Merge branch 'doc-add-changelog'

* add release notes to the manual
* merge API docs in one page `modules.rst`
* silence complaint about missing directory
* switch to sphinx_py3doc_enhanced_theme

Author: pavoljuhas

doc/manual/source/api/modules.rst

@@ -1,7 +1,134 @@
-pyobjcryst
-==========
+:tocdepth: 2
 
-.. toctree::
-   :maxdepth: 4
+##############
+pyobjcryst API
+##############
 
-   pyobjcryst
+
+pyobjcryst module
+-----------------
+
+.. automodule:: pyobjcryst
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.atom module
+----------------------
+
+.. automodule:: pyobjcryst.atom
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.crystal module
+-------------------------
+
+.. automodule:: pyobjcryst.crystal
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.general module
+-------------------------
+
+.. automodule:: pyobjcryst.general
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.io module
+--------------------
+
+.. automodule:: pyobjcryst.io
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.molecule module
+--------------------------
+
+.. automodule:: pyobjcryst.molecule
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.polyhedron module
+----------------------------
+
+.. automodule:: pyobjcryst.polyhedron
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.refinableobj module
+------------------------------
+
+.. automodule:: pyobjcryst.refinableobj
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.scatterer module
+---------------------------
+
+.. automodule:: pyobjcryst.scatterer
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.scatteringpower module
+---------------------------------
+
+.. automodule:: pyobjcryst.scatteringpower
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.scatteringpowersphere module
+---------------------------------------
+
+.. automodule:: pyobjcryst.scatteringpowersphere
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.spacegroup module
+----------------------------
+
+.. automodule:: pyobjcryst.spacegroup
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.unitcell module
+--------------------------
+
+.. automodule:: pyobjcryst.unitcell
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.utils module
+-----------------------
+
+.. automodule:: pyobjcryst.utils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.version module
+-------------------------
+
+.. automodule:: pyobjcryst.version
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyobjcryst.zscatterer module
+----------------------------
+
+.. automodule:: pyobjcryst.zscatterer
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/manual/source/api/pyobjcryst.rst

@@ -17,15 +17,20 @@
 # If your documentation needs a minimal Sphinx version, state it here.
 # needs_sphinx = '1.0'
 
-# 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.ifconfig', 'sphinx.ext.autodoc']
+# 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.ifconfig',
+    'sphinx.ext.autodoc',
+    'm2r',
+]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = ['.rst', '.md']
 
 # The encoding of source files.
 # source_encoding = 'utf-8-sig'
@@ -94,13 +99,17 @@
 
 # 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 = []
@@ -124,7 +133,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+# html_static_path = ['_static']
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.

doc/manual/source/conf.py

@@ -1,18 +1,12 @@
-.. _manual-index:
-
 ####################################################
 pyobjcryst documentation
 ####################################################
 
 pyobjcryst - Python bindings to the ObjCryst++ Object-Oriented
 Crystallographic Library
 
-===================
-Disclaimer
-===================
-
-.. literalinclude:: ../../../LICENSE.txt
-
+| Software version |release|.
+| Last updated |today|.
 
 ================
 Authors
@@ -32,18 +26,23 @@ https://github.com/diffpy/pyobjcryst/graphs/contributors.
 Installation
 ======================================
 
-See the `README.rst <https://github.com/diffpy/pyobjcryst#requirements>`_
+See the `README <https://github.com/diffpy/pyobjcryst#requirements>`_
 file included with the distribution.
 
 ======================================
-API
+Table of contents
 ======================================
 
 .. toctree::
-   :maxdepth: 3
+   :titlesonly:
 
-   api/modules.rst
+   license
+   release
+   api/modules
 
-* :ref:`genindex`
+========================================================================
+Indices
+========================================================================
 
-Last updated |today|.
+* :ref:`genindex`
+* :ref:`search`

doc/manual/source/index.rst

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