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

1.1.4

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...1.1.4

1.1.3

What's Changed

• Updated census tutorial by @canergen in #269
• Changes to not use secret keys by @canergen in #271
• style: update pre-commit and run auto-fixes by @martinkim0 in #274
• misc: manually update pre-commit versions by @martinkim0 in #275
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #276
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #277
• MrVI Quick Start Tutorial by @justjhong in #278
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #279
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #280
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #282
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #283
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #284
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #285
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #286

Full Changelog: 1.1.2...1.1.3

1.1.2

Full Changelog: 1.1.1...1.1.2

1.1.1

Full Changelog: 1.1.0.post2...1.1.1

1.1.0-post.2

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #211
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #214
• Update run workflows by @martinkim0 in #215
• Update pre-commit config by @martinkim0 in #216
• Fix formatting of scanvi tutorial by @martinkim0 in #218
• Update README by @martinkim0 in #219
• Add benchmark tutorial for scANVI logits fix by @martinkim0 in #217
• Update scanvi fix tutorial by @martinkim0 in #220
• Correct and rerun hub intro tutorial by @martinkim0 in #221
• Automated update for atac/PeakVI.ipynb by @github-actions in #223
• Add common notes to tutorials by @martinkim0 in #234
• Automated update for atac/PoissonVI.ipynb by @github-actions in #235
• Automated update for atac/PeakVI.ipynb by @github-actions in #236
• Automated update for dev/data_tutorial.ipynb by @github-actions in #237
• Automated update for dev/model_user_guide.ipynb by @github-actions in #238
• Automated update for dev/module_user_guide.ipynb by @github-actions in #239
• Automated update for hub/scvi_hub_intro_and_download.ipynb by @github-actions in #240
• Automated update for hub/scvi_hub_upload_and_large_files.ipynb by @github-actions in #241
• Automated update for hub/minification.ipynb by @github-actions in #242
• Automated update for multimodal/cite_scrna_integration_w_totalVI.ipynb by @github-actions in #243
• Automated update for multimodal/MultiVI_tutorial.ipynb by @github-actions in #244
• Automated update for multimodal/totalVI.ipynb by @github-actions in #245
• Automated update for quick_start/api_overview.ipynb by @github-actions in #246
• Automated update for quick_start/data_loading.ipynb by @github-actions in #247
• Automated update for multimodal/totalVI_reference_mapping.ipynb by @github-actions in #248
• Automated update for scrna/AutoZI_tutorial.ipynb by @github-actions in #249
• Automated update for scrna/cellassign_tutorial.ipynb by @github-actions in #250
• Automated update for scrna/amortized_lda.ipynb by @github-actions in #251
• Automated update for scrna/harmonization.ipynb by @github-actions in #252
• Automated update for scrna/linear_decoder.ipynb by @github-actions in #253
• Automated update for scrna/query_hlca_knn.ipynb by @github-actions in #254
• Automated update for scrna/contrastiveVI_tutorial.ipynb by @github-actions in #255
• Automated update for scrna/scanvi_fix.ipynb by @github-actions in #256
• Automated update for scrna/seed_labeling.ipynb by @github-actions in #257
• Automated update for scrna/scVI_DE_worm.ipynb by @github-actions in #258
• Automated update for spatial/gimvi_tutorial.ipynb by @github-actions in #259
• Automated update for scrna/tabula_muris.ipynb by @github-actions in #260
• Automated update for spatial/stereoscope_heart_LV_tutorial.ipynb by @github-actions in #261
• Automated update for tuning/autotune_new_model.ipynb by @github-actions in #262
• Use logging_dir for autotune by @martinkim0 in #264
• Automated update for tuning/autotune_scvi.ipynb by @github-actions in #265

