.. _install:

Installation
************

Spring has been successfully run on Linux and MacOSX systems with the help of `Conda <https://docs.conda.io/>`_
that is a popular open source package management system for python packages. We base our most recent 
distribution of Spring for standard Linux and Mac systems on EMAN2 version2.91. 


.. _prerequisites:

Prerequisites
=============

Mac
---

* Requirements: Xcode including Python with X11

.. _prereq_table_mac:

+--------------------------------+
| MacOSX (10.8 - 10.15, 11)      |
+--------------------------------+
| #. Xcode                       |
| #. +command line tools         |
| #. X-Quartz                    |
|                                |
|                                |
+--------------------------------+

Launch the App Store and download Xcode. After it is installed, you need to install the Command Line Tools. \
This will install the default OS X Python binary.

1. MacOSX 10.8: in Xcode's preferences, go to the Downloads tab and install Command Line Tools. 
2. MacOSX 10.9 - 10.15, 11 (Big Sur): 

.. code-block:: console

   % xcode-select --install

Wait until install completed. In order to activate Xcode developer tools, make sure to agree with the license:

.. code-block:: console

   % sudo xcodebuild -license

Acknowledge reading by typing agree after scrolling down. 


Install the X11 window manager `X-Qartz <http://xquartz.macosforge.org>`_ on your system.


.. _compile_install:

Install by Conda
======================
Due to the many python dependencies, we extended an EMAN2's base conda environment (version 2.91) for SPRING.

Linux
-----

Launch the install script below.

.. code-block:: console
   
   % wget https://spring.fz-juelich.de/_download/install_linux.sh
   % sh install_linux.sh

.. literalinclude:: install_linux.sh
   :language: sh


Mac
---

Launch the install script below. 

.. code-block:: console
   
   % curl --remote-name https://spring.fz-juelich.de/_download/install_mac.sh
   % sh install_mac.sh

.. literalinclude:: install_mac.sh
   :language: sh


Activation
==========
   
The conda environment base has been added to your startup shell script. After re-launch of your shell, you can now 
execute any of the programs from the spring package by typing the program, e.g.:

.. parsed-literal::

   % spring

Testing    
=======

Check functionality of installed code by running some tests.
    
.. code-block:: python

   from spring.tests.micprgs.test_micctfdetermine import TestMicCtfDetermineMpi
   t = TestMicCtfDetermineMpi()
   t.setup()
   t.do_end_to_end_test_sa_inputfile_with_MPI()
   t.do_end_to_end_test_sa_inputfile_no_CTFTILT_with_MPI()
   t.teardown()


.. include:: CHANGES.rst