Rename neurax to jaxley

CODE_OF_CONDUCT.md

@@ -60,7 +60,7 @@ representative at an online or offline event.
 ## Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported by contacting `neurax` developer Michael Deistler via email ([email protected]). All
+reported by contacting `jaxley` developer Michael Deistler via email ([email protected]). All
 complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the

CONTRIBUTING.md

@@ -1,7 +1,7 @@
 ## User experiences, bugs, and feature requests
 
 To report bugs and suggest features (including better documentation), please equally
-head over to [issues on GitHub](https://github.com/mackelab/neurax/issues).
+head over to [issues on GitHub](https://github.com/mackelab/jaxley/issues).
 
 ## Code contributions
 

README.md

@@ -1,13 +1,13 @@
-[![Contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/mackelab/neurax/blob/main/CONTRIBUTING.md)
-[![Tests](https://github.com/mackelab/neurax/workflows/Tests/badge.svg?branch=main)](https://github.com/mackelab/neurax/actions)
-[![GitHub license](https://img.shields.io/badge/license-MIT-green)](https://github.com/mackelab/neurax/blob/main/LICENSE)
+[![Contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/mackelab/jaxley/blob/main/CONTRIBUTING.md)
+[![Tests](https://github.com/mackelab/jaxley/workflows/Tests/badge.svg?branch=main)](https://github.com/mackelab/jaxley/actions)
+[![GitHub license](https://img.shields.io/badge/license-MIT-green)](https://github.com/mackelab/jaxley/blob/main/LICENSE)
 
 
 <p align="center">
   <img src="docs/logo.png?raw=true" width="360">
 </p>
 
-`neurax` is a differentiable simulator for networks of multicompartment neurons in [JAX](https://github.com/google/jax). Its key features are:
+`jaxley` 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  
@@ -17,32 +17,32 @@
 
 ### 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)
+Tutorial notebooks with some explanation are in [`tutorials`](https://github.com/mackelab/jaxley/tree/main/tutorials). We currently have tutorials on how to:
+- [run a simple network simulation](https://github.com/mackelab/jaxley/blob/main/tutorials/01_small_network.ipynb)
+- [set parameters](https://github.com/mackelab/jaxley/blob/main/tutorials/02_setting_parameters.ipynb)
+- [obtain a gradient and train](https://github.com/mackelab/jaxley/blob/main/tutorials/03_gradient.ipynb)
+- [define groups (aka sectionlists)](https://github.com/mackelab/jaxley/blob/main/tutorials/04_groups.ipynb)
+- [define your own channels and synapses](https://github.com/mackelab/jaxley/blob/main/tutorials/05_new_mechanisms.ipynb)
+- [use diverse channels](https://github.com/mackelab/jaxley/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).
+`jaxley` 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:
+`jaxley` requires that you first download and install [tridiax](https://github.com/mackelab/tridiax). Then, install `jaxley` via:
 ```sh
-git clone https://github.com/mackelab/neurax.git
-cd neurax
+git clone https://github.com/mackelab/jaxley.git
+cd jaxley
 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).
+We welcome any feedback on how jaxley is working for your neuron models and are happy to receive bug reports, pull requests and other feedback (see [contribute](https://github.com/mackelab/jaxley/blob/main/CONTRIBUTING.md)). We wish to maintain a positive community, please read our [Code of Conduct](https://github.com/mackelab/jaxley/blob/main/CODE_OF_CONDUCT.md).
 
 
 ### Acknowledgements
@@ -52,12 +52,12 @@ We greatly benefited from previous toolboxes for simulating multicompartment neu
 
 ### License
 
-[MIT License](https://github.com/mackelab/neurax/blob/main/LICENSE)
+[MIT License](https://github.com/mackelab/jaxley/blob/main/LICENSE)
 
 
 ### Citation
 
-If you use `neurax`, consider citing the corresponding paper:
+If you use `jaxley`, consider citing the corresponding paper:
 ```
 @article{}
 ```

docs/README.md

@@ -1,6 +1,6 @@
 # Documentation
 
-The documentation is available at: <http://mackelab.org/neurax>
+The documentation is available at: <http://mackelab.org/jaxley>
 
 ## Building the Documentation
 

docs/docs/credits.md

@@ -1,10 +1,10 @@
 # Credits
 
-`neurax` is a collaborative project between the groups of Jakob Macke (Uni Tübingen), Pedro Gonçalves (KU Leuven / NERF), and Philipp Berens (Uni Tübingen).
+`jaxley` is a collaborative project between the groups of Jakob Macke (Uni Tübingen), Pedro Gonçalves (KU Leuven / NERF), and Philipp Berens (Uni Tübingen).
 
 ## License
 
-`neurax` is licensed under the [Affero General Public License version 3 (AGPLv3)](https://www.gnu.org/licenses/agpl-3.0.html) and
+`jaxley` is licensed under the [Affero General Public License version 3 (AGPLv3)](https://www.gnu.org/licenses/agpl-3.0.html) and
 
 > Copyright (C) 2020 Michael Deistler.
 
@@ -15,7 +15,7 @@
 
 
 ## Citation
-If you use `neurax` consider citing the corresponding paper:
+If you use `jaxley` consider citing the corresponding paper:
 ```
 @article{deistler,
 }

