Convert to card structure (#80)

* Add new project types

* Update links

* First draft of electrophysiology page.

Please review

* Update collaborations.md

Please review, I think this is okay maybe I can run it by Pierre.

* Update docs/source/projects/developer_tools.md

Co-authored-by: Chang Huan Lo <[email protected]>

* Update docs/source/projects/electrophysiology.md

Co-authored-by: Chang Huan Lo <[email protected]>

* Update neuroblueprint link to website

* Update docs/source/projects/electrophysiology.md

Co-authored-by: Chang Huan Lo <[email protected]>

* Update docs/source/projects/electrophysiology.md

Co-authored-by: Chang Huan Lo <[email protected]>

* Added card images for data management and behaviour

* same backgrounds for all cards

* added collaborations card

* added ephys card

* Added movement text

* Standardise headings

* Remove collaborations for now

* Convert projects to cards

* Convert resources to cards

* Correct heading levels

* Make project descriptions higher level

* added fa icons to project-specific cards

* Remove unnecessary trailing colons

* changed TOC project links to refs

---------

Co-authored-by: Joe Ziminski <[email protected]>
Co-authored-by: Chang Huan Lo <[email protected]>
Co-authored-by: niksirbi <[email protected]>

docs/source/index.md

@@ -1,6 +1,6 @@
 # Neuroinformatics Unit
 
-The Neuroinformatics Unit (NIU) is a [Research Software Engineering](https://society-rse.org/) team based at the [Sainsbury Wellcome Centre](https://www.sainsburywellcome.org/web/) and the [Gatsby Computational Neuroscience Unit](https://www.ucl.ac.uk/gatsby/gatsby-computational-neuroscience-unit). 
+The Neuroinformatics Unit (NIU) is a [Research Software Engineering](https://society-rse.org/) team based at the [Sainsbury Wellcome Centre](https://www.sainsburywellcome.org/web/) and the [Gatsby Computational Neuroscience Unit](https://www.ucl.ac.uk/gatsby/gatsby-computational-neuroscience-unit).
 
 The NIU is dedicated to the development of high quality, accurate, robust, easy to use and maintainable open-source software for neuroscience and machine learning. We collaborate with researchers and other software engineers to advance research in the two research centres and make new algorithms and tools available to the global community.
 
@@ -12,42 +12,38 @@ The NIU is dedicated to the development of high quality, accurate, robust, easy
 
 :::{grid-item-card} {fas}`brain;sd-text-primary` Neuroanatomy
 :img-top: _static/neuroanatomy_card.png
-:link: projects/neuroanatomy
-:link-type: doc
+:link: projects-neuroanatomy
+:link-type: ref
 :::
 
 :::{grid-item-card} {fas}`video;sd-text-primary` Behaviour
 :img-top: _static/behaviour_card.png
-:link: projects/behaviour
-:link-type: doc
+:link: projects-behaviour
+:link-type: ref
 :::
 
 :::{grid-item-card} {fas}`bolt;sd-text-primary` Electrophysiology
 :img-top: _static/electrophysiology_card.png
-:link: projects/electrophysiology
-:link-type: doc
+:link: projects-electrophysiology
+:link-type: ref
 :::
 
 :::{grid-item-card} {fas}`database;sd-text-primary` Data Management
 :img-top: _static/data-management_card.png
-:link: projects/data_management
-:link-type: doc
+:link: projects-data-management
+:link-type: ref
 :::
 
 :::{grid-item-card} {fas}`code;sd-text-primary` Developer Tools
 :img-top: _static/dev-tools_card.png
-:link: projects/developer_tools
-:link-type: doc
+:link: projects-developer-tools
+:link-type: ref
 :::
 
 [//]: # (:::{grid-item-card} {fas}`handshake;sd-text-primary` Collaborations)
-
 [//]: # (:img-top: _static/collaborations_card.png)
-
-[//]: # (:link: projects/collaborations)
-
+[//]: # (:link: projects.html#collaborations)
 [//]: # (:link-type: doc)
-
 [//]: # (:::)
 
