-                      r2e66ef5
+                      r870a2f4
 Computational kernels
 ---------------------
+* :mod:`core`
+* :mod:`modelinfo`
+* :mod:`kernel`
+* :mod:`product`
+* :mod:`mixture`
 At the heart of *sasmodels* are the individual computational kernels.  These
 …
 return the expected scattering for that $q$. The instructions for writing
 a kernel are documented in :ref:`Writing_a_Plugin`.  The source code for
 the kernels is stored in :mod:`sasmodels.models`.
 The primary interface to the models is through :mod:`sasmodels.core`, which
+the kernels is stored in :mod:`models`.
+The primary interface to the models is through :mod:`core`, which
 provides functions for listing available models, loading the model definition
+and compiling the model.  Use :func:`sasmodels.core.load_model` to load in
+a model definition and compile it.
+The computational kernels are difficult to call directly, but an example
+was provided in :ref:`Scripting_Interface`.
+The code for loading the kernel is in
+:mod:`sasmodels.generate`, but a big part of it, which is interpreting the
+definition, lives in :mod:`sasmodels.modelinfo`.  This defines the properties
+of the model in :class:`sasmodels.modelinfo.ModelInfo`, the available
+model parameters in :class:`sasmodels.modelinfo.ParameterTable` and the
+individual parameter attributes such as units and hard limits in
+:class:`sasmodels.modelinfo.Parameter`.
+and compiling the model.  Use :func:`core.load_model` to load in
+a model definition and compile it.  This makes use of
+:func:`core.load_model_info` to load the model definition and
+:func:`core.build_model` to turn it into a computational kernel model
+:class:`kernel.KernelModel`.
+The :class:`modelinfo.ModelInfo` class defines the properties
+of the model including the available model parameters
+:class:`modelinfo.ParameterTable` with individual parameter attributes
+such as units and hard limits defined in :class:`modelinfo.Parameter`.
+The :class:`product.ProductModel` and :class:`mixture.MixtureModel` classes
+are derived models, created automatically for models with names like
+"hardsphere*sphere" and "cylinder+sphere".
+Data loaders
+------------
+* :mod:`data`
+In order to test models a minimal set of data management routines is
+provided in :mod:`data`.  In particular, it provides mock :class:`data.Data1D`
+and :class:`data.Data2D` classes which mimic those classes in *SasView*.
+The functions :func:`data.empty_data1D` and :func:`data.empty_data2D`
+are handy for creating containers with a particular set of $q$, $\Delta q$
+points which can later be evaluated, and :func:`data.plot_theory` to show
+the result.  If *SasView* is available on the path then :func:`data.load_data`
+can be used to load any data type defined in *SasView*.  The function
+:func:`data.plot_data` can plot that data alone without the theory value.
+Kernel execution
+----------------
+* :mod:`resolution`
+* :mod:`resolution2d`
+* :mod:`sesans`
+* :mod:`weights`
+* :mod:`details`
+* :mod:`direct_model`
+* :mod:`bumps_model`
+* :mod:`sasview_model`
+To execute a computational kernel at a particular set of $q$ values, the
+use :meth:`kernel.KernelModel.make_kernel`, which returns a callable
+:class:`kernel.Kernel` for that $q$ vector (or a pair of $q_x$, $q_y$
+for 2-D datasets).
+The calculated $q$ values should include the measured
+data points as well as additional $q$ values required to properly compute the
+$q$ resolution function.  The *Resolution* subclasses in :mod:`resolution`
+define the *q_calc* attribute for this purpose.  These are
+:class:`resolution.Perfect1D` for perfect resolution,
+:class:`resolution.Pinhole1D` for the usual SANS pinhole aperture,
+:class:`resolution.Slit1D` for the usual USANS slit aperture and
+:class:`resolution2d.Pinhole2D` for 2-D pinhole data.
