fix: green CI and align README Python version to 3.11+

.gitignore

@@ -3,6 +3,7 @@ __pycache__/
 *.egg-info/
 .pytest_cache/
 .codex_deps/
+.claude/
 tmp_*.log
 build/
 dist/

README.md

@@ -5,7 +5,7 @@
   <a href="https://anaconda.org/conda-forge/pyxenium"><img src="https://img.shields.io/conda/vn/conda-forge/pyxenium.svg" alt="Conda version"></a>
   <a href="https://pyxenium.readthedocs.io/en/latest/"><img src="https://readthedocs.org/projects/pyxenium/badge/?version=latest" alt="Read the Docs"></a>
   <a href="https://github.com/hutaobo/pyXenium/actions/workflows/ci.yml"><img src="https://github.com/hutaobo/pyXenium/actions/workflows/ci.yml/badge.svg?branch=main" alt="CI"></a>
-  <a href="https://pypi.org/project/pyXenium/"><img src="https://img.shields.io/pypi/pyversions/pyXenium.svg" alt="Python versions"></a>
+  <a href="https://pypi.org/project/pyXenium/"><img src="https://img.shields.io/badge/python-3.11%20%7C%203.12%20%7C%203.13-blue.svg" alt="Python versions"></a>
   <a href="https://github.com/hutaobo/pyXenium/blob/main/LICENSE"><img src="https://img.shields.io/badge/license-AGPL--3.0-0a7f5a.svg" alt="License"></a>
 </p>
 
@@ -39,7 +39,7 @@ and run separately; pyXenium does not vendor them or add them as core runtime de
 - Conda package: [conda-forge](https://anaconda.org/conda-forge/pyxenium)
 - Documentation site: [pyxenium.readthedocs.io](https://pyxenium.readthedocs.io/en/latest/)
 - Canonical build status: [GitHub Actions CI](https://github.com/hutaobo/pyXenium/actions/workflows/ci.yml)
-- Supported Python: `>=3.8`
+- Supported Python: `>=3.11`
 - License: [GNU AGPL v3.0 only](https://github.com/hutaobo/pyXenium/blob/main/LICENSE)
 - Maintained by: `SPATHO AB`
 
@@ -69,7 +69,7 @@ For documentation work:
 pip install -e ".[docs]"
 ```
 
-For the optional SpatialPerturb Bridge runtime on Python 3.9+:
+For the optional SpatialPerturb Bridge runtime on Python 3.11+:
 
 ```bash
 pip install -e ".[perturb]"

pyproject.toml

@@ -60,7 +60,7 @@ pyxenium = "pyXenium.__main__:main"
 
 [project.optional-dependencies]
 perturb = [
-  "SpatialPerturb>=0.3; python_version >= '3.9'",
+  "SpatialPerturb>=0.3; python_version >= '3.11'",
 ]
 
 lazyslide = [

tests/test_gmi_module.py

@@ -211,7 +211,7 @@ def test_gmi_docs_and_package_data_are_canonical():
     api_gmi = (repo_root / "docs" / "api" / "gmi.md").read_text(encoding="utf-8")
     pyproject = (repo_root / "pyproject.toml").read_text(encoding="utf-8")
 
-    assert "nine feature areas" in readme
+    assert "nine major sections" in readme
     assert "gmi" in api_index
     assert "pyXenium.gmi" in api_gmi
     assert "_vendor/Gmi/R/*" in pyproject