Fixing small pytest errors

ectyper/ectyper.py

@@ -65,6 +65,7 @@ def run_program():
 
     args = commandLineOptions.parse_command_line()
 
+
     output_directory = create_output_directory(args.output)
 
     # Create a file handler for log messages in the output directory for the root thread

ectyper/genomeFunctions.py

@@ -35,12 +35,14 @@ def get_files_as_list(files_or_directories, max_depth_level):
     """
 
     files_list = []
+
+
     init_min_dir_level = min([os.path.abspath(p).count(os.sep)+1 if os.path.isdir(p) else os.path.abspath(p).count(os.sep) for p in files_or_directories])
 
-    for file_or_directory in sorted([os.path.abspath(p) for p in files_or_directories]):
+    for file_or_directory in sorted([os.path.abspath(p) for p in files_or_directories if len(p) != 0]):
 
         dir_level_current = get_relative_directory_level(file_or_directory, init_min_dir_level)
-        
+
         if dir_level_current > max_depth_level:
             LOG.info(f"Directory level exceeded ({dir_level_current} > {max_depth_level}), skipping {file_or_directory} ...")
             continue

test/test_ectyper_integration.py

@@ -59,7 +59,7 @@ def test_integration_no_file():
     :return: None
     """
     file = ''
-    set_input(file)
+    set_input(input=file)
     with pytest.raises(FileNotFoundError) as se:
         ectyper.run_program()
     assert se.type == FileNotFoundError