Merge branch 'main' into feature/predict_batch

Author: LeonStadelmann

.github/workflows/build.yaml

@@ -15,10 +15,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python 3.10
+      - name: Set up Python 3.11
         uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: "3.11"
           cache: "pip"
           cache-dependency-path: "**/pyproject.toml"
       - name: Install build dependencies

.github/workflows/lint.yml

@@ -25,10 +25,10 @@ jobs:
       - uses: actions/checkout@v3
         with:
           submodules: true
-      - name: Set up Python 3.10
+      - name: Set up Python 3.11
         uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Cache pre-commit
         uses: actions/cache@v3

.github/workflows/test.yaml

@@ -23,12 +23,12 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - os: ubuntu-latest
-            python: "3.10"
           - os: ubuntu-latest
             python: "3.11"
           - os: ubuntu-latest
             python: "3.12"
+          - os: ubuntu-latest
+            python: "3.13"
           - os: macos-latest
             python: "3.12"
 

.pre-commit-config.yaml

@@ -1,16 +1,16 @@
 repos:
   # Hooks that are run everywhere
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.0.0-beta.3
+    rev: v2.0.0-beta.5
     hooks:
       - id: biome-format
   # Hooks that are run for scripts
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.5.1
+    rev: v2.6.0
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.9
+    rev: v0.11.11
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

.readthedocs.yaml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.11"
 sphinx:
   configuration: docs/conf.py
   # disable this for more lenient docs builds

docs/installation.rst

@@ -1,6 +1,6 @@
 Installation
 ============
-:mod:`cellflow` requires Python version >= 3.10 to run.
+:mod:`cellflow` requires Python version >= 3.11 to run.
 
 PyPI
 ----