Python 3.11 compatibility

Author: stevenweaver

hivclustering/mtnetwork.py

@@ -132,6 +132,7 @@ def _test_edge_support(cycles, sequence_records, hy_instance, p_value_cutoff, te
         except ImportError:
             raise ImportError("Optional dependencies not found. Please install the 'edgefiltering' extras to use this function: pip install hivclustering[edgefiltering]")
         hy_instance = hy.HyphyInterface()
+
     script_path = os.path.realpath(__file__)
 
     cycle_spec = []
@@ -173,6 +174,10 @@ def _batch_sequence_sim(spec):
 
 def _simulate_HIV_sequences(sequence, tree_matrix, hy_instance):
     if hy_instance is None:
+        try:
+            import hppy as hy
+        except ImportError:
+            raise ImportError("Optional dependencies not found. Please install the 'edgefiltering' extras to use this function: pip install hivclustering[edgefiltering]")
         hy_instance = hy.HyphyInterface()
 
     script_path = os.path.realpath(__file__)
@@ -930,6 +935,11 @@ def simulate_sequence_evolution(self, founders, founder_sequences, rate_per_year
         if self.adjacency_list is None:
             self.compute_adjacency()
 
+        try:
+            import hppy as hy
+        except ImportError:
+            raise ImportError("Optional dependencies not found. Please install the 'edgefiltering' extras to use this function: pip install hivclustering[edgefiltering]")
+
         hy_instance = hy.HyphyInterface()
         already_simulated = set()
 
@@ -2496,7 +2506,13 @@ def test_edge_support(self, sequence_records, cycles, adjacency_set, hy_instance
 
     def fit_degree_distribution(self, degree_option=None, hy_instance=None):
         if hy_instance is None:
+            try:
+                import hppy as hy
+            except ImportError:
+                raise ImportError("Optional dependencies not found. please install the 'edgefiltering' extras to use this function: pip install hivclustering[edgefiltering]")
+
             hy_instance = hy.HyphyInterface()
+
         script_path = os.path.realpath(__file__)
         hbl_path = os.path.join(os.path.dirname(script_path), "data", "HBL", "DegreeDistributions.bf")
         if degree_option == 'indegree':

setup.py

@@ -8,7 +8,7 @@
 sys.path.insert(0, join(split(abspath(__file__))[0], 'lib'))
 
 setup(name='hivclustering',
-      version="1.6.7",
+      version="1.6.8",
       description='HIV molecular clustering tools',
       author='Sergei Kosakovsky Pond',
       author_email='[email protected]',
@@ -19,7 +19,7 @@
             'data/HBL/*.bf',
     ]},
     extras_require={
-        'edgefiltering': ['bioext >= 0.19.0','hyphy-python >= 0.1.11','hppy >= 0.9.9'],
+        'edgefiltering': ['bioext >= 0.21.0','hyphy-python >= 0.1.11','hppy >= 0.9.9'],
     },
     scripts=[
         'scripts/hivnetworkcsv',