deprecate pd.SparseDataFrame, closes #190

KrishnaswamyLab · Oct 30, 2020 · 09e888c · 09e888c
1 parent 88eec77
commit 09e888c
Show file tree

Hide file tree

Showing 4 changed files with 10 additions and 11 deletions.
diff --git a/python/magic/magic.py b/python/magic/magic.py
@@ -200,8 +200,7 @@ def knn_max(self, value):
 
     @property
     def diff_op(self):
-        """The diffusion operator calculated from the data
-        """
+        """The diffusion operator calculated from the data"""
         if self.graph is not None:
             return self.graph.diff_op
         else:
@@ -501,7 +500,7 @@ def fit(self, X, graph=None):
     def _parse_genes(self, X, genes):
         if (
             genes is None
-            and isinstance(X, (pd.SparseDataFrame, sparse.spmatrix))
+            and (sparse.issparse(X) or scprep.utils.is_sparse_dataframe(X))
             and np.prod(X.shape) > 5000 * 20000
         ):
             warnings.warn(
@@ -867,7 +866,10 @@ def _impute(
                 ax.plot(x, error_vec)
                 if t_opt is not None:
                     ax.plot(
-                        t_opt, error_vec[t_opt - 1], "ro", markersize=10,
+                        t_opt,
+                        error_vec[t_opt - 1],
+                        "ro",
+                        markersize=10,
                     )
                 ax.plot(x, np.full(len(error_vec), threshold), "k--")
                 ax.set_xlabel("t")

diff --git a/python/magic/plot.py b/python/magic/plot.py
@@ -127,10 +127,7 @@ def animate_magic(
         show = False
 
     data_magic = scprep.select.select_cols(data, idx=genes)
-    if isinstance(data_magic, pd.SparseDataFrame):
-        data_magic = data_magic.to_dense()
-    elif sparse.issparse(data_magic):
-        data_magic = data_magic.toarray()
+    data_magic = scprep.utils.toarray(data_magic)
     c = data_magic[gene_color] if gene_color is not None else None
     sc = ax.scatter(data_magic[gene_x], data_magic[gene_y], c=c, cmap=cmap)
     ax.set_title("t = 0")

diff --git a/python/magic/utils.py b/python/magic/utils.py
@@ -132,11 +132,11 @@ def matrix_is_equivalent(X, Y):
 
 def convert_to_same_format(data, target_data, columns=None, prevent_sparse=False):
     # create new data object
-    if isinstance(target_data, pd.SparseDataFrame):
+    if scprep.utils.is_sparse_dataframe(target_data):
         if prevent_sparse:
             data = pd.DataFrame(data)
         else:
-            data = pd.SparseDataFrame(data)
+            data = scprep.utils.SparseDataFrame(data)
         pandas = True
     elif isinstance(target_data, pd.DataFrame):
         data = pd.DataFrame(data)

diff --git a/python/magic/version.py b/python/magic/version.py
@@ -1 +1 @@
-__version__ = "2.0.4a0"
+__version__ = "2.0.4"