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neuroinformatics-unit · Sep 22, 2023 · 0324a55 · 0324a55
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diff --git a/.buildinfo b/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 440ea43027b1235374accd9f6188e588
+config: b330c0af511c89d23f08cc73f851023f
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/index.doctree b/.doctrees/index.doctree
diff --git a/.doctrees/specification.doctree b/.doctrees/specification.doctree
diff --git a/CNAME b/CNAME
@@ -1 +1 @@
-swc-blueprint.neuroinformatics.dev
+neuroblueprint.neuroinformatics.dev
diff --git a/_images/swc-blueprint_logo-dark_no-text.png → _images/NeuroBlueprint_logo-dark_no-text.png b/_images/swc-blueprint_logo-dark_no-text.png → _images/NeuroBlueprint_logo-dark_no-text.png
diff --git a/_images/swc-blueprint_logo-light_no-text.png → ...ges/NeuroBlueprint_logo-light_no-text.png b/_images/swc-blueprint_logo-light_no-text.png → ...ges/NeuroBlueprint_logo-light_no-text.png
diff --git a/_images/swc-blueprint_project_tree_dark.png → _images/NeuroBlueprint_project_tree_dark.png b/_images/swc-blueprint_project_tree_dark.png → _images/NeuroBlueprint_project_tree_dark.png
diff --git a/_images/swc-blueprint_project_tree_light.png → ...ges/NeuroBlueprint_project_tree_light.png b/_images/swc-blueprint_project_tree_light.png → ...ges/NeuroBlueprint_project_tree_light.png
diff --git a/_sources/index.md.txt b/_sources/index.md.txt
@@ -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/_sources/specification.md.txt b/_sources/specification.md.txt
@@ -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.

diff --git a/_static/swc-blueprint_logo-dark_no-text.png → _static/NeuroBlueprint_logo-dark_no-text.png b/_static/swc-blueprint_logo-dark_no-text.png → _static/NeuroBlueprint_logo-dark_no-text.png
diff --git a/_static/swc-blueprint_logo-light_no-text.png → ...tic/NeuroBlueprint_logo-light_no-text.png b/_static/swc-blueprint_logo-light_no-text.png → ...tic/NeuroBlueprint_logo-light_no-text.png
diff --git a/_static/swc-blueprint_project_tree_dark.png → _static/NeuroBlueprint_project_tree_dark.png b/_static/swc-blueprint_project_tree_dark.png → _static/NeuroBlueprint_project_tree_dark.png
diff --git a/_static/swc-blueprint_project_tree_light.png → ...tic/NeuroBlueprint_project_tree_light.png b/_static/swc-blueprint_project_tree_light.png → ...tic/NeuroBlueprint_project_tree_light.png
diff --git a/_static/scripts/pydata-sphinx-theme.js b/_static/scripts/pydata-sphinx-theme.js
diff --git a/_static/scripts/pydata-sphinx-theme.js.map b/_static/scripts/pydata-sphinx-theme.js.map
diff --git a/_static/styles/pydata-sphinx-theme.css b/_static/styles/pydata-sphinx-theme.css
diff --git a/_static/webpack-macros.html b/_static/webpack-macros.html
@@ -4,28 +4,28 @@
 -->
 {# Load FontAwesome icons #}
 {% macro head_pre_icons() %}
-  <link href="{{ pathto('_static/vendor/fontawesome/6.1.2/css/all.min.css', 1) }}?digest=927b94d3fcb96560df09" rel="stylesheet" />
+  <link href="{{ pathto('_static/vendor/fontawesome/6.1.2/css/all.min.css', 1) }}?digest=ac02cc09edc035673794" rel="stylesheet" />
   <link rel="preload" as="font" type="font/woff2" crossorigin href="{{ pathto('_static/vendor/fontawesome/6.1.2/webfonts/fa-solid-900.woff2', 1) }}" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="{{ pathto('_static/vendor/fontawesome/6.1.2/webfonts/fa-brands-400.woff2', 1) }}" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="{{ pathto('_static/vendor/fontawesome/6.1.2/webfonts/fa-regular-400.woff2', 1) }}" />
 {% endmacro %}
 