 ::::
@@ -59,7 +55,7 @@ The NIU is dedicated to the development of high quality, accurate, robust, easy
 
 about
 people
-projects/index
+projects
 blog/index
 resources
 ```

docs/source/projects.md

@@ -0,0 +1,92 @@
+# Projects
+
+(projects-neuroanatomy)=
+## Neuroanatomy
+::::{grid} 1 1 1 1
+
+:::{grid-item-card} {fas}`brain;sd-text-primary` BrainGlobe
+:link: https://brainglobe.info/
+
+The BrainGlobe Initiative exists to facilitate the development of interoperable Python-based tools for computational 
+neuroanatomy with three core aims:
+
+* Develop specialist software for specific analysis and visualisation needs
+* Develop core tools to help others to build interoperable tools in Python
+* Build a community of neuroscientists and developers to share knowledge, build software and engage with the scientific, 
+and open-source community (e.g., by organising hackathons).
+:::
+::::
+
+(projects-behaviour)=
+## Behaviour
+::::{grid} 1 1 1 1
+
+:::{grid-item-card} {fas}`video;sd-text-primary` movement
+:link: https://movement.neuroinformatics.dev/
+
+Pose estimation tools (such as DeepLabCut and SLEAP) are now commonplace when processing video data of animal 
+behaviour. There is not yet a standardised, easy to use way to process the pose tracks from these software packages.
+
+movement aims to provide a consistent modular interface to analyse pose tracks, allowing steps such as data cleaning, 
+visualisation and motion quantification. We aim to support a range of pose estimation packages, along with 2D or 3D 
+tracking of single or multiple animals. 
+
+:::
+::::
+
+(projects-electrophysiology)=
+## Electrophysiology
+::::{grid} 1 1 1 1
+:::{grid-item-card} {fas}`bolt;sd-text-primary` SpikeWrap
+:link: https://github.com/neuroinformatics-unit/spikewrap
+Spikewrap simplifies the execution and visualisation of extracellular electrophysiology pre-processing and 
+spike-sorting pipelines. Taking input organised to our NeuroBlueprint standard, it provides an easy and flexible way to 
+process extracellular electrophysiology data from multiple subjects and sessions. 
+
+SpikeWrap is built upon SpikeInterface, abstracting away the implementation details to allow researchers to easily 
+test different pipeline configurations.
+
+:::
+::::
+
+(projects-data-management)=
+## Data Management
+::::{grid} 1 1 1 1
+:gutter: 3
+
+:::{grid-item-card} {fas}`database;sd-text-primary` NeuroBlueprint
+:link: https://neuroblueprint.neuroinformatics.dev
+NeuroBlueprint is a project folder structure specification designed for systems neuroscience in animal models.
+It is inspired by, and based on the BIDS specification, widely used in human neuroimaging.
+
+The NeuroBlueprint specification provides a set of rules and guidelines for project folder organisation, ensuring 
+consistent data management within and between labs.
+This standardisation makes data-sharing and collaboration much simpler, and allows sharing of analysis tools that 
+can operate on predictable folder structures.
+:::
+
+:::{grid-item-card} {fas}`database;sd-text-primary` DataShuttle
+:link: https://datashuttle.neuroinformatics.dev
+DataShuttle is a tool for automated generation of project folders formatted to the NeuroBlueprint specification. 
+It also allows these folders to be easily synchronised between computers.
+:::
+::::
+
+(projects-developer-tools)=
+## Developer Tools
+::::{grid} 1 1 1 1
+:gutter: 3
+
+:::{grid-item-card} {fas}`code;sd-text-primary` Python Cookiecutter
+:link: https://github.com/neuroinformatics-unit/python-cookiecutter
+The Python Cookiecutter template allows quick and easy setup of new python projects.
+Projects built using this template contain pre-set configurations for code quality checks, formatting,
+automated testing (pytest, both locally and through GitHub Actions), versioning and release on PyPI.
+:::
+
+:::{grid-item-card} {fas}`code;sd-text-primary` Actions
+:link: https://github.com/neuroinformatics-unit/actions
+The actions repository hosts reliable, maintained and versioned GitHub Actions
+workflows for common tasks such as linting, testing, and releasing Python projects to PyPI.
+:::
+::::