-                      r39674a0
+                      r8ae8532
+             ]
+# Redirect mathjax to a different CDN
+mathjax_path = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-MML-AM_CHTML"
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

doc/genapi.py

-                      ra5b8477
+                      r8ae8532
 import os.path
 MODULE_TEMPLATE=""".. Autogenerated by genmods.py
+MODULE_TEMPLATE = """.. Autogenerated by genmods.py
 ******************************************************************************
 …
 """
 INDEX_TEMPLATE=""".. Autogenerated by genmods.py
+INDEX_TEMPLATE = """.. Autogenerated by genmods.py
 .. _api-index:
 …
         os.makedirs(dir)
     for module,name in modules:
         with open(os.path.join(dir,module+'.rst'), 'w') as f:
+    for module, name in modules:
+        with open(os.path.join(dir, module+'.rst'), 'w') as f:
             f.write(MODULE_TEMPLATE%locals())
     rsts = "\n   ".join(module+'.rst' for module,name in modules)
     with open(os.path.join(dir,'index.rst'),'w') as f:
+    rsts = "\n   ".join(module+'.rst' for module, name in modules)
+    with open(os.path.join(dir, 'index.rst'), 'w') as f:
         f.write(INDEX_TEMPLATE%locals())
 modules=[
     #('__init__', 'Top level namespace'),
+modules = [
+    ('__init__', 'Top level namespace'),
     #('alignment', 'GPU data alignment [unused]'),
     ('bumps_model', 'Bumps interface'),
+    ('compare_many', 'Batch compare models on different compute engines'),
     ('compare', 'Compare models on different compute engines'),
     ('convert', 'Sasview to sasmodel converter'),
 …
     ('direct_model', 'Simple interface'),
     ('exception', 'Annotate exceptions'),
-    #('frozendict', 'Freeze a dictionary to make it immutable'),
     ('generate', 'Model parser'),
     ('kernel', 'Evaluator type definitions'),
 …
     ('resolution', '1-D resolution functions'),
     ('resolution2d', '2-D resolution functions'),
+    ('rst2html', 'Convert doc strings the web pages'),
     ('sasview_model', 'Sasview interface'),
     ('sesans', 'SESANS calculation routines'),
-    #('transition', 'Model stepper for automatic model selection'),
     ('weights', 'Distribution functions'),
+]
 package='sasmodels'
 package_name='Reference'
+package = 'sasmodels'
+package_name = 'Reference'
 genfiles(package, package_name, modules)

doc/gentoc.py

-                      r40a87fa
+                      r8ae8532
     from sasmodels.modelinfo import ModelInfo
 TEMPLATE="""\
+TEMPLATE = """\
 ..
     Generated from doc/gentoc.py -- DO NOT EDIT --
 …
 """
 MODEL_TOC_PATH = "ref/models"
+MODEL_TOC_PATH = "guide/models"
 def _make_category(category_name, label, title, parent=None):
 …
         # assume model is in sasmodels/models/name.py, and ignore the full path
         model_name = basename(item)[:-3]
+        if model_name.startswith('_'): continue
+        if model_name.startswith('_'):
+            continue
         model_info = load_model_info(model_name)
         if model_info.category is None:
             print("Missing category for", item, file=sys.stderr)
         else:
             category.setdefault(model_info.category,[]).append(model_name)
+            category.setdefault(model_info.category, []).append(model_name)
     # Check category names
     for k,v in category.items():
+    for k, v in category.items():
         if len(v) == 1:
             print("Category %s contains only %s"%(k,v[0]), file=sys.stderr)
+            print("Category %s contains only %s"%(k, v[0]), file=sys.stderr)
     # Generate category files for the table of contents.
 …
     # alphabetical order before them.
+    if not exists(MODEL_TOC_PATH): mkdir(MODEL_TOC_PATH)
+    if not exists(MODEL_TOC_PATH):
+        mkdir(MODEL_TOC_PATH)
     model_toc = _make_category(
         'index',  'Models', 'Model Functions')
+        'index', 'Models', 'Model Functions')
     #shape_toc = _make_category(
     #    'shape',  'Shapes', 'Shape Functions', model_toc)
     free_toc = _make_category(
         'shape-independent',  'Shape-independent',
+        'shape-independent', 'Shape-independent',
         'Shape-Independent Functions')
     struct_toc = _make_category(
         'structure-factor',  'Structure-factor', 'Structure Factors')
+        'structure-factor', 'Structure-factor', 'Structure Factors')
     custom_toc = _make_category(
         'custom-models',  'Custom-models', 'Custom Models')
+        'custom-models', 'Custom-models', 'Custom Models')
     # remember to top level categories
 …
     # Process the model lists
     for k,v in sorted(category.items()):
+    for k, v in sorted(category.items()):
         if ':' in k:
             cat,subcat = k.split(':')
+            cat, subcat = k.split(':')
             _maybe_make_category(cat, v, cat_files, model_toc)
             cat_file = cat_files[cat]
             label = "-".join((cat,subcat))
+            label = "-".join((cat, subcat))
             filename = label
             title = subcat.capitalize()+" Functions"
+            title = subcat.capitalize() + " Functions"
             sub_toc = _make_category(filename, label, title, cat_file)
             for model in sorted(v):
 …
     _add_subcategory('shape-independent', model_toc)
     _add_subcategory('structure-factor', model_toc)
     _add_subcategory('custom-models', model_toc)
+    #_add_subcategory('custom-models', model_toc)
     # Close the top-level category files
     #model_toc.close()
+    for f in cat_files.values(): f.close()
+    for f in cat_files.values():
+        f.close()

