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

Python Package Index (PyPI)
---------------------------
MyMesh can be installed from the `python package index (PyPI) <https://pypi.org/project/mymesh/>`_: 

.. code-block::

    pip install mymesh[all]

Installing from source:
-----------------------
Download/clone the repository from `github <https://github.com/BU-SMBL/mymesh>`_, 
then run:

.. code-block::

    pip install -e <path>/mymesh[all]

with :code:`<path>` replaced with the file path to the mymesh root directory. 
To install with only the required dependencies, the :code:`[all]` can be omitted.
To install additional dependencies used for testing, documentation, and benchmarking,

.. code-block::

    pip install -e <path>/mymesh[all,test]

Dependencies
------------

MyMesh depends on a small number of built-in or well established python packages. 
Additionally, there are several optional dependencies that are required only for 
specific functions or use-cases.

Core dependencies
^^^^^^^^^^^^^^^^^

================ ======================
Package          Install
================ ======================
`numpy`_         ``pip install numpy``
`scipy`_         ``pip install scipy``
`sympy`_         ``pip install sympy``
================ ======================

Optional dependencies
^^^^^^^^^^^^^^^^^^^^^

======================= ==================== ================================================================================================= =============================
Package                 Purpose              Used in                                                                                           Install
======================= ==================== ================================================================================================= =============================
`numba`_                Enhanced efficiency  :mod:`~mymesh.delaunay`, :mod:`~mymesh.utils`, :mod:`~mymesh.improvement`, :mod:`~mymesh.quality` ``pip install numba``
`meshio`_               Mesh file I/O        :class:`~mymesh.mesh`                                                                             ``pip install meshio``
`pydicom`_              DICOM image file I/O :mod:`~mymesh.image`                                                                              ``pip install pydicom``  
`tifffile`_             TIFF image file I/O  :mod:`~mymesh.image`                                                                              ``pip install tifffile``  
`opencv (cv2)`_ [#f1]_  Image file I/O       :mod:`~mymesh.image`                                                                              ``pip install opencv-python``
`triangle`_             Constrained Delaunay :mod:`~mymesh.delaunay`                                                                           ``pip install triangle``
`vispy`_                Mesh visualization   :mod:`~mymesh.visualize`                                                                          ``pip install vispy``
`matplotlib`_           Mesh visualization   :mod:`~mymesh.visualize`                                                                          ``pip install matplotlib``
`pillow`_               Mesh visualization   :mod:`~mymesh.visualize`                                                                          ``pip install pillow``
`jupyter_rfb`_          Mesh visualization   :mod:`~mymesh.visualize`                                                                          ``pip install jupyter_rfb``
`colorspacious`_        Mesh visualization   :mod:`~mymesh.visualize`                                                                          ``pip install colorspacious``
`pyvista`_              Mesh visualization   :class:`~mymesh.mesh`                                                                             ``pip install pyvista``
`triangle`_             Triangulation        :mod:`~mymesh.delaunay`                                                                           ``pip install triangle``
`tetgen`_               Tetrahedralization   :mod:`~mymesh.delaunay`                                                                           ``pip install tetgen``
======================= ==================== ================================================================================================= =============================

MyMesh can be used without these optional dependencies and if a function requires them, an error will be raised instructing the user to install the needed dependency.

.. _numpy: https://numpy.org/
.. _scipy: https://scipy.org/
.. _sympy: https://sympy.org/
.. _meshio: https://github.com/nschloe/meshio
.. _numba: http://numba.pydata.org/
.. _pydicom: https://github.com/pydicom/pydicom
.. _tifffile: https://github.com/cgohlke/tifffile/
.. _opencv (cv2): https://github.com/opencv/opencv-python
.. _triangle: https://github.com/drufat/triangle
.. _vispy: https://vispy.org/
.. _matplotlib: https://matplotlib.org/
.. _pillow: https://github.com/python-pillow/Pillow
.. _jupyter_rfb: https://github.com/vispy/jupyter_rfb
.. _colorspacious: https://github.com/njsmith/colorspacious
.. _pyvista: https://pyvista.org/
.. _triangle: https://github.com/drufat/triangle
.. _tetgen: https://github.com/pyvista/tetgen

.. [#f1] OpenCV may require additional non-python libraries on some operating systems (for example libgl1-mesa-dev, libglib2.0-0).