Merge branch 'main' into preprocess-tutorial

Author: lordy5

.github/workflows/run_linux_cuda.yml

@@ -47,7 +47,7 @@ on:
           - spatial/stereoscope_heart_LV_tutorial.ipynb
           - spatial/tangram_scvi_tools.ipynb
           - spatial/resolVI_tutorial.ipynb
-          - spatial/NicheVI_tutorial.ipynb
+          - spatial/scVIVA_tutorial.ipynb
           - use_cases/autotune_scvi.ipynb
           - use_cases/interpretability.ipynb
           - use_cases/minification.ipynb

.github/workflows/run_notebook_all.yaml

@@ -52,7 +52,7 @@ jobs:
           - spatial/stereoscope_heart_LV_tutorial.ipynb
           - spatial/tangram_scvi_tools.ipynb
           - spatial/resolVI_tutorial.ipynb
-          - spatial/NicheVI_tutorial.ipynb
+          - spatial/scVIVA_tutorial.ipynb
           - use_cases/autotune_scvi.ipynb
           - use_cases/interpretability.ipynb
           - use_cases/minification.ipynb

.github/workflows/run_notebook_individual.yaml

@@ -47,7 +47,7 @@ on:
           - spatial/stereoscope_heart_LV_tutorial.ipynb
           - spatial/tangram_scvi_tools.ipynb
           - spatial/resolVI_tutorial.ipynb
-          - spatial/NicheVI_tutorial.ipynb
+          - spatial/scVIVA_tutorial.ipynb
           - use_cases/autotune_scvi.ipynb
           - use_cases/interpretability.ipynb
           - use_cases/minification.ipynb

.github/workflows/run_notebook_individual_macos.yaml

@@ -47,7 +47,7 @@ on:
           - spatial/stereoscope_heart_LV_tutorial.ipynb
           - spatial/tangram_scvi_tools.ipynb
           - spatial/resolVI_tutorial.ipynb
-          - spatial/NicheVI_tutorial.ipynb
+          - spatial/scVIVA_tutorial.ipynb
           - use_cases/autotune_scvi.ipynb
           - use_cases/interpretability.ipynb
           - use_cases/minification.ipynb

.pre-commit-config.yaml

@@ -34,7 +34,7 @@ repos:
           )$
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.11
+    rev: v0.11.13
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2025, The scvi-tools development team
+Copyright (c) 2025, Yosef Lab, Weizmann Institute of Science
 
 All rights reserved.
 

README.md

@@ -44,3 +44,5 @@ Copyright (c) 2025, Yosef Lab, Weizmann Institute of Science
 [pytorch]: https://pytorch.org
 [scvi-tools]: https://scvi-tools.org/
 [tutorials]: https://docs.scvi-tools.org/en/stable/tutorials/index.html
+
+Copyright (c) 2025, Yosef Lab, Weizmann Institute of Science