neuroinformatics-unit · adamltyson · Sep 22, 2023 · Sep 21, 2023
diff --git a/README.md b/README.md
@@ -1,13 +1,13 @@
-# SWC-Blueprint
+# NeuroBlueprint
 
-![](docs/source/_static/swc-blueprint_logo-dark_no-text.png)
+![](docs/source/_static/NeuroBlueprint_logo-dark_no-text.png)
 
-`SWC-Blueprint` is a folder structure specification for (systems) neuroscience research projects. It is inspired by, and based on the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/), widely used in human neuroimaging.
+`NeuroBlueprint` is a folder structure specification for (systems) neuroscience research projects. It is inspired by, and based on the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/), widely used in human neuroimaging.
 
-The [SWC-Blueprint specification](specification.md) provides a set of rules and guidelines for project folder organisation, ensuring consistent data management within and between labs. The focus is on ensuring minimal overhead for researchers.
+The [NeuroBlueprint specification](specification.md) provides a set of rules and guidelines for project folder organisation, ensuring consistent data management within and between labs. The focus is on ensuring minimal overhead for researchers.
 
-`SWC-Blueprint` is being developed at the [Sainsbury Wellcome Centre (SWC) for Neural Circuits and Behaviour](https://www.sainsburywellcome.org/) by members of the [Neuroinformatics Unit (NIU)](https://neuroinformatics.dev/). As such, it prioritizes interoperability with NIU-developed data analysis tools.
+`NeuroBlueprint` is being developed at the [Sainsbury Wellcome Centre (SWC) for Neural Circuits and Behaviour](https://www.sainsburywellcome.org/) by members of the [Neuroinformatics Unit (NIU)](https://neuroinformatics.dev/). As such, it prioritizes interoperability with NIU-developed data analysis tools.
 
-That said, the specification is designed to be as general as possible, and should be useful to anyone within the neuroscience field. We (the NIU) welcome [feedback](https://github.com/neuroinformatics-unit/SWC-Blueprint/discussions) and contributions from the wider community and commit to maintaining the specification as a living and evolving document. We will also collaborate with [ongoing efforts](https://github.com/INCF/neuroscience-data-structure) by the [INCF](https://www.incf.org/) and [BIDS community](https://bids.neuroimaging.io/) to extend the BIDS specification to non-human animal research.
+That said, the specification is designed to be as general as possible, and should be useful to anyone within the neuroscience field. We (the NIU) welcome [feedback](https://github.com/neuroinformatics-unit/NeuroBlueprint/discussions) and contributions from the wider community and commit to maintaining the specification as a living and evolving document. We will also collaborate with [ongoing efforts](https://github.com/INCF/neuroscience-data-structure) by the [INCF](https://www.incf.org/) and [BIDS community](https://bids.neuroimaging.io/) to extend the BIDS specification to non-human animal research.
 
-This repository hosts the source code for the [SWC-Blueprint website](https://swc-blueprint.neuroinformatics.dev).
+This repository hosts the source code for the [NeuroBlueprint website](https://neuroblueprint.neuroinformatics.dev).
diff --git a/...tatic/swc-blueprint_logo-dark_no-text.png → ...atic/NeuroBlueprint_logo-dark_no-text.png b/...tatic/swc-blueprint_logo-dark_no-text.png → ...atic/NeuroBlueprint_logo-dark_no-text.png
diff --git a/...atic/swc-blueprint_logo-light_no-text.png → ...tic/NeuroBlueprint_logo-light_no-text.png b/...atic/swc-blueprint_logo-light_no-text.png → ...tic/NeuroBlueprint_logo-light_no-text.png
diff --git a/...tatic/swc-blueprint_project_tree_dark.png → ...atic/NeuroBlueprint_project_tree_dark.png b/...tatic/swc-blueprint_project_tree_dark.png → ...atic/NeuroBlueprint_project_tree_dark.png
diff --git a/...atic/swc-blueprint_project_tree_light.png → ...tic/NeuroBlueprint_project_tree_light.png b/...atic/swc-blueprint_project_tree_light.png → ...tic/NeuroBlueprint_project_tree_light.png
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -17,7 +17,7 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'SWC-Blueprint'
+project = 'NeuroBlueprint'
 copyright = '2022, UCL'
 author = 'Neuroinformatics Unit'
 