doc/guide/gpu/gpu_computations.rst

-                      r3f5a566
+                      r8ae8532
 GPU Computations
 ****************
 SasView model evaluations can run on your graphics card (GPU) or they can run
+sasmodels evaluations can run on your graphics card (GPU) or they can run
 on the processor (CPU). In general, calculations performed on the GPU will run faster.
 …
 SasView prefers AMD or NVIDIA drivers for GPU, and prefers Intel or
 Apple drivers for CPU. Both GPU and CPU are included on the assumption that CPU
+Apple drivers for CPU. Both GPU and CPU are included on the assumption that CPU
 is always available and supports double precision.
 …
+.. note::
+    This help document was last changed by Steve King, 08Oct2016
+*Document History*
+| 2016-10-08 Steve King
+| 2017-05-07 Paul Kienzle

doc/guide/index.rst

-                      rbb6f0f3
+                      r8ae8532
 **********
 SAS Models
 **********
+****************
+SAS Models Guide
+****************
+Small angle X-ray and Neutron (SAXS and SANS) scattering examines the
+scattering patterns produced by a beam travelling through the sample
+and scattering at low angles.  The scattering is computed as a function
+of $q_x$ and $q_y$, which for a given beam wavelength corresponds to
+particular scattering angles. Each pixel on the detector corresponds to
+a different scattering angle. If the sample is unoriented, the scattering
+pattern will appear as rings on the detector.  In this case, a circular
+average can be taken with 1-dimension data at $q = \surd (q_x^2 + q_y^2)$
+compared to the orientationally averaged SAS scattering pattern.
+.. toctree::
+   :numbered: 4
+   :maxdepth: 4
+Models have certain features in common.
+Every model has a *scale* and a *background*.
+Talk about orientation, with diagrams for orientation so that we don't need
+a link on every model page?
+.. _orientation:
+.. figure: img/orientation1.jpg
+    Orientation in 3D
+.. figure: img/orientation2.jpg
+    Orientation cross sections
+Talk about polydispersity.
+Talk about magnetism, converting the magnetism help file to inline text here,
+with links so that models can point back to it.
+Need to talk about structure factors even though we don't have any
+implemented yet.
+   intro.rst
+   gpu/gpu_computations.rst
+   gpu/opencl_installation.rst
+   magnetism/magnetism.rst
+   sesans/sans_to_sesans.rst
+   sesans/sesans_fitting.rst
+   refs.rst

