From 06c9b5cdbfa99fcf8788d0e75e4636f354800c61 Mon Sep 17 00:00:00 2001
From: Alan Garny <agarny@hellix.com>
Date: Thu, 5 Dec 2019 10:19:30 +1300
Subject: [PATCH] Python support: provide some user documentation (#2216).

---
 doc/python/OpenCOR_Python.rst | 190 ----------------------------------
 1 file changed, 190 deletions(-)
 delete mode 100644 doc/python/OpenCOR_Python.rst

diff --git a/doc/python/OpenCOR_Python.rst b/doc/python/OpenCOR_Python.rst
deleted file mode 100644
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--- a/doc/python/OpenCOR_Python.rst
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-Python in OpenCOR
-=================
-
-IPython console window
-----------------------
-
-A dockable window running `IPython <https://ipython.readthedocs.io/en/stable/index.html>`__ that includes `NumPy <https://numpy.org/>`__, `Scipy library <https://scipy.org/scipylib/index.html>`__ and `matplotlib <https://matplotlib.org/>`__.
-
-If not visible then enable it from OpenCOR's menu: ``View/Windows/PythonQtConsole``.
-
-An IPython tutorial is `here <https://ipython.readthedocs.io/en/stable/interactive/tutorial.html>`__. Some keys are different than in the tutorial:
-
-    ``Control-Enter``
-        start multi-line input.
-    ``Shift-Enter``
-        execute code block.
-    ``Escape``
-        clear input.
-
-Command history:
-
-    Up/down keys
-        History filtered with currently typed characters.
-    %history
-        All commands in current session.
-
-Change font size in Python console:
-
-    Linux and Windows
-        ``Control +/-``
-    MacOS
-        ``Command +/-``
-
-OpenCOR Python module
----------------------
-
-.. code:: python
-
-    import OpenCOR as oc
-
-Methods:
-
-    ``openSimulation()``
-        Open a model. Corresponds to ``File/Open``.
-
-        Returns the simulation.
-
-    ``openRemoteSimulation()``
-        Open a remote model. Corresponds to ``File/Open Remote``.
-
-        Returns the simulation.
-
-    ``simulation()``
-        Returns the current simulation.
-
-    ``simulations()``
-        Returns a dictionary of open simulations.
-
-Objects:
-
-    ``Simulation``
-
-    ``DataStore``
-
-    ``DataStoreVariable``
-
-Sample code
------------
-
-.. code:: python
-
-    # Change the current directory
-    %cd ~/biosignalml/workspace/cellml/workspaces/dbrooks/noble62
-
-    # Import OpenCOR's Python module
-    import OpenCOR as oc
-
-    # Current (visible) simulation
-    s = oc.simulation()
-
-    # Dictionary of all open simulations
-    s = oc.simulations()
-
-    # Open a simulation (Name of CellML or SEDML file)
-    s = oc.openSimulation('noble_1962.cellml')
-
-    # Open a remote simulation (URL of a CellML or SEDML file)
-    s = oc.openRemoteSimulation('https://models.physiomeproject.org/workspace/25d/rawfile/f0e63e292ebb1d6798da08914b4217aec434af96/lorenz.sedml')
-
-    # Access a simulation's initial conditions
-    d = s.data()
-
-    # Time constraints
-    d.startingPoint()
-    d.endingPoint()
-    d.pointInterval()
-
-    # Changing values
-    d.setStartingPoint(1)
-    d.setEndingPoint(2)
-    d.setPointInterval(0.1)
-
-    # Parameters (as Python dictionaries)
-    d.constants()
-    d.states()
-    d.rates()
-
-    # Changing values
-    d.constants()['main/k'] = 1.0
-
-    # Run a simulation
-    s.run()
-
-    # Reset a simulation's parameters
-    s.resetParameters()
-
-    # Clear a simulation's results
-    s.clearResults()
-
-    # Access a simultaion's results
-    r = s.results()
-
-    # Time points
-    t = r.points()
-    t.values()
-
-    # Dictionaries of DataStore variables
-    r.constants()
-    r.states()
-    r.rates()
-    r.algebraic()
-
-    # Individual variables
-    x = r.states()['main/k']
-    x.values()
-
-    # Data also accessible via the simulation's DataStore
-    ds = r.dataStore()
-
-    # Variable of integration (r.points())
-    ds.voi()
-
-    # Dictionaries of DataStore variables
-    ds.variables()
-    ds.voiAndVariables()
-
-    # Individual variables
-    x = ds.variables()['main/k']
-
-
-matplotlib example
-------------------
-
-A matplotlib tutorial is `available here <https://matplotlib.org/users/pyplot_tutorial.html>`__.
-
-.. code:: python
-
-    import matplotlib.pyplot as plt
-    from mpl_toolkits.mplot3d import Axes3D
-
-    # The following assumes a simulation of the Lorenz model has been run
-    states = s.results().states()
-
-    fig = plt.figure()
-    ax = fig.gca(projection='3d')
-    ax.plot(states['main/x'].values(), states['main/y'].values(), states['main/z'].values(), linewidth=0.5)
-    ax.set_xlabel(states['main/x'].label())
-    ax.set_ylabel(states['main/y'].label())
-    ax.set_zlabel(states['main/z'].label())
-    plt.show()
-
-..
-    Other code: ::
-
-    fig = plt.figure()
-
-    ax = fig.add_subplot(2, 1, 1, projection='3d')
-    ax.plot(t.values(), states['main/x'].values(), states['main/y'].values())
-    ax.set_xlabel(t.label())
-    ax.set_ylabel(states['main/x'].label())
-    ax.set_zlabel(states['main/y'].label())
-
-    ax = fig.add_subplot(2, 1, 2, projection='3d')
-    ax.plot(states['main/x'].values(), states['main/y'].values(), states['main/z'].values())
-    ax.set_ylabel(states['main/x'].label())
-    ax.set_zlabel(states['main/y'].label())
-    ax.set_zlabel(states['main/z'].label())
-
-    plt.show()
-