@@ -82,12 +82,12 @@
 # a list of builtin themes.
 #
 html_theme = 'pydata_sphinx_theme'
-html_title = 'SWC-Blueprint'
+html_title = 'NeuroBlueprint'
 
 # Redirect the webpage to another URL
 # Sphinx will create the appropriate CNAME file in the build directory
 # https://www.sphinx-doc.org/en/master/usage/extensions/githubpages.html
-html_baseurl = 'https://swc-blueprint.neuroinformatics.dev/'
+html_baseurl = 'https://neuroblueprint.neuroinformatics.dev/'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -108,15 +108,15 @@
             # Label for this link
             "name": "GitHub",
             # URL where the link will redirect
-            "url": "https://github.com/neuroinformatics-unit/SWC-Blueprint",  # required
+            "url": "https://github.com/neuroinformatics-unit/NeuroBlueprint",  # required
             # Icon class (if "type": "fontawesome"), or path to local image (if "type": "local")
             "icon": "fa-brands fa-github",
             # The type of image to be used (see below for details)
             "type": "fontawesome",
         }
     ],
     "logo": {
-        "text": f"SWC-Blueprint v{release}",
+        "text": f"NeuroBlueprint v{release}",
         "image_light": "logo_light.png",
         "image_dark": "logo_dark.png",
     },

diff --git a/docs/source/index.md b/docs/source/index.md
@@ -1,15 +1,15 @@
-# SWC-Blueprint
+# NeuroBlueprint
 
-<img src="_static/swc-blueprint_logo-light_no-text.png" alt="SWC-Blueprint logo" class="only-light img-responsive"/>
-<img src="_static/swc-blueprint_logo-dark_no-text.png" alt="SWC-Blueprint logo" class="only-dark img-responsive"/>
+<img src="_static/NeuroBlueprint_logo-light_no-text.png" alt="NeuroBlueprint logo" class="only-light img-responsive"/>
+<img src="_static/NeuroBlueprint_logo-dark_no-text.png" alt="NeuroBlueprint logo" class="only-dark img-responsive"/>
 
-**SWC-Blueprint** is a folder structure specification for (systems) neuroscience research projects. It is inspired by, and based on the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/), widely used in human neuroimaging.
+**NeuroBlueprint** is a folder structure specification for (systems) neuroscience research projects. It is inspired by, and based on the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/), widely used in human neuroimaging.
 
-The [SWC-Blueprint specification](specification.md) provides a set of rules and guidelines for project folder organisation, ensuring consistent data management within and between labs. The focus is on ensuring minimal overhead for researchers.
+The [NeuroBlueprint specification](specification.md) provides a set of rules and guidelines for project folder organisation, ensuring consistent data management within and between labs. The focus is on ensuring minimal overhead for researchers.
 
-**SWC-Blueprint** is being developed at the [Sainsbury Wellcome Centre (SWC) for Neural Circuits and Behaviour](https://www.sainsburywellcome.org/) by members of the [Neuroinformatics Unit (NIU)](https://neuroinformatics.dev/). As such, it prioritizes interoperability with NIU-developed data analysis tools.
+**NeuroBlueprint** is being developed at the [Sainsbury Wellcome Centre (SWC) for Neural Circuits and Behaviour](https://www.sainsburywellcome.org/) by members of the [Neuroinformatics Unit (NIU)](https://neuroinformatics.dev/). As such, it prioritizes interoperability with NIU-developed data analysis tools.
 
