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
#2489 - Backport PR #2485 on branch 1.1.x (Use anndata `CSCDataset` and `CSRDataset` for type checks)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
Labels: on-merge: backport to 1.1.x
#2488 - Backport PR #2487 on branch 1.1.x (Add token to codecov action)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
Labels: on-merge: backport to 1.1.x
#2487 - Add token to codecov action
Pull Request -
State: closed - Opened by martinkim0 8 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2486 - Address various deprecation warnings
Pull Request -
State: closed - Opened by martinkim0 8 months ago
- 1 comment
#2485 - Use anndata `CSCDataset` and `CSRDataset` for type checks
Pull Request -
State: closed - Opened by martinkim0 8 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2484 - Backport PR #2467 on branch 1.1.x (Add API for custom dataloaders in `SCVI`)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
Labels: on-merge: backport to 1.1.x
#2483 - Backport PR #2482 on branch 1.1.x (Remove chex dependency)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
Labels: on-merge: backport to 1.1.x
#2482 - Remove chex dependency
Pull Request -
State: closed - Opened by martinkim0 8 months ago
- 2 comments
Labels: on-merge: backport to 1.1.x
#2481 - Backport PR #2480 on branch 1.1.x (Make xarray and sparse optional deps, lazy load criticism)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
Labels: on-merge: backport to 1.1.x
#2480 - Make xarray and sparse optional deps, lazy load criticism
Pull Request -
State: closed - Opened by martinkim0 8 months ago
Labels: on-merge: backport to 1.1.x
#2479 - Backport PR #2478 on branch 1.1.x (Add support for Ray 2.8-2.9)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
Labels: on-merge: backport to 1.1.x
#2478 - Add support for Ray 2.8-2.9
Pull Request -
State: closed - Opened by martinkim0 8 months ago
Labels: on-merge: backport to 1.1.x
#2477 - Backport PR #2475 on branch 1.1.x (Remove Pandas pin)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
#2476 - Backport PR #2474 on branch 1.1.x (Temporarily remove cellxgene-census dependency, remove chex upperbound)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
#2475 - Remove Pandas pin
Pull Request -
State: closed - Opened by martinkim0 8 months ago
- 1 comment
#2474 - Temporarily remove cellxgene-census dependency, remove chex upperbound
Pull Request -
State: closed - Opened by martinkim0 8 months ago
- 1 comment
#2473 - Add back cellxgene-census as optional dep
Issue -
State: closed - Opened by martinkim0 8 months ago
Labels: enhancement
#2472 - Make xarray and sparse optional deps, remove chex dep, remove Pandas pin, support newest Ray, temp remove cellxgene dep
Pull Request -
State: closed - Opened by martinkim0 8 months ago
- 1 comment
#2471 - mamba receipt to use gpu for scvitools
Issue -
State: closed - Opened by qiyubio 8 months ago
- 1 comment
Labels: enhancement
#2470 - Backport PR #2469 on branch 1.1.x (Update to codecov-action v4)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
Labels: on-merge: backport to 1.1.x
#2469 - Update to codecov-action v4
Pull Request -
State: closed - Opened by martinkim0 8 months ago
Labels: on-merge: backport to 1.1.x
#2468 - Backport PR #2466 on branch 1.1.x (Update tutorials head)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
#2467 - Add API for custom dataloaders in `SCVI`
Pull Request -
State: closed - Opened by martinkim0 8 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2466 - Update tutorials head
Pull Request -
State: closed - Opened by martinkim0 8 months ago
- 1 comment
#2465 - Backport PR #2463 on branch 1.1.x (Add scANVI fix tutorial to index)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
Labels: on-merge: backport to 1.1.x
#2464 - Backport PR #2462 on branch 1.1.x (Bump version to 1.1.0)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
Labels: on-merge: backport to 1.1.x
#2463 - Add scANVI fix tutorial to index
Pull Request -
State: closed - Opened by martinkim0 8 months ago
Labels: on-merge: backport to 1.1.x
#2462 - Bump version to 1.1.0
Pull Request -
State: closed - Opened by martinkim0 8 months ago
Labels: on-merge: backport to 1.1.x
#2461 - Scvi project
Pull Request -
State: closed - Opened by yoavnahum21 8 months ago
#2460 - Backport PR #2458 on branch 1.1.x (Update codecov and readthedocs yaml)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
Labels: on-merge: backport to 1.1.x
#2459 - Backport PR #2457 on branch 1.1.x (Remove unused files)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
Labels: on-merge: backport to 1.1.x
#2458 - Update codecov and readthedocs yaml
Pull Request -
State: closed - Opened by martinkim0 8 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2457 - Remove unused files
Pull Request -
State: closed - Opened by martinkim0 8 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2456 - Backport PR #2455 on branch 1.1.x (Add macos m1 test workflow)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2455 - Add macos m1 test workflow
Pull Request -
State: closed - Opened by martinkim0 8 months ago
Labels: on-merge: backport to 1.1.x
