SingleCellExperiment 0.4.3__tar.gz → 0.4.5__tar.gz

{SingleCellExperiment-0.4.3 → singlecellexperiment-0.4.5}/.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: '^docs/conf.py'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v4.6.0
   hooks:
   - id: trailing-whitespace
   - id: check-added-large-files
@@ -26,14 +26,14 @@ repos:
       # --config, ./pyproject.toml
 
 - repo: https://github.com/psf/black
-  rev: 23.12.1
+  rev: 24.4.0
   hooks:
   - id: black
     language_version: python3
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.1.14
+  rev: v0.3.7
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

{SingleCellExperiment-0.4.3 → singlecellexperiment-0.4.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SingleCellExperiment
-Version: 0.4.3
+Version: 0.4.5
 Summary: Container class for single-cell experiments
 Home-page: https://github.com/BiocPy/SingleCellExperiment
 Author: jkanche
@@ -19,6 +19,8 @@ Provides-Extra: optional
 Requires-Dist: anndata; extra == "optional"
 Requires-Dist: h5py; extra == "optional"
 Requires-Dist: mudata; extra == "optional"
+Requires-Dist: delayedarray; extra == "optional"
+Requires-Dist: hdf5array; extra == "optional"
 Provides-Extra: testing
 Requires-Dist: setuptools; extra == "testing"
 Requires-Dist: pytest; extra == "testing"
@@ -26,6 +28,8 @@ Requires-Dist: pytest-cov; extra == "testing"
 Requires-Dist: anndata; extra == "testing"
 Requires-Dist: h5py; extra == "testing"
 Requires-Dist: mudata; extra == "testing"
+Requires-Dist: delayedarray; extra == "testing"
+Requires-Dist: hdf5array; extra == "testing"
 
 [![Project generated with PyScaffold](https://img.shields.io/badge/-PyScaffold-005CA0?logo=pyscaffold)](https://pyscaffold.org/)
 [![PyPI-Server](https://img.shields.io/pypi/v/SingleCellExperiment.svg)](https://pypi.org/project/SingleCellExperiment/)

{SingleCellExperiment-0.4.3 → singlecellexperiment-0.4.5}/setup.cfg

@@ -36,6 +36,8 @@ optional =
 	anndata
 	h5py
 	mudata
+	delayedarray
+	hdf5array
 testing = 
 	setuptools
 	pytest
@@ -43,6 +45,8 @@ testing =
 	anndata
 	h5py
 	mudata
+	delayedarray
+	hdf5array
 
 [options.entry_points]
 

{SingleCellExperiment-0.4.3 → singlecellexperiment-0.4.5}/setup.py

@@ -4,6 +4,7 @@ This file was generated with PyScaffold 4.5.
 PyScaffold helps you to put up the scaffold of your new Python project.
 Learn more under: https://pyscaffold.org/
 """
+
 from setuptools import setup
 
 if __name__ == "__main__":

{SingleCellExperiment-0.4.3 → singlecellexperiment-0.4.5}/src/SingleCellExperiment.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SingleCellExperiment
-Version: 0.4.3
+Version: 0.4.5
 Summary: Container class for single-cell experiments
 Home-page: https://github.com/BiocPy/SingleCellExperiment
 Author: jkanche
@@ -19,6 +19,8 @@ Provides-Extra: optional
 Requires-Dist: anndata; extra == "optional"
 Requires-Dist: h5py; extra == "optional"
 Requires-Dist: mudata; extra == "optional"
+Requires-Dist: delayedarray; extra == "optional"
+Requires-Dist: hdf5array; extra == "optional"
 Provides-Extra: testing
 Requires-Dist: setuptools; extra == "testing"
 Requires-Dist: pytest; extra == "testing"
@@ -26,6 +28,8 @@ Requires-Dist: pytest-cov; extra == "testing"
 Requires-Dist: anndata; extra == "testing"
 Requires-Dist: h5py; extra == "testing"
 Requires-Dist: mudata; extra == "testing"
+Requires-Dist: delayedarray; extra == "testing"
+Requires-Dist: hdf5array; extra == "testing"
 
 [![Project generated with PyScaffold](https://img.shields.io/badge/-PyScaffold-005CA0?logo=pyscaffold)](https://pyscaffold.org/)
 [![PyPI-Server](https://img.shields.io/pypi/v/SingleCellExperiment.svg)](https://pypi.org/project/SingleCellExperiment/)

{SingleCellExperiment-0.4.3 → singlecellexperiment-0.4.5}/src/SingleCellExperiment.egg-info/requires.txt

@@ -7,6 +7,8 @@ importlib-metadata
 anndata
 h5py
 mudata
+delayedarray
+hdf5array
 
 [testing]
 setuptools
@@ -15,3 +17,5 @@ pytest-cov
 anndata
 h5py
 mudata
+delayedarray
+hdf5array

{SingleCellExperiment-0.4.3 → singlecellexperiment-0.4.5}/src/singlecellexperiment/SingleCellExperiment.py

