Double check phenopy data files are there.

phenoscore/hpo_phenotype/calc_hpo_sim.py

@@ -1,4 +1,5 @@
 from phenopy.build_hpo import generate_annotated_hpo_network
+from phenopy.config import download_resource_files
 from phenopy.score import Scorer
 import networkx as nx
 import os
@@ -91,10 +92,12 @@ def _init_calc_similarity(self, scoring_method, sum_method):
         scorer: phenopy scorer instance
             Scorer object that can be used to calculate semantic similarity between lists of HPO terms
         """
+
         # files used in building the annotated HPO network
         phenopy_data_directory = os.path.join(os.path.expanduser("~"), '.phenopy', 'data')
         obo_file = os.path.join(phenopy_data_directory, 'hp.obo')
         disease_to_phenotype_file = os.path.join(phenopy_data_directory, 'phenotype.hpoa')
+        download_resource_files()
         hpo_network, alt2prim, disease_records = generate_annotated_hpo_network(obo_file,
                                                                                 disease_to_phenotype_file, )