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
#2389 - Backport PR #2361 on branch 1.1.x (Can criticism indices)
Pull Request -
State: closed - Opened by meeseeksmachine 9 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2388 - Segmentation error on scvi-tools
Issue -
State: closed - Opened by alexanderchang1 9 months ago
- 22 comments
Labels: bug
#2387 - Incompability between Pandas <2 and >=2 saved models
Issue -
State: closed - Opened by martinkim0 9 months ago
- 3 comments
Labels: bug
#2386 - Address xarray sparse issues in criticism
Issue -
State: closed - Opened by martinkim0 9 months ago
- 1 comment
Labels: bug
#2385 - Backport PR #2382 on branch 1.1.x (Add `save` method to `HubModel` and `HubMetadata`)
Pull Request -
State: closed - Opened by meeseeksmachine 9 months ago
- 1 comment
#2384 - Backport PR #2377 on branch 1.1.x (Clean up posterior predictive sample methods)
Pull Request -
State: closed - Opened by meeseeksmachine 9 months ago
- 1 comment
#2383 - Adding cycle consistency loss and VampPrior to scVI
Issue -
State: open - Opened by Hrovatin 9 months ago
- 23 comments
Labels: enhancement, P1
#2382 - Add `save` method to `HubModel` and `HubMetadata`
Pull Request -
State: closed - Opened by martinkim0 9 months ago
- 2 comments
#2381 - Manually update ruff pre-commit
Pull Request -
State: closed - Opened by martinkim0 9 months ago
- 1 comment
#2380 - Manually update ruff pre-commit
Pull Request -
State: closed - Opened by martinkim0 9 months ago
#2379 - Can hub paper
Pull Request -
State: open - Opened by canergen 9 months ago
- 2 comments
Labels: P0
#2378 - Add support for S3 in `HubModel`
Pull Request -
State: closed - Opened by martinkim0 9 months ago
- 2 comments
Labels: on-merge: backport to 1.1.x
#2377 - Clean up posterior predictive sample methods
Pull Request -
State: closed - Opened by martinkim0 9 months ago
- 2 comments
#2376 - No validation_step for scANVI
Issue -
State: closed - Opened by marcovarrone 9 months ago
- 3 comments
Labels: bug
#2375 - Cannot train model
Issue -
State: closed - Opened by stefraptis 9 months ago
- 3 comments
Labels: bug
#2374 - Backport PR #2373 on branch 1.1.x (Add seed argument for pymde)
Pull Request -
State: closed - Opened by meeseeksmachine 10 months ago
#2373 - Add seed argument for pymde
Pull Request -
State: closed - Opened by martinkim0 10 months ago
- 1 comment
#2372 - PyMDE seed fixation suggestion
Issue -
State: closed - Opened by seyoon-lee 10 months ago
- 1 comment
Labels: enhancement
#2371 - Add option to error on url response
Pull Request -
State: closed - Opened by martinkim0 10 months ago
- 2 comments
#2370 - PoissonVI Error in Pre-release
Issue -
State: closed - Opened by shahrozeabbas 10 months ago
- 14 comments
Labels: bug
#2369 - Backport PR #2368 on branch 1.1.x (Fix error message in `LayerField.transfer_field`)
Pull Request -
State: closed - Opened by meeseeksmachine 10 months ago
Labels: on-merge: backport to 1.1.x
#2368 - Fix error message in `LayerField.transfer_field`
Pull Request -
State: closed - Opened by martinkim0 10 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2367 - Backport PR #2366 on branch 1.1.x (Properly use `batch_size` in `GIMVI._make_scvi_dls`)
Pull Request -
State: closed - Opened by meeseeksmachine 10 months ago
Labels: on-merge: backport to 1.1.x
#2366 - Properly use `batch_size` in `GIMVI._make_scvi_dls`
Pull Request -
State: closed - Opened by martinkim0 10 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2365 - Move external tests into separate subdirectories
Pull Request -
State: closed - Opened by martinkim0 10 months ago
- 1 comment
#2364 - multi-GPU vs. single GPU - scvi 1.1.x branch
Issue -
State: open - Opened by zhenxingjian 10 months ago
- 3 comments
Labels: bug, P0
#2363 - POISSONVI Availability
Issue -
State: closed - Opened by shahrozeabbas 10 months ago
- 2 comments
Labels: bug
#2362 - Fixes error in get losses functions
Pull Request -
State: closed - Opened by canergen 10 months ago
- 3 comments
Labels: on-merge: backport to 1.2.x
#2361 - Can criticism indices
Pull Request -
State: closed - Opened by canergen 10 months ago
- 5 comments
Labels: on-merge: backport to 1.1.x
#2360 - Release scvi-tools 1.1.0-rc.2
Issue -
State: closed - Opened by martinkim0 10 months ago
Labels: releases
#2359 - Backport PR #2358 on branch 1.1.x (Add rc to version)
Pull Request -
State: closed - Opened by meeseeksmachine 10 months ago
Labels: on-merge: backport to 1.1.x
#2358 - Add rc to version
Pull Request -
State: closed - Opened by martinkim0 10 months ago
Labels: on-merge: backport to 1.1.x
#2357 - Backport PR #2356 on branch 1.1.x (Update tutorials head for release candidate)
Pull Request -
State: closed - Opened by meeseeksmachine 10 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2356 - Update tutorials head for release candidate
Pull Request -
State: closed - Opened by martinkim0 10 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2355 - multi-GPU support?