@@ -4,7 +4,6 @@ from warnings import warn
 
 import biocframe
 import biocutils as ut
-from genomicranges import GenomicRanges
 from summarizedexperiment._combineutils import (
     check_assays_are_equal,
     merge_assays,
@@ -984,25 +983,16 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         Returns:
             A tuple with ``AnnData`` main experiment and a list of alternative experiments.
         """
-        from anndata import AnnData
+        obj = super().to_anndata()
 
-        layers = OrderedDict()
-        for asy, mat in self.assays.items():
-            layers[asy] = mat.transpose()
+        if self.reduced_dims is not None:
+            obj.obsm = self.reduced_dims
 
-        trows = self.row_data
-        if isinstance(self.row_data, GenomicRanges):
-            trows = self.row_data.to_pandas()
-
-        obj = AnnData(
-            obs=self.col_data,
-            var=trows,
-            uns=self.metadata,
-            obsm=self.reduced_dims,
-            layers=layers,
-            varp=self.row_pairs,
-            obsp=self.column_pairs,
-        )
+        if self.row_pairs is not None:
+            obj.varp = self.row_pairs
+
+        if self.column_pairs is not None:
+            obj.obsp = self.column_pairs
 
         if include_alternative_experiments is True:
             adatas = None
@@ -1014,8 +1004,6 @@ class SingleCellExperiment(RangedSummarizedExperiment):
                 ) in self.alternative_experiments.items():
                     adatas[alt_name] = alternative_experiment.to_anndata()
 
-            return obj, adatas
-
         return obj, None
 
     @classmethod
@@ -1027,7 +1015,9 @@ class SingleCellExperiment(RangedSummarizedExperiment):
                 Input data.
 
         Returns:
-            A ``SingleCellExperiment`` object.
+            A ``SingleCellExperiment`` object. If the input contains any data
+            in the ``uns`` attribute, the `metadata` slot of the ``SingleCellExperiment``
+            will contain a key ``uns``.
         """
 
         layers = OrderedDict()
@@ -1040,12 +1030,13 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         obsm = _to_normal_dict(input.obsm)
         varp = _to_normal_dict(input.varp)
         obsp = _to_normal_dict(input.obsp)
+        _metadata = {"uns": input.uns} if input.uns is not None else None
 
         return cls(
             assays=layers,
             row_data=biocframe.BiocFrame.from_pandas(input.var),
             column_data=biocframe.BiocFrame.from_pandas(input.obs),
-            metadata=input.uns,
+            metadata=_metadata,
             reduced_dims=obsm,
             row_pairs=varp,
             column_pairs=obsp,

{SingleCellExperiment-0.4.3 → singlecellexperiment-0.4.5}/src/singlecellexperiment/io/tenx.py

@@ -58,7 +58,7 @@ def read_tenx_h5(path: str) -> SingleCellExperiment:
     """
 
     import h5py
-    from scipy.sparse import csc_matrix, csr_matrix
+    from hdf5array import Hdf5CompressedSparseMatrix
 
     h5 = h5py.File(path, mode="r")
 
@@ -68,16 +68,11 @@ def read_tenx_h5(path: str) -> SingleCellExperiment:
     groups = h5["matrix"].keys()
 
     # read the matrix
-    data = h5["matrix"]["data"][:]
-    indices = h5["matrix"]["indices"][:]
-    indptr = h5["matrix"]["indptr"][:]
     shape = tuple(h5["matrix"]["shape"][:])
 
-    counts = None
-    if len(indptr) == shape[1] + 1:
-        counts = csc_matrix((data, indices, indptr), shape=shape)
-    else:
-        counts = csr_matrix((data, indices, indptr), shape=shape)
+    counts = Hdf5CompressedSparseMatrix(
+        path=path, group_name="matrix", by_column=True, shape=shape
+    )
 
     # read features
     features = None
@@ -106,6 +101,8 @@ def read_tenx_h5(path: str) -> SingleCellExperiment:
         barcodes["barcodes"] = [x.decode("ascii") for x in h5["matrix"]["barcodes"]]
         barcodes = BiocFrame(barcodes, number_of_rows=counts.shape[1])
 
+    h5.close()
+
     return SingleCellExperiment(
         assays={"counts": counts}, row_data=features, column_data=barcodes
     )

{SingleCellExperiment-0.4.3 → singlecellexperiment-0.4.5}/tests/test_sce_io.py

@@ -61,6 +61,8 @@ def test_SCE_to_anndata():
     adata = tse.to_anndata()
     assert adata is not None
     assert isinstance(adata[0], anndata.AnnData)
+    assert adata[0].shape[0] == counts.shape[1]
+    assert adata[0].shape[1] == counts.shape[0]
 
 
 def test_SCE_fromH5AD():
@@ -127,6 +129,14 @@ def test_SCE_randomAnnData():
     assert tse is not None
     assert isinstance(tse, SingleCellExperiment)
 
+    # to avoid unknown mapping types;
+    # ran into an issue with anndata.compat._overloaded_dict.OverloadedDict when loading a h5ad
+    adata.uns = {".internal": [f"obs_{i+1}" for i in range(n)]}
+    tse = singlecellexperiment.SingleCellExperiment.from_anndata(adata)
+
+    assert tse is not None
+    assert isinstance(tse, SingleCellExperiment)
+
 
 def test_SCE_to_mudata():
     tse = SingleCellExperiment(