wip: updating website with API refs, logo and fixing bug in mkdocs.ym…

…l that prevented building of website. closes #213 (#387)

docs/docs/index.md

@@ -1,7 +1,5 @@
 
-<h1 align="center">
-jaxley
-</h1>
+![jaxley_logo](logo.png)
 
 `jaxley` is a differentiable simulator for networks of multicompartment neurons in [JAX](https://github.com/google/jax). Its key features are:
 
@@ -38,6 +36,8 @@ cd jaxley
 pip install -e .
 ```
 
+Note that `pip>=21.3` is required to install the editable version with `pyproject.toml` see [pip docs](https://pip.pypa.io/en/latest/reference/build-system/pyproject-toml/#editable-installation). 
+
 
 ### Feedback and Contributions
 

docs/docs/install.md

@@ -1,3 +1,8 @@
-```
+`jaxley` requires that you first download and install [tridiax](https://github.com/jaxleyverse/tridiax). Then, install `jaxley` via:
+```sh
+git clone https://github.com/jaxleyverse/jaxley.git
+cd jaxley
 pip install -e .
-```
+```
+
+Note that `pip>=21.3` is required to install the editable version with `pyproject.toml` see [pip docs](https://pip.pypa.io/en/latest/reference/build-system/pyproject-toml/#editable-installation). 

docs/docs/reference/connection.md

@@ -0,0 +1 @@
+::: jaxley.connection

docs/docs/reference/integration.md

@@ -0,0 +1,5 @@
+::: jaxley.integrate
+
+::: jaxley.solver_gate
+
+::: jaxley.solver_voltage

docs/docs/reference/mechanisms.md

@@ -0,0 +1,85 @@
+# Channels
+## Channel
+::: jaxley.channels.channel.Channel
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+## HH
+::: jaxley.channels.hh.HH
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+## Pospischil
+::: jaxley.channels.pospischil.Leak
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+::: jaxley.channels.pospischil.Na
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+::: jaxley.channels.pospischil.K
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+::: jaxley.channels.pospischil.Km
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+::: jaxley.channels.pospischil.CaL
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+::: jaxley.channels.pospischil.CaT
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+# Synapses
+
+## Synapse
+::: jaxley.synapses.synapse.Synapse
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+## Ionotropic Synapse
+::: jaxley.synapses.ionotropic.IonotropicSynapse
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+## TanH Rate Synapse
+::: jaxley.synapses.tanh_rate.TanhRateSynapse
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true

docs/docs/reference/modules.md

@@ -0,0 +1,39 @@
+## Module
+::: jaxley.modules.base.Module
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+## Compartment
+::: jaxley.modules.compartment.Compartment
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+## Branch
+::: jaxley.modules.branch.Branch
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+## Cell
+::: jaxley.modules.cell.Cell
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true
+
+## Network
+::: jaxley.modules.network.Network
+    rendering:
+      show_root_heading: true
+    selection:
+      filters: [ "!^_", "^__", "!^__class__" ]
+      inherited_members: true

docs/docs/reference/optimize.md

@@ -0,0 +1,2 @@
+::: jaxley.optimize.optimizer
+::: jaxley.optimize.transforms

docs/docs/reference/utils.md

@@ -0,0 +1,5 @@
+::: jaxley.utils.cell_utils
+::: jaxley.utils.plot_utils
+::: jaxley.utils.swc
+::: jaxley.utils.jax_utils
+::: jaxley.utils.syn_utils

docs/mkdocs.yml

@@ -4,18 +4,24 @@ site_url: "https://mackelab.org/jaxley/"
 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
+    - Getting started: tutorial/01_morph_neurons.md
+    - Run a network simulation: tutorial/02_small_network.md
+    - Set parameters: tutorial/03_setting_parameters.md
+    - Accelerate simulations: tutorial/04_jit_and_vmap.md
+    - Define your own channels: tutorial/05_channel_and_synapse_models.md
+    - Define groups: tutorial/06_groups.md
+    - Optimization: tutorial/07_gradient_descent.md
   - Installation: install.md
   - Contributing: 
     - Guide: contribute.md
     - Code of Conduct: code_of_conduct.md
-  - API Reference: reference.md
+  - API Reference: 
+    - Modules: reference/modules.md
+    - Simulation: reference/integration.md
+    - Mechansims: reference/mechanisms.md
+    - Connecting Cells: reference/connection.md
+    - Optimization: reference/optimze.md
+    - Utils: reference/utils.md
   - FAQ: faq.md
   - Credits: credits.md
 
@@ -24,9 +30,12 @@ repo_url: http://github.com/jaxleyverse/jaxley
 
 theme:
   name: 'material'
+  features:
+  - content.code.copy
   palette:
     primary: 'indigo'
     accent: 'indigo'
+  logo: logo_white.png
   collapse_navigation: False
 
 markdown_extensions:
@@ -65,9 +74,10 @@ plugins:
       default_handler: python
       handlers:
         python:
-          rendering:
+          options:
             show_source: true
             heading_level: 3
+          paths: [..]
 
 watch:
   - ../jaxley