+In addition, :class:`resolution2d.Slit2D` defines 1-D slit smeared data
+for oriented samples, which require calculation at particular $q_x$ and
+$q_y$ values instead of $|q|$ as is the case for orientationally averaged
+USANS.  The :class:`sesans.SesansTransform` class acts like a 1-D resolution,
+having a *q_calc* attribute that defines the calculated $q$ values for
+the SANS models that get converted to spin-echo values by the
+:meth:`sesnas.SesansTransform.apply` method.
+Polydispersity is defined by :class:`weights.Dispersion` classes,
+:class:`weights.RectangleDispersion`, :class:`weights.ArrayDispersion`,
+:class:`weights.LogNormalDispersion`, :class:`weights.GaussianDispersion`,
+:class:`weights.SchulzDispersion`.  The :func:`weights.get_weights`
+function creates a dispersion object of the class matching
+:attr:`weights.Dispersion.type`, and calls it with the current value
+of the parameter.  This returns a vector of values and weights for a
+weighted average polydispersity.
+In order to call the :class:`kernel.Kernel`, the values and weights for
+all parameters must be composed into a :class:`details.CallDetails` object.
+This is a compact vector representation of the entire polydispersity
+loop that can be passed easily to the kernel.  Additionally, the magnetic
+parameters must be converted from polar to cartesian coordinates.  This
+work is done by the :func:`details.make_kernel_args` function, which returns
+values that can be sent directly to the kernel.  It uses
+:func:`details.make_details` to set the details object and
+:func:`details.convert_magnetism` for the coordinate transform.
+In the end, making a simple theory function evaluation requires a lot of
+setup. To make calling them a little easier, the *DirectModel* and
+*BumpsModel* interfaces are provided.  See :ref:`Scripting_Interface`
+for an example.
+The :class:`direct_model.DirectModel` interface accepts a data object
+and a kernel model.  Within the class,
+the :meth:`direct_model.DataMixin._interpret_data` method is called to
+query the data and set the resolution.
+The :meth:`direct_model.DataMixin._calc_theory` takes a set of parameter
+values, builds the kernel arguments, calls the kernel, and applies the
+resolution function, returning the predicted value for the data $q$ values.
+The :class:`bumps_model.Experiment` class is like the DirectModel class,
+but it defines a Fitness class that can be handed directly to the
+bumps optimization and uncertainty analysis program.
+The :class:`sasview_model.SasviewModel` class defines a SasView 4.x
+compatible interface to the sasmodels definitions, allowing sasmodels
+to be used directly from SasView.  Over time the SasView shim should
+disappear as SasView access the :class:`modelinfo.ModelInfo` and
+computational kernels directly.
+Kernel execution
+----------------
+* :mod:`kernelcl`
+* :mod:`kerneldll`
+* :mod:`kernelpy`
+* :mod:`generate`
 The kernel functions for the most part do not define polydispersity,
+resolution functions or magnetism.  Instead, code for these is generated in
+:mod:`sasmodels.generate`
+Sasview kernels:
+* :mod:`
+    ('kernel', 'Evaluator type definitions'),
+    ('kernelcl', 'OpenCL model evaluator'),
+    ('kerneldll', 'Ctypes model evaluator'),
+    ('kernelpy', 'Python model evaluator'),
+Bumps fitting routines:
+* :mod:`sasmodels.bumps_model` is a wrapper around
+    ('bumps_model', 'Bumps interface'),
+    ('direct_model', 'Simple interface'),
+Utility functions:
+* :mod:`sasmodels` provides :func:`sasmodels.__init__.data_files` for the installer.
+* :mod:`sasmodels.rst2html` provides tools for converting model docs to html and viewing
+  the html.  When run as a main program, it can display arbitrary rst files.
+* :mod:`sasmodels.exception` annotates the current exception with a context string,
+  such as "while opening myfile.dat" without adjusting the traceback.
