More small tidy ups.

JoeZiminski · JoeZiminski · commit 223715248149 · 2025-05-22T16:55:23.000+01:00
diff --git a/docs/source/pages/get_started/getting-started.md b/docs/source/pages/get_started/getting-started.md
@@ -1,6 +1,13 @@
 (getting-started-walkthrough)=
 ## Getting Started Walkthrough
 
+:::{note}
+
+This walkthrough was written at ``datashuttle`` version `0.3.0`. While the
+interface may look slightly different, core functionality remains the same.
+
+:::
+
 This tutorial will give a full introduction to managing
 a neuroscience project with ``datashuttle``.
 
diff --git a/docs/source/pages/get_started/index.md b/docs/source/pages/get_started/index.md
@@ -45,7 +45,7 @@ formatting issues.
 Start a new project or manage an existing project.
 :::
 
-:::{grid-item-card} {fas}`desktop;sd-text-primary` Full Walkthrough
+:::{grid-item-card} {fas}`desktop;sd-text-primary` Walkthrough
 :link: getting-started
 :link-type: doc
 :class-img-top: tutorial-link-image
diff --git a/docs/source/pages/get_started/quick-validate-project.md b/docs/source/pages/get_started/quick-validate-project.md
@@ -2,23 +2,20 @@
 
 # Quickly Validate an Existing Project
 
-Datashuttle provides the functionality to validate an existing
-[NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/latest/index.html)-formatted project.
-All NeuroBlueprint issues will be flagged, including a filepath pointing to
-problematic folders.
-
-Below, we explore how to quickly validate a NeuroBlueprint-formatted
-project without setting up a full project in ``datashuttle``.
+``datashuttle`` can validate an existing
+[NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/latest/index.html)-formatted project given only the filepath.
+All [NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/latest/index.html) issues will be flagged along with the full filepath
+to any problematic folders.
 
 ::::{tab-set}
 
 :::{tab-item} Graphical Interface
 :sync: gui
 
 To quickly validate a project, start the terminal user interface with
-``datashuttle launch`` and click ``"Validate Project at Path"``.
+``datashuttle launch`` and click ``Validate Project at Path``.
 
-This will open the screen below. To validate an existing project,
+The screen below will show. To validate an existing project,
 enter the full filepath to the project folder in the top input box
 and click ``Validate``:
 
@@ -35,19 +32,19 @@ and click ``Validate``:
 <br>
 
 Any validation errors detected in the project will be displayed in the logging box.
-See ``Strict Mode`` below for key details on how the validation is performed.
+See ``Strict Mode`` below for details on how the validation is performed.
 
 **Options:**
 
 Top level folder dropdown
 : The top-level folder to validate the folders within.
 
 Strict Mode
-: If `True`, only allow NeuroBlueprint-formatted folders to exist in
-the project. By default, non-NeuroBlueprint folders (e.g. a folder
-called 'my_stuff' in the 'rawdata') are allowed, and only folders
-starting with sub- or ses- prefix are checked. In `Strict Mode`,
-any folder not prefixed with sub-, ses- or a valid datatype will
+: If `True`, only [NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/latest/index.html)-formatted folders are allowed
+in the project. By default, non-[NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/latest/index.html) folders (e.g. a folder
+called `my_stuff` in the `rawdata`) are allowed, and only folders
+starting with `sub-` or `ses-` prefix are checked. In `Strict Mode`,
+any folder not prefixed with `sub-`, `ses-` or a valid datatype will
 raise a validation issue.
 
 :::
@@ -68,8 +65,8 @@ quick_validate_project(
 
 ```
 
-In this case, display_mode=error will result in an error on the first encountered validation issue.
-Otherwise "warn" will show a python warning for all detected issues, while "print" will print directly to console.
+In this case, `display_mode=error` will result in an error on the first encountered validation issue.
+Otherwise, `"warn"` will show a python warning for all detected issues, while `"print"` will print directly to console.
 
 See the [](datashuttle.quick_validate_project) API documentation at the link,
 for full details of parameters including the important argument ``strict_mode``
@@ -78,3 +75,5 @@ that controls how validation is performed.
 :::
 
 ::::
+\
+More detail on validation options can be found in the [Validation](tutorial-validation) user guide.
diff --git a/docs/source/pages/get_started/set-up-a-project.md b/docs/source/pages/get_started/set-up-a-project.md
@@ -1,14 +1,13 @@
 (set-up-a-project_)=
 ## Set up a Project
 
-``datashuttle`` can be used to create, validate and transfer
-[NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/latest/index.html) projects. The first section will
-set up a local-only project that can manage creation
+The first section of this guide will
+set up a "local-only" project that can manage creation
 and validation of project folders. This requires
-only minimal configurations to get started.
+only minimal configuration to get started.
 
 To see how a datashuttle project can be set up for transfer,
-see the [Set up a project for transfer](set-up-a-project-for-transfer) section.
+visit [Set up a project for transfer](set-up-a-project-for-transfer) section.
 
 
 ::::{tab-set}
@@ -19,8 +18,8 @@ see the [Set up a project for transfer](set-up-a-project-for-transfer) section.
 Selecting `Make New Project` will take you to the project set up screen.
 
 Enter the name of your project, the path to your project folder and
-select `No connection (local only)` (note that the central-path options
-are now disabled).
+select `No connection (local only)` (note that the central-path option
+is now disabled).
 
