neuroinformatics-unit · JoeZiminski · Sep 4, 2025 · Sep 5, 2025 · Sep 26, 2025
diff --git a/datashuttle/datashuttle_class.py b/datashuttle/datashuttle_class.py
@@ -1071,7 +1071,17 @@ def make_config_file(
         ds_logger.close_log_filehandler()
 
     def update_config_file(self, **kwargs) -> None:
-        """Update the configuration file."""
+        """Update the configuration file.
+
+        Parameters
+        ----------
+        **kwargs
+            A dictionary of key-value pairs containing the config
+            settings to update. For example,
+            ``{"connection_method": "local_filesystem", "central_path": "/my/local/path"}``
+            will update the ``connection_method`` and ``central_path`` settings.
+
+        """
         if not self.cfg:
             utils.log_and_raise_error(
                 "Must have a config loaded before updating configs.",

diff --git a/docs/source/_static/screenshots/how-to-create-folders-example-dark.png b/docs/source/_static/screenshots/how-to-create-folders-example-dark.png
diff --git a/docs/source/_static/screenshots/how-to-create-folders-example-light.png b/docs/source/_static/screenshots/how-to-create-folders-example-light.png
diff --git a/docs/source/_static/screenshots/how-to-create-project-aws-dark.png b/docs/source/_static/screenshots/how-to-create-project-aws-dark.png
diff --git a/docs/source/_static/screenshots/how-to-create-project-aws-light.png b/docs/source/_static/screenshots/how-to-create-project-aws-light.png
diff --git a/docs/source/_static/screenshots/how-to-create-project-gdrive-dark.png b/docs/source/_static/screenshots/how-to-create-project-gdrive-dark.png
diff --git a/docs/source/_static/screenshots/how-to-create-project-gdrive-light.png b/docs/source/_static/screenshots/how-to-create-project-gdrive-light.png
diff --git a/docs/source/_static/screenshots/how-to-create-project-ssh-dark.png b/docs/source/_static/screenshots/how-to-create-project-ssh-dark.png
diff --git a/docs/source/_static/screenshots/how-to-create-project-ssh-light.png b/docs/source/_static/screenshots/how-to-create-project-ssh-light.png
diff --git a/docs/source/_static/screenshots/how-to-quick-validate-project-dark.png b/docs/source/_static/screenshots/how-to-quick-validate-project-dark.png
diff --git a/docs/source/_static/screenshots/how-to-quick-validate-project-light.png b/docs/source/_static/screenshots/how-to-quick-validate-project-light.png
diff --git a/docs/source/_static/screenshots/tutorial-1-create-datatype-dark.png b/docs/source/_static/screenshots/tutorial-1-create-datatype-dark.png
diff --git a/docs/source/_static/screenshots/tutorial-1-create-datatype-light.png b/docs/source/_static/screenshots/tutorial-1-create-datatype-light.png
diff --git a/docs/source/_static/screenshots/tutorial-1-create-screen-dark.png b/docs/source/_static/screenshots/tutorial-1-create-screen-dark.png
diff --git a/docs/source/_static/screenshots/tutorial-1-create-screen-light.png b/docs/source/_static/screenshots/tutorial-1-create-screen-light.png
diff --git a/docs/source/_static/screenshots/tutorial-1-landing-screen-dark.png b/docs/source/_static/screenshots/tutorial-1-landing-screen-dark.png
diff --git a/docs/source/_static/screenshots/tutorial-1-landing-screen-light.png b/docs/source/_static/screenshots/tutorial-1-landing-screen-light.png
diff --git a/docs/source/_static/screenshots/tutorial-1-make-screen-dark.png b/docs/source/_static/screenshots/tutorial-1-make-screen-dark.png
diff --git a/docs/source/_static/screenshots/tutorial-1-make-screen-light.png b/docs/source/_static/screenshots/tutorial-1-make-screen-light.png
diff --git a/docs/source/_static/screenshots/tutorial-1-make-screen-local-filesystem-dark.png b/docs/source/_static/screenshots/tutorial-1-make-screen-local-filesystem-dark.png
diff --git a/docs/source/_static/screenshots/tutorial-1-make-screen-local-filesystem-light.png b/docs/source/_static/screenshots/tutorial-1-make-screen-local-filesystem-light.png
diff --git a/docs/source/_static/screenshots/tutorial-validation-dark.png b/docs/source/_static/screenshots/tutorial-validation-dark.png
diff --git a/docs/source/_static/screenshots/tutorial-validation-light.png b/docs/source/_static/screenshots/tutorial-validation-light.png
diff --git a/docs/source/_static/screenshots/updating-configs-dark.png b/docs/source/_static/screenshots/updating-configs-dark.png
diff --git a/docs/source/_static/screenshots/updating-configs-light.png b/docs/source/_static/screenshots/updating-configs-light.png
diff --git a/docs/source/pages/get_started/getting-started.md b/docs/source/pages/get_started/getting-started.md
@@ -94,7 +94,7 @@ We need to set the:
 