#2454 - Backport PR #2453 on branch 1.1.x (Update tutorials head)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2453 - Update tutorials head
Pull Request -
State: closed - Opened by martinkim0 8 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2452 - Index error when using totalVI
Issue -
State: closed - Opened by HafsaKM 8 months ago
- 4 comments
Labels: bug
#2451 - Backport PR #2450 on branch 1.1.x (Remove black and flake8 as deps)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2450 - Remove black and flake8 as deps
Pull Request -
State: closed - Opened by martinkim0 8 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2449 - UserWarning: The value argument must be within the support of the distribution reconst_loss = -px.log_prob(x).sum(-1)
Issue -
State: open - Opened by FZ-hajji 8 months ago
- 1 comment
Labels: bug
#2448 - Make `drop_last` configurable in data loaders
Issue -
State: closed - Opened by aksarkar 8 months ago
- 9 comments
Labels: enhancement
#2447 - Backport PR #2446 on branch 1.1.x (Fix reinitialization error in GIMVI)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
Labels: on-merge: backport to 1.1.x, cuda tests
#2446 - Fix reinitialization error in GIMVI
Pull Request -
State: closed - Opened by martinkim0 8 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x, cuda tests
#2445 - Backport PR #2444 on branch 1.1.x (Change workflow names)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
Labels: on-merge: backport to 1.1.x, all tests, prerelease tests
#2444 - Change workflow names
Pull Request -
State: closed - Opened by martinkim0 8 months ago
Labels: on-merge: backport to 1.1.x, all tests, prerelease tests
#2443 - Update workflow for pushes
Pull Request -
State: closed - Opened by martinkim0 8 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x, all tests
#2442 - Backport PR #2441 on branch 1.1.x (Update workflows)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x, all tests
#2441 - Update workflows
Pull Request -
State: closed - Opened by martinkim0 8 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x, all tests
#2440 - Backport PR #2438 on branch 1.1.x (Add label triage to cuda, private test workflows)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
Labels: all tests
#2439 - Backport PR #2437 on branch 1.1.x (Switch cuda docker image tag)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2438 - Add label triage to cuda, private test workflows
Pull Request -
State: closed - Opened by martinkim0 8 months ago
- 2 comments
Labels: all tests
#2437 - Switch cuda docker image tag
Pull Request -
State: closed - Opened by martinkim0 8 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2436 - Backport PR #2435 on branch 1.1.x (Upgrade actions to setup-python v5)
Pull Request -
State: closed - Opened by meeseeksmachine 8 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2435 - Upgrade actions to setup-python v5
Pull Request -
State: closed - Opened by martinkim0 8 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2434 - Add user API for using arbitrary dataloaders
Issue -
State: closed - Opened by martinkim0 8 months ago
Labels: enhancement
#2433 - AttributeError: module 'optax' has no attribute 'additive_weight_decay'
Issue -
State: closed - Opened by Zethson 8 months ago
- 1 comment
Labels: bug
#2432 - Update typing in all files to match new format
Issue -
State: closed - Opened by martinkim0 8 months ago
- 2 comments
Labels: enhancement, good first issue, backlog
#2431 - Switch to new typing
Pull Request -
State: closed - Opened by martinkim0 8 months ago
Labels: on-merge: backport to 1.1.x
#2430 - Replace `scvi.nn._utils.one_hot` in favor of the PyTorch version
Issue -
State: closed - Opened by martinkim0 9 months ago
- 6 comments
Labels: enhancement
#2429 - `SCANVI.loss` fails when `n_samples>1`
Issue -
State: closed - Opened by martinkim0 9 months ago
Labels: bug, P0
#2428 - Clean up tests and code
Pull Request -
State: closed - Opened by martinkim0 9 months ago
- 1 comment
#2427 - Tag commit for scvi-hub manuscript
Issue -
State: closed - Opened by martinkim0 9 months ago
Labels: enhancement
#2426 - Backport PR #2425 on branch 1.1.x (Fix hub model test names)
Pull Request -
State: closed - Opened by meeseeksmachine 9 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2425 - Fix hub model test names
Pull Request -
State: closed - Opened by martinkim0 9 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2424 - Error Importing - dadapt_adamw; 'type' object is not subscriptable
Issue -
State: closed - Opened by rigelsison 9 months ago
- 2 comments
Labels: bug
#2423 - Backport PR #2422 on branch 1.1.x (Add clearer error message to `poisson_gene_selection`)
Pull Request -
State: closed - Opened by meeseeksmachine 9 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2422 - Add clearer error message to `poisson_gene_selection`
Pull Request -
State: closed - Opened by martinkim0 9 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2421 - Adding model with cycle consistency and VampPrior
Pull Request -
State: open - Opened by Hrovatin 9 months ago
- 8 comments
Labels: cuda tests, P1
#2420 - `Trainer.fit` stopped: `max_epochs=1` reached.
