####################
User's Documentation
####################


Getting start
=============

Upgrade from OpenAlea <= 1.2
============================

.. include:: upgrade.rst

Features
========

.. s'inspirer de https://support.rstudio.com/hc/en-us/categories/200035113-Documentation


.. toctree::
    :maxdepth: 1
    
    project
    model



.. warning::

    Move it


Command History
---------------

OpenAleaLab automatically store all the commands that you use in the interpreter (bottom red circle) during the current session into the *history* panel (right red circle).

.. container:: custom-float-right

    .. image:: ../../images/history.png
        :height: 500px
        :align:   center

You can browse this history into the panel *History*.
The commands are displayed in order (most recent at the bottom).

This components is useful to check what you have done previously and how you have done it.
You can copy/paste a line that you have already used from the history into the interpreter.

Help
----

This graphical component display informations about objects that you can select.

It can display help from models, packages and nodes.



Metadata
########

Project Loading
###############

Project Viewer
##############

Text Editor
-----------

  - Syntax Coloring
  - Tab Completion (Work in progress)
  - search (Ctrl+F)
  - go to (Ctrl+G)
  - execute selected code (Ctrl+R)
  - run model
      - run (F1)
      - step (F2)
      - animate (F3)
      - stop (F4) (Work in progress)
      - init (F5)

.. image:: ../../images/text_editor.png
    :height: 500px
    :align:   center

Workflow Editor
---------------

  - package manager
  - create node from PM
  - create node from models
  - create node from control

.. image:: ../../images/workflow_editor.png
    :height: 500px
    :align:   center


IPython Interpreter
-------------------

  - Syntax Coloring
  - Tab Completion (Work in progress)
  - magic commands
  - plots
  - interactive documentation

.. image:: ../../images/ipython.png
    :height: 300px
    :align:   center

Store
-----

Work in progress

.. install package, plugin, labs

Control Panel
-------------

Work in progress

Logger
------

Permit to show many informations about Application execution (useful to debug but unusable for beginner).

.. image:: ../../images/logger.png
    :height: 300px
    :align:   center


File Browser
------------

A simple file browser which allow to check what is on your computer and to show and edit files.

World Viewer
------------

3D Viewer
---------

Plot2d
------

The Plot2d plugin add interactive 2D plot to OpenAleaLab, using matplotlib.
When loaded, all plot  functionalities from matplotlib pyplot_ or pylab_ (which is included in ipython after running `pylab`) are automatically send to this applet. For Example, you can write in a python model::
    
    from matplotlib import pyplot as plt
    import numpy as np

    plt.clf()
    x = np.arange(0,12*np.pi,.1)
    plt.plot(np.exp(-x/12)*np.cos(x))
    
Running this model gives the following result:

.. image:: ../../images/plot2d_plugin_ex1.png
    :width: 70%

Another example, using pylab_::
    
    from scipy import stats
    %pylab
    
    dist = randn(10000)
    n = stats.norm(*stats.norm.fit(dist))
    
    # ploting
    clf()
    x = arange(dist.min(),dist.max(),.1)
    hist(dist,100,normed=1)
    plot(x,n.pdf(x),'r')
    
Produce this:

.. image:: ../../images/plot2d_plugin_ex2.png
    :width: 70%


.. _pyplot: http://matplotlib.org/api/pyplot_api.html
.. _pylab:  http://wiki.scipy.org/PyLab