Support Python 3.13 (#720)

* Support Python 3.13

* Remove scikit-misc

* Add  scikit-misc

* docs

Author: Zethson

.github/workflows/build.yml

@@ -19,7 +19,7 @@ jobs:
             - name: Set up Python
               uses: actions/setup-python@v5
               with:
-                  python-version: "3.12"
+                  python-version: "3.13"
                   cache: "pip"
                   cache-dependency-path: "**/pyproject.toml"
 

.github/workflows/release.yml

@@ -13,10 +13,10 @@ jobs:
             - name: Checkout code
               uses: actions/checkout@v4
 
-            - name: Set up Python 3.12
+            - name: Set up Python
               uses: actions/setup-python@v5
               with:
-                  python-version: "3.12"
+                  python-version: "3.x"
 
             - name: Install hatch
               run: pip install hatch

.github/workflows/test.yml

@@ -22,13 +22,13 @@ jobs:
             matrix:
                 include:
                     - os: ubuntu-22.04 # ubuntu-latest is currently broken for joblib
-                      python: "3.12"
+                      python: "3.13"
                       run_mode: "slow"
                     - os: ubuntu-22.04
-                      python: "3.12"
+                      python: "3.13"
                       run_mode: "fast"
                     # - os: ubuntu-latest
-                    #   python: "3.12"
+                    #   python: "3.13"
                     #   run_mode: slow
                     #   pip-flags: "--pre"
 

.readthedocs.yml

@@ -2,7 +2,7 @@ version: 2
 build:
     os: ubuntu-24.04
     tools:
-        python: "3.12"
+        python: "3.12" # 3.13 breaks because scikit-misc cannot be installed
     commands:
         - asdf plugin add uv
         - asdf install uv latest

pyproject.toml

@@ -7,7 +7,7 @@ name = "pertpy"
 version = "0.10.0"
 description = "Perturbation Analysis in the scverse ecosystem."
 readme = "README.md"
-requires-python = ">=3.10,<3.13"
+requires-python = ">=3.10,<3.14"
 license = {file = "LICENSE"}
 authors = [
     {name = "Lukas Heumos"},
@@ -44,6 +44,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Topic :: Scientific/Engineering :: Visualization",
 ]