 {% macro head_pre_assets() %}
   <!-- Loaded before other Sphinx assets -->
-  <link href="{{ pathto('_static/styles/theme.css', 1) }}?digest=927b94d3fcb96560df09" rel="stylesheet" />
-<link href="{{ pathto('_static/styles/bootstrap.css', 1) }}?digest=927b94d3fcb96560df09" rel="stylesheet" />
-<link href="{{ pathto('_static/styles/pydata-sphinx-theme.css', 1) }}?digest=927b94d3fcb96560df09" rel="stylesheet" />
+  <link href="{{ pathto('_static/styles/theme.css', 1) }}?digest=ac02cc09edc035673794" rel="stylesheet" />
+<link href="{{ pathto('_static/styles/bootstrap.css', 1) }}?digest=ac02cc09edc035673794" rel="stylesheet" />
+<link href="{{ pathto('_static/styles/pydata-sphinx-theme.css', 1) }}?digest=ac02cc09edc035673794" rel="stylesheet" />
 {% endmacro %}
 
 {% macro head_js_preload() %}
   <!-- Pre-loaded scripts that we'll load fully later -->
-  <link rel="preload" as="script" href="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=927b94d3fcb96560df09" />
-<link rel="preload" as="script" href="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=927b94d3fcb96560df09" />
-  <script src="{{ pathto('_static/vendor/fontawesome/6.1.2/js/all.min.js', 1) }}?digest=927b94d3fcb96560df09"></script>
+  <link rel="preload" as="script" href="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=ac02cc09edc035673794" />
+<link rel="preload" as="script" href="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=ac02cc09edc035673794" />
+  <script src="{{ pathto('_static/vendor/fontawesome/6.1.2/js/all.min.js', 1) }}?digest=ac02cc09edc035673794"></script>
 {% endmacro %}
 
 {% macro body_post() %}
   <!-- Scripts loaded after <body> so the DOM is not blocked -->
-  <script src="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=927b94d3fcb96560df09"></script>
-<script src="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=927b94d3fcb96560df09"></script>
+  <script src="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=ac02cc09edc035673794"></script>
+<script src="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=ac02cc09edc035673794"></script>
 {% endmacro %}
diff --git a/genindex.html b/genindex.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Index &#8212; SWC-Blueprint</title>
+    <title>Index &#8212; NeuroBlueprint</title>
 
 
 
@@ -17,12 +17,12 @@
   </script>
 
   <!-- Loaded before other Sphinx assets -->
-  <link href="_static/styles/theme.css?digest=927b94d3fcb96560df09" rel="stylesheet" />
-<link href="_static/styles/bootstrap.css?digest=927b94d3fcb96560df09" rel="stylesheet" />
-<link href="_static/styles/pydata-sphinx-theme.css?digest=927b94d3fcb96560df09" rel="stylesheet" />
+  <link href="_static/styles/theme.css?digest=ac02cc09edc035673794" rel="stylesheet" />
+<link href="_static/styles/bootstrap.css?digest=ac02cc09edc035673794" rel="stylesheet" />
+<link href="_static/styles/pydata-sphinx-theme.css?digest=ac02cc09edc035673794" rel="stylesheet" />
 
 
-  <link href="_static/vendor/fontawesome/6.1.2/css/all.min.css?digest=927b94d3fcb96560df09" rel="stylesheet" />
+  <link href="_static/vendor/fontawesome/6.1.2/css/all.min.css?digest=ac02cc09edc035673794" rel="stylesheet" />
   <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.1.2/webfonts/fa-solid-900.woff2" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.1.2/webfonts/fa-brands-400.woff2" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.1.2/webfonts/fa-regular-400.woff2" />
@@ -32,17 +32,17 @@
     <link rel="stylesheet" type="text/css" href="_static/css/custom.css?v=1015aea7" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
-  <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=927b94d3fcb96560df09" />
-<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=927b94d3fcb96560df09" />
-  <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=927b94d3fcb96560df09"></script>
+  <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=ac02cc09edc035673794" />
+<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=ac02cc09edc035673794" />
+  <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=ac02cc09edc035673794"></script>
 