Issue -
State: closed - Opened by zhenxingjian 10 months ago
- 4 comments
Labels: enhancement
#2354 - Backport PR #2353 on branch 1.1.x (Add gdown to tutorial deps)
Pull Request -
State: closed - Opened by meeseeksmachine 10 months ago
- 1 comment
#2353 - Add gdown to tutorial deps
Pull Request -
State: closed - Opened by martinkim0 10 months ago
- 2 comments
#2352 - Backport PR #2351 on branch 1.1.x (Add jupyter to tutorials deps)
Pull Request -
State: closed - Opened by meeseeksmachine 10 months ago
Labels: on-merge: backport to 1.1.x
#2351 - Add jupyter to tutorials deps
Pull Request -
State: closed - Opened by martinkim0 10 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2350 - Update docs
Pull Request -
State: closed - Opened by martinkim0 10 months ago
- 1 comment
#2349 - Implement conditional batch/layer normalization
Issue -
State: open - Opened by martinkim0 10 months ago
- 1 comment
Labels: enhancement, good first issue, P1
#2348 - Remove unused files
Pull Request -
State: closed - Opened by martinkim0 10 months ago
- 1 comment
#2347 - Update docs
Pull Request -
State: closed - Opened by martinkim0 10 months ago
- 1 comment
#2346 - Update tutorials
Pull Request -
State: closed - Opened by martinkim0 10 months ago
- 1 comment
#2345 - Add `POISSONVI` to docs API
Pull Request -
State: closed - Opened by martinkim0 10 months ago
#2344 - Pin fsspec
Pull Request -
State: closed - Opened by martinkim0 10 months ago
#2343 - Format timestamps for compatibility with new `fsspec`
Pull Request -
State: closed - Opened by martinkim0 10 months ago
- 1 comment
#2342 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 10 months ago
- 1 comment
#2341 - I get error 'warnings.warn("Initializing zero-element tensors is a no-op") ' when looking at 10x multiom data
Issue -
State: closed - Opened by jeffpkamp 10 months ago
- 2 comments
Labels: bug, P2
#2340 - Add indices to scvi criticism if using other subset AnnData object
Issue -
State: closed - Opened by canergen 10 months ago
Labels: bug
#2339 - Change `SemiSupervisedTrainingPlan` accuracy and F1 to micro average
Pull Request -
State: closed - Opened by martinkim0 10 months ago
- 1 comment
#2338 - Model trained on 0.14 and model load on 0.20, error shows: no "ind_x"
Issue -
State: closed - Opened by zhenxingjian 10 months ago
- 3 comments
Labels: bug, P0
#2337 - question on mismatch peak to gene association
Issue -
State: closed - Opened by marjorieb12345 11 months ago
- 1 comment
Labels: bug
#2336 - Unable to change gene_likelihood in scvi.model.SCVI.setup_anndata
Issue -
State: closed - Opened by gamabunta313 11 months ago
- 1 comment
Labels: bug
#2335 - Possible mistake in error formating - `scvi.data.fields._layer`
Issue -
State: closed - Opened by yotamcons 11 months ago
- 3 comments
Labels: bug
#2334 - Lazy load autotune, hub modules
Pull Request -
State: closed - Opened by martinkim0 11 months ago
- 1 comment
#2333 - scvi-tools fails
Issue -
State: closed - Opened by joseagraz 11 months ago
- 14 comments
Labels: bug
#2332 - Change chex from default to test dependency
Pull Request -
State: open - Opened by martinkim0 11 months ago
- 1 comment
#2331 - batch and max_kl_weight parameters ignored when mapping to scvi reference
Issue -
State: closed - Opened by LisaSikkema 11 months ago
- 8 comments
Labels: bug, P0
#2330 - Fix uncaught bug in scANVI logits fix load, bump version to 1.1.0
Pull Request -
State: closed - Opened by martinkim0 11 months ago
- 1 comment
#2329 - Update experimental tags for consistency
Pull Request -
State: closed - Opened by martinkim0 11 months ago
- 1 comment
#2328 - Bump version to 1.1.0
Pull Request -
State: closed - Opened by martinkim0 11 months ago
- 1 comment
#2327 - Release scvi-tools 1.1.0-rc.1
Issue -
State: closed - Opened by martinkim0 11 months ago
Labels: releases
#2326 - Fix release template formatting
Pull Request -
State: closed - Opened by martinkim0 11 months ago
#2325 - Add link to model hub in docs
Pull Request -
State: closed - Opened by martinkim0 11 months ago
- 1 comment
#2324 - Release scvi-tools 1.1
Issue -
State: closed - Opened by martinkim0 11 months ago
Labels: releases
#2323 - Add a release checklist
Pull Request -
State: closed - Opened by martinkim0 11 months ago
