Add python3.13 support to wk-libs (#1240)

* Update dependencies.

* Update pylibczirw.

* Update scipy.

* Update uv version in CI.

* Updated changelog.

Author: markbader

.github/workflows/ci.yml

@@ -38,7 +38,7 @@ jobs:
       max-parallel: 4
       matrix:
         executors: [multiprocessing, slurm, kubernetes, dask]
-        python-version: ["3.12", "3.11", "3.10", "3.9"]
+        python-version: ["3.13", "3.12", "3.11", "3.10", "3.9"]
     defaults:
       run:
         working-directory: cluster_tools
@@ -151,7 +151,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.12", "3.11", "3.10", "3.9"]
+        python-version: ["3.13", "3.12", "3.11", "3.10", "3.9"]
         group: [1, 2, 3]
       fail-fast: false
     defaults:
@@ -165,7 +165,7 @@ jobs:
         uses: astral-sh/setup-uv@v3
         with:
           # Install a specific version of uv.
-          version: "0.4.22"
+          version: "0.5.22"
 
       - name: Install proxay
         run: npm install -g proxay

.github/workflows/nightly.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
         group: [1, 2, 3]
       fail-fast: false
     defaults:
@@ -24,7 +24,7 @@ jobs:
     - name: Install uv
       uses: astral-sh/setup-uv@v3
       with:
-        version: "0.4.19"
+        version: "0.5.22"
 
     - name: Install proxay
       run: npm install -g proxay

.github/workflows/verify_published.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.12", "3.11", "3.10", "3.9"]
+        python-version: ["3.13", "3.12", "3.11", "3.10", "3.9"]
         extras: ["", "[all]"]
     steps:
       - name: Set up Python ${{ matrix.python-version }}

webknossos/Changelog.md

@@ -15,6 +15,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 ### Breaking Changes
 
 ### Added
+- Added support for python 3.13. [#1240](https://github.com/scalableminds/webknossos-libs/pull/1240)
 
 ### Changed
 

webknossos/pyproject.toml

@@ -29,7 +29,7 @@ classifiers = [
     "Programming Language :: Python :: 3.12", 
 ]
 
-requires-python = ">=3.9,<3.13"
+requires-python = ">=3.9,<=3.13"
 
 dependencies = [
     "aiohttp ~=3.10.5",
@@ -48,7 +48,7 @@ dependencies = [
     "python-dateutil ~=2.8.0",
     "python-dotenv ~=1.0.1",
     "rich ~=13.8.0",
-    "scipy ~=1.13",
+    "scipy >=1.13",
     "tensorstore~=0.1.69",
     "typer ~=0.12.5",
     "typing-extensions ~=4.0",
@@ -68,7 +68,7 @@ Changelog = "https://github.com/scalableminds/webknossos-libs/blob/master/webkno
 tifffile = ["tifffile >=2024.8.24"]
 imagecodecs = ["imagecodecs >=2021.11.20"]
 bioformats = ["JPype1 ~=1.5.0"]
-czi = ["pylibCZIrw ==4.1.1"]
+czi = ["pylibCZIrw ==4.1.3"]
 examples = [
     "fastremap ~=1.15.0",
     "pandas ~=2.2.0",