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
#2289 - Backport PR #2285 on branch 1.0.x (Update notebook links in user guides)
Pull Request -
State: closed - Opened by martinkim0 12 months ago
#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
#2276 - ImportError: cannot import name 'SparseDataset' from 'anndata._core.sparse_dataset'
Issue -
State: closed - Opened by knadia07 12 months ago
- 5 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
#2253 - Long (never ending???) runtime of scvi.model.SCVI.differential_expression with "weights = 'importance'"
Issue -
State: closed - Opened by MaximilianNuber about 1 year ago
- 2 comments
Labels: bug
#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
#2244 - Error `TypeError: '<' not supported between instances of 'str' and 'float'` raised when I run `scvi.model.SCVI.load_query_data`
Issue -
State: closed - Opened by lconan about 1 year ago
- 4 comments
Labels: bug
#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
#2236 - scvi.model.SCVI.train() on GPU with multiple devices error: object of type numpy.int64 has no len()
Issue -
State: closed - Opened by MaximilianNuber about 1 year ago
- 3 comments
Labels: bug
#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
#2214 - Expected more than 1 value per channel when training, input size torch.Size([1, 128])
Issue -
State: closed - Opened by Josuerinho about 1 year ago
- 4 comments
#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
#2206 - Backport PR #2180 on branch 1.0.x (Update tutorial indexes with subdirectories)
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
#2190 - Backport PR #2189 on branch 1.0.x (Add docstring for scanvi unlabeled category)
Pull Request -
State: closed - Opened by meeseeksmachine about 1 year ago