Merge branch 'doc-add-changelog'

* fix inclusion of moved source files
* add release-notes page
* clean up autogenerated API docs
* move license to a separate page
* fix documentation project name
* activate intersphinx extension
* switch to sphinx_py3doc_enhanced_theme

Author: pavoljuhas

CHANGELOG.md

@@ -0,0 +1,33 @@
+# Release notes
+
+## unreleased - Version 3.0.0
+
+Differences from version 1.3.
+
+### Added
+
+- Support for Python 3.7, 3.6, 3.5 in addition to 2.7.
+
+### Changed
+
+- Always use lower-case imports from `diffpy.structure`.
+- Use numeric-value sort to order variables in `PrintFitHook`.
+
+### Deprecated
+
+- Variable `__gitsha__` in the `version` module renamed to `__git_commit__`.
+
+### Removed
+
+- Optional upper and lower-bound arguments in `Parameter.setValue`.
+  The bounds can be set with `Parameter.boundRange` instead.
+- Unused classes `ListOperator`, `SetOperator`.
+
+### Fixed
+
+- Metadata retrieval from `PDFContribution` hierarchy.
+- Refresh `PDFGenerator` when its `rgrid` is changed in-place.
+- Zero division in the `nppdfsas.py` example.
+- Crash in `ellipsoidsas.py` example because of bug in `Parameter.setValue`.
+- Pickling of `ProfileGenerator` objects and of bound class methods.
+- Invalid escape sequences in string values.

doc/manual/source/api/diffpy.rst

@@ -1,10 +1,13 @@
+:tocdepth: 2
+
 diffpy.srfit package
 ====================
 
 Subpackages
 -----------
 
 .. toctree::
+    :maxdepth: 2
 
     diffpy.srfit.equation
     diffpy.srfit.fitbase

doc/manual/source/api/diffpy.srfit.rst

@@ -31,14 +31,20 @@
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.intersphinx',
-              'sphinx.ext.napoleon']
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.intersphinx',
+    'm2r',
+]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
-# The suffix of source filenames.
-source_suffix = '.rst'
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+source_suffix = ['.rst', '.md']
 
 # The encoding of source files.
 # source_encoding = 'utf-8-sig'
@@ -47,7 +53,7 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'SrFit'
+project = u'diffpy.srfit'
 copyright = u'%Y, Brookhaven National Laboratory'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -107,13 +113,15 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'default'
+html_theme = 'sphinx_py3doc_enhanced_theme'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-# html_theme_options = {}
-html_theme_options = {'collapsiblesidebar' : 'true'}
+html_theme_options = {
+    'collapsiblesidebar' : 'true',
+    'navigation_with_keys' : 'true',
+}
 
 # Add any paths that contain custom themes here, relative to this directory.
 # html_theme_path = []
@@ -181,7 +189,7 @@
 # html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'SrFitdoc'
+htmlhelp_basename = 'srfitdoc'
 
 
 # -- Options for LaTeX output --------------------------------------------------
@@ -200,7 +208,7 @@
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('index', 'SrFit_manual.tex', u'SrFit Documentation',
+  ('index', 'srfit_manual.tex', u'diffpy.srfit documentation',
    ab_authors, 'manual'),
 ]
 
@@ -230,7 +238,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'srfit', u'SrFit Documentation',
+    ('index', 'diffpy.srfit', u'diffpy.srfit documentation',
      ab_authors, 1)
 ]
 
@@ -244,8 +252,8 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'SrFit', u'SrFit Documentation',
-   ab_authors, 'SrFit', 'One line description of project.',
+  ('index', 'diffpy.srfit', u'diffpy.srfit documentation',
+   ab_authors, 'diffpy.srfit', 'One line description of project.',
    'Miscellaneous'),
 ]
 
@@ -260,4 +268,7 @@
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-# intersphinx_mapping = {'http://docs.python.org/': None}
+intersphinx_mapping = {
+    'numpy': ('https://docs.scipy.org/doc/numpy', None),
+    'python' : ('https://docs.python.org/3.7', None),
+}

doc/manual/source/api/modules.rst

@@ -180,7 +180,7 @@ external program before or after interfacing with SrFit. An example of a
 customized Profile is the ``SASProfile`` class in the
 ``diffpy.srfit.sas.sasprofile`` module:
 
