Type hints and f string

loqusdb/commands/identity.py

@@ -22,7 +22,7 @@ def identity(ctx, variant_id):
 
     variant_count: int = adapter.db.identity.count_documents({"variant_id": variant_id})
     if variant_count == 0:
-        LOG.info("No hits for variant %s", variant_id)
+        LOG.info(f"No hits for variant {variant_id}")
         return
 
     for res in result:

tests/commands/test_export.py

@@ -2,7 +2,7 @@
 
 from loqusdb.commands.cli import cli as base_command
 
-def test_export_base(real_db_name):
+def test_export_base(real_db_name:str):
     """Test the base command that exports variants."""
 
     runner = CliRunner()

tests/commands/test_identity.py

@@ -2,7 +2,7 @@
 
 from loqusdb.commands.cli import cli as base_command
 
-def test_identity(real_db_name):
+def test_identity(real_db_name:str):
     """Test the SV identity base command."""
 
     runner = CliRunner()

tests/commands/test_view.py

@@ -1,8 +1,8 @@
 from click.testing import CliRunner
-
+from loqusdb.plugins.mongo.adapter import MongoAdapter
 from loqusdb.commands.cli import cli as base_command
 
-def test_view_cases_base(real_mongo_adapter, real_db_name):
+def test_view_cases_base(real_mongo_adapter, real_db_name:str):
     """Test the base command that returns database cases."""
 
     ## GIVEN an empty database