python313Packages.scanpy: init at 1.11.4 (#433795)
This commit is contained in:
Samuel Ainsworth
@@ -1,4 +1,5 @@
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{
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anndata,
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array-api-compat,
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awkward,
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boltons,
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@@ -17,17 +18,15 @@
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numba,
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numpy,
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openpyxl,
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packaging,
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pandas,
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pyarrow,
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pytest-mock,
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pytest-xdist,
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pytestCheckHook,
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pythonOlder,
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scanpy,
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scikit-learn,
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scipy,
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stdenv,
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typing-extensions,
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zarr,
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}:
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@@ -56,6 +55,7 @@ buildPythonPackage rec {
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numpy
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pandas
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scipy
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zarr
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];
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nativeCheckInputs = [
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@@ -72,7 +72,7 @@ buildPythonPackage rec {
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pytest-xdist
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pytestCheckHook
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scikit-learn
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zarr
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scanpy
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];
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# Optionally disable pytest-xdist to make it easier to debug the test suite.
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@@ -80,43 +80,22 @@ buildPythonPackage rec {
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# fail when running without pytest-xdist ("worker_id not found").
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# pytestFlags = [ "-oaddopts=" ];
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disabledTestPaths = [
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# Tests that require scanpy, creating a circular dependency chain
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"src/anndata/_core/anndata.py"
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"src/anndata/_core/merge.py"
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"src/anndata/_core/sparse_dataset.py"
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"src/anndata/_io/specs/registry.py"
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"src/anndata/_io/utils.py"
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"src/anndata/_warnings.py"
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"src/anndata/experimental/merge.py"
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"src/anndata/experimental/multi_files/_anncollection.py"
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"src/anndata/utils.py"
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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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doCheck = false; # use passthru.tests instead to prevent circularity with `scanpy`
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passthru.tests = anndata.overridePythonAttrs { doCheck = true; };
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disabledTests = [
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# requires data from a previous test execution:
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"test_no_diff"
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# doctests that require scanpy, creating a circular dependency chain. These
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# do not work in disabledTestPaths for some reason.
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"anndata._core.anndata.AnnData.concatenate"
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"anndata._core.anndata.AnnData.obs_names_make_unique"
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"anndata._core.anndata.AnnData.var_names_make_unique"
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"anndata._core.extensions.register_anndata_namespac"
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"anndata._core.merge.concat"
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"anndata._core.merge.gen_reindexer"
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"anndata._core.sparse_dataset.sparse_dataset"
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"anndata._io.specs.registry.read_elem_as_dask"
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# try to download data:
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"anndata._io.specs.registry.read_elem_lazy"
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"anndata._io.utils.report_read_key_on_error"
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"anndata._io.utils.report_write_key_on_error"
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"anndata._warnings.ImplicitModificationWarning"
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"anndata.experimental.backed._io.read_lazy"
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"anndata.experimental.merge.concat_on_disk"
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"anndata.experimental.multi_files._anncollection.AnnCollection"
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"anndata.utils.make_index_unique"
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"ci.scripts.min-deps.min_dep"
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"concatenation.rst"
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# Tests that require cupy and GPU access. Introducing cupy as a dependency
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# would make this package unfree and GPU access is not possible within the
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@@ -0,0 +1,182 @@
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{
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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 = "1.11.4";
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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-EvNelorfLOpYLGGZ1RSq4+jk6emuCWCKBdUop24iLf4=";
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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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];
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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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@@ -0,0 +1,58 @@
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{
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lib,
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buildPythonPackage,
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fetchFromGitHub,
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hatch-docstring-description,
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hatch-vcs,
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hatchling,
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coverage,
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ipykernel,
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jupyter-client,
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pytestCheckHook,
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pytest-asyncio,
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pytest-subprocess,
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testing-common-database,
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writableTmpDirAsHomeHook,
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}:
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buildPythonPackage rec {
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pname = "session-info2";
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version = "0.2";
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pyproject = true;
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src = fetchFromGitHub {
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owner = "scverse";
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repo = "session-info2";
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tag = "v${version}";
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hash = "sha256-DsI2mFM7xZgSm24yVzF6B+2aruKsjkTKZAmJPg7mWgg=";
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};
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build-system = [
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hatch-docstring-description
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hatch-vcs
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hatchling
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];
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nativeCheckInputs = [
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coverage
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ipykernel
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jupyter-client
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pytestCheckHook
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pytest-asyncio
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pytest-subprocess
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testing-common-database
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writableTmpDirAsHomeHook
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];
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pythonImportsCheck = [
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"session_info2"
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];
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meta = {
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description = "Report Python session information";
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homepage = "https://session-info2.readthedocs.io";
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changelog = "https://github.com/scverse/session-info2/releases/tag/${src.tag}";
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license = lib.licenses.mpl20;
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maintainers = with lib.maintainers; [ bcdarwin ];
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};
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}
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@@ -16185,6 +16185,8 @@ self: super: with self; {
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scancode-toolkit = callPackage ../development/python-modules/scancode-toolkit { };
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scanpy = callPackage ../development/python-modules/scanpy { };
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scapy = callPackage ../development/python-modules/scapy {
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inherit (pkgs) libpcap; # Avoid confusion with python package of the same name
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};
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@@ -16435,6 +16437,8 @@ self: super: with self; {
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service-identity = callPackage ../development/python-modules/service-identity { };
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session-info2 = callPackage ../development/python-modules/session-info2 { };
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setproctitle = callPackage ../development/python-modules/setproctitle { };
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setupmeta = callPackage ../development/python-modules/setupmeta { };
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