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

#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

#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

#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

#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