Replace pandas.read_table with read_csv

Merges #5

pandas.read_table deprecated in pandas v0.24
https://pandas.pydata.org/pandas-docs/version/0.24/whatsnew/v0.24.0.html#deprecations

Author: dhimmel

hetmatpy/degree_group.py

@@ -78,11 +78,11 @@ def dwpc_to_degrees(graph, metapath, damping=0.5, ignore_zeros=False):
     del source_adj_mat, target_adj_mat
 
     source_path = graph.get_nodes_path(metapath.source(), file_format='tsv')
-    source_node_df = pandas.read_table(source_path)
+    source_node_df = pandas.read_csv(source_path, sep='\t')
     source_node_names = list(source_node_df['name'])
 
     target_path = graph.get_nodes_path(metapath.target(), file_format='tsv')
-    target_node_df = pandas.read_table(target_path)
+    target_node_df = pandas.read_csv(target_path, sep='\t')
     target_node_names = list(target_node_df['name'])
 
     row_names, col_names, dwpc_matrix = graph.read_path_counts(metapath, 'dwpc', damping)

hetmatpy/hetmat/__init__.py

@@ -366,7 +366,7 @@ def get_node_identifiers(self, metanode):
         Returns a list of node identifiers for a metapath
         """
         path = self.get_nodes_path(metanode, file_format='tsv')
-        node_df = pandas.read_table(path)
+        node_df = pandas.read_csv(path, sep='\t')
         return list(node_df['identifier'])
 
     @functools.lru_cache()

hetmatpy/pipeline.py

@@ -38,7 +38,7 @@ def combine_dwpc_dgp(graph, metapath, damping, ignore_zeros=False, max_p_value=1
     Includes gamma-hurdle significance estimates.
     """
     stats_path = graph.get_running_degree_group_path(metapath, 'dwpc', damping, extension='.tsv.gz')
-    dgp_df = pandas.read_table(stats_path)
+    dgp_df = pandas.read_csv(stats_path, sep='\t')
     dgp_df = add_gamma_hurdle_to_dgp_df(dgp_df)
     degrees_to_dgp = dgp_df.set_index(['source_degree', 'target_degree']).to_dict(orient='index')
     dwpc_row_generator = hetmatpy.degree_group.dwpc_to_degrees(