mkdocs.yml

site_name: xolotl
repo_url: https://github.com/sg-s/xolotl/
site_author: Srinivas Gorur-Shandilya
docs_dir: 'docs'
theme:
  name: 'material'
  logo: 'images/Xlogo.png'
  palette:
    primary: 'deep-purple'
    accent: 'deep-purple'
pages:
  - Home: index.md
  - Tutorials:
    - Getting Started: 'tutorials/start-here.md'
    - Demos: 'tutorials/built-in-demos.md'
    - Your first neuron: 'tutorials/first-neuron.md'
    - Your first network: 'tutorials/first-network.md'
  - How to:
    - Install and configure: how-to/install-configure.md
    - Construct models: how-to/construct-models.md
    - Discover existing components: how-to/discover-components.md
    - Specify initial conditions: how-to/specify-initial-conditions.md
    - Modify existing models: how-to/change-existing-models.md
    - Copy a model: how-to/copy-models.md
    - Save and load models: how-to/save-load-models.md
    - Run simulations: how-to/run-simulations.md
    - Inspect conductances and mechanism: how-to/inspect-channels-and-mechanisms.md
    - Voltage clamp a compartment: how-to/voltage-clamp.md
    - Inject current: how-to/inject-current.md
    - Make plots: how-to/make-plots.md
    - Save configurations and use snapshots: how-to/snapshots.md
    - Make your own components: how-to/make-own-models.md
    - Manipulate a model: how-to/manipulate.md
    - Create multi-compartment models: how-to/create-multi-compartment-models.md
    - Fit a model to arbitrary constraints: how-to/fit-parameters.md
    - Run simulations in parallel: how-to/run-simulations-in-parallel.md
    - Use stochastic channels: how-to/stochastic-channels.md
    - Construct complex self-assembling models: how-to/write-mechanisms-that-self-assemble.md
    - Generate a database of models using random search: how-to/database-search.md
  - Reference:
    - Units: 'reference/units.md'
    - C++ classes:
      - conductance: 'reference/c++/conductance.md'
      - compartment: 'reference/c++/compartment.md'
      - synapse: 'reference/c++/synapse.md'
      - network: 'reference/c++/network.md'
      - mechanism: 'reference/c++/mechanism.md'
    - MATLAB:
      - conductance: reference/matlab/conductance.md
      - xtools: reference/matlab/xtools.md
      - xtest: reference/matlab/xtest.md
      - xolotl: reference/matlab/xolotl.md
      - cpplab: reference/matlab/cpplab.md
      - xfit: reference/matlab/xfit.md
      - xgrid: reference/matlab/xgrid.md
  - How xolotl works:
    - How cpplab binds code: explanation/cpplab.md
    - How equations are integrated: explanation/integration.md
    - How xolotl transpiles code: explanation/transpile.md
    - How xolotl interfaces with its binary: explanation/mex-interface.md
    - How hashing works in xolotl and cpplab: explanation/hashing.md
  - Performance tips:
    - Speed: 'performance/speed.md'
    - Memory: 'performance/memory.md'
  - Troubleshooting:
    - Fixes to common problems: troubleshooting.md
  - Meta:
    - Development and future: 'meta/future.md'
    - Documentation: 'meta/documentation.md'
    - Testing: 'meta/testing.md'
  - FAQ: 'faq.md'
  - Contributing: 'contributing.md'
  - Bibliography: 'bibliography.md'
  - License: 'license.md'

use_directory_urls: true

markdown_extensions:
  - admonition
  - mdx_math:
      enable_dollar_delimiter: True #for use of inline $..$
  - toc:
      permalink: true
  - codehilite

# Required to load the MathJax javascript for the mdx_math.py
extra_javascript: ['https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS_HTML']