Solved issues with testing, now all tests pass.

Mikado/loci/superlocus.py

@@ -14,6 +14,7 @@
 from sqlalchemy.engine import Engine
 from sqlalchemy.ext import baked
 from sqlalchemy.orm.session import sessionmaker
+from sqlalchemy.orm import session as sasession
 from sqlalchemy.sql.expression import and_
 from ..transcripts.transcript import Transcript
 from .abstractlocus import Abstractlocus
@@ -658,7 +659,8 @@ def load_all_transcript_data(self, engine=None, data_dict=None):
             self.logger.debug("Finished retrieving data for %d transcripts",
                               len(tid_keys))
             self.session.close()
-            self.sessionmaker.close_all()
+            sasession.close_all_sessions()
+            # self.sessionmaker.close_all_sessions()
 
         for tid in tid_keys:
             remove_flag, new_transcripts = self.load_transcript_data(tid, data_dict)

Mikado/tests/assigner_test.py

@@ -1107,6 +1107,7 @@ def test_false_fusion(self):
         args.self = False
         args.extended_refmap = False
         args.gzip = False
+        args.processes = 1
 
         scales.compare.compare(args)
 

Mikado/tests/test_system_calls.py

@@ -810,6 +810,7 @@ def test_compare_trinity(self):
             with self.subTest(ref=ref, pred=pred):
                 namespace.reference = to_gff(ref)
                 namespace.prediction = to_gff(pred)
+                namespace.processes = 2
                 dir = tempfile.TemporaryDirectory()
                 namespace.log = os.path.join(dir.name, "compare_{}_{}.log".format(
                     files.index(ref), files.index(pred)))

Mikado/tests/test_transcript_methods.py

@@ -669,7 +669,9 @@ def test_conversion(self):
         self.assertEqual(t1, self.t1)
 
     def test_get_coding_exons(self):
-        correct = [(5697,5891), (5256, 5576)]
+        correct = sorted([(5697,5891), (5256, 5576)])
+        self.t1.finalize()
+        self.assertIsNotNone(self.t1.coding_exons)
         self.assertEqual(sorted(self.t1.coding_exons), sorted(correct))
         t1 = self.t1.copy()
         t1.strip_cds()

Mikado/transcripts/transcript.py

@@ -2085,6 +2085,7 @@ def _wrapped(combined_cds, combined_cds_length, exons):
                         coding.append(exon)
                         break
                     continue
+            return coding
 
         return _wrapped(tuple(self.combined_cds), self.combined_cds_length, tuple(self.exons))
 

setup.cfg

@@ -3,7 +3,7 @@ test=pytest
 
 [tool:pytest]
 addopts = --cov Mikado
-norecursedirs = datrie*
+norecursedirs = datrie* build
 # filterwarnings =
 #     # Fail the tests if there are any warnings.
 #     error