Merge pull request #11 from mvinyard/bug-fixes

Bug fixes

setup.py

@@ -5,10 +5,6 @@
 __email__ = ", ".join(["[email protected]"])
 
 
-# -- specify package version: --------------------------------------------------
-__version__ = "0.0.21"
-
-
 # -- import packages: ----------------------------------------------------------
 import setuptools
 import re
@@ -19,7 +15,7 @@
 # -- run setup: ----------------------------------------------------------------
 setuptools.setup(
     name="torch-adata",
-    version="0.0.21",
+    version="0.0.22rc0",
     python_requires=">3.9.0",
     author="Michael E. Vinyard",
     author_email="[email protected]",

torch_adata/__init__.py

@@ -6,7 +6,7 @@
 
 
 # -- specify package version: --------------------------------------------------
-__version__ = "0.0.21"
+__version__ = "0.0.22rc0"
 
 
 # -- import modules: -----------------------------------------------------------

torch_adata/_core/_core_ancilliary/_data_typing.py

@@ -9,6 +9,7 @@
 import numpy
 import pandas
 import torch
+import scipy
 
 
 # -- data type handlers: -----------------------------------------------------------------
@@ -46,6 +47,23 @@ def is_pandas_categorical(x_arr) -> bool:
     return x_arr.__class__ is pandas.Categorical
 
 
+def is_scipy_sparse(x_arr):
+    """
+    Inspects and indicates if input is a subclass of: scipy.sparse.spmatrix, the base class for all scipy sparse matrices.
+
+    Parameters:
+    -----------
+    x_arr
+        type: unknown
+
+    Returns:
+    --------
+    indicator
+        type: bool
+    """
+    return isinstance(x_arr, scipy.sparse.spmatrix)
+
+
 def to_np_array(x_arr) -> numpy.ndarray:
     """
     Inspects input. If input is not, numpy.ndarray, it is transformed to numpy.ndarray.
@@ -62,6 +80,8 @@ def to_np_array(x_arr) -> numpy.ndarray:
     """
     if is_numpy_array(x_arr):
         return x_arr
+    if is_scipy_sparse(x_arr):
+        return x_arr.toarray()
     if is_pandas_categorical(x_arr):
         return x_arr.to_numpy()
     return x_arr.toarray()
@@ -89,4 +109,4 @@ def as_list(item):
         if not isinstance(item, list):
             return [item]
         return item
-    return []
+    return []