doc/guide/sesans/sesans_fitting.rst

-                      r3330bb4
+                      r8ae8532
 ===================
+.. note:: A proper installation of the developers setup of SasView (http://trac.sasview.org/wiki/AnacondaSetup) is a prerequisite for using these instructions.
+.. note::
+    A proper installation of the developers setup of SasView
+    (http://trac.sasview.org/wiki/AnacondaSetup) is a prerequisite for
+    using these instructions.
 It is possible to fit SESANS measurements from the command line in Python.
 …
 Simple Fits
 ...........
+In the folder sasmodels/example the file sesans_sphere_2micron.py gives an example of how to fit a shape to a measurement.
+In the folder sasmodels/example the file sesans_sphere_2micron.py gives
+an example of how to fit a shape to a measurement.
 The command::
 …
 .. image:: sesans_img/SphereLineFitSasView.png
+All the parameters and names in sesans_sphere_2micron.py (shown below) can be adjusted to fit your own problem::
+All the parameters and names in sesans_sphere_2micron.py (shown below) can
+be adjusted to fit your own problem::
   """
 …
   # Constraints
   # model.param_name = f(other params)
   # EXAMPLE: model.scale = model.radius*model.radius*(1 - phi) - where radius and scale are model functions and phi is
   # a custom parameter
+  # EXAMPLE: model.scale = model.radius*model.radius*(1 - phi) - where radius
+  # and scale are model functions and phi is a custom parameter
   model.scale = phi*(1-phi)
 …
 Incorporating a Structure Factor
 ................................
+An example of how to also include a structure factor can be seen in the following example taken from Washington et al.,
+*Soft Matter*\, (2014), 10, 3016 (dx.doi.org/10.1039/C3SM53027B). These are time-of-flight measurements, which is the
+reason that not the polarisation is plotted, but the :math:`\frac{log(P/P_0)}{\lambda^2}` . The sample is a dispersion
+of core-shell colloids at a high volume fraction with hard sphere interactions.
+An example of how to also include a structure factor can be seen in the
+following example taken from Washington et al., *Soft Matter*\, (2014), 10, 3016
+(dx.doi.org/10.1039/C3SM53027B). These are time-of-flight measurements, which
+is the reason that not the polarisation is plotted, but the
+:math:`\frac{log(P/P_0)}{\lambda^2}` . The sample is a dispersion of
+core-shell colloids at a high volume fraction with hard sphere interactions.
 The fit can be started by::
 …
 .. image:: sesans_img/HardSphereLineFitSasView.png
+The code sesans_parameters_css-hs.py can then be used as a template for a fitting problem with a structure factor::
+The code sesans_parameters_css-hs.py can then be used as a template for a
+fitting problem with a structure factor::
  """
 …
  # Constraints
  # model.param_name = f(other params)
  # EXAMPLE: model.scale = model.radius*model.radius*(1 - phi) - where radius and scale are model functions and phi is
  # a custom parameter
+ # EXAMPLE: model.scale = model.radius*model.radius*(1 - phi) - where radius
+ # and scale are model functions and phi is a custom parameter
  model.scale = phi*(1-phi)
  model.volfraction = phi

doc/index.rst

-                      r7bb290c
+                      r8ae8532
+Introduction
+============
+sasmodels
+=========
+Small angle X-ray and Neutron scattering (SAXS and SANS) examines the
+scattering patterns produced by a beam travelling through the sample
+and scattering at low angles.  The scattering is computed as a function
+of reciprocal space $q$, which arises from a combination of beam wavelength
+and scattering angles. Each pixel on the detector corresponds to
+a different scattering angle, and has a distinct $q_x$ and $q_y$. If the
+sample is unoriented, the scattering pattern will appear as rings on the
+detector.  In this case, a circular average can be taken with 1-dimension
+data at $q = \surd (q_x^2 + q_y^2)$ compared to the orientationally
+averaged SAS scattering pattern.
 The sasmodels package provides theory functions for small angle scattering
+calculations.
+calculations for different shapes, including the effects of resolution,
+polydispersity and orientational dispersion.
 .. htmlonly::
 …
    guide/index.rst
+   guide/models/index.rst
    developer/index.rst
-   ref/index.rst
-   ref/models/index.rst
    api/index.rst
 …
 .. htmlonly::
   * :ref:`search`

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