 ``datashuttle`` supports connecting to the central storage machine
 either as a mounted drive or through SHH. \
-See [Set up configs for transfer(set-up-a-project-for-transfer)
+See [Set up configs for transfer](set-up-a-project-for-transfer)
 for detailed instructions for
 connecting a mounted drive or by using SSH.
 
@@ -198,7 +198,7 @@ from datashuttle import DataShuttle
 project = DataShuttle("my_first_project")
 ```
 
-Next, we will use the `make_config_file()` method set the
+Next, we will use the [](make_config_file()) method set the
 configurations ('configs') for our project.
 
 
@@ -220,7 +220,7 @@ project.make_config_file(
 )
 ```
 
-If you want to change any config in the future, use the `update_config_file()` method
+If you want to change any config in the future, use the [](update_config_file()) method
 
 ```python
 project.update_config_file(
@@ -315,20 +315,20 @@ we only create `behav` and `ephys` folders.
 ```{image} /_static/screenshots/tutorial-1-create-datatype-dark.png
    :align: center
    :class: only-dark
-   :width: 400px
+   :width: 375px
 ```
 ```{image} /_static/screenshots/tutorial-1-create-datatype-light.png
    :align: center
    :class: only-light
-   :width: 400px
+   :width: 375px
 ```
 <br>
 
 Finally, click `Create Folders` to create the project folders.
 :::
 :::{tab-item} Python API
 :sync: python
-We will create project folders with the `create_folders()` method.
+We will create project folders with the [](create_folders()) method.
 
 Following the [NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/)
 style we will  call the first subject `sub-001`. Additional key-value pairs
@@ -360,8 +360,8 @@ An error will be raised if names break with the specification and
 the folders will not be created.
 ```
 
-Two useful methods to automate folder creation are `get_next_sub()` and
-`get_next_ses()`. These can be used to automatically get the next subject
+Two useful methods to automate folder creation are [](get_next_sub()) and
+[](get_next_ses()). These can be used to automatically get the next subject
 and session names in a project.
 
 To get the next subject  in this project (`sub-002`) and the next
@@ -450,7 +450,7 @@ Finally, hover the mouse over the `Directory Tree` and press `CTRL+R` to refresh
 :::{tab-item} Python API
 :sync: python
 
-`create_folders()` returns the full filepaths of created datatype folders.
+[](create_folders()) returns the full filepaths of created datatype folders.
 
 These can be used in acquisition scripts to save data to these folders:
 
@@ -543,7 +543,7 @@ Next, we will use `Custom` transfers to move only a subset of the dataset.
 :::{tab-item} Python API
 :sync: python
 
-`upload_entire_project()` is a high level method that uploads all files
+[](upload_entire_project()) is a high level method that uploads all files
 in the project.
 This includes both the `rawdata` and `derivatives` top-level folders—see the
 [NeuroBlueprint specification](https://neuroblueprint.neuroinformatics.dev/latest/specification.html)
@@ -560,7 +560,7 @@ All files will be uploaded from the local version of the project to central stor
 Navigating to the `central_path` in your systems file browser, the newly transferred data
 will have appeared.
 