Full Changelog: 1.1.0rc2...1.1.0.post2

1.1.0

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #156
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #158
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #159
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #161
• PoissonVI tutorial by @lauradmartens in #160
• contrastiveVI tutorial by @ethanweinberger in #162
• Update workflow by @martinkim0 in #164
• Automated update for atac/PeakVI.ipynb by @github-actions in #165
• Automated update for atac/scbasset_batch.ipynb by @github-actions in #166
• Automated update for dev/model_user_guide.ipynb by @github-actions in #167
• Automated update for dev/module_user_guide.ipynb by @github-actions in #168
• Automated update for hub/minification.ipynb by @github-actions in #169
• Automated update for hub/scvi_hub_upload_and_large_files.ipynb by @github-actions in #170
• Automated update for multimodal/cite_scrna_integration_w_totalVI.ipynb by @github-actions in #171
• Automated update for multimodal/MultiVI_tutorial.ipynb by @github-actions in #172
• Fix tutorials by @martinkim0 in #173
• Automated update for multimodal/totalVI_reference_mapping.ipynb by @github-actions in #175
• Automated update for multimodal/totalVI.ipynb by @github-actions in #176
• Automated update for quick_start/api_overview.ipynb by @github-actions in #177
• Automated update for quick_start/data_loading.ipynb by @github-actions in #178
• Automated update for atac/PoissonVI.ipynb by @github-actions in #179
• Automated update for dev/data_tutorial.ipynb by @github-actions in #180
• Automated update for scrna/amortized_lda.ipynb by @github-actions in #181
• Automated update for scrna/AutoZI_tutorial.ipynb by @github-actions in #182
• Automated update for scrna/linear_decoder.ipynb by @github-actions in #183
• Automated update for scrna/query_hlca_knn.ipynb by @github-actions in #184
• Automated update for scrna/scVI_DE_worm.ipynb by @github-actions in #185
• Automated update for scrna/harmonization.ipynb by @github-actions in #186
• Automated update for scrna/seed_labeling.ipynb by @github-actions in #187
• Automated update for scrna/tabula_muris.ipynb by @github-actions in #189
• Automated update for scrna/cellassign_tutorial.ipynb by @github-actions in #190
• Fix contrastivevi tutorial by @martinkim0 in #191
• Fix stereoscope tutorial by @martinkim0 in #192
• Fix autotune tutorial by @martinkim0 in #193
• Automated update for tuning/autotune_new_model.ipynb by @github-actions in #194
• Fix stereoscope tutorial by @martinkim0 in #196
• Fix gimvi tutorial by @martinkim0 in #198
• Automated update for spatial/stereoscope_heart_LV_tutorial.ipynb by @github-actions in #197
• Automated update for spatial/gimvi_tutorial.ipynb by @github-actions in #199
• Fix autotune tutorial by @martinkim0 in #200
• Automated update for tuning/autotune_scvi.ipynb by @github-actions in #201
• Fix contrastivevi tutorial by @martinkim0 in #202
• Remove use_gpu from model user guide by @martinkim0 in #203
• Automated update for scrna/contrastiveVI_tutorial.ipynb by @github-actions in #204
• Increase timeout minutes for workflows by @martinkim0 in #207
• Add rerun release checklist by @martinkim0 in #208
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #163
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #211
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #214
• Update run workflows by @martinkim0 in #215
• Update pre-commit config by @martinkim0 in #216
• Fix formatting of scanvi tutorial by @martinkim0 in #218
• Update README by @martinkim0 in #219
• Add benchmark tutorial for scANVI logits fix by @martinkim0 in #217
• Update scanvi fix tutorial by @martinkim0 in #220
• Correct and rerun hub intro tutorial by @martinkim0 in #221
• Automated update for atac/PeakVI.ipynb by @github-actions in #223
• Add common notes to tutorials by @martinkim0 in #234
• Automated update for atac/PoissonVI.ipynb by @github-actions in #235
• Automated update for atac/PeakVI.ipynb by @github-actions in #236
• Automated update for dev/data_tutorial.ipynb by @github-actions in #237
• Automated update for dev/model_user_guide.ipynb by @github-actions in #238
• Automated update for dev/module_user_guide.ipynb by @github-actions in #239
• Automated update for hub/scvi_hub_intro_and_download.ipynb by @github-actions in #240
• Automated update for hub/scvi_hub_upload_and_large_files.ipynb by @github-actions in #241
• Automated update for hub/minification.ipynb by @github-actions in #242
• Automated update for multimodal/cite_scrna_integration_w_totalVI.ipynb by @github-actions in #243
• Automated update for multimodal/MultiVI_tutorial.ipynb by @github-actions in #244
• Automated update for multimodal/totalVI.ipynb by @github-actions in #245
• Automated update for quick_start/api_overview.ipynb by @github-actions in #246
• Automated update for quick_start/data_loading.ipynb by @github-actions in #247
• Automated update for multimodal/totalVI_reference_mapping.ipynb by @github-actions in #248
• Automated update for scrna/AutoZI_tutorial.ipynb by @github-actions in #249
• Automated update for scrna/cellassign_tutorial.ipynb by @github-actions in #250
• Automated update for scrna/amortized_lda.ipynb by @github-actions in #251
• Automated update for scrna/harmonization.ipynb by @github-actions in #252
• Automated update for scrna/linear_decoder.ipynb by @github-actions in #253
• Automated update for scrna/query_hlca_knn.ipynb by @github-actions in #254
• Automated update for scrna/contrastiveVI_tutorial.ipynb by @github-actions in #255
• Automated update for scrna/scanvi_fix.ipynb by @github-actions in #256
• Automated update for scrna/seed_labeling.ipynb by @github-actions in #257
• Automated update for scrna/scVI_DE_worm.ipynb by @github-actions in #258
• Automated update for spatial/gimvi_tutorial.ipynb by @github-actions in #259
• Automated update for scrna/tabula_muris.ipynb by @github-actions in #260
• Automated update for spatial/stereoscope_heart_LV_tutorial.ipynb by ...

1.1.0-rc.2

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #163

Full Changelog: 1.1.0rc1...1.1.0rc2