168a68e7db
Diff: https://github.com/scverse/scanpy/compare/1.11.4...1.11.5 Changelog: https://github.com/scverse/scanpy/releases/tag/1.11.5
186 lines
3.0 KiB
Nix
186 lines
3.0 KiB
Nix
{
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lib,
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buildPythonPackage,
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fetchFromGitHub,
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hatch-vcs,
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hatchling,
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anndata,
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h5py,
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joblib,
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legacy-api-wrap,
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matplotlib,
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natsort,
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networkx,
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numba,
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numpy,
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packaging,
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pandas,
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patsy,
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pynndescent,
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scikit-learn,
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scipy,
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seaborn,
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session-info2,
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statsmodels,
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tqdm,
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typing-extensions,
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umap-learn,
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dask,
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dask-ml,
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igraph,
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leidenalg,
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scikit-image,
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scikit-misc,
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zarr,
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pytestCheckHook,
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pytest-cov-stub,
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pytest-mock,
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pytest-randomly,
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pytest-rerunfailures,
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pytest-xdist,
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tuna,
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}:
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buildPythonPackage rec {
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pname = "scanpy";
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version = "1.11.5";
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pyproject = true;
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src = fetchFromGitHub {
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owner = "scverse";
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repo = "scanpy";
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tag = version;
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hash = "sha256-GnZ1qJ4SaTLDzfLAH6IHrYeuMBo8PglKUlj4f3ljeR0=";
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};
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build-system = [
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hatch-vcs
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hatchling
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];
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dependencies = [
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anndata
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h5py
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joblib
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legacy-api-wrap
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matplotlib
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natsort
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networkx
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numba
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numpy
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packaging
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pandas
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patsy
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pynndescent
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scikit-learn
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scipy
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seaborn
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session-info2
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statsmodels
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tqdm
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typing-extensions
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umap-learn
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];
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optional-dependencies = {
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# commented attributes are due to some dependencies not being in Nixpkgs
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#bbknn = [
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# bbknn
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#];
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dask = [
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anndata
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dask
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];
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dask-ml = [
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dask-ml
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];
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#harmony = [
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# harmonypy
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#];
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leiden = [
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igraph
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leidenalg
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];
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#louvain = [
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# igraph
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# louvain
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#];
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#magic = [
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# magic-impute
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#];
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paga = [
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igraph
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];
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#rapids = [
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# cudf
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# cugraph
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# cuml
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#];
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#scanorama = [
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# scanorama
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#];
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scrublet = [
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scikit-image
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];
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skmisc = [
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scikit-misc
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];
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};
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nativeCheckInputs = [
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pytestCheckHook
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pytest-cov-stub
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pytest-mock
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pytest-randomly
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pytest-rerunfailures
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pytest-xdist
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tuna
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zarr
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];
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preCheck = ''
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export NUMBA_CACHE_DIR=$(mktemp -d);
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'';
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disabledTestPaths = [
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# try to download data:
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"tests/test_aggregated.py"
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"tests/test_highly_variable_genes.py"
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"tests/test_normalization.py"
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"tests/test_pca.py"
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"tests/test_plotting.py"
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"tests/test_plotting_embedded/"
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];
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disabledTests = [
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# try to download data:
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"scanpy.get._aggregated.aggregate"
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"scanpy.plotting._tools.scatterplots.spatial"
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"test_clip"
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"test_download_failure"
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"test_mean_var"
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"test_regress_out_int"
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"test_score_with_reference"
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# fails to find the trivial test script for some reason:
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"test_external"
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# AssertionError: Not equal to tolerance rtol=1e-07, atol=0
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"test_connectivities_euclidean"
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];
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pythonImportsCheck = [
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"scanpy"
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];
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meta = {
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description = "Single-cell analysis in Python which scales to >100M cells";
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homepage = "https://scanpy.readthedocs.io";
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changelog = "https://github.com/scverse/scanpy/releases/tag/${src.tag}";
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license = lib.licenses.bsd3;
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maintainers = with lib.maintainers; [ bcdarwin ];
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mainProgram = "scanpy";
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};
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}
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