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

#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

#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

#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

#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