Pull Request -
State: closed - Opened by martinkim0 5 months ago
- 2 comments
#2756 - feat(external): add mrvi
Pull Request -
State: closed - Opened by martinkim0 5 months ago
- 6 comments
Labels: cuda tests, on-merge: backport to 1.2.x
#2755 - Can we have a scVI with reconstruction distirbution as normal distribution?
Issue -
State: closed - Opened by HelloWorldLTY 5 months ago
- 4 comments
Labels: enhancement
#2754 - Assistance Required with scvi-tools GPU Setup on Ubuntu
Issue -
State: closed - Opened by qweasdf1354 5 months ago
- 7 comments
Labels: bug
#2753 - Backport PR #2751 on branch 1.2.x (build: remove explicit upperbounds for ray and lightning)
Pull Request -
State: closed - Opened by meeseeksmachine 5 months ago
Labels: on-merge: backport to 1.2.x
#2752 - Backport PR #2748 on branch 1.2.x (feat(model): support custom dataloaders in vaemixin)
Pull Request -
State: closed - Opened by meeseeksmachine 5 months ago
Labels: on-merge: backport to 1.2.x
#2751 - build: remove explicit upperbounds for ray and lightning
Pull Request -
State: closed - Opened by martinkim0 5 months ago
- 1 comment
Labels: on-merge: backport to 1.2.x
#2750 - Backport PR #2749 on branch 1.2.x (refactor: rename data_module to datamodule)
Pull Request -
State: closed - Opened by meeseeksmachine 5 months ago
Labels: on-merge: backport to 1.2.x
#2749 - refactor: rename data_module to datamodule
Pull Request -
State: closed - Opened by martinkim0 5 months ago
- 1 comment
Labels: on-merge: backport to 1.2.x
#2748 - feat(model): support custom dataloaders in vaemixin
Pull Request -
State: closed - Opened by martinkim0 5 months ago
- 2 comments
Labels: on-merge: backport to 1.2.x
#2747 - Backport PR #2745 on branch 1.2.x (docs: remove contrastive dataloader and splitter from api ref)
Pull Request -
State: closed - Opened by meeseeksmachine 5 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x
#2746 - Backport PR #2745 on branch 1.1.x (docs: remove contrastive dataloader and splitter from api ref)
Pull Request -
State: closed - Opened by meeseeksmachine 5 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x
#2745 - docs: remove contrastive dataloader and splitter from api ref
Pull Request -
State: closed - Opened by martinkim0 5 months ago
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x
#2744 - misc: add node_modules to gitignore
Pull Request -
State: closed - Opened by martinkim0 5 months ago
#2743 - build: fail rtd on warnings
Pull Request -
State: closed - Opened by martinkim0 5 months ago
- 1 comment
#2742 - feat(model): save mudata var_names per modality
Pull Request -
State: closed - Opened by martinkim0 5 months ago
Labels: on-merge: backport to 1.2.x
#2741 - Backport PR #2739 on branch 1.2.x (feat(data): add explicit synthetic protein and region var names)
Pull Request -
State: closed - Opened by meeseeksmachine 5 months ago
- 1 comment
Labels: on-merge: backport to 1.2.x
#2740 - 'SCVI' object has no attribute 'eval'
Issue -
State: closed - Opened by FZ-hajji 5 months ago
- 2 comments
#2739 - feat(data): add explicit synthetic protein and region var names
Pull Request -
State: closed - Opened by martinkim0 5 months ago
- 1 comment
Labels: on-merge: backport to 1.2.x
#2738 - feat(model): support saving models initialized without anndata
Pull Request -
State: closed - Opened by martinkim0 5 months ago
- 1 comment
Labels: on-merge: backport to 1.2.x
#2737 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 5 months ago
- 1 comment
#2736 - Training models with torch.Tensor input
Issue -
State: open - Opened by j-bac 5 months ago
- 4 comments
Labels: enhancement, P1
#2735 - Poissonmultivi
Pull Request -
State: open - Opened by lauradmartens 6 months ago
- 3 comments
Labels: P2
#2734 - Backport PR #2733 on branch 1.2.x (refactor(model): substitute save file names with constants)
Pull Request -
State: closed - Opened by martinkim0 6 months ago
#2733 - refactor(model): substitute save file names with constants
Pull Request -
State: closed - Opened by martinkim0 6 months ago
- 1 comment
Labels: Still Needs Manual Backport, on-merge: backport to 1.2.x
#2732 - Backport PR #2731 on branch 1.2.x (refactor(model): move base model utils to new files)
Pull Request -
State: closed - Opened by meeseeksmachine 6 months ago
Labels: on-merge: backport to 1.2.x
#2731 - refactor(model): move base model utils to new files
Pull Request -
State: closed - Opened by martinkim0 6 months ago
- 1 comment
Labels: on-merge: backport to 1.2.x
#2730 - feat: support per mod var names saves for mudata
Pull Request -
State: closed - Opened by martinkim0 6 months ago
Labels: on-merge: backport to 1.2.x
#2729 - SemiSupervisedDataSplitter not properly separating unlabelled cells into train/val/test
Issue -
State: closed - Opened by ethanweinberger 6 months ago
- 1 comment
Labels: bug
#2728 - Backport PR #2727 on branch 1.2.x (build: remove criticism from optional deps)
Pull Request -
State: closed - Opened by meeseeksmachine 6 months ago
- 1 comment
Labels: on-merge: backport to 1.2.x
#2727 - build: remove criticism from optional deps
Pull Request -
State: closed - Opened by martinkim0 6 months ago
- 1 comment
Labels: on-merge: backport to 1.2.x
#2726 - scvi tools train with multi gpus
Issue -
State: closed - Opened by shanzha9 6 months ago
- 3 comments
Labels: bug, P0
