Prerequisites and Installation
=================================

Prerequisites
----------------

To run CyTRACK, you need

- `Python 3.8+ <https://www.python.org/downloads/release/python-380/>`__ 
- `Git <https://git-scm.com/>`__ 
- `Anaconda 3 <https://www.anaconda.com/>`__ 
- `Linux <https://www.linux.org/>`__ 



The main Python packages that must be installed are the following:

.. code-block:: bash

    - netCDF4
    - numpy 
    - scipy 
    - mpi4py
    - time
    - datetime
    - functools
    - math 
    - sys
    - os
    - matplotlib
    - imp
    - xarray
    - sklearn
    - argparse

Installation
------------------

**1 - First Method**

.. code-block:: bash

    conda install -c tramo-ephyslab cytrack

or

.. code-block:: bash

    conda install -c apa_py cytrack


**2 - Second Method**
  
You must check that all the packages are installed and that there is no error message when they are imported.

- Clone the repository:

.. code-block:: bash

    git clone https://github.com/apalarcon/CyTRACK.git


- Verify you have installed all packages requiered for CyTRACK. If you use an Anaconda environment, please be sure you have activated the environment

- Copy the src/cytrack directory to your Anaconda installation

.. code-block:: bash

    cp -r src/cytrack path_to_anaconda_installation/lib/python3.x/site-packages/

To knnow the exactly path of your Anaconda installation (patho_to_anaconda_installation/.../site-packages/), you can follow these instructions:

.. code-block:: python

    from distutils.sysconfig import get_python_lib
    print(get_python_lib())

**3 - Third Method**

- Clone CyTRACK repository.

.. code-block:: bash

    git clone https://github.com/apalarcon/CyTRACK.git

- Verify you have installed all packages requiered for CyTRACK. If you use an Anaconda environment, please be sure you have activated the environment.

- Go to src directory

.. code-block:: bash

    run install_CyTRACK.sh.


.. note::
    From now on it should be installed in the python environment and can be used like any other Python package.

Possible problems with python packages:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

If you have a problem with the `mpi4py` library, try these steps:

- Remove the `mpi4py` library conda remove `mpi4py`
- Install the `openmpi` library `conda install conda-forge::openmpi`
- Install again the `mpi4py` library conda install `mpi4py`
- If the problem continue (the problem is frequently related with the `libmpi.so.12`  or similar), you can also try

Search the mising library on your system and link it to your Anaconda lib path.

.. code-block:: bash

    ln -s path_to_missing_library/libmpi.so.12 patho_to_anaconda_installation/lib/

or

Contact your system administrator