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

#2288 - Add FAQ page in documentation

Issue - State: closed - Opened by martinkim0 12 months ago
Labels: enhancement

#2287 - Move over Docker images from scvi-tools-docker

Issue - State: closed - Opened by martinkim0 12 months ago
Labels: enhancement

#2286 - Bump version to 1.0.4

Pull Request - State: closed - Opened by martinkim0 12 months ago - 1 comment
Labels: on-merge: backport to 1.0.x

#2285 - Update notebook links in user guides

Pull Request - State: closed - Opened by martinkim0 12 months ago - 2 comments
Labels: on-merge: backport to 1.0.x

#2284 - Change mde to use accelerator and device

Pull Request - State: closed - Opened by martinkim0 12 months ago - 3 comments

#2283 - Add option for covariates in synthetic data

Pull Request - State: closed - Opened by martinkim0 12 months ago

#2282 - Make `mde()` consistent with docstring for `device` argument

Pull Request - State: closed - Opened by pablo-gar 12 months ago - 2 comments

#2281 - Make JAX an optional dependency

Issue - State: open - Opened by martinkim0 12 months ago - 4 comments
Labels: enhancement, P1

#2280 - Log learning rate when `reduce_lr_on_plateau=True`

Pull Request - State: closed - Opened by martinkim0 12 months ago - 1 comment

#2279 - Refactor tests

Pull Request - State: closed - Opened by martinkim0 12 months ago - 1 comment

#2278 - Backport PR #2271: Add support for AnnData 0.10.0

Pull Request - State: closed - Opened by martinkim0 12 months ago - 1 comment

#2277 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 12 months ago - 2 comments

#2275 - ImportError: cannot import name 'settings' from 'scvi' (unknown location)

Issue - State: closed - Opened by Kiliankleemann 12 months ago - 4 comments
Labels: bug

#2274 - Refactor tests

Pull Request - State: closed - Opened by martinkim0 almost 1 year ago

#2273 - Observed a bug in GimVI

Issue - State: closed - Opened by HelloWorldLTY almost 1 year ago - 2 comments
Labels: bug, gimvi

#2272 - [pre-commit.ci] pre-commit autoupdate

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

#2271 - Add support for AnnData 0.10.0

Pull Request - State: closed - Opened by martinkim0 about 1 year ago - 3 comments
Labels: on-merge: backport to 1.0.x

#2270 - Log learning rate when `reduce_lr_on_plateau=True`

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

#2269 - [pre-commit.ci] pre-commit autoupdate

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

#2268 - Support for upcoming AnnData 0.10.0rc1 for compatibility with the latest rapids_singlecell

Issue - State: closed - Opened by ktravaglini about 1 year ago - 1 comment
Labels: enhancement

#2267 - [pre-commit.ci] pre-commit autoupdate

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

#2266 - Load model don't use the GPU

Issue - State: closed - Opened by Quentin-bioinfo about 1 year ago - 2 comments
Labels: bug

#2265 - Implement ContrastiveVI

Pull Request - State: closed - Opened by chris522229197 about 1 year ago - 10 comments

#2264 - Add changes to make saving intermediate checkpoints easier

Issue - State: closed - Opened by martinkim0 about 1 year ago
Labels: enhancement

#2263 - Sgrouard/sanity checks updated

Pull Request - State: closed - Opened by SimonGrouard about 1 year ago - 1 comment

#2262 - MultiVI Tensor shape invalid values nan

Issue - State: closed - Opened by bhhlee about 1 year ago - 4 comments
Labels: bug, P0

#2261 - [pre-commit.ci] pre-commit autoupdate

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

#2260 - Add tensorboard default logging in autotune

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

#2259 - ModuleNotFoundError: No module named 'anndata._io.specs'

Issue - State: closed - Opened by zhangnan0107 about 1 year ago - 2 comments
Labels: bug

#2258 - Fix device conversion in autotune

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

#2257 - MultiVI with Poisson/NB likelihood for ATAC?

