Merge pull request #383 from CORE-GATECH-GROUP/docs

DOC Fix a lot of documentation issues

Author: Andrew Johnson

docs/_templates/myclass.rst

@@ -6,3 +6,5 @@
 
 .. autoclass:: {{ objname }}
     :members: 
+    :special-members:
+    :exclude-members: __init__

docs/changelog.rst

@@ -113,7 +113,7 @@ Incompatible API Changes
 * Setting ``expectGcu`` has been removed as :pull:`324` fixed how files without
   group constants are handled.
 * Keys to |BranchedUniv| objects stored in
-  :attr:`serpentTools.BranchCollector.universes` are stored as strings,
+  :attr:`serpentTools.xs.BranchCollector.universes` are stored as strings,
   rather than integers, e.g. ``0`` is replaced with ``"0"`` - :pull:`321`
 * Keys to |HomogUniv| instances stored on
   :class:`~serpentTools.objects.BranchContainer` are now
@@ -320,11 +320,13 @@ Deprecations
   files with unique random seeds - :mod:`serpentTools.seed`
 * :pull:`229` - :meth:`serpentTools.SensitivityReader.plot`
   now respects the option to not set x nor y labels.
-* :pull:`231` - |ResultsReader| objects
-  can now read files that do not contain group constant data. The setting
-  :ref:`results-expectGcu` should be used to inform the reader that no
-  group constant data is anticipated
+* :pull:`231` - |ResultsReader| objects can now read files that do not
+  contain group constant data. The setting ``results-expectGcu`` should
+  be used to inform the reader that no group constant data is anticipated
+
+    .. note::
 
+        This setting was removed in :ref:`v0.8.0` and in :pull:`324`
 
 .. _v0.5.2:
 

docs/conf.py

@@ -208,8 +208,8 @@
 .. |DetectorReader| replace:: :class:`~serpentTools.DetectorReader`
 .. |DepletionReader| replace:: :class:`~serpentTools.DepletionReader`
 .. |DepmtxReader| replace:: :class:`~serpentTools.DepmtxReader`
-.. |BranchCollector| replace:: :class:`~serpentTools.BranchCollector`
-.. |BranchedUniv| replace:: :class:`~serpentTools.BranchedUniv`
+.. |BranchCollector| replace:: :class:`~serpentTools.xs.BranchCollector`
+.. |BranchedUniv| replace:: :class:`~serpentTools.xs.BranchedUniv`
 .. |BranchingReader| replace:: :class:`~serpentTools.BranchingReader`
 .. |XSPlotReader| replace:: :class:`~serpentTools.XSPlotReader`
 .. |HistoryReader| replace:: :class:`~serpentTools.HistoryReader`

docs/defaultSettings.rst

@@ -9,13 +9,13 @@ reviewing pull requests (PR):
 
 #. The content of the PR fits within the scope of the project - :ref:`project-scope`
 #. The code included in the PR is written in good
-   `pythonic  <https://stackoverflow.com/a/25011492>`_
+   `pythonic <https://stackoverflow.com/a/25011492>`_
    fashion, and follows the style of the project - :ref:`code-style`
 #. The code directly resolves a previously raised issue - :ref:`issues`
 #. PR does not cause unit tests and builds to fail
 #. Changes are reflected in documentation - :ref:`documentation`
 
-.. _dev-ci
+.. _dev-ci:
 
 CI Testing
 ==========
@@ -27,7 +27,7 @@ notebooks. The former are used to perform more granular testing
 over the project, while the latter ensure our example notebooks
 are runnable.
 
-.. _dev-unittests
+.. _dev-unittests:
 
 Unit Tests
 ----------
@@ -51,7 +51,7 @@ deviations are acceptable. The coverage is not a factor in passing or failing
 CI, but substantial changes to the test suite should serve a valid purpose if
 the coverage does decrease.
 
-.. _dev-notebooks
+.. _dev-notebooks:
 
 Notebook Tests
 --------------
@@ -65,7 +65,7 @@ converts these to python scripts and runs them using
 It is beneficial to run this script during major changes to the API, as well as correcting any
 errors or deprecated/removed features.
 
-.. _dev-lint
+.. _dev-lint:
 
 Lint
 ====

docs/develop/checklist.rst

@@ -87,7 +87,7 @@ appropriately.
 
 .. autofunction:: serpentTools.utils.compare.logDirectCompare
 
-.. autofunction:: serpentTools.utils.compare.splitdictByKeys
+.. autofunction:: serpentTools.utils.compare.splitDictByKeys
 
 .. autofunction:: serpentTools.utils.compare.getKeyMatchingShapes
 

docs/develop/comparisons.rst

@@ -30,7 +30,7 @@ where ``"debug"`` can be one of ``"debug"``, ``"info"``, ``"warning"``,
 ``"error"`` or ``"critical"``.
 
 Alternatively, the level can be adjusting using the python 
-:module:`logging` module::
+:mod:`logging` module::
 
     >>> logging.getLogger("serpentTools").setLevel(logging.DEBUG)
 

docs/develop/logging.rst

@@ -24,7 +24,7 @@ Checklist
 =========
 
 #. Include the version as an option in the `serpentVersion` setting - :ref:`serpentVersion`
-#. Update the :ref:`defaultSettings` using the script ``docs/rstDefaultSettings.py``
+#. Update the :ref:`default-settings`
 #. Update |vars.yaml| to include the version and any new variable groups
    present in the results files - :ref:`dev-sss-versions-newVars`
 #. If |vars.yaml| is updated, update :ref:`variable-groups` using the script 
@@ -115,7 +115,7 @@ Loading such a file would return a dictionary like::
      childV: {childV:{vx0, vx1, ...}}}
 
 
-.. _dev-sss-versions-newFormats
+.. _dev-sss-versions-newFormats:
 
 Versions with New File Formats
 ==============================