Remove superfluous warnings from tests.

datashuttle/tui/screens/create_folder_settings.py

@@ -75,7 +75,7 @@ def compose(self) -> ComposeResult:
         sub_on = True if self.input_mode == "sub" else False
         ses_on = not sub_on
 
-        explanation = """
+        explanation = r"""
         A 'Template' can be set check subject or session names are
         formatted in a specific way.
 

datashuttle/utils/getters.py

@@ -233,7 +233,7 @@ def get_num_value_digits_from_project(
 def get_num_value_digits_from_regexp(
     prefix: Prefix, name_template_regexp: str
 ) -> Union[Literal[False], int]:
-    """
+    r"""
     Given a name template regexp, find the number of values for the
     sub or ses key. These will be fixed with "\d" (digit) or ".?" (wildcard).
     If there is length-unspecific wildcard (.*) in the sub key, then skip.

datashuttle/utils/validation.py

@@ -310,7 +310,7 @@ def get_path_and_name(path_or_name: Path | str) -> Tuple[Optional[Path], str]:
 
 
 def replace_tags_in_regexp(regexp: str) -> str:
-    """
+    r"""
     Before validation, all tags in the names are converted to
     their final values (e.g. @DATE@ -> _date-<date>). We also want to
     allow template to be formatted like `sub-\d\d_@DATE@` as it
@@ -321,8 +321,8 @@ def replace_tags_in_regexp(regexp: str) -> str:
     Note `replace_date_time_tags_in_name()` operates in place on a list.
     """
     regexp_list = [regexp]
-    date_regexp = "\d\d\d\d\d\d\d\d"
-    time_regexp = "\d\d\d\d\d\d"
+    date_regexp = r"\d\d\d\d\d\d\d\d"
+    time_regexp = r"\d\d\d\d\d\d"
 
     formatting.replace_date_time_tags_in_name(
         regexp_list,

tests/test_utils.py

@@ -34,16 +34,12 @@ def setup_project_default_configs(
     """
     delete_project_if_it_exists(project_name)
 
-    warnings.filterwarnings("ignore")
-
-    project = DataShuttle(project_name)
+    project = make_project(project_name)
 
     default_configs = get_test_config_arguments_dict(
         tmp_path, project_name, set_as_defaults=True
     )
 
-    #  make_project_paths(default_configs)
-
     project.make_config_file(**default_configs)
 
     rclone.setup_rclone_config_for_ssh(
@@ -52,8 +48,6 @@ def setup_project_default_configs(
         project.cfg.ssh_key_path,
     )
 
-    warnings.filterwarnings("default")
-
     if local_path:
         os.makedirs(local_path, exist_ok=True)
         project.update_config_file(local_path=local_path)
@@ -147,7 +141,7 @@ def setup_project_fixture(tmp_path, test_project_name, project_type="full"):
             ),
         )
     elif project_type == "local":
-        project = DataShuttle(test_project_name)
+        project = make_project(test_project_name)
         project.make_config_file(
             local_path=make_test_path(tmp_path, "local", test_project_name)
         )
@@ -699,3 +693,10 @@ def get_task_by_name(name):
 async def await_task_by_name_if_present(name: str) -> None:
     if task := get_task_by_name(name):
         await task
+
+
+def make_project(project_name):
+    warnings.filterwarnings("ignore")
+    project = DataShuttle(project_name)
+    warnings.filterwarnings("default")
+    return project

tests/tests_integration/base.py

@@ -3,8 +3,6 @@
 import pytest
 import test_utils
 
-from datashuttle import DataShuttle
-
 TEST_PROJECT_NAME = "test_project"
 
 
@@ -19,7 +17,7 @@ def no_cfg_project(test):
         test_utils.delete_project_if_it_exists(TEST_PROJECT_NAME)
 
         warnings.filterwarnings("ignore")
-        no_cfg_project = DataShuttle(TEST_PROJECT_NAME)
+        no_cfg_project = test_utils.make_project(TEST_PROJECT_NAME)
         warnings.filterwarnings("default")
 
         yield no_cfg_project
@@ -51,7 +49,7 @@ def project(self, tmp_path, request):
             )
         elif project_type == "local":
             test_utils.delete_project_if_it_exists(TEST_PROJECT_NAME)
-            project = DataShuttle(TEST_PROJECT_NAME)
+            project = test_utils.make_project(TEST_PROJECT_NAME)
             project.make_config_file(local_path=tmp_path / TEST_PROJECT_NAME)
 
         else:

tests/tests_integration/test_configs.py

@@ -71,6 +71,8 @@ def test_bad_path_syntax(self, project, bad_pattern, path_type, tmp_path):
 
         Note pathlib strips "./" so not checked.
         """
+        os.chdir(tmp_path)
+
         if bad_pattern != ".":
             bad_pattern = f"{bad_pattern}/{project.project_name}"
         good_pattern = f"{tmp_path}/my/path/{project.project_name}"
@@ -236,7 +238,7 @@ def patch_get_datashuttle_path():
             patch_get_datashuttle_path,
         )
 
