diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a77f7a0..93f66e5 100644 --- a/.github/workflows/ci.yml +++ b/.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 diff --git a/CHANGELOG.md b/CHANGELOG.md index e525495..1045418 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/README.md b/README.md index a481c1f..4dacb9e 100644 --- a/README.md +++ b/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 diff --git a/docker/novae/Dockerfile b/docker/novae/Dockerfile index 364f47c..de362b8 100644 --- a/docker/novae/Dockerfile +++ b/docker/novae/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.10-slim +FROM python:3.12-slim ARG NOVAE_VERSION diff --git a/docs/getting_started.md b/docs/getting_started.md index 4978524..ff116cb 100644 --- a/docs/getting_started.md +++ b/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)" diff --git a/novae/data/_load/_toy.py b/novae/data/_load/_toy.py index ef71055..7e3f711 100644 --- a/novae/data/_load/_toy.py +++ b/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() diff --git a/pyproject.toml b/pyproject.toml index 34268d1..57835f0 100644 --- a/pyproject.toml +++ b/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 = "quentin.blampey@gmail.com" }] -requires-python = ">=3.10,<3.13" +requires-python = ">=3.11" readme = "README.md" license = "BSD-3-Clause" classifiers = [ diff --git a/uv.lock b/uv.lock index ffd17de..c7e99fd 100644 --- a/uv.lock +++ b/uv.lock @@ -1,27 +1,15 @@ version = 1 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