-Other methods (e.g. `upload_rawdata()` and `upload_custom()`) provide customisable
+Other methods (e.g. [](upload_rawdata()) and [](upload_custom())) provide customisable
 transfers (and every `upload` method has an equivalent `download` method).
 
 See the  [How to Transfer Data](how-to-transfer-data) page for full details
@@ -683,8 +683,8 @@ of files will now be available in the **local path**.
 :::{tab-item} Python API
 :sync: python
 
-We will use the `download_custom()` method (the download equivalent method of
-the `upload_custom()`).
+We will use the [](download_custom()) method (the download equivalent method of
+the [](upload_custom())).
 
 Convenience tags can be used to make downloading subsets of data easier:
 

diff --git a/docs/source/pages/get_started/set-up-a-project.md b/docs/source/pages/get_started/set-up-a-project.md
@@ -20,12 +20,12 @@ Enter the name of your project, the path to your project folder and
 select `No connection (local only)` (note that the `Central Path` option
 will be disabled).
 
-```{image} /_static/screenshots/how-to-make-local-project-configs-dark.png
+```{image} /_static/screenshots/tutorial-1-make-screen-dark.png
    :align: center
    :class: only-dark
    :width: 900px
 ```
-```{image} /_static/screenshots/how-to-make-local-project-configs-light.png
+```{image} /_static/screenshots/tutorial-1-make-screen-light.png
    :align: center
    :class: only-light
    :width: 900px
@@ -74,11 +74,13 @@ project.make_config_file(
 
 ```
 \
-The project is now ready for use, and in future can be instantiated
-with the line ``project = DataShuttle("my_project_name")`` (i.e. you will not
-have to set the `local_path` again).
+The project is now ready for use, and in future can be instantiated with the line:
+```python
+project = DataShuttle("my_project_name")
+```
+(i.e. you will not have to set the `local_path` again).
 
-If you wish to change the project settings at a later time, use ``project.update_config_file()``.
+If you wish to change the project settings at a later time, use [](update_config_file()).
 
 :::
 ::::
@@ -159,12 +161,12 @@ First, click the `Make New Project` button from the launch page.
 
 The `Make New Project` screen will be displayed:
 
-```{image} /_static/screenshots/tutorial-1-make-screen-dark.png
+```{image} /_static/screenshots/tutorial-1-make-screen-local-filesystem-dark.png
    :align: center
    :class: only-dark
    :width: 900px
 ```
-```{image} /_static/screenshots/tutorial-1-make-screen-light.png
+```{image} /_static/screenshots/tutorial-1-make-screen-local-filesystem-light.png
    :align: center
    :class: only-light
    :width: 900px
@@ -201,7 +203,7 @@ project = DataShuttle("my_first_project")
 
 ```
 
-Next, the `make_config_file()` method can be used to set up a new
+Next, the [](make_config_file()) method can be used to set up a new
 project with the desired **local path**, **central path** and
 **connection method**.
 

diff --git a/docs/source/pages/user_guides/create-folders.md b/docs/source/pages/user_guides/create-folders.md
@@ -161,7 +161,7 @@ any alphanumeric character, rather than restricted to integers.
 :::{tab-item} Python API
 :sync: python
 
-The `create_folders()` method is used for folder creation.
+The [](create_folders()) method is used for folder creation.
 
