[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -31,12 +31,12 @@ repos:
         - id: rst-directive-colons
         - id: rst-inline-touching-normal
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.15.20
+      rev: v0.16.6
       hooks:
         - id: ruff
         - id: ruff-format
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v2.1.0
+      rev: v2.3.1
       hooks:
           - id: mypy
             additional_dependencies:
@@ -48,7 +48,7 @@ repos:
                 - types-simplejson
                 - pandas-stubs
     - repo: https://github.com/codespell-project/codespell
-      rev: v2.4.2
+      rev: v2.4.3
       hooks:
       - id: codespell
         additional_dependencies:

docs/source/pages/examples/acquisition-script.md

@@ -22,15 +22,16 @@ def get_file_path():
     # the function get_next_ses() normally checks for the next session
     # if you are recording for a new subject you can use it as well to create
     # the first session folder for this subject.
-    session = project.get_next_ses(top_level_folder="rawdata",
-                                   sub=f"sub-{sub}_id-{id_number}")
+    session = project.get_next_ses(
+        top_level_folder="rawdata", sub=f"sub-{sub}_id-{id_number}"
+    )
 
     # create the folders
     created_folders = project.create_folders(
         top_level_folder="rawdata",
         sub_names=f"sub-{sub}_id-{id_number}",
         ses_names=f"{session}_@DATETIME@",
-        datatype=["behav"]
+        datatype=["behav"],
     )
     # create a prompt to enter the experiment information and
     # conspecific ID for social experiments.
@@ -46,7 +47,7 @@ def get_file_path():
     file_name_video_1 = f"{exp_number}_{comsp_id}.avi"
 
     # create the path to the video file
-    file_path1 = created_folders['behav'][0] / file_name_video_1
+    file_path1 = created_folders["behav"][0] / file_name_video_1
     file_path1.touch()
 
     return file_path1

docs/source/pages/examples/lab-project-checker.md

@@ -8,7 +8,6 @@ This runs weekly to catch any formatting issues introduced into projects.
 
 
 ```python
-
 from datashuttle import DataShuttle
 import os
 
@@ -27,7 +26,9 @@ for p in project_list:
     if os.path.isdir(project_path):  # Only process directories
         project = DataShuttle(p)
         try:
-            errors = project.validate_project("rawdata", display_mode="print", strict_mode=True)
+            errors = project.validate_project(
+                "rawdata", display_mode="print", strict_mode=True
+            )
             error_messages[p] = errors if errors else "No errors"
         except Exception as e:
             error_messages[p] = f"Validation failed: {e}"
@@ -41,5 +42,4 @@ with open(log_file, "w") as f:
 # Optional: Print summary of error messages
 for project, message in error_messages.items():
     print(f"{project}: {message}")
-
 ```

docs/source/pages/get_started/getting-started.md

@@ -223,9 +223,7 @@ project.make_config_file(
 If you want to change any config in the future, use the [](update_config_file()) method
 
 ```python
-project.update_config_file(
-    local_path=r"C:\a\new\path"
-)
+project.update_config_file(local_path=r"C:\a\new\path")
 ```
 
 We are now ready to create our standardised project folders.
@@ -347,7 +345,7 @@ project.create_folders(
     top_level_folder="rawdata",
     sub_names="sub-001",
     ses_names="ses-001_@DATE@",
-    datatype=["behav", "ephys"]
+    datatype=["behav", "ephys"],
 )
 ```
 
@@ -368,14 +366,11 @@ To get the next subject  in this project (`sub-002`) and the next
 session for that subject (`ses-001`) we can run:
 
 ```python
-next_sub = project.get_next_sub("rawdata")                # returns "sub-001"
+next_sub = project.get_next_sub("rawdata")  # returns "sub-001"
 next_ses = project.get_next_ses("rawdata", sub=next_sub)  # returns "ses-001"
 
 project.create_folders(
-    "rawdata",
-    next_sub,
-    f"{next_ses}_@DATE@",
-    datatype=["behav", "ephys"]
+    "rawdata", next_sub, f"{next_ses}_@DATE@", datatype=["behav", "ephys"]
 )
 ```
 
@@ -459,8 +454,7 @@ folder_path_dict = project.create_folders(
     top_level_folder="rawdata",
     sub_names=["sub-001"],
     ses_names=["ses-001_@DATE@"],
-    datatype=["behav", "ephys"]
-
+    datatype=["behav", "ephys"],
 )
 
 print([path_ for path_ in folder_path_dict["behav"]])
@@ -693,7 +687,7 @@ project.download_custom(
     top_level_folder="rawdata",
     sub_names="all",
     ses_names="ses-001_@*@",
-    datatype="behav"
+    datatype="behav",
 )
 ```
 

docs/source/pages/get_started/quick-validate-project.md

@@ -53,7 +53,6 @@ validate_project_from_path(
     project_path="/mydrive/path/to/project/project_name",
     display_mode="error",
 )
-
 ```
 
 In this case, `display_mode=error` will result in an error on the first encountered validation issue.

docs/source/pages/user_guides/create-folders.md

@@ -174,7 +174,7 @@ created_folders = project.create_folders(
     top_level_folder="rawdata",
     sub_names=["sub-001", "002"],
     ses_names="ses-001_@DATE@",
-    datatype=["behav", "funcimg"]
+    datatype=["behav", "funcimg"],
 )
 ```
 

docs/source/pages/user_guides/set-up-a-project.md

@@ -56,22 +56,16 @@ If a project already exists, this should match the project folder name (i.e. the
 
 
 ```python
-
 from datashuttle import DataShuttle
 
 project = DataShuttle("my_project_name")
-
 ```
 
 Next, give ``datashuttle`` the path to the project folder (this can,
 but doesn't have to, include the ``project_name``)
 
 ```python
-
-project.make_config_file(
-    local_path=r"C:\MyUsername\my_data\my_project_name"
-)
-
+project.make_config_file(local_path=r"C:\MyUsername\my_data\my_project_name")
 ```
 \
 The project is now ready for use, and in future can be instantiated with the line:

docs/source/pages/user_guides/update-configs.md

@@ -41,8 +41,7 @@ For example, to change the `local_path` and `central_path`:
 
 ```python
 project.update_config_file(
-    local_path="/a/new/local/path",
-    central_path="/a/new/central/path"
+    local_path="/a/new/local/path", central_path="/a/new/central/path"
 )
 ```
 

docs/source/pages/user_guides/validate.md

@@ -63,7 +63,9 @@ from datashuttle import DataShuttle
 
 project = DataShuttle("my_project")
 
-project.make_config_file(local_path="/path/to/my/project")  # only required once, on initial project set up
+project.make_config_file(
+    local_path="/path/to/my/project"
+)  # only required once, on initial project set up
 
 error_messages = project.validate_project(
     "rawdata",
@@ -126,14 +128,9 @@ In ``strict_mode``, non-[NeuroBlueprint](https://neuroblueprint.neuroinformatics
 Therefore, any additional folders at the subject or session level will raise a validation error, for example:
 
 ```python
-project.validate_project(
-    "rawdata",
-    display_mode="print",
-    strict_mode=True
-)
+project.validate_project("rawdata", display_mode="print", strict_mode=True)
 
 # BAD_NAME: The name: some_other_folder of type: sub- is not valid. Path: <path to folder>
-
 ```
 
 ## ``include_central``
@@ -149,9 +146,7 @@ The ``include_central`` argument must be set to ``True``:
 
 ```python
 error_messages = project.validate_project(
-    "rawdata",
-    display_mode="warn",
-    include_central=True
+    "rawdata", display_mode="warn", include_central=True
 )
 ```