docs/docs/faq.md

@@ -1,3 +1,3 @@
 # Frequently asked questions
 
-[What makes `neurax` different from other libraries?](faq/question_01.md)
+[What makes `jaxley` different from other libraries?](faq/question_01.md)

docs/docs/faq/question_01.md

@@ -1,3 +1,3 @@
-# What makes `neurax` different from other libraries?
+# What makes `jaxley` different from other libraries?
 
 Differentiable, jit-compilable, and implements implicit Euler for multicompartment models.

docs/docs/index.md

@@ -1,9 +1,9 @@
 
 <h1 align="center">
-neurax
+jaxley
 </h1>
 
-`neurax` is a differentiable simulator for networks of multicompartment neurons in [JAX](https://github.com/google/jax). Its key features are:
+`jaxley` 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  
@@ -14,33 +14,33 @@ neurax
 
 ### Tutorial
 
-Tutorial notebooks with some explanation are in [`tutorials`](https://github.com/mackelab/neurax/tree/main/tutorials). We currently have tutorials on how to:
+Tutorial notebooks with some explanation are in [`tutorials`](https://github.com/mackelab/jaxley/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)
+- [run a simple network simulation](https://github.com/mackelab/jaxley/blob/main/tutorials/01_small_network.ipynb)
+- [set parameters](https://github.com/mackelab/jaxley/blob/main/tutorials/02_setting_parameters.ipynb)
+- [obtain a gradient and train](https://github.com/mackelab/jaxley/blob/main/tutorials/03_gradient.ipynb)
+- [define groups (aka sectionlists)](https://github.com/mackelab/jaxley/blob/main/tutorials/04_groups.ipynb)
+- [define your own channels and synapses](https://github.com/mackelab/jaxley/blob/main/tutorials/05_new_mechanisms.ipynb)
+- [use diverse channels](https://github.com/mackelab/jaxley/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).
+`jaxley` 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:
+`jaxley` requires that you first download and install [tridiax](https://github.com/mackelab/tridiax). Then, install `jaxley` via:
 ```sh
-git clone https://github.com/mackelab/neurax.git
-cd neurax
+git clone https://github.com/mackelab/jaxley.git
+cd jaxley
 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).
+We welcome any feedback on how jaxley is working for your neuron models and are happy to receive bug reports, pull requests and other feedback (see [contribute](https://github.com/mackelab/jaxley/blob/main/CONTRIBUTING.md)). We wish to maintain a positive community, please read our [Code of Conduct](https://github.com/mackelab/jaxley/blob/main/CODE_OF_CONDUCT.md).
 
 
 ### Acknowledgements
@@ -50,12 +50,12 @@ We greatly benefited from previous toolboxes for simulating multicompartment neu
 
 ### License
 
-[MIT License](https://github.com/mackelab/neurax/blob/main/LICENSE)
+[MIT License](https://github.com/mackelab/jaxley/blob/main/LICENSE)
 
 
 ### Citation
 
-If you use `neurax`, consider citing the corresponding paper:
+If you use `jaxley`, consider citing the corresponding paper:
 ```
 @article{}
 ```

docs/docs/reference.md

@@ -2,28 +2,28 @@
 
 ## Modules
 
-::: neurax.modules.compartment.Compartment
+::: jaxley.modules.compartment.Compartment
     rendering:
       show_root_heading: true
     selection:
       filters: [ "!^_", "^__", "!^__class__" ]
       inherited_members: true
 
-::: neurax.modules.branch.Branch
+::: jaxley.modules.branch.Branch
     rendering:
       show_root_heading: true
     selection:
       filters: [ "!^_", "^__", "!^__class__" ]
       inherited_members: true
 
-::: neurax.modules.cell.Cell
+::: jaxley.modules.cell.Cell
     rendering:
       show_root_heading: true
     selection:
       filters: [ "!^_", "^__", "!^__class__" ]
       inherited_members: true
 