 ```{image} /_static/screenshots/how-to-make-local-project-configs-dark.png
    :align: center
@@ -47,11 +46,6 @@ You will now be able to go to the project manager screen:
    :class: only-light
    :width: 900px
 ```
-<br>
-
-
-See the [create folders](how-to-create-folders) and [validate folders](tutorial-validation)
-for details on how to create and validate your project.
 
 :::
 
@@ -80,7 +74,7 @@ project.make_config_file(
 )
 
 ```
-
+\
 The project is now ready for use, and in future can be instantiated only
 with the line ``project = DataShuttle("my_project_name")`` (i.e. you will not
 have to set the `local_path` again).
@@ -102,24 +96,23 @@ New project folders can also be created in the local folder:
 project.create_folders("rawdata", "sub-001", "ses-001_@DATE@", datatype=["ephys", "behav"])
 ```
 
-see  [Create Folders](how-to-create-folders)  for more details.
-
 :::
 ::::
 
-
 Now, this project is ready for creating and validating
-folders to the [NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/latest/index.html) standard.
+folders to the [NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/latest/index.html) standard. See the [create folders](how-to-create-folders)
+and [validate folders](tutorial-validation) for details.
+
 If you would also like to transfer files to a central machine, see the next section.
 
 (set-up-a-project-for-transfer)=
 ## Set up a project for transfer
 
 Above, we have set up a ``datashuttle`` project by providing the **project name**
-and **local path**. For data transfer, transfer across the local filesystem or via SSH
-is supported. Therefore, we will need to provide:
+and **local path**. Transfer across the local filesystem or via SSH is supported.
+Therefore, we will need to provide:
 
-1) **central path**: location of the project on the central data storage machine.
+1) **central path**: location of the project on the central storage machine.
 2) Connection-specific settings (e.g. if using SSH).
 
 ```{image} /_static/datashuttle-overview-dark.png
@@ -313,7 +306,6 @@ Clicking `Save` will save these project configs. A button
 confirm the server ID and enter your password
 (you will only need to do this once).
 
-
 :::
 :::{tab-item} Python API
 :sync: python
diff --git a/docs/source/pages/user_guides/validate.md b/docs/source/pages/user_guides/validate.md
@@ -14,7 +14,8 @@ Below we will cover how to validate a datashuttle-managed project
 # Validating a local project
 
 Validation will highlight validation errors within a project. For example, consider
-``my_project``, which has a NeuroBlueprint error (a subject that does not have an integer value):
+``my_project``, which has a [NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/latest/index.html)
+error (a subject that does not have an integer value):
 
 ```shell
 └── my_project/
@@ -54,7 +55,7 @@ for details on the options.
 
 Project validation can be run with the [](datashuttle.DataShuttle.validate_project) function.
 
-Violations of the NeuroBlueprint can be set to raise an error, be displayed as warnings or printed as output.
+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.
 
 ```python
@@ -71,7 +72,7 @@ error_messages = project.validate_project(
 # UserWarning: BAD_VALUE: The value for prefix sub in name sub-abc is not an integer. Path: <path to folder>
 ```
 
-This outputs any NeuroBlueprint validation as a warning.
+This outputs any [NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/latest/index.html) validation as a warning.
 
 The returned ``error_messages`` is a last of strings containing all validation errors, to be used if required e.g.:
 
@@ -81,7 +82,7 @@ print(error_messages)
 ```
 
 The options for `display_mode` and ``"error"``, ``"warn"`` and ``"print"``.
-For `"error"`, only the first  encountered NeuroBlueprint violation will be raised.
+For `"error"`, only the first  encountered [NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/latest/index.html) violation will be raised.
 
 :::
 
@@ -100,11 +101,10 @@ use ``strict_mode``.
 
 ## ``strict_mode``
 
-In strict-mode, all folders outside the
-``datatype`` ]()
-folder (e.g. ``"ephys"``) must be NeuroBlueprint-formatted.
+In strict-mode, all folders outside the ``datatype`` folder (e.g. ``"ephys"``)
+must be [NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/latest/index.html)-formatted.
 
-NeuroBlueprint does not require all folders in the project to be NeuroBlueprint-formatted ``sub-``, ``ses-`` or
+[NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/latest/index.html) does not require all folders in the project to be [NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/latest/index.html)-formatted ``sub-``, ``ses-`` or
 datatype folders.
 
 For example, ``some_other_folder``:
@@ -119,10 +119,10 @@ For example, ``some_other_folder``:
 ```
 
 However, this means it is hard to validate all folder names, as it is not possible to determine whether
-these are mistkaes e.g. ``rat-001`` or auxiliary folders. By default, ``datashuttle`` will only look for
+these are mistakes e.g. ``rat-001`` or auxiliary folders. By default, ``datashuttle`` will only look for
 ``sub-`` or ``ses-`` prefixed files to validate.
 
-In ``strict_mode``, non-NeuroBlueprint formatted folders are not allowed (except within datatype folders).
+In ``strict_mode``, non-[NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/latest/index.html) formatted folders are not allowed (except within datatype folders).
 Therefore, any additional folders at the subject or session level will raise a validation error, for example:
 
 ```python
@@ -140,9 +140,9 @@ project.validate_project(
 
 Validation can be performed across all folders in projects in which data is transferred
 between a 'local' and 'central' machine. The validation will combine ``sub-`` and ``ses-``
-folders across 'local' and 'central' before validation. This is useful check against inconsistent value lengths
+folders across local and central before validation. This is useful check against inconsistent value lengths
 (e.g. `sub-001` vs `sub-02`) and duplicate names (e.g. ``sub-001`` and ``sub-001_date-20240101``) across
-the 'local' and 'central' project.
+the local and central project.
 
 To perform this type of validation, connection configurations [must be set](set-up-a-project-for-transfer).
 The ``include_central`` argument must be set to ``True``:
