1.3.3

What's Changed

• fix bad tutorials file names by @ori-kron-wis in #456
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #457
• docs: New AnnCollection Tutorial by @ori-kron-wis in #450
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #458
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #459
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #461

Full Changelog: 1.3.2...1.3.3

1.3.2

What's Changed

• Tutorials New Location Because of New RTD tutorials Filtering Scheme by @ori-kron-wis in #436
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #437
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #438
• updates by @ori-kron-wis in #439
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #452
• NicheVI tuto by @LevyNat in #423
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #454
• automated update for atac/PeakVI.ipynb by @github-actions in #447
• automated update for multimodal/totalVI.ipynb by @github-actions in #448
• Taho100M cells Hub tutorial by @ori-kron-wis in #453
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #455
• automated update for scrna/harmonization.ipynb by @github-actions in #449
• automated update for spatial/DestVI_tutorial.ipynb by @github-actions in #451
• automated update for multimodal/MultiVI_tutorial.ipynb by @github-actions in #441
• add preprocessing tutorial with multiple examples by @lordy5 in #398

New Contributors

• @LevyNat made their first contribution in #423
• @lordy5 made their first contribution in #398

Full Changelog: 1.3.1...1.3.2

1.3.1.post1

Merge pull request #454 from scverse/pre-commit-ci-update-config

[pre-commit.ci] pre-commit autoupdate

1.3.1

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #426
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #427
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #428
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #429
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #430
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #431
• added custom dataloaders initial tutos by @ori-kron-wis in #425

Full Changelog: 1.3.0...1.3.1

1.3.0

What's Changed

• docs: Fix DE broken link by @ori-kron-wis in #387
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #388
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #389
• totalvi update with explenations about pre filtering procedures by @ori-kron-wis in #390
• ResolVI tutorial. by @canergen in #392
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #393
• api_overview: latent_subset fix by @ryan-williams in #391
• updated with ext tutorial by @ori-kron-wis in #394
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #395
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #396
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #397
• Basic Decipher Tutorial by @justjhong in #373
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #403
• SysVI tutorial by @Hrovatin in #212
• update tutorials by @ori-kron-wis in #404
• update tutorials by @ori-kron-wis in #407
• update tutorials by @ori-kron-wis in #409
• docs: change structure of tutorials by @ori-kron-wis in #413
• docs: scib-autotune addition to tune tutorial by @ori-kron-wis in #412
• add tutorial for interpretability by @ori-kron-wis in #414
• added scverse symbol by @ori-kron-wis in #416
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #417
• Update interpretability.ipynb by @ori-kron-wis in #418
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #419
• updated tuto with fast shap by @ori-kron-wis in #420
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #421
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #424

New Contributors

• @ryan-williams made their first contribution in #391
• @Hrovatin made their first contribution in #212

Full Changelog: 1.2.2...1.3.0

1.2.2

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #377
• docs: updated tutorials without pymde + HF bug by @ori-kron-wis in #378
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #379
• test: Added localy manual macos tests for mps by @ori-kron-wis in #380
• Update run_notebook_macos.yaml by @ori-kron-wis in #381
• Update run_notebook_macos.yaml by @ori-kron-wis in #382
• Update run_notebook_macos.yaml by @ori-kron-wis in #384
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #386

Full Changelog: 1.2.1...1.2.2

1.2.1

What's Changed

• automated update for scrna/cellassign_tutorial.ipynb by @github-actions in #360
• fix in tangram - anndata uniq vars by @ori-kron-wis in #361
• automated update for multimodal/totalVI.ipynb by @github-actions in #333
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #362
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #364
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #365
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #366
• docs: bad link in minification.ipynb by @ori-kron-wis in #369
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #368
• docs: Remove autotune hyperparameters info from tutorial by @ori-kron-wis in #371
• MethylVI batch effect tutorial by @ethanweinberger in #363
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #372
• ci: Added run links for Methylvi by @ori-kron-wis in #374
• automated update for scbs/MethylVI_batch.ipynb by @github-actions in #376
• automated update for scrna/MrVI_tutorial.ipynb by @github-actions in #375

Full Changelog: 1.2.0...1.2.1

1.2.0

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #301
• Update cellassign_tutorial.ipynb with numpy dummy by @ori-kron-wis in #310
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #308
• automated update for scrna/scVI_DE_worm.ipynb by @github-actions in #309
• automated update for atac/PeakVI.ipynb by @github-actions in #304
• automated update for tuning/autotune_scvi.ipynb by @github-actions in #307
• automated update for tuning/autotune_new_model.ipynb by @github-actions in #306
• automated update for atac/PoissonVI.ipynb by @github-actions in #305
• automated update for scrna/cellassign_tutorial.ipynb by @github-actions in #312
• automated update for quick_start/api_overview.ipynb by @github-actions in #311
• Changes scarches tutorial by @ori-kron-wis in #314
• Drop Python 3.9 by @ori-kron-wis in #317
• Update run_notebook.yaml by @ori-kron-wis in #318
• automated update for quick_start/api_overview.ipynb by @github-actions in #316
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #315
• automated update for quick_start/api_overview.ipynb by @github-actions in #319
• Update pyproject.toml by @ori-kron-wis in #322
• docs: updated several tutorials by @ori-kron-wis in #346
• Update several tutorials so they will work in scvi-tools 1.2.0, py312… by @ori-kron-wis in #351
• Update several tutorials so they will work in scvi-tools 1.2.0, py312… by @ori-kron-wis in #353
• automated update for atac/PeakVI.ipynb by @github-actions in #321
• automated update for atac/PoissonVI.ipynb by @github-actions in #320
• automated update for dev/data_tutorial.ipynb by @github-actions in #323
• automated update for dev/model_user_guide.ipynb by @github-actions in #324
• automated update for dev/module_user_guide.ipynb by @github-actions in #325
• automated update for hub/cellxgene_census_model.ipynb by @github-actions in #326
• automated update for hub/minification.ipynb by @github-actions in #327
• automated update for hub/scvi_hub_intro_and_download.ipynb by @github-actions in #328
• automated update for hub/scvi_hub_upload_and_large_files.ipynb by @github-actions in #329
• automated update for multimodal/cite_scrna_integration_w_totalVI.ipynb by @github-actions in #330
• automated update for multimodal/MultiVI_tutorial.ipynb by @github-actions in #331
• automated update for quick_start/api_overview.ipynb by @github-actions in #334
• automated update for scrna/amortized_lda.ipynb by @github-actions in #335
• automated update for scrna/AutoZI_tutorial.ipynb by @github-actions in #336
• automated update for scrna/contrastiveVI_tutorial.ipynb by @github-actions in #337
• automated update for scrna/query_hlca_knn.ipynb by @github-actions in #338
• automated update for scrna/scVI_DE_worm.ipynb by @github-actions in #340
• automated update for scrna/seed_labeling.ipynb by @github-actions in #341
• automated update for scrna/tabula_muris.ipynb by @github-actions in #342
• automated update for spatial/gimvi_tutorial.ipynb by @github-actions in #344
• automated update for spatial/stereoscope_heart_LV_tutorial.ipynb by @github-actions in #345
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #347
• automated update for scrna/scanvi_fix.ipynb by @github-actions in #348
• automated update for scrna/MrVI_tutorial.ipynb by @github-actions in #343
• automated update for scrna/linear_decoder.ipynb by @github-actions in #349
• automated update for tuning/autotune_scvi.ipynb by @github-actions in #354
• automated update for scrna/harmonization.ipynb by @github-actions in #352
• automated update for quick_start/data_loading.ipynb by @github-actions in #350

Full Changelog: 1.1.6...1.2.0

1.1.6

What's Changed

• ci: refactor run notebook workflows by @martinkim0 in #295
• ci: add notebooks yaml by @martinkim0 in #298
• revert previous commit by @martinkim0 in #299
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #300
• added numpy to cellassign tutorial by @ori-kron-wis in #302

New Contributors

• @ori-kron-wis made their first contribution in #302

Full Changelog: 1.1.5...1.1.6

1.1.5

What's Changed

• misc: update license by @martinkim0 in #287
• feat: update dev module tutorial for lossoutput by @martinkim0 in #288
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #289
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #290
• ci: add release workflow by @martinkim0 in #291
• ci: fix release workflow by @martinkim0 in #292

Full Changelog: 1.1.3...1.1.5