-.. literalinclude:: ../../../diffpy/srfit/sas/sasprofile.py
+.. literalinclude:: ../../../src/diffpy/srfit/sas/sasprofile.py
    :pyobject: SASProfile
 
 The ``__init__`` method sets the ``xobs``, ``yobs`` and ``dyobs`` attributes of
@@ -218,7 +218,7 @@ to keep the restraint cost comparable to the residual of a single data point.
 ``Restraint`` whose penalty is the root-mean-square deviation from the expected
 and calculated BVS of a structure.
 
-.. literalinclude:: ../../../diffpy/srfit/structure/bvsrestraint.py
+.. literalinclude:: ../../../src/diffpy/srfit/structure/bvsrestraint.py
    :pyobject: BVSRestraint
 
 Note that the penalty scaling is optional (selected by the `scaled` flag) and
@@ -230,7 +230,7 @@ restrainable object. A ``BVSRestraint`` is used to restrain a ``SrRealParSet``,
 which is a ``ParameterSet`` wrapper base class for SrReal-compatible
 structures.  The restraint is applied with the ``restrainBVS`` method.
 
-.. literalinclude:: ../../../diffpy/srfit/structure/srrealparset.py
+.. literalinclude:: ../../../src/diffpy/srfit/structure/srrealparset.py
    :pyobject: SrRealParSet.restrainBVS
 
 The purpose of the method is to create the custom ``Restraint`` object,

doc/manual/source/conf.py

@@ -1,14 +1,13 @@
 .. _developers-guide-index:
 
 ####################################################
-SrFit developer's documentation
+diffpy.srfit documentation
 ####################################################
 
-Software version |release|.
+diffpy.srfit - configurable code for solving atomic structures.
 
-Last updated |today|.
-
-Configurable code for solving atomic structures.
+| Software version |release|.
+| Last updated |today|.
 
 The diffpy.srfit package provides the framework for building a global optimizer
 on the fly from components such as function calculators (that calculate
@@ -32,31 +31,25 @@ obtain the total cost function. Additionally, diffpy.srfit is designed to be
 extensible, allowing the user to integrate external calculators to perform
 co-refinements with other techniques.
 
-===================
-Disclaimer
-===================
-
-.. literalinclude:: ../../../LICENSE.txt
-
-================
-Acknowledgments
-================
-
-Developers
------------
-
-diffpy.sifit is developed and maintained by
+========================================
+Authors
+========================================
 
-.. literalinclude:: ../../../AUTHORS.txt
+diffpy.srfit is developed by members of the Billinge Group at
+Columbia University and at Brookhaven National Laboratory including
+Christopher L. Farrow, Pavol Juhás, Simon J.L. Billinge.
 
 The source code in *observable.py* was derived from the 1.0 version
 of the Caltech "Pyre" project.
 
+For a detailed list of contributors see
+https://github.com/diffpy/diffpy.srfit/graphs/contributors.
+
 ======================================
 Installation
 ======================================
 
-See the `README.rst <https://github.com/diffpy/diffpy.srfit#requirements>`_
+See the `README <https://github.com/diffpy/diffpy.srfit#requirements>`_
 file included with the distribution.
 
 ======================================
@@ -70,15 +63,22 @@ Where next?
    extending.rst
 
 ======================================
-API
+Table of contents
 ======================================
 
 .. toctree::
-   :maxdepth: 3
+   :titlesonly:
 
-   api/diffpy.srfit.rst
+   license
+   release
+   Package API <api/diffpy.srfit>
 
 .. faq.rst
 
+======================================
+Indices
+======================================
+
 * :ref:`genindex`
+* :ref:`modindex`
 * :ref:`search`

doc/manual/source/extending.rst

@@ -1,3 +1,5 @@
+.. index:: license
+
 License
 #######
 

doc/manual/source/index.rst

@@ -0,0 +1,3 @@
+.. index:: release notes
+
+.. mdinclude:: ../../../CHANGELOG.md