#2322 - Default to settings `dl_num_workers` in `AnnDataLoader`
Pull Request -
State: closed - Opened by martinkim0 11 months ago
- 1 comment
#2321 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 11 months ago
- 1 comment
#2320 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 11 months ago
- 1 comment
#2319 - Move chex to test dep
Pull Request -
State: open - Opened by justjhong 11 months ago
Labels: dependencies
#2318 - Split JAX into optional extra dependency
Pull Request -
State: closed - Opened by justjhong 11 months ago
- 1 comment
Labels: dependencies
#2317 - Add `SaveCheckpoint` callback for checkpointing
Pull Request -
State: closed - Opened by martinkim0 11 months ago
- 2 comments
#2316 - Upperbound ray to 2.8
Pull Request -
State: closed - Opened by martinkim0 11 months ago
- 2 comments
#2315 - Make autotune tests optional
Pull Request -
State: closed - Opened by martinkim0 11 months ago
- 2 comments
#2314 - ValueError: Expected more than 1 value per channel when training, got input size torch.Size([1, 128])
Issue -
State: closed - Opened by Huiflorazhan 11 months ago
- 2 comments
Labels: bug
#2313 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 11 months ago
- 1 comment
#2312 - ImportError: cannot import name 'Doc' from 'typing_extensions'
Issue -
State: closed - Opened by jheonsuh 11 months ago
- 4 comments
Labels: bug
#2311 - Separate out unit and integration tests
Issue -
State: open - Opened by martinkim0 11 months ago
Labels: good first issue, tests, CI/CD, P2
#2310 - Add pre logits fix scANVI model to test data
Pull Request -
State: closed - Opened by martinkim0 11 months ago
- 1 comment
#2309 - Match Flax batch norm params to PyTorch defaults
Pull Request -
State: closed - Opened by martinkim0 11 months ago
- 1 comment
#2308 - Pin Pandas to not 2.1.2
Pull Request -
State: closed - Opened by martinkim0 11 months ago
- 1 comment
#2307 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 11 months ago
#2306 - Make pbmc test optional
Pull Request -
State: closed - Opened by martinkim0 11 months ago
#2305 - Replace Black with Ruff formatter
Pull Request -
State: closed - Opened by martinkim0 11 months ago
- 1 comment
Labels: ready to merge
#2304 - Replace Black with Ruff formatter
Pull Request -
State: closed - Opened by martinkim0 11 months ago
- 1 comment
#2303 - Bump Lightning upperbound to 2.2
Pull Request -
State: closed - Opened by martinkim0 11 months ago
- 1 comment
#2302 - ImportError when Installing scvi-colab: Cannot Import 'Doc' from 'typing_extensions'
Issue -
State: closed - Opened by aasingh2 12 months ago
- 4 comments
Labels: bug
#2301 - Patch SCANVI classifier logits bug
Pull Request -
State: closed - Opened by martinkim0 12 months ago
- 1 comment
Labels: scanvi, ready to merge
#2300 - Bump lowerbound on scib-metrics
Pull Request -
State: closed - Opened by martinkim0 12 months ago
- 1 comment
#2299 - Switch to functional torchmetrics, add calibration error
Pull Request -
State: closed - Opened by martinkim0 12 months ago
- 1 comment
#2298 - [pre-commit.ci] pre-commit autoupdate
Pull Request -
State: closed - Opened by pre-commit-ci[bot] 12 months ago
- 1 comment
#2297 - Fix a bug in the imputation process of Gimvi
Pull Request -
State: closed - Opened by HelloWorldLTY 12 months ago
- 7 comments
#2296 - Update _model.py
Pull Request -
State: closed - Opened by HelloWorldLTY 12 months ago
#2295 - Fix scarches tutorial links
Pull Request -
State: closed - Opened by martinkim0 12 months ago
- 1 comment
#2294 - scvi.settings.seed cannot generate same UMAP embeddings.
Issue -
State: closed - Opened by Lijunyao8 12 months ago
- 5 comments
Labels: bug
#2293 - Remove sparse array tests and arguments
Pull Request -
State: closed - Opened by martinkim0 12 months ago
- 1 comment
#2292 - Allow for other registry keys in dtype conversion
Pull Request -
State: closed - Opened by martinkim0 12 months ago
- 1 comment
#2291 - Add FAQ page
Pull Request -
State: closed - Opened by martinkim0 12 months ago
- 1 comment
#2290 - Backport PR #2286 on branch 1.0.x (Bump version to 1.0.4)
Pull Request -
State: closed - Opened by meeseeksmachine 12 months ago
- 1 comment
Labels: on-merge: backport to 1.0.x