#2725 - Backport PR #2724 on branch 1.2.x (docs: remove velovi preprocess from api)
Pull Request -
State: closed - Opened by meeseeksmachine 6 months ago
- 1 comment
Labels: on-merge: backport to 1.2.x
#2724 - docs: remove velovi preprocess from api
Pull Request -
State: closed - Opened by martinkim0 6 months ago
Labels: on-merge: backport to 1.2.x
#2723 - Backport PR #2721 on branch 1.2.x (fix(train): address typo in save checkpoint callback)
Pull Request -
State: closed - Opened by meeseeksmachine 6 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x
#2722 - Backport PR #2721 on branch 1.1.x (fix(train): address typo in save checkpoint callback)
Pull Request -
State: closed - Opened by meeseeksmachine 6 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x
#2721 - fix(train): address typo in save checkpoint callback
Pull Request -
State: closed - Opened by martinkim0 6 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x
#2720 - benign typo in kwarg
Issue -
State: closed - Opened by ghwatson 6 months ago
- 1 comment
Labels: bug
#2719 - Backport PR #2636 on branch 1.2.x (docs: update installation instructions)
Pull Request -
State: closed - Opened by meeseeksmachine 6 months ago
- 1 comment
Labels: on-merge: backport to 1.2.x
#2718 - Backport PR #2692 on branch 1.2.x (Add Beta-Binomial distribution for modeling scBS-seq data)
Pull Request -
State: closed - Opened by meeseeksmachine 6 months ago
- 1 comment
Labels: on-merge: backport to 1.2.x
#2717 - docs: rearrange api reference
Pull Request -
State: closed - Opened by martinkim0 6 months ago
- 1 comment
#2716 - Update CI description in maintenance guide
Issue -
State: closed - Opened by martinkim0 6 months ago
- 1 comment
#2715 - Backport PR #2712 on branch 1.2.x (docs: update contributing and developer guides)
Pull Request -
State: closed - Opened by meeseeksmachine 6 months ago
Labels: on-merge: backport to 1.2.x
#2714 - Backport PR #2713 on branch 1.2.x (docs: update readme)
Pull Request -
State: closed - Opened by meeseeksmachine 6 months ago
Labels: on-merge: backport to 1.2.x
#2713 - docs: update readme
Pull Request -
State: closed - Opened by martinkim0 6 months ago
Labels: on-merge: backport to 1.2.x
#2712 - docs: update contributing and developer guides
Pull Request -
State: closed - Opened by martinkim0 6 months ago
- 1 comment
Labels: on-merge: backport to 1.2.x
#2711 - Backport PR #2710 on branch 1.2.x (chore: transition to src layout)
Pull Request -
State: closed - Opened by meeseeksmachine 6 months ago
- 1 comment
Labels: on-merge: backport to 1.2.x
#2710 - chore: transition to src layout
Pull Request -
State: closed - Opened by martinkim0 6 months ago
- 1 comment
Labels: on-merge: backport to 1.2.x
#2709 - Fail to accerlerate scvi analysis using gpu on mac M1
Issue -
State: closed - Opened by xylinwc 6 months ago
- 7 comments
Labels: bug
#2708 - Backport PR #2707 on branch 1.2.x (chore(misc): update github stars badge)
Pull Request -
State: closed - Opened by meeseeksmachine 6 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x
#2707 - chore(misc): update github stars badge
Pull Request -
State: closed - Opened by martinkim0 6 months ago
Labels: on-merge: backport to 1.2.x
#2706 - Backport PR #2704 on branch 1.2.x (chore(release): bump version to 1.1.3)
Pull Request -
State: closed - Opened by meeseeksmachine 6 months ago
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x
#2705 - Backport PR #2704 on branch 1.1.x (chore(release): bump version to 1.1.3)
Pull Request -
State: closed - Opened by meeseeksmachine 6 months ago
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x
#2704 - chore(release): bump version to 1.1.3
Pull Request -
State: closed - Opened by martinkim0 6 months ago
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x
#2703 - Backport PR #2702 on branch 1.2.x (chore(misc): add markdown lint and format)
Pull Request -
State: closed - Opened by meeseeksmachine 6 months ago
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x
#2702 - chore(misc): add markdown lint and format
Pull Request -
State: closed - Opened by martinkim0 6 months ago
- 1 comment
Labels: on-merge: backport to 1.2.x
#2701 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 6 months ago
- 1 comment
#2700 - chore(misc): add markdown lint and format
Pull Request -
State: closed - Opened by martinkim0 6 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x
#2699 - Backport PR #2697 on branch 1.2.x (chore(external): add note and warning for solo predict breaking change)
Pull Request -
State: closed - Opened by meeseeksmachine 6 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x
#2698 - Backport PR #2697 on branch 1.1.x (chore(external): add note and warning for solo predict breaking change)
Pull Request -
State: closed - Opened by meeseeksmachine 6 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x
#2697 - chore(external): add note and warning for solo predict breaking change
Pull Request -
State: closed - Opened by martinkim0 6 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x, on-merge: backport to 1.2.x
#2696 - Save per-modality feature names for MuData models
Pull Request -
State: closed - Opened by ethanweinberger 6 months ago
- 4 comments
#2695 - Fixes to pyro model initialisation & sampling [WIP]
Pull Request -
State: open - Opened by vitkl 6 months ago
- 6 comments
Labels: P1