Pushing version 2.0.0 to main (#28)

* Update conf.py * Update setup.py * Updated docs * Updated documentation with usage examples * Updated models documentation * Removing some dendrite-specific features from Soma * Implemented a simple logging function * Updated gitignore * Updated ephys to account for dimensionless * Updated ephys: dimensionless, better errors, logging * updated gitignore * Improving compartment.py * Syncing changes from main to development (#21) * Update README.rst * Update README.rst * Updated Fig2_notebook.ipynb !pip install dendrify==1.0.8 --quiet * Updating development (#22) * Update README.rst * Update README.rst * Updated Fig2_notebook.ipynb !pip install dendrify==1.0.8 --quiet * Update Fig3_notebook.ipynb * Update Fig4_notebook.ipynb * Update Fig5_notebook.ipynb * Made from scratch a new dSpike mechanism * Updated __str__ method and implemented pprint. * Updated custom events, __str__ and type checking * Implemented default params functionality * Added config_dspikes and did minor changes * Added some files to .gitignore * Reduced checks for dSpikes and added timesteps * Minor improvements * Updated gitignore * Added PointNeuronModel * Added PointNeuronModel to init * Resolved double connection when using ipython * Added more methods to PointNeuronModel * NeuronModel uses copies of compartments * Improved compartment parsing for NeuronModel. * Updated PointNeuronModel class * Updated .gitignore * Added option to just view default_params * Changed order of processes within connect() * Added a check for dimensionless within connect * Fixed a bug in connect * Added option for figsize in as_graph() * install requires brian 2.5.4 * Added more parameters to make_neurongroup * added second reset functionality to neuronmodel * Updated docs of ephysproperties * Finished docs of compartment and cleared code * Simplified docstrings * Added tutorials and pointneuronmodel to docs * Improved installation guidelines * Minor changes * Fixed index file * Updated installation guidelines * Finished docstrings of all classes * Fixed tuple bug when creating a NeuronGroup * Documentation changes * Documentation improvements * Fixed a weird bug that was raising silly errors * Minor changes * Experimenting with pytest * Created using Colaboratory * Colab test * Fixed docs * Made PointNeuronModel from scratch * added 3 examples with point adex * cleared repo * Minor changes * Updated tutorials * Updated docs * Automated examples to rst * Added point neuron models * Fixed a bug in _set_properties * Removed scale & spine factor from NeuronModel init * Many documentation updates * Added tau validation to docs * Minor changes * Minor documentation changes * FIxed duplicate label warning from sphinx * Added FI curve to docs * Minor changes * Added more validation tests to docs * Dendritic IO + other docs improvements * Added more examples * minor * Fixed bug that initialized area_factors with None * Fixed _set_properties bug with area factors * Finished all validation examples * More documentation changes * Added logo * Fixed intro images in docs * Improved colors for docs * Changed hover color * Minor * Improved model library in docs * Changed changelog :) * Minor changes docs * Minor * Added understanding dSpikes to docs * Minor changes * Fixed background color for intro figs * Updated readme and docs * Updated Readme * Updated changelog * Updated release noted and COC * Updated release notes * Finished docs * Updated conf * Updated rtd config file
Poirazi-Lab · Sep 19, 2023 · f3a0c99 · f3a0c99
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diff --git a/.gitignore b/.gitignore
@@ -132,3 +132,14 @@ dmypy.json
 test.py
 .vscode/settings.json
 .vscode/
+test.ipynb
+test2.ipynb
+minitest.ipynb
+dspikes_benchmarks.ipynb
+dspikes.ipynb
+nikos.ipynb
+viz.py
+bench_test_old.py
+bench_test.py
+test2.py
+examples_new/val_tau.py
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -18,5 +18,4 @@ formats:
 # Optionally declare the Python requirements required to build your docs
 python:
    install:
-   - requirements: docs_sphinx/source/requirements_docs.txt
-   system_packages: true
+   - requirements: docs_sphinx/source/requirements_docs.txt
diff --git a/README.rst b/README.rst
@@ -14,18 +14,37 @@ Dendrify
         :target: CODE_OF_CONDUCT.md
         :alt: Contributor Covenant
 
-Although neuronal dendrites greatly influence how single neurons process incoming information, their role in network-level functions remain largely unexplored. Current SNNs are usually quite simplistic, overlooking essential dendritic properties. Conversely, circuit models with morphologically detailed neuron models are computationally costly, thus impractical for large-network simulations.
 