Issue - State: open - Opened by vitkl about 1 year ago - 8 comments
Labels: enhancement, P1

#2256 - Using torch.compile in Pyro models

Issue - State: open - Opened by vitkl about 1 year ago - 10 comments
Labels: enhancement, P2

#2255 - Import Error : ModuleNotFoundError: No module named 'torch.utils.model_zoo'

Issue - State: closed - Opened by HaoyeYang about 1 year ago - 1 comment
Labels: bug

#2254 - [pre-commit.ci] pre-commit autoupdate

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

#2252 - Support fractional accelerator usage in autotune

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

#2251 - [pre-commit.ci] pre-commit autoupdate

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

#2250 - Refactor anntorchdataset, add correct default dtypes

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

#2249 - PoissonVI to model quantitative scATAC-seq fragment counts

Pull Request - State: closed - Opened by lauradmartens about 1 year ago - 11 comments

#2248 - [pre-commit.ci] pre-commit autoupdate

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

#2247 - Revalidate devices when auto switching mps to cpu

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

#2246 - Type error when I run vae.train()

Issue - State: closed - Opened by Huiflorazhan about 1 year ago - 6 comments
Labels: bug

#2245 - Khalil/signatures

Pull Request - State: closed - Opened by khalilouardini about 1 year ago - 2 comments

#2243 - AttributeError: 'NoneType' object has no attribute 'numel'

Issue - State: closed - Opened by simomounir about 1 year ago - 18 comments
Labels: bug

#2242 - Implement contrastiveVI

Issue - State: closed - Opened by chris522229197 about 1 year ago - 1 comment

#2241 - Update pypi downloads badge

Pull Request - State: closed - Opened by martinkim0 about 1 year ago - 2 comments

#2240 - Implement batch embeddings for `SCVI`

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

#2239 - Fix tunable detection for new type annotation

Pull Request - State: closed - Opened by martinkim0 about 1 year ago - 2 comments

#2238 - CUDA memory error in lvm-DE

Issue - State: closed - Opened by joseph-siefert about 1 year ago - 4 comments
Labels: bug

#2237 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago - 2 comments

#2235 - Backport PR #2234 on branch 1.0.x (Add date to 1.0.3 release)

Pull Request - State: closed - Opened by meeseeksmachine about 1 year ago
Labels: on-merge: backport to 1.0.x

#2234 - Add date to 1.0.3 release

Pull Request - State: closed - Opened by martinkim0 about 1 year ago
Labels: on-merge: backport to 1.0.x

#2233 - Backport PR #2232 on branch 1.0.x (Update tutorials)

Pull Request - State: closed - Opened by meeseeksmachine about 1 year ago - 1 comment

#2232 - Update tutorials

Pull Request - State: closed - Opened by martinkim0 about 1 year ago - 2 comments

#2231 - Backport PR #2226 on branch 1.0.x (Fix references to tutorials)

Pull Request - State: closed - Opened by meeseeksmachine about 1 year ago - 1 comment
Labels: on-merge: backport to 1.0.x

#2230 - Saved `user_attributes` dict is massive (> 150 gb) which creates memory issues

Issue - State: closed - Opened by yanwu2014 about 1 year ago - 2 comments
Labels: bug

#2229 - Pass in `n_hidden` to `Encoder` in `AmortizedLDA`

Pull Request - State: closed - Opened by canergen about 1 year ago - 2 comments

#2228 - Pass in shape to torch sparse conversion

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

#2227 - [pre-commit.ci] pre-commit autoupdate

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

#2226 - Fix references to tutorials

Pull Request - State: closed - Opened by martinkim0 about 1 year ago - 1 comment
Labels: on-merge: backport to 1.0.x

#2225 - Add NumFocus logo and badges

Pull Request - State: closed - Opened by mikelkou about 1 year ago

#2224 - Add `use_posterior_mean` option to scanvi `predict`

Pull Request - State: closed - Opened by martinkim0 about 1 year ago - 3 comments

