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Neuroinformatics Unit Website

Website shields.io made-with-sphinx-doc

The main website of the SWC/GCNU Neuroinformatics Unit.

Website structure

The website is built using Sphinx and the PyData Sphinx Theme.

  • Build requirements are listed in docs/requirements.txt.
  • The source files are located in docs/source and include:
    • conf.py: Sphinx configuration file
    • index.md: landing page linking to all other pages
    • Other pages are defined as <page-name>.md files in the source directory, or its subdirectories.
  • The built website is deployed from the gh-pages branch to the neuroinformatics.dev domain.

Editing the website

  • Clone the GitHub repository, and create your new_branch.
  • Edit the website and commit your changes to the new_branch.
  • Check how the edited website looks by building it locally.
  • Push the new_branch to GitHub and create a pull request. This will automatically trigger a GitHub Action that checks if the website still builds correctly.
  • If the checks pass, assign someone to review your changes.
  • When the reviewer merges your changes into the main branch, a different GitHub Action will be triggered, which will build the website and publish it to the gh-pages branch.
  • Check the deployed build at neuroinformatics.dev

Local build

If you wish to view the website locally before you push it, you can do so by running the following commands from the root of the repository:

# only need to do this once
pip install -r docs/requirements.txt
# do this every time you want to refresh the build
rm -rf docs/build # remove existing local build
sphinx-build docs/source docs/build # make new build

You can view the local build at docs/build/index.html

SWC/GCNU Neuroinformatics Unit's Projects

datashuttle icon datashuttle

Tool for the creation, validation and transfer of neuroscience project folders.

datasquash icon datasquash

Data compression utilities for systems neuroscience.

derotation icon derotation

Derotate images acquired via 2-photon or 3-photon calcium imaging

ethology icon ethology

Data processing tools for animal behavioural analysis

howto icon howto

NIU website on common software problems and their troubleshooting

in2research-2024 icon in2research-2024

Repository used as a playground for the In2Research placement we hosted in summer 2024.

movement icon movement

Python tools for analysing body movements across space and time

neuroblueprint icon neuroblueprint

Lightweight data specification for systems neuroscience, inspired by BIDS.

rsp-vision icon rsp-vision

Analysis and visualization of calcium imaging data from retrosplenial cortex

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