-That said, the specification is designed to be as general as possible, and should be useful to anyone within the neuroscience field. We (the NIU) welcome [feedback](https://github.com/neuroinformatics-unit/SWC-Blueprint/discussions) and contributions from the wider community and commit to maintaining the specification as a living and evolving document. We will also collaborate with [ongoing efforts](https://github.com/INCF/neuroscience-data-structure) by the [INCF](https://www.incf.org/) and [BIDS community](https://bids.neuroimaging.io/) to extend the BIDS specification to non-human animal research.
+That said, the specification is designed to be as general as possible, and should be useful to anyone within the neuroscience field. We (the NIU) welcome [feedback](https://github.com/neuroinformatics-unit/NeuroBlueprint/discussions) and contributions from the wider community and commit to maintaining the specification as a living and evolving document. We will also collaborate with [ongoing efforts](https://github.com/INCF/neuroscience-data-structure) by the [INCF](https://www.incf.org/) and [BIDS community](https://bids.neuroimaging.io/) to extend the BIDS specification to non-human animal research.
 
 ```{toctree}
 :maxdepth: 3

diff --git a/docs/source/specification.md b/docs/source/specification.md
@@ -1,6 +1,6 @@
 # The specification
 
-The current version of **SWC-Blueprint** mainly aims to enforce a uniform and consistent [project folder structure](#project-folder-structure).
+The current version of **NeuroBlueprint** mainly aims to enforce a uniform and consistent [project folder structure](#project-folder-structure).
 In addition, it also includes some non-mandatory conventions for [naming files](#file-naming-conventions) and storing [tabular metadata](#tabular-metadata).
 
 :::{note}
@@ -13,8 +13,8 @@ Standardised project folders contain data that are hierarchically structured acc
 
 For example:
 
-<img src="_static/swc-blueprint_project_tree_light.png" alt="SWC-Blueprint logo" class="only-light img-responsive"/>
-<img src="_static/swc-blueprint_project_tree_dark.png" alt="SWC-Blueprint logo" class="only-dark img-responsive"/>
+<img src="_static/NeuroBlueprint_project_tree_light.png" alt="NeuroBlueprint logo" class="only-light img-responsive"/>
+<img src="_static/NeuroBlueprint_project_tree_dark.png" alt="NeuroBlueprint logo" class="only-dark img-responsive"/>
 
 ### Basic principles
 
@@ -110,7 +110,7 @@ A real project folder might look like:
 
 ## File naming conventions
 
-**SWC-Blueprint** imposes no absolute requirements on file names. That said, below we provide some recommendations for file names, based on the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#filenames).
+**NeuroBlueprint** imposes no absolute requirements on file names. That said, below we provide some recommendations for file names, based on the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#filenames).
 
 :::{admonition} What makes a good file name?
 :class: tip
@@ -130,7 +130,7 @@ A real project folder might look like:
 * Anything after the left-most stop (`.`) is considered as the file extension.
 * `sub` and `ses` *should* be included in the filename. This can seem redundant, given that the file is already in a `sub-<label>/ses-<label>` folder, but it makes it easier to identify the file if it is moved out of its original folder.
 * Additional information, such as the task name, or run number, *may* be included as further key-value pairs, e.g. `sub-001_ses-001_task-escape_run-001.csv`
-* If the acquisition software outputs data with its own mandatory file naming convention, these *should* be placed under a folder that follows the **SWC-Blueprint** naming conventions, e.g.:
+* If the acquisition software outputs data with its own mandatory file naming convention, these *should* be placed under a folder that follows the **NeuroBlueprint** naming conventions, e.g.:
 
 ```
 └── my_project/
@@ -144,7 +144,7 @@ A real project folder might look like:
 ```
 
 ### Example file names
-Below we provide some example file names adhering to the **SWC-Blueprint** naming conventions.
+Below we provide some example file names adhering to the **NeuroBlueprint** naming conventions.
 
 ```
 └── project/
@@ -165,7 +165,7 @@ Below we provide some example file names adhering to the **SWC-Blueprint** namin
 
 ## Metadata conventions
 
-**SWC-Blueprint** imposes no absolute requirements on how to store metadata. That said, we do outline some best practices, in accordance with the [BIDS specification on tabular files](https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#tabular-files).
+**NeuroBlueprint** imposes no absolute requirements on how to store metadata. That said, we do outline some best practices, in accordance with the [BIDS specification on tabular files](https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#tabular-files).
 
 ### Tabular metadata
 Tabular metadata, e.g. a table describing the animals in the project, *should* be saved as a tab-separated value file (TSV, ending with `.tsv`) , that is, a CSV file where commas are replaced by tabs. The tab character is a less ambiguous delimiter compared to commas, as it is less likely to appear in data. This makes TSV less prone to parsing errors.