change doc/manual/source dir to doc/source (#120)

doc/source/extending.rst

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+.. _extending-srmise:
+
+===================
+Extending SrMise
+===================
+
+The :ref:`tutorial` gives an overview of how to use SrMise with the existing
+peak and baseline functions.  These inherit from classes providing generic peak
+and baseline functionality, and from which additional peaks and baselines can be
+implemented.  The process for adding new peaks and baselines is summarized
+below, but see the source code for additional details.
+
+If you implement a peak or baseline likely to be of broad interest to the PDF
+community, please consider submitting a pull request to the GitHub
+`SrMise repository  <https://github.com/diffpy/diffpy.srmise>`_.
+
+Organization of Functions
+-------------------------
+
+The ``BaseFunction`` class in ``diffpy.srmise.basefunction`` implements the
+functionality common to all SrMise baseline and peak functions, which are
+separately implemented in the ``diffpy.srmise.baselines`` and
+``diffpy.srmise.peaks`` subpackages.  Specific baseline and peak functions
+inherit from the ``BaselineFunction`` and ``PeakFunction`` classes in those
+subpackges, as shown below.
+
+* .. py:class:: BaseFunction
+
+    + .. py:class:: BaselineFunction
+
+        - .. py:class:: FromSequence
+        - .. py:class:: NanoSpherical
+        - .. py:class:: Polynomial
+        - *etc.*
+
+    + .. py:class:: PeakFunction
+
+        - .. py:class:: Gaussian
+        - .. py:class:: GaussianOverR
+        - *etc.*
+
+Adding Baselines
+-------------------------------------
+
+To add a baseline, create a new module which defines a class inheriting from
+``diffpy.srmise.baselines.base.BaselineFunction``.  The class data and methods
+which need to be implemented are summarized in the source code.
+
+
+.. literalinclude:: ../../../diffpy/srmise/baselines/base.py
+    :pyobject: BaselineFunction
+    :end-before: __init__
+
+The class methods should follow these specifications.  See existing baselines
+for examples.
+
+.. py:method:: estimate_parameters(r, y)
+
+    Return a Numpy array of parameters estimated from the data.
+
+    :param r: Grid on which the data are defined.
+    :param y: The data.
+    :type r: `Sequence`
+    :type y: `Sequence`
+    :returns: Estimated parameters
+    :rtype: `numpy.ndarray`
+    :raises: NotImplementedError if estimation has not been implemented.
+    :raises: SrMiseEstimationError if estimation fails.
+
+
+.. py:method:: _jacobian_raw(pars, r, free)
+   
+    Return Jacobian for parameters evaluated over `r`.
+
+    :param pars: The parameters of the baseline.
+    :param r: Scalar or grid on which to calculate the Jacobian.
+    :param free: Boolean values indicating if corresponding parameter is free (True) or fixed (False).
+    :type pars: `Sequence(float)`
+    :type r: `int`, `float`, or `Sequence(int` or `float)`
+    :type free: `Sequence(boolean)`
+    :returns: List of Jacobian values (or None if parameter is not free) for each parameter evaluated at `r`.
+    :rtype: `list(numpy.ndarray(float) or float or None)`
+
+.. py:method:: _transform_derivativesraw(pars, in_format, out_format)
+
+    Return the gradient matrix of `pars` represented in format 'out_format'.
+
+    :param pars: The parameters of the baseline.
+    :param in_format: The format of `pars`.
+    :param out_format: The desired format of `pars`.
+    :type pars: `Sequence(float)`
+    :type in_format: `str`
+    :type out_format: `str`
+    :returns: The gradient matrix for the transformation.
+    :rtype: `numpy.ndarray`
+
+.. py:method:: _transform_parametersraw(pars, in_format, out_format)
+
+    Return parameters transformed into format 'out_format'.
+
+    :param pars: The parameters of the baseline.
+    :param in_format: The format of `pars`.
+    :param out_format: The desired format of `pars`.
+    :type pars: `Sequence(float)`
+    :type in_format: `str`
+    :type out_format: `str`
+    :returns: The transformed parameters.
+    :rtype: `numpy.ndarray`
+
+.. py:method:: _valueraw(pars, r)
+
+    Return value of baseline with given parameters at r.
+
+    :param pars: The parameters of the baseline.
+    :param r: Scalar or grid on which to calculate the baseline.
+    :type pars: `Sequence(float)`
+    :type r: `int`, `float`, or `Sequence(int` or `float)`
+    :returns: The value of the baseline.
+    :rtype: `float` or `numpy.ndarray(float)`.
+
+
+Adding Peaks
+--------------------------
+
+To add a new peak function, create a new module which defines a class
+inheriting from ``diffpy.srmise.peaks.base.PeakFunction``.  Implementing a peak
+function is nearly identical to implementing a baseline function, with the
+following differences:
+
+1) The ``estimate_parameters`` method is required.
+2) The "position" key must be defined in the ``parameterdict`` class member.
+3) Peak functions must implement the additional method ``scale_at``.
+
+.. py:method:: scale_at(pars, r, scale)
+
+    Return peak parameters such that the value at ``r`` is scaled by ``scale``
+    while the position of the peak's maxima remains unchanged.
+
+    :param pars: The parameters of the peak.
+    :param r: Position where the peak will be rescaled.
+    :param scale: A scale factor > 0.
+    :type pars: `Sequence(float)`
+    :type r: `int` or `float`
+    :type scale: `float`
+    :returns: The adjusted peak parameters.
+    :rtype: `numpy.ndarray(float)`.