Warning fixes

anndata2ri/conv.py

@@ -23,7 +23,7 @@ def full_converter() -> conversion.Converter:
 
 
 def activate():
-    """
+    r"""
     Activate conversion for :class:`~anndata.AnnData` objects
     as well as :doc:`numpy` arrays and :class:`pandas.DataFrame`\ s
     via ``rpy2.robjects.numpy2ri`` and ``rpy2.robjects.pandas2ri``.

anndata2ri/scipy2ri/__init__.py

@@ -1,4 +1,4 @@
-"""
+r"""
 Convert scipy.sparse matrices between Python and R.
 
 For a detailed comparison between the two languages‘,

anndata2ri/scipy2ri/py2r.py

@@ -21,7 +21,7 @@
 def get_type_conv(dtype: np.dtype) -> Tuple[str, Callable[[np.ndarray], Sexp], Type[Vector]]:
     if np.issubdtype(dtype, np.floating):
         return "d", as_double, FloatVector
-    elif np.issubdtype(dtype, bool):
+    elif np.issubdtype(dtype, np.bool_):
         return "l", as_logical, BoolVector
     else:
         raise ValueError(f"Unknown dtype {dtype!r} cannot be converted to ?gRMatrix.")

pytest.ini

@@ -0,0 +1,13 @@
+[pytest]
+# eventlet 0.24.1 imports dns.hash: https://github.com/eventlet/eventlet/pull/563
+# igraph 0.7.1post6 imports SafeConfigParser: https://github.com/igraph/python-igraph/pull/203
+# ipywidgets 7.4.2 imports ABCs from collections: https://github.com/jupyter-widgets/ipywidgets/pull/2395
+# jinja2 2.10.1 imports ABCs from collections: https://github.com/pallets/jinja/pull/867
+# rpy2 3.0.2 imports ABCs from collections: https://bitbucket.org/rpy2/rpy2/pull-requests/74/fix-deprecationwarning/diff
+filterwarnings =
+    ignore::DeprecationWarning:dns.hash
+    ignore::DeprecationWarning:igraph.configuration
+    ignore::DeprecationWarning:ipywidgets.widgets.widget_selection
+    ignore::DeprecationWarning:jinja2.utils
+    ignore::DeprecationWarning:jinja2.runtime
+    ignore::DeprecationWarning:rpy2.rinterface_lib.sexp

tests/test_py2rpy.py

@@ -42,7 +42,11 @@ def check_pca(ex):
 @pytest.mark.parametrize("conversion", conversions_py2rpy)
 @pytest.mark.parametrize("check,shape,dataset", datasets)
 def test_py2rpy(conversion, check, shape, dataset):
-    ex = conversion(anndata2ri, dataset())
+    if dataset is sc.datasets.krumsiek11:
+        with pytest.warns(UserWarning, match=r"Duplicated obs_names"):
+            ex = conversion(anndata2ri, dataset())
+    else:
+        ex = conversion(anndata2ri, dataset())
     assert tuple(baseenv["dim"](ex)[::-1]) == shape
     check(ex)
 

tests/test_scipy_rpy2py.py

@@ -21,7 +21,7 @@
 
 @pytest.mark.parametrize("conversion", conversions_rpy2py)
 @pytest.mark.parametrize("shape,dataset,cls", mats)
-def test_py2rpy(conversion, shape, dataset,cls):
+def test_py2rpy(conversion, shape, dataset, cls):
     sm = conversion(scipy2ri, dataset)
     assert isinstance(sm, cls)
     assert sm.shape == shape