-To bridge the gap between these two, we introduce Dendrify, a free, open-source Python package compatible with the `Brian 2 simulator <https://brian2.readthedocs.io/en/stable/>`_. Dendrify, through simple commands, automatically generates reduced compartmental neuron models with simplified yet biologically relevant dendritic and synaptic integrative properties. Such models strike a good balance between flexibility, performance, and biological accuracy, allowing us to explore dendritic contributions to network-level functions.
+Although neuronal dendrites play a crucial role in shaping how individual 
+neurons process synaptic information, their contribution to network-level 
+functions has remained largely unexplored. Current spiking neural networks 
+(SNNs) often oversimplify dendritic properties or overlook their essential 
+functions. On the other hand, circuit models with morphologically detailed 
+neuron representations are computationally intensive, making them impractical 
+for simulating large networks.
+
+In an effort to bridge this gap, we present Dendrify—a freely available,
+open-source Python package that seamlessly integrates with the
+`Brian 2 simulator <https://brian2.readthedocs.io/en/stable/>`_. Dendrify,
+through simple commands, automatically generates reduced compartmental neuron
+models with simplified yet biologically relevant dendritic and synaptic
+integrative properties. These models offer a well-rounded compromise between
+flexibility, performance, and biological accuracy, enabling us to investigate
+the impact of dendrites on network-level functions.
 
 .. image:: https://github.com/Poirazi-Lab/dendrify/blob/main/docs_sphinx/source/_static/intro.png
    :width: 70 %
    :align: center
 
 If you use Dendrify for your published research, we kindly ask you to cite our article:
 
-Pagkalos, M., Chavlis, S., & Poirazi, P. (2023). Introducing the Dendrify framework for incorporating dendrites to spiking neural networks. Nature Communications, 14(1), 131. https://doi.org/10.1038/s41467-022-35747-8
+Pagkalos, M., Chavlis, S., & Poirazi, P. (2023). Introducing the Dendrify framework
+for incorporating dendrites to spiking neural networks.
+Nature Communications, 14(1), 131. https://doi.org/10.1038/s41467-022-35747-8
+
 
 Documentation for Dendrify can be found at https://dendrify.readthedocs.io/en/latest/
 
-The project presentation for the INCF/OCNS Software Working Group is available `on google drive <https://docs.google.com/presentation/d/1LUUh2ja3YSHcmByU0Vyn7vcDEnDq6fWfVxFfuK8FzE0/edit?usp=sharing>`_ and an interactive notebook with a short demo `on google colab <https://colab.research.google.com/drive/1-bGp15eWfjNuF7ETCNSsL3ovOanS_R_7?usp=sharing>`_.
+
+The project presentation for the INCF/OCNS Software Working Group is available 
+`on google drive <https://docs.google.com/presentation/d/1LUUh2ja3YSHcmByU0Vyn7vcDEnDq6fWfVxFfuK8FzE0/edit?usp=sharing>`_.
diff --git a/dendrify/__init__.py b/dendrify/__init__.py
@@ -1,4 +1,5 @@
 from .compartment import Compartment, Dendrite, Soma
-from .ephysproperties import EphysProperties
+from .ephysproperties import (EphysProperties, default_params,
+                              update_default_params)
 from .equations import library
-from .neuronmodel import NeuronModel
+from .neuronmodel import NeuronModel, PointNeuronModel