diff --git a/README.md b/README.md index 6af1a92..af27513 100644 --- 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/docs/source/_static/swc-blueprint_logo-dark_no-text.png b/docs/source/_static/NeuroBlueprint_logo-dark_no-text.png similarity index 100% rename from docs/source/_static/swc-blueprint_logo-dark_no-text.png rename to docs/source/_static/NeuroBlueprint_logo-dark_no-text.png diff --git a/docs/source/_static/swc-blueprint_logo-light_no-text.png b/docs/source/_static/NeuroBlueprint_logo-light_no-text.png similarity index 100% rename from docs/source/_static/swc-blueprint_logo-light_no-text.png rename to docs/source/_static/NeuroBlueprint_logo-light_no-text.png diff --git a/docs/source/_static/swc-blueprint_project_tree_dark.png b/docs/source/_static/NeuroBlueprint_project_tree_dark.png similarity index 100% rename from docs/source/_static/swc-blueprint_project_tree_dark.png rename to docs/source/_static/NeuroBlueprint_project_tree_dark.png diff --git a/docs/source/_static/swc-blueprint_project_tree_light.png b/docs/source/_static/NeuroBlueprint_project_tree_light.png similarity index 100% rename from docs/source/_static/swc-blueprint_project_tree_light.png rename to docs/source/_static/NeuroBlueprint_project_tree_light.png diff --git a/docs/source/conf.py b/docs/source/conf.py index 9381d3d..fe89d09 100644 --- 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, @@ -108,7 +108,7 @@ # 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) @@ -116,7 +116,7 @@ } ], "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 index 365a75d..7d10b8d 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -1,15 +1,15 @@ -# SWC-Blueprint +# NeuroBlueprint -SWC-Blueprint logo -SWC-Blueprint logo +NeuroBlueprint logo +NeuroBlueprint logo -**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 index 32e50f7..218f994 100644 --- 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: -SWC-Blueprint logo -SWC-Blueprint logo +NeuroBlueprint logo +NeuroBlueprint logo ### 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-