build!: drop Python 3.11 and upgrade the spatialdata cluster

.github/workflows/complexity-monitoring.yml

@@ -25,7 +25,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.12'
 
     - name: Install Poetry
       uses: snok/install-poetry@v1

.github/workflows/release.yml

@@ -39,7 +39,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: '3.12'
 
       - name: Install dependencies
         run: |
@@ -108,7 +108,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: '3.12'
 
       - name: Install build tools
         run: |

.github/workflows/tests.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest]
-        python-version: ['3.11', '3.12', '3.13']
+        python-version: ['3.12', '3.13']
 
     steps:
     - uses: actions/checkout@v4
@@ -46,7 +46,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.11', '3.13']
+        python-version: ['3.12', '3.13']
 
     steps:
     - uses: actions/checkout@v4

README.md

@@ -4,7 +4,7 @@
 
 [![Tests](https://img.shields.io/github/actions/workflow/status/M4i-Imaging-Mass-Spectrometry/thyra/tests.yml?branch=main&logo=github)](https://github.com/M4i-Imaging-Mass-Spectrometry/thyra/actions/workflows/tests.yml)
 [![PyPI](https://img.shields.io/pypi/v/thyra?logo=pypi&logoColor=white)](https://pypi.org/project/thyra/)
-[![Python 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
+[![Python 3.12+](https://img.shields.io/badge/python-3.12+-blue.svg)](https://www.python.org/downloads/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![Docs](https://img.shields.io/badge/docs-mkdocs-blue)](https://M4i-Imaging-Mass-Spectrometry.github.io/thyra)

docs/contributing.md

@@ -15,7 +15,7 @@ Thank you for your interest in contributing to Thyra! This document provides gui
 
 ### Prerequisites
 
-- Python 3.11 or 3.12
+- Python 3.12 or 3.13
 - Poetry for dependency management
 - Git
 

docs/getting-started.md

@@ -17,7 +17,7 @@
     ```
 
 !!! note "Requirements"
-    Python 3.11 or 3.12. Windows, macOS, and Linux are all supported.
+    Python 3.12 or 3.13. Windows, macOS, and Linux are all supported.
     Bruker readers require the vendor SDK DLLs (bundled for Windows).
 
 ---

docs/index.md

@@ -4,7 +4,7 @@
 
 [![PyPI](https://img.shields.io/pypi/v/thyra?logo=pypi&logoColor=white)](https://pypi.org/project/thyra/)
 [![Tests](https://img.shields.io/github/actions/workflow/status/M4i-Imaging-Mass-Spectrometry/thyra/tests.yml?branch=main&logo=github)](https://github.com/M4i-Imaging-Mass-Spectrometry/thyra/actions/workflows/tests.yml)
-[![Python 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
+[![Python 3.12+](https://img.shields.io/badge/python-3.12+-blue.svg)](https://www.python.org/downloads/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
 **Thyra** (from Greek *thyra*, meaning "door" or "portal") converts Mass Spectrometry Imaging (MSI) data into the standardized [SpatialData](https://spatialdata.scverse.org/)/Zarr format -- your portal to spatial omics analysis workflows.

docs/tutorial.md

@@ -23,7 +23,7 @@ paper.
 pip install thyra
 ```
 
-Thyra requires Python 3.11 or 3.12. Check what you have:
+Thyra requires Python 3.12 or 3.13. Check what you have:
 
 ```bash
 thyra --version