 We simply need to provide the subject, session and datatypes to create:
 
@@ -178,9 +178,8 @@ created_folders = project.create_folders(
 )
 ```
 
-The method outputs `created_folders`, which contains the
-`Path`s to created datatype folders. See the below section for
-details on the `@DATE@` and other convenience tags.
+`created_folders` is a list containing  `Path`s to created datatype folders.
+See the below section for details on the `@DATE@` and other convenience tags.
 
 By default, an error will be raised if the folder names break
 with [Neuroblueprint](https://neuroblueprint.neuroinformatics.dev/)

diff --git a/docs/source/pages/user_guides/read-logs.md b/docs/source/pages/user_guides/read-logs.md
@@ -44,7 +44,7 @@ Clicking `Open Most Recent` will open the most recently saved logs.
 :sync: python
 
 The path where logs are stored can be accessed by running
-`get_logging_path()`:
+[](get_logging_path()):
 
 ```python
 logs_path = project.get_logging_path()

diff --git a/docs/source/pages/user_guides/transfer-data.md b/docs/source/pages/user_guides/transfer-data.md
@@ -146,7 +146,7 @@ Click `Transfer` to begin.
 :::{tab-item} Python API
 :sync: python
 
-The `upload_rawdata()`, `upload_derivatives()` and `download_rawdata()`, `download_derivatives()`
+The [](upload_rawdata()), [](upload_derivatives()) and [](download_rawdata()), [](download_derivatives())
 methods target transfer to a particular top-level folder.
 
 The below example will upload `rawdata` then download `derivatives`.
@@ -221,7 +221,7 @@ Finally, click `Transfer` to begin.
 :::{tab-item} Python API
 :sync: python
 
-The `upload_custom()` and `download_custom()` methods can be used for custom
+The [](upload_custom()) and [](download_custom()) methods can be used for custom
 data transfers. For example, to perform a custom upload:
 
 ```python

diff --git a/docs/source/pages/user_guides/update-configs.md b/docs/source/pages/user_guides/update-configs.md
@@ -11,12 +11,12 @@ The project configs can be updated at any time following the initial set up.
 ```{image} /_static/screenshots/updating-configs-dark.png
    :align: center
    :class: only-dark
-   :width: 900px
+   :width: 1100px
 ```
 ```{image} /_static/screenshots/updating-configs-light.png
    :align: center
    :class: only-light
-   :width: 900px
+   :width: 1100px
 ```
 <br>
 
@@ -35,7 +35,7 @@ If SSH configs are changed the connection may need to be
 :sync: python
 
 The project configs on the local machine can be selectively
-updated with the `update_config_file()` method.
+updated with the [](update_config_file()) method.
 
 For example, to change the `local_path` and `central_path`:
 
@@ -46,12 +46,8 @@ project.update_config_file(
 )
 ```
 
-If SSH configs are changed the connection may need to be
-[set up again](new-project-ssh) with:
-
-```python
-project.setup_ssh_connection()
-```
+If SSH, AWS or Google Drive configs are changed the connection
+may need to be [set up again](new-project-ssh).
 
 :::
 ::::
diff --git a/docs/source/pages/user_guides/use-name-templates.md b/docs/source/pages/user_guides/use-name-templates.md
@@ -61,10 +61,10 @@ will be automatically saved. These settings will persist across
 :::{tab-item} Python API
 :sync: python
 
-The `set_name_templates()` and `get_name_templates()` can be used
+The [](set_name_templates()) and [](get_name_templates()) can be used
 to set and get current name template settings.
 
-`set_name_templates` takes as input the `name_template` dictionary,
+[](set_name_templates()) takes as input the `name_template` dictionary,
 which is formatted as below:
 
 ```

diff --git a/docs/source/pages/user_guides/validate.md b/docs/source/pages/user_guides/validate.md
@@ -38,13 +38,13 @@ for details on the options.
 ```{image} /_static/screenshots/tutorial-validation-light.png
 :align: center
 :class: only-light
-:width: 600px
+:width: 800px
 ```
 
 ```{image} /_static/screenshots/tutorial-validation-dark.png
 :align: center
 :class: only-dark
-:width: 600px
+:width: 800px
 ```
 
 :::
@@ -53,7 +53,7 @@ for details on the options.
 :sync: python
 
 
-Project validation can be run with the [](datashuttle.DataShuttle.validate_project) function.
+Project validation can be run with the [](validate_project) function.
 
 Violations of the [NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/latest/index.html) can be set to raise an error, be displayed as warnings or printed as output.
 They are also returned in a list of strings.