#2223 - Backport PR #2222 on branch 1.0.x (Migrate flax frozen dicts to dict)

Pull Request - State: closed - Opened by meeseeksmachine about 1 year ago - 1 comment
Labels: on-merge: backport to 1.0.x

#2222 - Migrate flax frozen dicts to dict

Pull Request - State: closed - Opened by martinkim0 about 1 year ago - 1 comment
Labels: on-merge: backport to 1.0.x

#2221 - Fix scanvi training

Pull Request - State: closed - Opened by watiss about 1 year ago - 1 comment

#2220 - Jax tests failing due to module init

Issue - State: closed - Opened by martinkim0 about 1 year ago - 1 comment
Labels: bug

#2219 - [pre-commit.ci] pre-commit autoupdate

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

#2218 - Conda recipe broken due to flax

Issue - State: closed - Opened by martinkim0 about 1 year ago - 3 comments
Labels: bug

#2217 - AttributeError: module 'scvi' has no attribute 'model'

Issue - State: closed - Opened by 183136 about 1 year ago - 8 comments
Labels: bug

#2216 - JAX issue

Issue - State: closed - Opened by anhducnguyen0122 about 1 year ago - 3 comments
Labels: bug

#2215 - ValueError with NaN tensors in gimVI training

Issue - State: open - Opened by sunericd about 1 year ago - 12 comments
Labels: bug, P0

#2213 - Backport PR #2212 on branch 1.0.x (Fix legacy convert for pandas 2.0)

Pull Request - State: closed - Opened by meeseeksmachine about 1 year ago - 1 comment
Labels: on-merge: backport to 1.0.x

#2212 - Fix legacy convert for pandas 2.0

Pull Request - State: closed - Opened by martinkim0 about 1 year ago - 2 comments
Labels: on-merge: backport to 1.0.x

#2211 - Legacy model convert fails because of pandas 2

Issue - State: closed - Opened by martinkim0 about 1 year ago
Labels: bug

#2210 - Update tutorial dependencies

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

#2209 - Backport PR #2208 on branch 1.0.x (Bump to 1.0.3, update tutorials)

Pull Request - State: closed - Opened by meeseeksmachine about 1 year ago - 1 comment
Labels: on-merge: backport to 1.0.x

#2208 - Bump to 1.0.3, update tutorials

Pull Request - State: closed - Opened by martinkim0 about 1 year ago - 1 comment
Labels: on-merge: backport to 1.0.x

#2207 - Backport PR #2185 on branch 1.0.x (Fix references page)

Pull Request - State: closed - Opened by meeseeksmachine about 1 year ago

#2205 - Remove devcontainer

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

#2204 - Expose `datasplitter_kwargs` in model `train` methods

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

#2203 - Expose fixed model and train kwargs in autotune

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

#2202 - Update cuda test image

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

#2201 - Add `accelerator` and `devices` options in pytest

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

#2200 - Expose `torch.save` kwargs

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

#2199 - [pre-commit.ci] pre-commit autoupdate

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

#2198 - Pretrained scvi-tools Hugging Face models mismatches

Issue - State: closed - Opened by juliebehr about 1 year ago - 3 comments
Labels: bug

#2197 - change python-igraph to igraph

Pull Request - State: closed - Opened by szhorvat about 1 year ago - 2 comments

#2196 - Issue converting scanpy back to seurat

Issue - State: closed - Opened by zacharyjxy2020 about 1 year ago - 2 comments
Labels: bug

#2195 - model.save() fails for large models

Issue - State: closed - Opened by yanwu2014 about 1 year ago - 2 comments
Labels: bug

#2194 - Expose model and train kwargs in autotune

Issue - State: closed - Opened by martinkim0 about 1 year ago
Labels: enhancement

#2193 - Update README with new badges

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

#2192 - Unable to import scvi

Issue - State: closed - Opened by raman91 about 1 year ago - 3 comments
Labels: bug

#2191 - [pre-commit.ci] pre-commit autoupdate

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