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

#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

#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

#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

#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