Installation
============

DendroTweaks is included in the Python package index: https://pypi.org/project/dendrotweaks.

1. We recommend using a virtual environment to install DendroTweaks. You can create a new virtual environment using :code:`conda`:

.. code-block:: bash

   conda create -n dendrotweaks python=3.11

2. Activate the environment:

.. code-block:: bash

   conda activate dendrotweaks

3. Install the :code:`dendrotweaks` package and its dependencies:
  
.. code-block:: bash

   pip install dendrotweaks

If you are working on Windows, you will need to separately install NEURON according to the official instructions: 
https://nrn.readthedocs.io/en/8.2.6/install/install_instructions.html#windows

3. (Alternative) If you want to install the package from source, you can clone the repository and run the following command:

.. code-block:: bash

   git clone https://github.com/Poirazi-Lab/DendroTweaks.git
   cd DendroTweaks
   pip install .

4. Once installed, you can import the package in your Python scripts or Jupyter notebooks:

.. code-block:: python

   import dendrotweaks as dd
   dd.__version__

If the installation was successful, this command will return the version number of the package.

If you want to use the package in Jupyter notebooks, you will need to install Jupyter:

.. code-block:: bash

   pip install jupyter

Development
---------------

If you want to contribute to the development of DendroTweaks, you can install the package in editable mode with
the development dependencies. To do this, clone the repository and run the following command:

.. code-block:: bash

   git clone https://github.com/Poirazi-Lab/DendroTweaks.git
   cd DendroTweaks
   pip install -e .[dev]


Troubleshooting
---------------

Debian-based systems (e.g., Ubuntu)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


If you encounter any issues with compiling MOD files in the NEURON simulator, you could try to 
manually compile the MOD files. To do this,
navigate to a folder containing MOD files, activate your virtual environment, 
and run the following command:

.. code-block:: bash

   nrnivmodl

This command will compile the MOD files and result in the following directory 
structure:

.. code-block:: bash

   /path/to/mod/
   ├── mechanism.mod
   └── x86_64
      └── ...

You should be able to load the mechanisms from the compiled MOD files 
in Python using the following command:

.. code-block:: python

   import neuron
   neuron.load_mechanisms('path/to/mod/')

If you encounter any issues with the compilation of the MOD files, 
you may need to install the C++ compiler and make utility. 
Make sure you have the following packages installed:

.. code-block:: bash

   gcc --version
   g++ --version
   make --version

If you don't have them installed, you can install them using the following commands:

.. code-block:: bash

   sudo apt install gcc
   sudo apt install g++
   sudo apt install make