Merge aea005a into abcfda0

qiime2 · Feb 10, 2020 · f6e1c9c · f6e1c9c
2 parents abcfda0 + aea005a
commit f6e1c9c
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Showing 3 changed files with 8 additions and 6 deletions.
diff --git a/ci/recipe/meta.yaml b/ci/recipe/meta.yaml
@@ -21,7 +21,7 @@ requirements:
     - scikit-bio >=0.5.4
     - numpy
     - blas=*=openblas
-    - pandas
+    - pandas >=1
     - biom-format >=2.1.5,<2.2.0
     - ijson
     - h5py

diff --git a/q2_types/feature_data/_transformer.py b/q2_types/feature_data/_transformer.py
@@ -80,13 +80,14 @@ def _taxonomy_formats_to_dataframe(filepath, has_header=None):
     if df.index.has_duplicates:
         raise ValueError(
             "Taxonomy format feature IDs must be unique. The following IDs "
-            "are duplicated: %s" % ', '.join(df.index.get_duplicates()))
+            "are duplicated: %s" %
+            ', '.join(df.index[df.index.duplicated()].unique()))
 
     if df.columns.has_duplicates:
         raise ValueError(
             "Taxonomy format column names must be unique. The following "
             "column names are duplicated: %s" %
-            ', '.join(df.columns.get_duplicates()))
+            ', '.join(df.columns[df.columns.duplicated()].unique()))
 
     df['Taxon'] = df['Taxon'].str.strip()
     return df
@@ -117,13 +118,14 @@ def _dataframe_to_tsv_taxonomy_format(df):
     if df.index.has_duplicates:
         raise ValueError(
             "Taxonomy format feature IDs must be unique. The following IDs "
-            "are duplicated: %s" % ', '.join(df.index.get_duplicates()))
+            "are duplicated: %s" %
+            ', '.join(df.index[df.index.duplicated()].unique()))
 
     if df.columns.has_duplicates:
         raise ValueError(
             "Taxonomy format column names must be unique. The following "
             "column names are duplicated: %s" %
-            ', '.join(df.columns.get_duplicates()))
+            ', '.join(df.columns[df.columns.duplicated()].unique()))
 
     ff = TSVTaxonomyFormat()
     df.to_csv(str(ff), sep='\t', header=True, index=True)

diff --git a/q2_types/feature_data/tests/test_transformer.py b/q2_types/feature_data/tests/test_transformer.py
@@ -338,7 +338,7 @@ def test_has_header_with_headerless(self):
                 has_header=True)
 
     def test_jagged(self):
-        with self.assertRaises(pandas.io.common.CParserError):
+        with self.assertRaises(pandas.io.common.ParserError):
             _taxonomy_formats_to_dataframe(
                 self.get_data_path(os.path.join('taxonomy', 'jagged.tsv')))