Fix config test

WrightonLabCSU · Jan 7, 2023 · c97cf0f · c97cf0f
1 parent 076fcc4
commit c97cf0f
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Showing 3 changed files with 6 additions and 10 deletions.
diff --git a/mag_annotator/CONFIG b/mag_annotator/CONFIG
@@ -25,3 +25,4 @@
   },
   "description_db": null,
   "dram_version": null
+}
diff --git a/mag_annotator/summarize_vgfs.py b/mag_annotator/summarize_vgfs.py
@@ -119,8 +119,8 @@ def look_up_metabolic_info(search_db, match_db, match_db_name):
             .assign(gene_id_origin=match_db_name))
 
     amg_database_frame = (amg_database
-                          .melt(value_vars=['KO', 'EC', 'PFAM'], 
-                                id_vars=['gene', 'module', 'metabolism', 
+                          .melt(value_vars=['KO', 'EC', 'PFAM'],
+                                id_vars=['gene', 'module', 'metabolism',
                                          'reference', 'verified'],
                                 value_name='gene_id')
                           .drop('variable', axis=1)

diff --git a/tests/test_config_cleen.py b/tests/test_config_cleen.py
@@ -11,14 +11,8 @@
 from mag_annotator.utils import setup_logger
 
 
-@pytest.fixture()
-def logger(tmpdir):
-    logger = logging.getLogger('test_log')
-    setup_logger(logger)
-    return logger
-
 
-def db_w_entries(logger):
+def test_clean_config():
     empty_config = {
         "search_databases": {
         "kegg": None,
@@ -47,5 +41,6 @@ def db_w_entries(logger):
       "description_db": None,
       "dram_version": None
     }
-    db_handler = DatabaseHandler(logger, path.join('tests', 'data', 'test_CONFIG'))
+    logger = logging.getLogger('test_log')
+    db_handler = DatabaseHandler(logger)
     assert db_handler.config == empty_config
-Original file line number
+Diff line change
@@ Expand Up / @@ -25,3 +25,4 @@ @@
       },
       "description_db": null,
       "dram_version": null
+    }