diff --git a/.github/workflows/register-template-repos.yml b/.github/workflows/register-template-repos.yml
index 40cf2f8..8e1239b 100644
--- a/.github/workflows/register-template-repos.yml
+++ b/.github/workflows/register-template-repos.yml
@@ -13,10 +13,10 @@ jobs:
       - uses: actions/checkout@v4
         with:
           token: ${{ secrets.BOT_GH_TOKEN }}
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+      - name: Set up Python 3.13
+        uses: actions/setup-python@6
         with:
-          python-version: "3.11"
+          python-version: "3.13"
           cache: "pip"
           cache-dependency-path: "**/pyproject.toml"
       - name: Install build dependencies
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index aa9eff3..f631a49 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -17,8 +17,8 @@ repos:
         args: [--fix=lf]
       - id: trailing-whitespace
       - id: check-case-conflict
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v4.0.0-alpha.8
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: v3.6.2
     hooks:
       - id: prettier
   # package metadata
@@ -47,6 +47,6 @@ repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.13.3
     hooks:
-      - id: ruff
+      - id: ruff-check
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
diff --git a/scripts/pyproject.toml b/scripts/pyproject.toml
index abcb537..603b1e7 100644
--- a/scripts/pyproject.toml
+++ b/scripts/pyproject.toml
@@ -29,7 +29,7 @@ source = "vcs"
 fallback-version = "0.0"
 
 [tool.hatch.envs.default]
-python = "3.11"
+python = "3.13"
 
 [tool.ruff]
 line-length = 120
diff --git a/template-repos.yml b/template-repos.yml
index 9e0a0f4..bf19c5b 100644
--- a/template-repos.yml
+++ b/template-repos.yml
@@ -118,6 +118,7 @@
 - url: https://github.com/scverse/spatial-sample-aggregation
 - url: https://github.com/scverse/spatialdata-plot
 - url: https://github.com/scverse/squidpy
+- url: https://github.com/scverse/pertpy
 - url: https://github.com/smgoggin10/ESCHR
 - url: https://github.com/srivarra/anatomize
 - url: https://github.com/srivarra/annsel
@@ -132,6 +133,7 @@
 - url: https://github.com/theislab/cellflow_reproducibility
 - url: https://github.com/theislab/devVI
 - url: https://github.com/theislab/ehrdata
+- url: https://github.com/theislab/ehrapy
 - url: https://github.com/theislab/geome
 - url: https://github.com/theislab/mapqc
 - url: https://github.com/theislab/multigrate