update docs

.gitignore

@@ -1,3 +1,8 @@
+# Project specific
+/docs/docs/tutorial/*
+/docs/docs/examples/*
+/docs/site/*
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

docs/docs/index.md

@@ -1,2 +1,61 @@
-# `neurax`: differentiable networks of multicompartment neurons
 
+<h1 align="center">
+neurax
+</h1>
+
+`neurax` is a differentiable simulator for networks of multicompartment neurons in [JAX](https://github.com/google/jax). Its key features are:
+
+- automatic differentiation, allowing gradient-based optimization of thousands of parameters  
+- support for CPU and GPU without any changes to the code  
+- `jit`-compilation, making it as fast as other packages while being fully written in python  
+- backward-Euler solver for stable numerical solution of multicompartment neurons  
+- elegant mechanisms for parameter sharing
+
+
+### Tutorial
+
+Tutorial notebooks with some explanation are in [`tutorials`](https://github.com/mackelab/neurax/tree/main/tutorials). We currently have tutorials on how to:
+
+- [run a simple network simulation](https://github.com/mackelab/neurax/blob/main/tutorials/01_small_network.ipynb)
+- [set parameters](https://github.com/mackelab/neurax/blob/main/tutorials/02_setting_parameters.ipynb)
+- [obtain a gradient and train](https://github.com/mackelab/neurax/blob/main/tutorials/03_gradient.ipynb)
+- [define groups (aka sectionlists)](https://github.com/mackelab/neurax/blob/main/tutorials/04_groups.ipynb)
+- [define your own channels and synapses](https://github.com/mackelab/neurax/blob/main/tutorials/05_new_mechanisms.ipynb)
+- [use diverse channels](https://github.com/mackelab/neurax/blob/main/tutorials/06_diverse_channels.ipynb)
+
+
+### Units
+
+`neurax` uses the same [units as `NEURON`](https://www.neuron.yale.edu/neuron/static/docs/units/unitchart.html).
+
+
+### Installation
+`neurax` requires that you first download and install [tridiax](https://github.com/mackelab/tridiax). Then, install `neurax` via:
+```sh
+git clone https://github.com/mackelab/neurax.git
+cd neurax
+pip install -e .
+```
+
+
+### Feedback and Contributions
+
+We welcome any feedback on how neurax is working for your neuron models and are happy to receive bug reports, pull requests and other feedback (see [contribute](https://github.com/mackelab/neurax/blob/main/CONTRIBUTING.md)). We wish to maintain a positive community, please read our [Code of Conduct](https://github.com/mackelab/neurax/blob/main/CODE_OF_CONDUCT.md).
+
+
+### Acknowledgements
+
+We greatly benefited from previous toolboxes for simulating multicompartment neurons, in particular [NEURON](https://github.com/neuronsimulator/nrn).
+
+
+### License
+
+[MIT License](https://github.com/mackelab/neurax/blob/main/LICENSE)
+
+
+### Citation
+
+If you use `neurax`, consider citing the corresponding paper:
+```
+@article{}
+```

docs/docs/reference.md

@@ -0,0 +1,110 @@
+# API Reference
+
+## Modules
+
+::: neurax.modules.compartment.Compartment
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+::: neurax.modules.branch.Branch
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+::: neurax.modules.cell.Cell
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+::: neurax.modules.network.Network
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+
+## Channels
+
+::: neurax.channels.hh.HHChannel
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+::: neurax.channels.pospischil.CaLChannelPospi
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+::: neurax.channels.pospischil.CaTChannelPospi
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+::: neurax.channels.pospischil.KChannelPospi
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+::: neurax.channels.pospischil.KmChannelPospi
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+::: neurax.channels.pospischil.Leak
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+::: neurax.channels.pospischil.NaChannelPospi
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+
+## Synapses
+
+::: neurax.synapses.glutamate.GlutamateSynapse
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+
+## Optimization
+
+::: neurax.optimize.transforms.ParamTransform
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+
+## Utils
+
+::: neurax.read_swc
+    rendering:
+      show_root_heading: true

docs/mkdocs.yml

@@ -3,6 +3,14 @@ site_url: "https://mackelab.org/neurax/"
 
 nav:
   - Home: index.md
+  - Tutorials:
+    - Getting started: tutorial/01_small_network.md
+    - Run a network simulation: tutorial/01_small_network.md
+    - Set parameters: tutorial/02_setting_parameters.md
+    - Obtain gradient and train: tutorial/03_gradient.md
+    - Define groups: tutorial/04_groups.md
+    - Define your own channels: tutorial/05_new_mechanisms.md
+    - Use diverse channels: tutorial/06_diverse_channels.md
   - Installation: install.md
   - Contributing: 
     - Guide: contribute.md
@@ -48,4 +56,18 @@ markdown_extensions:
   - pymdownx.superfences
   - pymdownx.tasklist:
       custom_checkbox: true
-  - pymdownx.tilde
+  - pymdownx.tilde
+
+
+plugins:
+  - search
+  - mkdocstrings:
+      default_handler: python
+      handlers:
+        python:
+          rendering:
+            show_source: true
+            heading_level: 3
+
+watch:
+  - ../neurax

setup.py

@@ -13,9 +13,11 @@
         "black",
         "isort",
         "jupyter",
-        "markdown-include",
         "mkdocs",
         "mkdocs-material",
+        "markdown-include",
+        "mkdocs-redirects",
+        "mkdocstrings[python]>=0.18",
         "neuron",
         "pytest",
         "pyright",