Use python versions 3.11 to 3.13 included

.github/workflows/ci.yml

@@ -22,7 +22,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
 
     steps:
       - uses: actions/checkout@v4

CHANGELOG.md

@@ -14,6 +14,7 @@
 
 ### Fixed
 - Retrieve `mode=multimodal` when saving the model and re-loading the model after H&E training (#24)
+- Fix tests for recent AnnData versions only supporting CSR/CSC sparse matrices
 
 ## [1.0.0] - 2025-08-09
 

README.md

@@ -38,7 +38,7 @@ Check [Novae's documentation](https://mics-lab.github.io/novae/) to get started.
 
 ## Installation
 
-`novae` can be installed from `PyPI` on all OS, for any Python version from `3.10` to `3.12` (included).
+`novae` can be installed from `PyPI` on all OS, for any Python version `>=3.11` and `<3.14` (3.14 support coming soon).
 
 ```
 pip install novae

docker/novae/Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.10-slim
+FROM python:3.12-slim
 
 ARG NOVAE_VERSION
 

docs/getting_started.md

@@ -1,6 +1,6 @@
 ## Installation
 
-Novae can be installed on every OS and for any Python version from `3.10` to `3.12` (included).
+Novae can be installed on every OS and for any Python version `>=3.11` and `<3.14` (3.14 support coming soon).
 
 !!! note "Advice (optional)"
 

novae/data/_load/_toy.py

@@ -118,10 +118,10 @@ def toy_dataset(
 
 def _drop_neighbors(adata: AnnData, index: int):
     for key in ["spatial_connectivities", "spatial_distances"]:
-        adata.obsp[key] = adata.obsp[key].tolil()
-        adata.obsp[key][index] = 0
-        adata.obsp[key][:, index] = 0
-        adata.obsp[key] = adata.obsp[key].tocsr()
+        connectivities = adata.obsp[key].tolil()
+        connectivities[index] = 0
+        connectivities[:, index] = 0
+        adata.obsp[key] = connectivities.tocsr()
         adata.obsp[key].eliminate_zeros()
 
 

pyproject.toml

@@ -3,7 +3,7 @@ name = "novae"
 version = "1.0.0"
 description = "Graph-based foundation model for spatial transcriptomics data"
 authors = [{ name = "Quentin Blampey", email = "[email protected]" }]
-requires-python = ">=3.10,<3.13"
+requires-python = ">=3.11"
 readme = "README.md"
 license = "BSD-3-Clause"
 classifiers = [