+And so on::
+    ('compare_many', 'Batch compare models on different compute engines'),
+    ('compare', 'Compare models on different compute engines'),
+    ('convert', 'Sasview to sasmodel converter'),
+    ('core', 'Model access'),
+    ('data', 'Data layout and plotting routines'),
+    ('details', 'Parameter packing for kernel calls'),
+    ('generate', 'Model parser'),
+    ('list_pars', 'Identify all parameters in all models'),
+    ('mixture', 'Mixture model evaluator'),
+    ('model_test', 'Unit test support'),
+    ('modelinfo', 'Parameter and model definitions'),
+    ('product', 'Product model evaluator'),
+    ('resolution', '1-D resolution functions'),
+    ('resolution2d', '2-D resolution functions'),
+    ('sasview_model', 'Sasview interface'),
+    ('sesans', 'SESANS calculation routines'),
+    ('weights', 'Distribution functions'),
+resolution or magnetism directly.  Instead sasmodels automatically
+applies these, calling the computation kernel as needed.
+The outermost loop is the resolution calculation.  For the 1-D case
+this computes a single vector of $I(q)$ values and applies the convolution
+to the resulting set.  Since the same $I(q)$ vector is used to compute the
+convolution at each point, it can be precomputed before the convolution,
+and so the convolution is reasonably efficient.  The 2-D case is not
+that efficient, and instead recomputes the entire shifted/scaled set
+of $q_x$, $q_y$ values many times, or very many times depending on the
+accuracy requested.
+Polydispersity is handled as a mesh over the polydisperse parameters.
+This is the next level of the loop.  For C kernels run in a DLL or
+using OpenCL, the polydisperisty loop is generated separately for each
+model as C code.  Inside the polydispersity loop there is a loop over
+the magnetic cross sections for magnetic models, updating the SLD
+parameters with the effective magnetic SLD for that particular $q$
+value. For OpenCL, each $q$ value loops over the
+polydispersity mesh on a separate processor. For DLL, the outer loop
+cycles through polydispersity, and the inner loop distributes q values
+amongst the processors.  Like the DLL, the Python kernel execution
+cycles over the polydisperse parameters and the magnetic cross sections,
+calling the computation kernel with a vector of $q$ values.  Assuming
+the kernel code accepts vectors, this can be fast enough (though it is
+painfully slow if not vectorized).
+Further details are provided in the next section,
+:ref:`Calculator_Interface`
+Testing
+-------
+* :mod:`model_test`
+* :mod:`compare`
+* :mod:`compare_many`
+* :mod:`rst2html`
+* :mod:`list_pars`
+Individual models should all have test values to make sure that the
+evaluation is correct.  This is particularly important in the context
+of OpenCL since sasmodels doesn't control the compiler or the hardware,
+and since GPUs are notorious for preferring speed over precision.  The
+tests can be run as a group using :mod:`model_test` as main::
+    $ python -m sasmodels.model_test all
+Individual models can be listed instead of *all*, which is convenient when
+adding new models.
+The :mod:`compare` module, usually invoked using *./sascomp* provides a
+rich interface for exploring model accuracy, execution speed and parameter
+ranges.  It also allows different models to be compared.
+The :mod:`compare_many` module does batch comparisons, keeping a list of
+the particular random seeds which lead to large differences in output
+between different computing platforms.
+The :mod:`rst2html` module provides tools for converting model docs to
+html and viewing the html.  This is used by :mod:`compare` to display
+the model description, such as::
+    $ ./sascomp -html sphere
+This makes debugging the latex much faster, though this may require
+Qt in order for mathjax to work correctly.
+When run as main, it can display arbitrary ReStructuredText files. E.g.,
+::
+    $ python -m sasmodels.rst2html doc/developer/overview.rst
+This is handy for sorting out rst and latex syntax.  With some work
+the results could be improved so that it recognizes sphinx roles
+such as *mod*, *class* and *func*, and so that it uses the style sheets
+from the sasmodels docs.