Issue -
State: closed - Opened by yubin-ai 9 months ago
- 4 comments
Labels: bug
#2419 - Backport PR #2418 on branch 1.1.x (Check build on PR to backport branches)
Pull Request -
State: closed - Opened by meeseeksmachine 9 months ago
- 1 comment
#2418 - Check build on PR to backport branches
Pull Request -
State: closed - Opened by martinkim0 9 months ago
- 1 comment
#2417 - Backport PR #2416 on branch 1.1.x (Update workflows)
Pull Request -
State: closed - Opened by meeseeksmachine 9 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2416 - Update workflows
Pull Request -
State: closed - Opened by martinkim0 9 months ago
Labels: on-merge: backport to 1.1.x
#2415 - Backport PR #2378 on branch 1.1.x (Add support for S3 in `HubModel`)
Pull Request -
State: closed - Opened by meeseeksmachine 9 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2414 - Backport PR #2413 on branch 1.1.x (Add workflow for private tests)
Pull Request -
State: closed - Opened by meeseeksmachine 9 months ago
Labels: on-merge: backport to 1.1.x
#2413 - Add workflow for private tests
Pull Request -
State: closed - Opened by martinkim0 9 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2412 - Backport PR #2410 on branch 1.1.x (Change release checklist)
Pull Request -
State: closed - Opened by meeseeksmachine 9 months ago
#2411 - Release scvi-tools 1.1.0
Issue -
State: open - Opened by martinkim0 9 months ago
Labels: releases
#2410 - Change release checklist
Pull Request -
State: closed - Opened by martinkim0 9 months ago
- 1 comment
#2409 - Auto backport of pr 2408 on 1.1.x
Pull Request -
State: closed - Opened by martinkim0 9 months ago
#2408 - Copy cookiecutter release workflow
Pull Request -
State: closed - Opened by martinkim0 9 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2407 - Backport PR #2406 on branch 1.1.x (Add write permissions to release workflow)
Pull Request -
State: closed - Opened by meeseeksmachine 9 months ago
Labels: on-merge: backport to 1.1.x
#2406 - Add write permissions to release workflow
Pull Request -
State: closed - Opened by martinkim0 9 months ago
Labels: on-merge: backport to 1.1.x
#2405 - Backport PR #2404 on branch 1.1.x (Remove pypi token from workflow)
Pull Request -
State: closed - Opened by meeseeksmachine 9 months ago
Labels: on-merge: backport to 1.1.x
#2404 - Remove pypi token from workflow
Pull Request -
State: closed - Opened by martinkim0 9 months ago
Labels: on-merge: backport to 1.1.x
#2403 - Backport PR #2402 on branch 1.1.x (Update tutorials head)
Pull Request -
State: closed - Opened by meeseeksmachine 9 months ago
Labels: on-merge: backport to 1.1.x
#2402 - Update tutorials head
Pull Request -
State: closed - Opened by martinkim0 9 months ago
Labels: on-merge: backport to 1.1.x
#2401 - Backport PR #2400 on branch 1.1.x (Bump version to 1.1.0rc2)
Pull Request -
State: closed - Opened by meeseeksmachine 9 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2400 - Bump version to 1.1.0rc2
Pull Request -
State: closed - Opened by martinkim0 9 months ago
Labels: on-merge: backport to 1.1.x
#2399 - poisson_gene_selection
Issue -
State: closed - Opened by xianjieshen 9 months ago
- 6 comments
Labels: bug
#2398 - Backport PR #2395 on branch 1.1.x (Fix repr for custom distributions, add optional constraint)
Pull Request -
State: closed - Opened by meeseeksmachine 9 months ago
Labels: on-merge: backport to 1.1.x
#2397 - Backport PR #2396 on branch 1.1.x (Switch from `optax.additive_weight_decay` to `optax.add_decayed_weights`)
Pull Request -
State: closed - Opened by meeseeksmachine 9 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2396 - Switch from `optax.additive_weight_decay` to `optax.add_decayed_weights`
Pull Request -
State: closed - Opened by martinkim0 9 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2395 - Fix repr for custom distributions, add optional constraint
Pull Request -
State: closed - Opened by martinkim0 9 months ago
- 1 comment
Labels: on-merge: backport to 1.1.x
#2394 - Support Optax 0.1.8
Issue -
State: closed - Opened by martinkim0 9 months ago
Labels: enhancement, dependencies
#2393 - Multimodal reference mapping with MuData objects
Issue -
State: closed - Opened by ethanweinberger 9 months ago
- 6 comments
Labels: enhancement
#2392 - PyTorch distribution `__repr__` error with custom distributions
Issue -
State: closed - Opened by martinkim0 9 months ago
Labels: bug
#2391 - AttributeError occurred when I use scVI method in R
Issue -
State: closed - Opened by redtorrentCN 9 months ago
- 2 comments
Labels: bug
#2390 - Add support for NumPy 2
Issue -
State: open - Opened by martinkim0 9 months ago
Labels: enhancement, dependencies, P0