Merge branch 'main' into main

Author: jsnagai

.pre-commit-config.yaml

@@ -23,13 +23,13 @@ repos:
       - id: prettier
   # package metadata
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.36.2
+    rev: 0.37.0
     hooks:
       - id: check-jsonschema
         files: "scripts/src/ecosystem_scripts/schema.json"
         args: ["--check-metaschema"]
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.36.2
+    rev: 0.37.0
     hooks:
       - id: check-jsonschema
         files: "packages/.*/meta.yaml"
@@ -45,7 +45,7 @@ repos:
         exclude: "^packages/.*/(meta.yaml|logo\\..*)$"
   # scripts
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.2
+    rev: v0.15.5
     hooks:
       - id: ruff-check
         args: [--fix, --exit-non-zero-on-fix]

template-repos.yml

@@ -46,6 +46,7 @@
 - url: https://github.com/bunina-lab/scDoRI_tools
 - url: https://github.com/cameronraysmith/perturbvelo
 - url: https://github.com/carmonalab/pyucell
+- url: https://github.com/cellannotation/pairOT
 - url: https://github.com/clinicalomx/napari-prism
 - url: https://github.com/cobioda/scispy
 - url: https://github.com/const-ae/pyLemur
@@ -142,6 +143,7 @@
 - url: https://github.com/theislab/troutpy
 - url: https://github.com/timtreis/gefslim
 - url: https://github.com/vitkl/cell2module
+- url: https://github.com/vitkl/regularizedvi
 - url: https://github.com/wangd12rpi/hescape_changed
 - url: https://github.com/yizhak-lab-ccg/scXpand
 - url: https://github.com/zunderlab/eschr