-        project_1 = DataShuttle("project_1")
+        project_1 = test_utils.make_project("project_1")
         project_1.make_config_file(
             tmp_path / "project_1",
             tmp_path / "project_1",
@@ -247,7 +249,7 @@ def patch_get_datashuttle_path():
         # have a config file.
         os.mkdir(tmp_path / "projects" / "project_2")
 
-        project_2 = DataShuttle("project_3")
+        project_2 = test_utils.make_project("project_3")
         project_2.make_config_file(
             tmp_path / "project_3",
             tmp_path / "project_3",
@@ -276,6 +278,6 @@ def check_config_reopen_and_check_config_again(self, project, *kwargs):
 
         del project  # del project is almost certainly unnecessary
 
-        project = DataShuttle(project_name)
+        project = test_utils.make_project(project_name)
 
         test_utils.check_configs(project, kwargs[0])

tests/tests_integration/test_filesystem_transfer.py

@@ -336,7 +336,7 @@ def test_transfer_with_keyword_parameters(
                     (base_local / "rawdata" / sub / "ses*").as_posix()
                 )
 
-                datetime_regexp = "datetime-\d{8}T\d{6}"
+                datetime_regexp = r"datetime-\d{8}T\d{6}"
 
                 assert re.fullmatch(
                     "ses-001_" + datetime_regexp, sessions_in_path[0]

tests/tests_integration/test_local_only_mode.py

@@ -4,7 +4,6 @@
 import test_utils
 from base import BaseTest
 
-from datashuttle import DataShuttle
 from datashuttle.utils.custom_exceptions import (
     ConfigError,
 )
@@ -21,7 +20,7 @@ def test_bad_setup(self, tmp_path):
         """
         local_path = tmp_path / "test_local"
 
-        project = DataShuttle("this_project_is_not_torn_down")
+        project = test_utils.make_project("this_project_is_not_torn_down")
 
         with pytest.raises(ConfigError) as e:
             project.make_config_file(

tests/tests_integration/test_logging.py

@@ -7,7 +7,6 @@
 import pytest
 import test_utils
 
-from datashuttle import DataShuttle
 from datashuttle.configs import canonical_configs
 from datashuttle.configs.canonical_tags import tags
 from datashuttle.utils import ds_logger
@@ -154,7 +153,7 @@ def test_log_filename(self, project):
 
     def test_logs_make_config_file(self, clean_project_name, tmp_path):
         """"""
-        project = DataShuttle(clean_project_name)
+        project = test_utils.make_project(clean_project_name)
 
         project.make_config_file(
             tmp_path / clean_project_name,
@@ -358,7 +357,7 @@ def test_temp_log_folder_moved_make_config_file(
         logs are moved to the passed `local_path` when
         `make_config_file()` is passed.
         """
-        project = DataShuttle(clean_project_name)
+        project = test_utils.make_project(clean_project_name)
 
         configs = test_utils.get_test_config_arguments_dict(
             tmp_path, clean_project_name
@@ -389,7 +388,7 @@ def test_clear_logging_path(self, clean_project_name, tmp_path):
         begins, this test checks the `_temp_log_path`
         is cleared correctly.
         """
-        project = DataShuttle(clean_project_name)
+        project = test_utils.make_project(clean_project_name)
 
         configs = test_utils.get_test_config_arguments_dict(
             tmp_path, clean_project_name

tests/tests_integration/test_settings.py

@@ -2,9 +2,9 @@
 import shutil
 
 import pytest
+import test_utils
 from base import BaseTest
 
-from datashuttle import DataShuttle
 from datashuttle.configs import canonical_configs
 from datashuttle.utils import validation
 from datashuttle.utils.custom_exceptions import NeuroBlueprintError
@@ -32,8 +32,8 @@ def test_persistent_settings_name_templates(self, project):
         assert name_templates["ses"] is None
 
         # Set some new settings and check they become persistent
-        sub_regexp = "sub-\d_id-.?.?_random-.*"
-        ses_regexp = "ses-\d\d_id-.?.?.?_random-.*"
+        sub_regexp = r"sub-\d_id-.?.?_random-.*"
+        ses_regexp = r"ses-\d\d_id-.?.?.?_random-.*"
 
         new_name_templates = {
             "on": True,
@@ -43,7 +43,7 @@ def test_persistent_settings_name_templates(self, project):
 
         project.set_name_templates(new_name_templates)
 
-        project_reload = DataShuttle(project.project_name)
+        project_reload = test_utils.make_project(project.project_name)
 
         reload_name_templates = project_reload.get_name_templates()
 
@@ -138,7 +138,7 @@ def test_persistent_settings_tui(self, project):
         project._update_persistent_setting("tui", new_tui_settings)
 
