Development (#10)

* Update conf.py * Update setup.py * Updated docs
Poirazi-Lab · Jan 11, 2023 · 6fec1b0 · 6fec1b0
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diff --git a/README.rst b/README.rst
@@ -34,15 +34,15 @@ contributions to network-level functions.
    :width: 75 %
    :align: center
 
-Note
-----
-If you use Dendrify for your published research, we kindly ask you to cite our
-article:|br|
-**Dendrify: a new framework for seamless incorporation of dendrites in Spiking Neural Networks** |br|
-M Pagkalos, S Chavlis, P Poirazi |br|
-DOI: https://doi.org/10.1101/2022.05.03.490412 |br|
-
-**Documentation** for Dendrify can be found at https://dendrify.readthedocs.io/en/latest/
+.. tip::
+   If you use Dendrify for your published research, we kindly ask you to cite our
+   article:|br|
+   **Introducing the Dendrify framework for incorporating dendrites to spiking neural networks** |br|
+   M Pagkalos, S Chavlis, P Poirazi |br|
+   DOI: https://doi.org/10.1038/s41467-022-35747-8 |br|
+
+Documentation for Dendrify can be found at https://dendrify.readthedocs.io/en/latest/
+
 
 .. |br| raw:: html
 

diff --git a/docs_sphinx/source/conf.py b/docs_sphinx/source/conf.py
@@ -13,7 +13,7 @@
 project = 'Dendrify'
 copyright = '2022, Michalis Pagkalos'
 author = 'Michalis Pagkalos'
-release = '1.0.6'
+release = '1.0.7'
 
 
 # -- General configuration -----------------------------------------------------
@@ -40,6 +40,7 @@
 intersphinx_mapping = {
     "brian2": ("https://brian2.readthedocs.io/en/stable/", None),
     "networkx": ("https://networkx.org/documentation/stable", None),
+    "brian2cuda": ("https://brian2cuda.readthedocs.io/en/latest/", None)
 }
 
 myst_url_schemes = ["http", "https", ]

diff --git a/docs_sphinx/source/index.rst b/docs_sphinx/source/index.rst
@@ -41,9 +41,9 @@ contributions to network-level functions.
 .. tip::
    If you use Dendrify for your published research, we kindly ask you to cite our
    article:|br|
-   **Dendrify: a new framework for seamless incorporation of dendrites in Spiking Neural Networks** |br|
+   **Introducing the Dendrify framework for incorporating dendrites to spiking neural networks** |br|
    M Pagkalos, S Chavlis, P Poirazi |br|
-   DOI: https://doi.org/10.1101/2022.05.03.490412 |br|
+   DOI: https://doi.org/10.1038/s41467-022-35747-8 |br|
 
 |
 

diff --git a/docs_sphinx/source/installation.rst b/docs_sphinx/source/installation.rst
@@ -10,10 +10,28 @@ The easiest way to install it is through ``pip``, using the command::
 Dependencies
 ------------
 
-* Brian 2 (required)
+* `Brian 2 <https://brian2.readthedocs.io/en/stable/index.html>`_ (required) is
+  a simulator for spiking neural networks. It is written in Python and is available
+  on almost all platforms. Brian is designed to be easy to learn and use, highly
+  flexible and easily extensible.
 
-  * :doc:`Brian installation guidelines <brian2:introduction/install>`
+  * :doc:`How to install Brian 2 <brian2:introduction/install>`
+
+* `Netwokx <https://networkx.org/>`_ (optional) is a Python package for the creation,
+  manipulation, and study of the structure, dynamics, and functions of complex
+  networks. If you wish Dendrify to have access to certain experimental model
+  visualization features, you can install it using the command::
+
+    pip install networkx
+
+
+GPU support
+-----------
+Dendrify is compatible with `Brian2CUDA <https://brian2cuda.readthedocs.io/>`_,
+a Python package for simulating spiking neural networks on graphics processing
+units (GPUs). Brian2CUDA is an extension of Brian2 that uses the code generation
+system of the latter to generate simulation code in C++/CUDA, which is then executed
+on NVIDIA GPUs.
 
-* `Netwokx <https://networkx.org/>`_ (optional, needed for few experimental features)::
+* :doc:`How to install Brian2CUDA <brian2cuda:introduction/install>`
 
-    pip install networkx
diff --git a/docs_sphinx/source/papers.rst b/docs_sphinx/source/papers.rst
@@ -4,9 +4,9 @@ Important literature
 
 .. list-table::
 
-   * - **Dendrify: a new framework for seamless incorporation of dendrites in Spiking Neural Networks** |br|
+   * - **Introducing the Dendrify framework for incorporating dendrites to spiking neural networks** |br|
        M Pagkalos, S Chavlis, P Poirazi |br|
-       DOI: https://doi.org/10.1101/2022.05.03.490412
+       DOI: https://doi.org/10.1038/s41467-022-35747-8 |br|
 
    * - |br| 
        **Brian 2, an intuitive and efficient neural simulator** |br|
@@ -31,7 +31,12 @@ Important literature
    * - |br| 
        **Book | Mathematical Foundations of Neuroscience (chapters 1, 2 & 7)** |br|
        G B Ermentrout, D H Terman |br|
-       Publisher's website: https://link.springer.com/book/10.1007/978-0-387-87708-2 
+       Publisher's website: https://link.springer.com/book/10.1007/978-0-387-87708-2
+
+   * - |br| 
+       **Brian2CUDA: flexible and efficient simulation of spiking neural network models on GPUs** |br|
+       D Alevi, M Stimberg, H Sprekeler, K Obermayer, M Augustin |br|
+       DOI: https://doi.org/10.3389/fninf.2022.883700 
 
 
 .. |br| raw:: html

diff --git a/setup.py b/setup.py
@@ -1,8 +1,9 @@
 from setuptools import find_packages, setup
 
-VERSION = '1.0.6'
+VERSION = '1.0.7'
 DESCRIPTION = 'A package for adding dendrites to SNNs'
-LONG_DESCRIPTION = 'A package for adding dendrites to SNNs in Brian 2'
+with open("README.rst") as f:
+    LONG_DESCRIPTION = f.read()
 
 # Setting up
 setup(
@@ -11,7 +12,7 @@
     author="Michalis Pagkalos",
     author_email="<mpagkalos93@gmail.com>",
     description=DESCRIPTION,
-    long_description_content_type="text/markdown",
+    long_description_content_type="text/x-rst; charset=UTF-8",
     long_description=LONG_DESCRIPTION,
     packages=find_packages(),
     install_requires=['brian2==2.5.1'],