Fix tests (#183)

* Rename so pytest finds files; remove duplicate test file

* Remove classes/setup/teardown, use pytest.fixture; all tests discoverable by pytest

* Bug fix where alt probes could be in wrong order

src/mykrobe/cmds/dump.py

@@ -32,7 +32,7 @@ def get_non_singelton_variants(db_name):
 
 def run(parser, args):
     db_name = '%s-%s' % (DB_PREFIX, args.db_name)
-    DB = connect(db_name, host=args.db_uri)
+    DB = connect(db_name, host=args.db_uri, uuidRepresentation="pythonLegacy")
     if args.verbose:
         logger.setLevel(level=logging.DEBUG)
     else:

src/mykrobe/cmds/makeprobes.py

@@ -39,7 +39,7 @@ def run(parser, args):
         logger.info("Not connecting to database, because --no-backgrounds option used")
         DB = None
     else:
-        DB = connect("%s-%s" % (DB_PREFIX, args.db_name), host=args.db_uri)
+        DB = connect("%s-%s" % (DB_PREFIX, args.db_name), host=args.db_uri, uuidRepresentation="pythonLegacy")
 
     if DB is not None:
         try:

src/mykrobe/cmds/variants/add.py

@@ -48,7 +48,7 @@ def run(parser, args):
     else:
         logger.setLevel(logging.INFO)
     DBNAME = "%s-%s" % (DB_PREFIX, args.db_name)
-    connect(DBNAME, host=args.db_uri)
+    connect(DBNAME, host=args.db_uri, uuidRepresentation="pythonLegacy")
     logger.debug("Using DB %s" % DBNAME)
 
     with open(args.reference_set) as fp:
@@ -58,7 +58,7 @@ def run(parser, args):
         reference_set = ReferenceSet.objects.get(name=reference_set_name)
     except DoesNotExist:
         reference_set = ReferenceSet.create_and_save(name=reference_set_name)
-        
+
     try:
         reference = Reference.create_and_save(
             name=reference_set_name, reference_sets=[reference_set], md5checksum="NA"

src/mykrobe/probes/models.py

@@ -204,6 +204,7 @@ def _generate_alternates_on_all_backgrounds(self, v, context):
                 for alt in v.alternate_bases:
                     alternate[i: i + len(v.reference_bases)] = alt
                     alternates.append(alternate)
+
         return alternates
 
     def _get_all_context_combinations(self, context):
@@ -379,7 +380,8 @@ def __init__(self, variant, refs, start, alts):
         self.refs = unique(["".join(ref) for ref in refs])
         self.start = start
         self.alts = unique(["".join(alt) for alt in alts])
-        self.alts=list(set(self.alts)-set(self.refs))
+        ref_set = set(self.refs)
+        self.alts = [x for x in self.alts if x not in ref_set]
 
 
 class Mutation(object):

tests/cmds_tests/amr_tests.py → tests/cmds_tests/amr_test.py

@@ -1,5 +1,4 @@
 import copy
-import pytest
 
 from mykrobe import amr
 

tests/end_to_end_test.py

@@ -1,6 +1,5 @@
 import json
 import os
-import pytest
 import subprocess
 
 from mykrobe.parser import parser

tests/metagenomics_tests/basic_test.py

@@ -1,54 +1,37 @@
-from unittest import TestCase
 from mykrobe.metagenomics import AMRSpeciesPredictor
 
 
-class MTBCSpeciesTests(TestCase):
-
-    def setUp(self):
-        pass
-
-    def teardown(self):
-        pass
-
-    def test_mixed_chimera(self):
-        species_predictor = AMRSpeciesPredictor(
-            phylo_group_covgs={},
-            sub_complex_covgs={},
-            species_covgs={},
-            lineage_covgs={}
-        )
-        species_predictor.out_json["phylogenetics"] = {
-            "sub_complex": {
-                "Mycobacterium_avium_complex": {
-                    "percent_coverage": 98.346,
-                    "median_depth": 54.0
-                }
-            },
-            "phylo_group": {
-                "Non_tuberculosis_mycobacterium_complex": {
-                    "percent_coverage": 82.846,
-                    "median_depth": 49
-                }
-            },
-            "species": {
-                "Mycobacterium_chimaera": {
-                    "percent_coverage": 99.162,
-                    "median_depth": 39
-                },
-                "Mycobacterium_intracellulare": {
-                    "percent_coverage": 98.662,
-                    "median_depth": 45
-                },
-                "Mycobacterium_bovis": {
-                    "percent_coverage": 9.894,
-                    "median_depth": 12.0
-                }
+def test_mixed_chimera():
+    species_predictor = AMRSpeciesPredictor(
+        phylo_group_covgs={}, sub_complex_covgs={}, species_covgs={}, lineage_covgs={}
+    )
+    species_predictor.out_json["phylogenetics"] = {
+        "sub_complex": {
+            "Mycobacterium_avium_complex": {
+                "percent_coverage": 98.346,
+                "median_depth": 54.0,
+            }
+        },
+        "phylo_group": {
+            "Non_tuberculosis_mycobacterium_complex": {
+                "percent_coverage": 82.846,
+                "median_depth": 49,
             }
-        }
+        },
+        "species": {
+            "Mycobacterium_chimaera": {"percent_coverage": 99.162, "median_depth": 39},
+            "Mycobacterium_intracellulare": {
+                "percent_coverage": 98.662,
+                "median_depth": 45,
+            },
+            "Mycobacterium_bovis": {"percent_coverage": 9.894, "median_depth": 12.0},
+        },
+    }
 
-        out_dict = species_predictor.choose_best(
-            species_predictor.out_json["phylogenetics"])
+    out_dict = species_predictor.choose_best(
+        species_predictor.out_json["phylogenetics"]
+    )
 
-        assert "Mycobacterium_chimaera" in out_dict["species"]
-        assert "Mycobacterium_intracellulare" in out_dict["species"]
-        assert "Mycobacterium_bovis" not in out_dict["species"]
+    assert "Mycobacterium_chimaera" in out_dict["species"]
+    assert "Mycobacterium_intracellulare" in out_dict["species"]
+    assert "Mycobacterium_bovis" not in out_dict["species"]