Remove 'all' default for datatype for make_sub_folders and change to …

…'' which will make no datatype by default.

datashuttle/command_line_interface.py

@@ -599,7 +599,7 @@ def construct_parser():
         type=str,
         nargs="+",
         required=False,
-        default="all",  # TODO: this is not nice, should read the default from API NOT duplicate in CLI
+        default="",  # TODO: this is not nice, should read the default from API NOT duplicate in CLI
         help=help("required_str_single_or_multiple_or_all"),
     )
 

datashuttle/datashuttle.py

@@ -159,7 +159,7 @@ def make_folders(
         self,
         sub_names: Union[str, list],
         ses_names: Optional[Union[str, list]] = None,
-        datatype: Union[List[str], str] = "all",
+        datatype: str = "",
     ) -> None:
         """
         Create a subject / session folder tree in the project
@@ -182,7 +182,8 @@ def make_folders(
                 The datatype to make in the sub / ses folders.
                 (e.g. "ephys", "behav", "histology"). If "all"
                 is selected, all datatypes permitted in
-                NeuroBlueprint will be created.
+                NeuroBlueprint will be created. If "" is passed
+                no datatype will be created.
 
         Notes
         -----

tests/tests_integration/test_filesystem_transfer.py

@@ -455,7 +455,8 @@ def test_rclone_overwrite_modified_file(
             Path("rawdata") / "sub-001" / "histology" / "test_file.txt"
         )
 
-        project.make_folders("sub-001")
+        project.make_folders("sub-001", datatype="histology")
+
         local_test_file_path = project.cfg["local_path"] / path_to_test_file
         central_test_file_path = (
             project.cfg["central_path"] / path_to_test_file
@@ -554,7 +555,9 @@ def test_specific_file_or_folder(
 
     def setup_specific_file_or_folder_files(self, project):
         """ """
-        project.make_folders(["sub-001", "sub-002"], "ses-003")
+        project.make_folders(
+            ["sub-001", "sub-002"], "ses-003", ["behav", "ephys"]
+        )
 
         path_to_test_file_behav = (
             Path("rawdata")

tests/tests_integration/test_make_folders.py

@@ -144,7 +144,8 @@ def test_explicitly_session_list(self, project):
         """
         subs = ["sub-001", "sub-002"]
         sessions = ["ses-001", "50432"]
-        project.make_folders(subs, sessions)
+
+        project.make_folders(subs, sessions, "all")
         base_folder = test_utils.get_top_level_folder_path(project)
 
         for sub in subs:
@@ -224,7 +225,8 @@ def test_custom_folder_names(self, project):
         # Make the folders
         sub = "sub-001"
         ses = "ses-001"
-        project.make_folders(sub, ses)
+
+        project.make_folders(sub, ses, "all")
 
         # Check the folders were not made / made.
         base_folder = test_utils.get_top_level_folder_path(project)
@@ -359,7 +361,7 @@ def test_all_top_level_folders(self, project, folder_name):
         subs = ["sub-001", "sub-2"]
         sessions = ["ses-001", "ses-03"]
 
-        project.make_folders(subs, sessions)
+        project.make_folders(subs, sessions, "all")
 
         # Check folder tree is made in the desired top level folder
         test_utils.check_working_top_level_folder_only_exists(