     <script src="_static/documentation_options.js?v=38b66d78"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/design-tabs.js?v=36754332"></script>
     <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'genindex';</script>
-    <link rel="canonical" href="https://swc-blueprint.neuroinformatics.dev/genindex.html" />
+    <link rel="canonical" href="https://neuroblueprint.neuroinformatics.dev/genindex.html" />
     <link rel="icon" href="_static/logo_light.png"/>
     <link rel="index" title="Index" href="#" />
     <link rel="search" title="Search" href="search.html" />
@@ -125,7 +125,7 @@
     <script>document.write(`<img src="_static/logo_dark.png" class="logo__image only-dark" alt="Logo image"/>`);</script>
 
 
-    <p class="title logo__title">SWC-Blueprint v0.1.0</p>
+    <p class="title logo__title">NeuroBlueprint v0.1.0</p>
 
 </a></div>
 
@@ -164,8 +164,8 @@
  document.write(`
    <button class="btn navbar-btn search-button-field search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
     <i class="fa-solid fa-magnifying-glass"></i>
-    <span class="search-button__kbd-shortcut">Search</span>
-    <span><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd class="kbd-shortcut__modifier">K</kbd></span>
+    <span class="search-button__default-text">Search</span>
+    <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd class="kbd-shortcut__modifier">K</kbd></span>
    </button>
  `);
  </script>
@@ -194,7 +194,7 @@
 
 
 
-          <a href="https://github.com/neuroinformatics-unit/SWC-Blueprint" title="GitHub" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-github fa-lg" aria-hidden="true"></i></span>
+          <a href="https://github.com/neuroinformatics-unit/NeuroBlueprint" title="GitHub" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-github fa-lg" aria-hidden="true"></i></span>
             <span class="sr-only">GitHub</span></a>
         </li>
 </ul></div>
@@ -209,8 +209,8 @@
  document.write(`
    <button class="btn navbar-btn search-button-field search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
     <i class="fa-solid fa-magnifying-glass"></i>
-    <span class="search-button__kbd-shortcut">Search</span>
-    <span><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd class="kbd-shortcut__modifier">K</kbd></span>
+    <span class="search-button__default-text">Search</span>
+    <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd class="kbd-shortcut__modifier">K</kbd></span>
    </button>
  `);
  </script>
@@ -280,7 +280,7 @@
 
 
 
-          <a href="https://github.com/neuroinformatics-unit/SWC-Blueprint" title="GitHub" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-github fa-lg" aria-hidden="true"></i></span>
+          <a href="https://github.com/neuroinformatics-unit/NeuroBlueprint" title="GitHub" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-github fa-lg" aria-hidden="true"></i></span>
             <span class="sr-only">GitHub</span></a>
         </li>
 </ul></div>
@@ -347,8 +347,8 @@ <h1 id="index">Index</h1>
   </div>
 
   <!-- Scripts loaded after <body> so the DOM is not blocked -->
-  <script src="_static/scripts/bootstrap.js?digest=927b94d3fcb96560df09"></script>
-<script src="_static/scripts/pydata-sphinx-theme.js?digest=927b94d3fcb96560df09"></script>
+  <script src="_static/scripts/bootstrap.js?digest=ac02cc09edc035673794"></script>
+<script src="_static/scripts/pydata-sphinx-theme.js?digest=ac02cc09edc035673794"></script>
 
   <footer class="bd-footer">
 <div class="bd-footer__inner bd-page-width">
@@ -362,7 +362,7 @@ <h1 id="index">Index</h1>
 <p class="theme-version">
 Built with the
 <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html">PyData Sphinx Theme</a>
-0.14.0.
+0.14.1.
 </p></div>
 
     </div>
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		swc-blueprint.neuroinformatics.dev
		neuroblueprint.neuroinformatics.dev