-::: neurax.modules.network.Network
+::: jaxley.modules.network.Network
     rendering:
       show_root_heading: true
     selection:
@@ -33,49 +33,49 @@
 
 ## Channels
 
-::: neurax.channels.hh.HHChannel
+::: jaxley.channels.hh.HHChannel
     rendering:
       show_root_heading: true
     selection:
       filters: [ "!^_", "^__", "!^__class__" ]
       inherited_members: true
 
-::: neurax.channels.pospischil.CaLChannelPospi
+::: jaxley.channels.pospischil.CaLChannelPospi
     rendering:
       show_root_heading: true
     selection:
       filters: [ "!^_", "^__", "!^__class__" ]
       inherited_members: true
 
-::: neurax.channels.pospischil.CaTChannelPospi
+::: jaxley.channels.pospischil.CaTChannelPospi
     rendering:
       show_root_heading: true
     selection:
       filters: [ "!^_", "^__", "!^__class__" ]
       inherited_members: true
 
-::: neurax.channels.pospischil.KChannelPospi
+::: jaxley.channels.pospischil.KChannelPospi
     rendering:
       show_root_heading: true
     selection:
       filters: [ "!^_", "^__", "!^__class__" ]
       inherited_members: true
 
-::: neurax.channels.pospischil.KmChannelPospi
+::: jaxley.channels.pospischil.KmChannelPospi
     rendering:
       show_root_heading: true
     selection:
       filters: [ "!^_", "^__", "!^__class__" ]
       inherited_members: true
 
-::: neurax.channels.pospischil.Leak
+::: jaxley.channels.pospischil.Leak
     rendering:
       show_root_heading: true
     selection:
       filters: [ "!^_", "^__", "!^__class__" ]
       inherited_members: true
 
-::: neurax.channels.pospischil.NaChannelPospi
+::: jaxley.channels.pospischil.NaChannelPospi
     rendering:
       show_root_heading: true
     selection:
@@ -85,7 +85,7 @@
 
 ## Synapses
 
-::: neurax.synapses.glutamate.GlutamateSynapse
+::: jaxley.synapses.glutamate.GlutamateSynapse
     rendering:
       show_root_heading: true
     selection:
@@ -95,7 +95,7 @@
 
 ## Optimization
 
-::: neurax.optimize.transforms.ParamTransform
+::: jaxley.optimize.transforms.ParamTransform
     rendering:
       show_root_heading: true
     selection:
@@ -105,6 +105,6 @@
 
 ## Utils
 
-::: neurax.read_swc
+::: jaxley.read_swc
     rendering:
       show_root_heading: true

docs/mkdocs.yml

@@ -1,5 +1,5 @@
-site_name: neurax
-site_url: "https://mackelab.org/neurax/"
+site_name: jaxley
+site_url: "https://mackelab.org/jaxley/"
 
 nav:
   - Home: index.md
@@ -19,8 +19,8 @@ nav:
   - FAQ: faq.md
   - Credits: credits.md
 
-repo_name: 'mackelab/neurax'
-repo_url: http://github.com/mackelab/neurax
+repo_name: 'mackelab/jaxley'
+repo_url: http://github.com/mackelab/jaxley
 
 theme:
   name: 'material'
@@ -40,23 +40,23 @@ markdown_extensions:
       toc_depth: 3
   - markdown_include.include:
       base_path: ../
-  - pymdownx.arithmatex:
+  - pymdowjx.arithmatex:
       generic: true
-  - pymdownx.betterem:
+  - pymdowjx.betterem:
       smart_enable: all
-  - pymdownx.caret
-  - pymdownx.critic
-  - pymdownx.details
-  - pymdownx.emoji:
-      emoji_generator: !!python/name:pymdownx.emoji.to_svg
-  - pymdownx.inlinehilite
-  - pymdownx.magiclink
-  - pymdownx.mark
-  - pymdownx.smartsymbols
-  - pymdownx.superfences
-  - pymdownx.tasklist:
+  - pymdowjx.caret
+  - pymdowjx.critic
+  - pymdowjx.details
+  - pymdowjx.emoji:
+      emoji_generator: !!python/name:pymdowjx.emoji.to_svg
+  - pymdowjx.inlinehilite
+  - pymdowjx.magiclink
+  - pymdowjx.mark
+  - pymdowjx.smartsymbols
+  - pymdowjx.superfences
+  - pymdowjx.tasklist:
       custom_checkbox: true
-  - pymdownx.tilde
+  - pymdowjx.tilde
 
 
 plugins:
@@ -70,4 +70,4 @@ plugins:
             heading_level: 3
 
 watch:
-  - ../neurax
+  - ../jaxley