+The :mod:`list_pars` module lists all instances of parameters across
+all models.  This helps to make sure that similar parameters have
+similar names across the different models.  With the verbose flag,
+the particular models which use each named parameter are listed.
+Model conversion
+----------------
+* :mod:`convert`
+* :mod:`conversion_table`
+Model definitions are not static.  As needs change or problems are found,
+models may be updated with new model names or may be reparameterized
+with new parameter definitions.  For example, in translating the
+Teubner-Strey model from SasView 3.x to sasmodels, the definition
+in terms of *drho*, *k*, *c1*, *c2*, *a2* and prefactor was replaced
+by the defintion in terms of *volfraction_a*, *xi*, *d*, *sld_a* and
+*sld_b*.  Within :mod:`convert`, the *_hand_convert_3_1_2_to_4_1*
+function must be called when loading a 3.x model definition to update it to
+.1, and then the model should be further updated to 4.2, 5.0, and so on.
+The :func:`convert.convert_model` function does this, using the conversion
+table in :mod:`conversion_table` (which handled the major renaming from
+SasView 3.x to sasmodels), and using the internal *_hand_convert* function
+for the more complicated cases.
+Other
+-----
+* :mod:`exception`
+* :mod:`alignment`
+The :func:`exception.annotate_exception` function annotates the current
+exception with a context string, such as "while opening myfile.dat" without
+adjusting the traceback.
+The :mod:`alignment` module is unused.

doc/guide/plugin.rst

-                      r990d8df
+                      r870a2f4
         :code:`source = ["lib/polevl.c", ...]`
         (`link to code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/polevl.c>`_)
+        (`polevl.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/polevl.c>`_)
     sas_gamma(x):
 …
         on some platforms.
         :code:`source = ["lib/sasgamma.c", ...]`
         (`link to code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_gamma.c>`_)
+        :code:`source = ["lib/sas_gamma.c", ...]`
+        (`sas_gamma.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_gamma.c>`_)
     sas_erf(x), sas_erfc(x):
 …
         :code:`source = ["lib/polevl.c", "lib/sas_erf.c", ...]`
         (`link to error functions' code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_erf.c>`_)
+        (`sas_erf.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_erf.c>`_)
     sas_J0(x):
 …
         :code:`source = ["lib/polevl.c", "lib/sas_J0.c", ...]`
         (`link to Bessel function's code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_J0.c>`_)
+        (`sas_J0.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_J0.c>`_)
     sas_J1(x):
 …
         :code:`source = ["lib/polevl.c", "lib/sas_J1.c", ...]`
         (`link to Bessel function's code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_J1.c>`_)
+        (`sas_J1.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_J1.c>`_)
     sas_JN(n, x):
 …
         :code:`source = ["lib/polevl.c", "lib/sas_J0.c", "lib/sas_J1.c", "lib/sas_JN.c", ...]`
         (`link to Bessel function's code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_JN.c>`_)
+        (`sas_JN.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_JN.c>`_)
     sas_Si(x):
 …
         :code:`source = ["lib/Si.c", ...]`
         (`link to code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/Si.c>`_)
+        (`Si.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/Si.c>`_)
     sas_3j1x_x(x):
 …
         :code:`source = ["lib/sas_3j1x_x.c", ...]`
         (`link to code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_3j1x_x.c>`_)
+        (`sas_3j1x_x.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_3j1x_x.c>`_)
 …
         :code:`source = ["lib/polevl.c", "lib/sas_J1.c", ...]`
         (`link to Bessel form's code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_J1.c>`_)
+        (`sas_J1.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_J1.c>`_)
 …
         :code:`source = ["lib/gauss76.c", ...]`
         (`link to code <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/gauss76.c>`_)
+        (`gauss76.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/gauss76.c>`_)

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Changeset 870a2f4 in sasmodels for doc

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