         # Reload and check
-        project = DataShuttle(project.project_name)
+        project = test_utils.make_project(project.project_name)
 
         reloaded_settings = project._load_persistent_settings()
         assert reloaded_settings["tui"] == new_tui_settings
@@ -155,7 +155,7 @@ def test_bypass_validation(self, project):
         # should not raise
         project.create_folders("rawdata", "sub-@@@", bypass_validation=True)
 
-        project = DataShuttle(project.project_name)
+        project = test_utils.make_project(project.project_name)
 
         with pytest.raises(BaseException) as e:
             project.create_folders("rawdata", "sub-@@@")

tests/tests_integration/test_validation.py

@@ -1,5 +1,6 @@
 import os.path
 import shutil
+import warnings
 
 import pytest
 from base import BaseTest
@@ -408,9 +409,12 @@ def test_validate_project_returned_list(self, project, prefix):
                 "rawdata", "sub-001", bad_names, bypass_validation=True
             )
 
+        warnings.filterwarnings("ignore")
         error_messages = project.validate_project(
             "rawdata", "warn", include_central=False
         )
+        warnings.filterwarnings("default")
+
         concat_error = "".join(error_messages)
 
         assert "DATETIME" in concat_error
@@ -426,9 +430,11 @@ def test_output_paths_are_valid(self, project):
             "rawdata", sub_name, ses_name, bypass_validation=True
         )
 
+        warnings.filterwarnings("ignore")
         error_messages = project.validate_project(
             "rawdata", "warn", include_central=False
         )
+        warnings.filterwarnings("default")
 
         sub_path = error_messages[0].split("Path: ")[-1]
         ses_path = error_messages[1].split("Path: ")[-1]
@@ -717,8 +723,8 @@ def test_tags_in_name_templates_pass_validation(self, project):
         """
         name_templates = {
             "on": True,
-            "sub": "sub-\d\d_@DATE@",
-            "ses": "ses-\d\d\d@DATETIME@",
+            "sub": r"sub-\d\d_@DATE@",
+            "ses": r"ses-\d\d\d@DATETIME@",
         }
 
         project.set_name_templates(name_templates)
@@ -745,7 +751,7 @@ def test_tags_in_name_templates_pass_validation(self, project):
         assert "TEMPLATE: The name: ses-001_datex-20241212" in str(e.value)
 
         # Do a quick test for time
-        name_templates["sub"] = "sub-\d\d_@TIME@"
+        name_templates["sub"] = r"sub-\d\d_@TIME@"
         project.set_name_templates(name_templates)
 
         # use time tag, should not raise
@@ -760,22 +766,23 @@ def test_tags_in_name_templates_pass_validation(self, project):
         assert "TEMPLATE: The name: ses-001_datex-20241212" in str(e.value)
 
     def test_name_templates_validate_project(self, project):
-        """
-        TODO
-        """
+
+        # set up name templates
         name_templates = {
             "on": True,
-            "sub": "sub-\d\d_id-\d.?",
-            "ses": "ses-\d\d_id-\d.?",
+            "sub": r"sub-\d\d_id-\d.?",
+            "ses": r"ses-\d\d_id-\d.?",
         }
         project.set_name_templates(name_templates)
 
+        # Create names that match, check this does not error
         project.create_folders(
             "rawdata", "sub-01_id-2b", "ses-01_id-1a", bypass_validation=True
         )
 
         project.validate_project("rawdata", "error", include_central=False)
 
+        # Create names that don't match, check they error
         project.create_folders(
             "rawdata", "sub-02_id-a1", "ses-02_id-aa", bypass_validation=True
         )

tests/tests_regression/test_backwards_compatibility.py

@@ -5,8 +5,6 @@
 import pytest
 import test_utils
 
-from datashuttle import DataShuttle
-
 TEST_PROJECT_NAME = "test_project"
 
 
@@ -20,7 +18,7 @@ def project(self):
         """
         test_utils.delete_project_if_it_exists(TEST_PROJECT_NAME)
 
-        project = DataShuttle(TEST_PROJECT_NAME)
+        project = test_utils.make_project(TEST_PROJECT_NAME)
 
         yield project
 
@@ -104,7 +102,7 @@ def load_and_check_old_version_yamls(
 
         # In the current version of datashuttle, get the settings. These are
         # thus correct for the most recent datashuttle version.
-        project = DataShuttle(TEST_PROJECT_NAME)
+        project = test_utils.make_project(TEST_PROJECT_NAME)
         project.make_config_file("cur_ver", "cur_ver", "local_filesystem")
 
         current_ver_configs = project.get_configs()
@@ -117,7 +115,7 @@ def load_and_check_old_version_yamls(
         shutil.copy(old_version_path / "config.yaml", config_path)
         shutil.copy(old_version_path / "persistent_settings.yaml", config_path)
 
-        project = DataShuttle(TEST_PROJECT_NAME)
+        project = test_utils.make_project(TEST_PROJECT_NAME)
 
         reloaded_ver_configs = project.get_configs()
         reloaded_ver_persistent_settings = project._load_persistent_settings()