explicitly convert spmatrix

scprep/run/conversion.py

@@ -3,6 +3,7 @@
 from .._lazyload import rpy2
 
 import numpy as np
+import scipy.sparse
 import warnings
 
 
@@ -46,6 +47,18 @@ def _pysce2rpy(pyobject):
     return pyobject
 
 
+def _rpyspmatrix2py(robject):
+    if utils._try_import("anndata2ri"):
+        robject = anndata2ri.scipy2ri.rpy2py(robject)
+    return robject
+
+
+def _pyspmatrix2rpy(pyobject):
+    if utils._try_import("anndata2ri") and isinstance(pyobject, scipy.sparse.spmatrix):
+        pyobject = anndata2ri.scipy2ri.py2rpy(pyobject)
+    return pyobject
+
+
 def _is_r_object(obj):
     return "rpy2.robjects" in str(type(obj)) or "rpy2.rinterface" in str(type(obj))
 
@@ -76,6 +89,7 @@ def rpy2py(robject):
     for converter in [
         _rpynull2py,
         _rpysce2py,
+        _rpyspmatrix2py,
         rpy2.robjects.pandas2ri.rpy2py,
         _rpylist2py,
         rpy2.robjects.numpy2ri.rpy2py,
@@ -119,6 +133,7 @@ def py2rpy(pyobject):
     for converter in [
         _pynull2rpy,
         _pysce2rpy,
+        _pyspmatrix2rpy,
         rpy2.robjects.pandas2ri.py2rpy,
         rpy2.robjects.numpy2ri.py2rpy,
         rpy2.robjects.conversion.py2rpy,

scprep/stats.py

@@ -11,7 +11,6 @@
 import numbers
 import numpy as np
 import pandas as pd
-import scipy.sparse
 import warnings
 
 plt = matplotlib.pyplot
@@ -550,7 +549,7 @@ def differential_expression(
     X, Y, measure="difference", direction="both", gene_names=None, n_jobs=-2
 ):
     """Calculate the most significant genes between two datasets.
-    
+
     If using ``measure="emd"``, the test statistic is multiplied by the sign of
     the mean differencein order to allow for distinguishing between positive
     and negative shifts. To ignore this, use ``direction="both"`` to sort by the

scprep/version.py

@@ -1 +1 @@
-__version__ = "1.2.0"
+__version__ = "1.2.1"

setup.py

@@ -25,7 +25,7 @@
     "mock",
     "h5py",
     "matplotlib>=3.0",
-    "rpy2>=3.0",
+    "rpy2>=3.0,<3.4.3",
     "black",
 ]
 

test/test_run.py

@@ -596,6 +596,8 @@ def test_conversion_spmatrix():
         assert isinstance(x, scipy.sparse.csc_matrix)
         assert x.shape == (2, 3)
         assert np.all(x.toarray() == np.array([[1, 3, 5], [2, 4, 6]]))
+        y = scprep.run.conversion.py2rpy(x)
+        assert (scprep.run.conversion.rpy2py(y) != x).nnz == 0
 
     def test_conversion_dataframe():
         x = scprep.run.conversion.rpy2py(

test/test_stats.py

@@ -7,7 +7,6 @@
 
 import numpy as np
 import os
-import scipy.sparse
 import scprep
 import warnings