MAINT: adjust to change in pd.DataFrame interaction with > (#940)

* MAINT: adjust to change in pd.DataFrame interaction with > * STY: adjust for flake8
biocore · Nov 8, 2023 · 5d1c921 · 5d1c921
1 parent d3f82fe
commit 5d1c921
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/biom/tests/test_table.py b/biom/tests/test_table.py
@@ -1593,7 +1593,7 @@ def test_to_dataframe_is_sparse(self):
         df = example_table.to_dataframe()
         density = (float(example_table.matrix_data.getnnz()) /
                    np.prod(example_table.shape))
-        df_density = (df > 0).sum().sum() / np.prod(df.shape)
+        df_density = (df.values > 0).sum().sum() / np.prod(df.shape)
         assert np.allclose(df_density, density)
 
     def test_to_dataframe_dense(self):

diff --git a/biom/util.py b/biom/util.py
@@ -441,11 +441,11 @@ def biom_open(fp, permission='r'):
         opener = h5py.File
 
     if mode in ['U', 'r', 'rb'] and is_gzip(fp):
-        def opener(fp, mode):
+        def opener(fp, mode):  # noqa
             return codecs.getreader('utf-8')(gzip_open(fp, mode))
         mode = 'rb' if permission in ['U', 'r'] else permission
     elif mode in ['w', 'wb'] and str(fp).endswith('.gz'):
-        def opener(fp, mode):
+        def opener(fp, mode):  # noqa
             codecs.getwriter('utf-8')(gzip_open(fp, mode))
 
     f = opener(fp, mode)