Add updated doc

Author: bobleesj

doc/source/api/diffpy.structure.example_package.rst

@@ -0,0 +1,31 @@
+.. _example_package documentation:
+
+|title|
+=======
+
+.. |title| replace:: diffpy.structure.example_package package
+
+.. automodule:: diffpy.structure.example_package
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+|foo|
+-----
+
+.. |foo| replace:: diffpy.structure.example_package.foo module
+
+.. automodule::  diffpy.structure.example_package.foo
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+|bar|
+-----
+
+.. |bar| replace:: diffpy.structure.example_package.bar module
+
+.. automodule:: diffpy.structure.example_package.foo
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/source/api/diffpy.structure.rst

@@ -1,7 +1,9 @@
 :tocdepth: -1
 
-diffpy.structure package
-========================
+|title|
+=======
+
+.. |title| replace:: diffpy.structure package
 
 .. automodule:: diffpy.structure
     :members:
@@ -12,107 +14,17 @@ Subpackages
 -----------
 
 .. toctree::
-    :titlesonly:
-
-    diffpy.structure.parsers
-    diffpy.structure.expansion
-    diffpy.structure.apps
+   diffpy.structure.example_package
 
 Submodules
 ----------
 
-diffpy.structure.spacegroups module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: diffpy.structure.spacegroups
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-diffpy.structure._legacy_importer module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: diffpy.structure._legacy_importer
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-diffpy.structure.structureerrors module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: diffpy.structure.structureerrors
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-diffpy.structure.spacegroupmod module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: diffpy.structure.spacegroupmod
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-diffpy.structure.utils module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: diffpy.structure.utils
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-diffpy.structure.lattice module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: diffpy.structure.lattice
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-diffpy.structure.structure module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: diffpy.structure.structure
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-diffpy.structure.mmlibspacegroups module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: diffpy.structure.mmlibspacegroups
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-diffpy.structure.symmetryutilities module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: diffpy.structure.symmetryutilities
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-diffpy.structure.atom module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: diffpy.structure.atom
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-diffpy.structure.pdffitstructure module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: diffpy.structure.pdffitstructure
-    :members:
-    :undoc-members:
-    :show-inheritance:
+|module|
+--------
 
-diffpy.structure.sgtbxspacegroups module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+.. |module| replace:: diffpy.structure.example_submodule module
 
-.. automodule:: diffpy.structure.sgtbxspacegroups
+.. automodule:: diffpy.structure.example_submodule
     :members:
     :undoc-members:
     :show-inheritance:

doc/source/conf.py

@@ -18,8 +18,6 @@
 from importlib.metadata import version
 from pathlib import Path
 
-autodoc_mock_imports = ["importlib.metadata"]
-
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use Path().resolve() to make it absolute, like shown here.
@@ -48,8 +46,6 @@
     "m2r",
 ]
 
-autodoc_member_order = "groupwise"
-
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
@@ -120,12 +116,6 @@
 # Display all warnings for missing links.
 nitpicky = True
 
-nitpick_ignore = [
-    ("py:class", "array_like"),
-    ("py:class", "Parser"),
-    ("py:class", "CifFile"),
-]
-
 # -- Options for HTML output ----------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
@@ -297,7 +287,3 @@
 
 # Example configuration for intersphinx: refer to the Python standard library.
 # intersphinx_mapping = {'http://docs.python.org/': None}
-intersphinx_mapping = {
-    "python": ("https://docs.python.org/3", None),
-    "numpy": ("https://numpy.org/doc/stable/", None),
-}

doc/source/index.rst

@@ -4,57 +4,21 @@
 
 .. |title| replace:: diffpy.structure documentation
 
-diffpy.structure - Crystal structure container and parsers for structure formats.
+diffpy.structure - Crystal structure container and parsers for structure formats..
 
 | Software version |release|.
 | Last updated |today|.
 
-The diffpy.structure package provides objects for storing atomic
-coordinates, displacement parameters and other crystal structure data.
-diffpy.structure supports import and export of structure data in several
-structure formats such as CIF, PDB, xyz.  It provides conversion
-between fractional and absolute Cartesian coordinates, functions for
-symmetry expansion from asymmetric unit and generation of symmetry
-constraints for atom positions and displacement parameters.  diffpy.structure
-includes definitions of all space groups in over 500 symmetry settings.
-
 =======
 Authors
 =======
 
-diffpy.structure is developed by members of the Billinge Group at
-Columbia University and at Brookhaven National Laboratory including
-Pavol Juhás, Christopher L. Farrow, Xiaohao Yang, Simon J.L. Billinge.
+diffpy.structure is developed by Billinge Group
+and its community contributors.
 
 For a detailed list of contributors see
 https://github.com/diffpy/diffpy.structure/graphs/contributors.
 
-Acknowledgments
-===============
-
-Space group codes in *spacegroupmod.py* and *mmlibspacegroups.py*
-originate from the pymmlib project, http://pymmlib.sourceforge.net.
-Less common settings of space groups were generating using the
-Computational Crystallography Toolbox,
-http://cctbx.sourceforge.net.
-
-
-.. index:: citation, reference
-
-Reference
-=========
-
-If you use this program for a scientific research that leads
-to publication, we ask that you acknowledge use of the program
-by citing the following paper in your publication:
-
-   P. Juhás, C. L. Farrow, X. Yang, K. R. Knox and S. J. L. Billinge,
-   `Complex modeling: a strategy and software program for combining
-   multiple information sources to solve ill posed structure and
-   nanostructure inverse problems
-   <http://dx.doi.org/10.1107/S2053273315014473>`__,
-   *Acta Crystallogr. A* **71**, 562-568 (2015).
-
 ============
 Installation
 ============
@@ -65,7 +29,6 @@ file included with the distribution.
 =================
 Table of contents
 =================
-
 .. toctree::
    :titlesonly: