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

1.1.0-rc.1

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

New Contributors

• @lauradmartens made their first contribution in #160
• @ethanweinberger made their first contribution in #162
• @github-actions made their first contribution in #165

Full Changelog: 1.0.3...1.1.0rc1

1.0.4

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #131
• Restructure tutorials by @martinkim0 in #133
• Add run notebook workflow by @martinkim0 in #134
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #136
• Install kernel in workflow by @martinkim0 in #135
• Update automated update PR by @martinkim0 in #138
• Add same seed and scvi version to tutorials by @martinkim0 in #140
• Explicitly add notebook paths to workflow by @martinkim0 in #141
• Add workflow to run from branch by @martinkim0 in #143
• Change workflow name by @martinkim0 in #144
• Rerun and refresh peakvi by @martinkim0 in #145
• Update data tutorial by @martinkim0 in #146
• Update and rerun model guides by @martinkim0 in #147
• Update and rerun quick start tutorials by @martinkim0 in #149
• Update and rerun totalvi tutorials by @martinkim0 in #150
• Update and rerun multivi by @martinkim0 in #151
• Update and rerun scrna tutorials by @martinkim0 in #152
• Update and rerun autotune by @martinkim0 in #153
• Update and rerun hub tutorials by @martinkim0 in #154
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #155

Full Changelog: 1.0.2...1.0.4

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #131
• Restructure tutorials by @martinkim0 in #133
• Add run notebook workflow by @martinkim0 in #134
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #136
• Install kernel in workflow by @martinkim0 in #135
• Update automated update PR by @martinkim0 in #138
• Add same seed and scvi version to tutorials by @martinkim0 in #140
• Explicitly add notebook paths to workflow by @martinkim0 in #141
• Add workflow to run from branch by @martinkim0 in #143
• Change workflow name by @martinkim0 in #144
• Rerun and refresh peakvi by @martinkim0 in #145
• Update data tutorial by @martinkim0 in #146
• Update and rerun model guides by @martinkim0 in #147
• Update and rerun quick start tutorials by @martinkim0 in #149
• Update and rerun totalvi tutorials by @martinkim0 in #150
• Update and rerun multivi by @martinkim0 in #151
• Update and rerun scrna tutorials by @martinkim0 in #152
• Update and rerun autotune by @martinkim0 in #153
• Update and rerun hub tutorials by @martinkim0 in #154
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #155

Full Changelog: 1.0.2...1.0.4

1.0.3

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #131
• Restructure tutorials by @martinkim0 in #133
• Add run notebook workflow by @martinkim0 in #134
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #136
• Install kernel in workflow by @martinkim0 in #135
• Update automated update PR by @martinkim0 in #138
• Add same seed and scvi version to tutorials by @martinkim0 in #140
• Explicitly add notebook paths to workflow by @martinkim0 in #141
• Add workflow to run from branch by @martinkim0 in #143
• Change workflow name by @martinkim0 in #144
• Rerun and refresh peakvi by @martinkim0 in #145
• Update data tutorial by @martinkim0 in #146
• Update and rerun model guides by @martinkim0 in #147
• Update and rerun quick start tutorials by @martinkim0 in #149
• Update and rerun totalvi tutorials by @martinkim0 in #150
• Update and rerun multivi by @martinkim0 in #151
• Update and rerun scrna tutorials by @martinkim0 in #152
• Update and rerun autotune by @martinkim0 in #153
• Update and rerun hub tutorials by @martinkim0 in #154
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #155

Full Changelog: 1.0.2...1.0.3

1.0.2

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #127
• Fix scanpy link in api tutorial by @martinkim0 in #128
• Fix link to Ray in autotune tutorial by @martinkim0 in #130

Full Changelog: 1.0.0...1.0.2

1.0.0

What's Changed

• Switch to myst admonitions by @adamgayoso in #109
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #110
• Fix data handling tutorial and rerun by @martinkim0 in #111
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #112
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #113
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #115
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #117
• Copy over issue and pr templates by @martinkim0 in #120
• DE tutorial update by @PierreBoyeau in #118
• Add motif scoring to main scbasset tutorial by @martinkim0 in #125

New Contributors

• @PierreBoyeau made their first contribution in #118

Full Changelog: 0.20.3...1.0.0

0.20.3

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #107
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #108

Full Changelog: 0.20.2...0.20.3

0.20.2

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #105

Full Changelog: 0.20.1...0.20.2

0.20.1

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #101
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #102

Full Changelog: 0.20.0...0.20.1