Merge branch 'master' into dev-backport

Backport of features included since 0.9.3 release Includes the following PRs git log --online --pretty="%s" --merges 0.9.3... Merge pull request CORE-GATECH-GROUP#407 from drewejohnson/fix-readme Merge pull request CORE-GATECH-GROUP#406 from drewejohnson/r0.9.3 Merge pull request CORE-GATECH-GROUP#405 from nicoloabrate/master Merge pull request CORE-GATECH-GROUP#404 from drewejohnson/update-git-attr Merge pull request CORE-GATECH-GROUP#402 from drewejohnson/xsplot-labels Merge pull request CORE-GATECH-GROUP#400 from drewejohnson/lib2-notes Merge pull request CORE-GATECH-GROUP#399 from CORE-GATECH-GROUP/docs-sphinx-2.0 Merge pull request CORE-GATECH-GROUP#397 from drewejohnson/port-list-of-arrays Merge pull request CORE-GATECH-GROUP#398 from drewejohnson/det-supers Merge pull request CORE-GATECH-GROUP#396 from drewejohnson/df-arg-renaming Merge pull request CORE-GATECH-GROUP#394 from drewejohnson/0.9.3-update-docs Merge pull request CORE-GATECH-GROUP#395 from drewejohnson/hist-branch-dictlike Merge pull request CORE-GATECH-GROUP#393 from drewejohnson/less-metadata Merge pull request CORE-GATECH-GROUP#392 from drewejohnson/better-access Merge pull request CORE-GATECH-GROUP#391 from drewejohnson/dep-dataframe Merge pull request CORE-GATECH-GROUP#390 from drewejohnson/api-dep-attributes Merge pull request CORE-GATECH-GROUP#388 from drewejohnson/xsplot-branch Merge pull request CORE-GATECH-GROUP#378 from drewejohnson/better-build Merge pull request CORE-GATECH-GROUP#376 from drewejohnson/unbundle-data-files Merge pull request CORE-GATECH-GROUP#370 from drewejohnson/results-loa Merge pull request CORE-GATECH-GROUP#369 from drewejohnson/merge-0.9.1-develop
drewejohnson · May 21, 2020 · 5f02cd9 · 5f02cd9
2 parents b3ee0ee + 6120e16
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diff --git a/.gitattributes b/.gitattributes
@@ -1,5 +1,5 @@
-serpentTools/_version.py export-subst
 * text eol=auto
 * text eol=lf
 *.py diff=py
 *.png binary
+*.m linguist-vendored
diff --git a/README.rst b/README.rst
@@ -33,12 +33,10 @@ Installation
 
    $ python -m pip install --user --upgrade pip serpentTools
 
-
 For more detailed instructions, including operating-system specific
 instructions and building from source, see
 `Installation Guide <http://serpent-tools.readthedocs.io/en/latest/install.html>`_.
 
-
 Issues
 ======
 
@@ -51,25 +49,19 @@ References
 
 The Annals of Nuclear Energy article should be cited for all work
 using ``SERPENT``. If you are using this project, please considering
-citing with::
+citing with
 
-    Andrew Johnson, Dan Kotlyar, Stefano Terlizzi, and Gavin Ridley,
-    "`serpentTools: A Python Package for Expediting Analysis with
-    Serpent <https://doi.org/10.1080/00295639.2020.1723992>`_,"
-    *Nuc. Sci. Eng*, (in press) (2020).
+* Andrew Johnson, Dan Kotlyar, Stefano Terlizzi, and Gavin Ridley,
+  "`serpentTools: A Python Package for Expediting Analysis with
+  Serpent <https://doi.org/10.1080/00295639.2020.1723992>`_,"
+  *Nuc. Sci. Eng*, (in press) (2020).
 
 Also, let us know if you publish work using this package! We try and
-keep an up-to-date list of `works using serpentTools`_, and would be
+keep an up-to-date list of works using serpentTools [2]_, and would be
 happy to include more.
 
-If you want to refer to a specific version, follow the `Zenodo DOI 
-<https://doi.org/10.5281/zenodo.1301035>`_. This will resolve to the latest
-version, with links to earlier releases.
-
- .. _works using serpentTools: https://github.com/CORE-GATECH-GROUP/serpent-tools/wiki/Publications-using-serpentTools
-
-If you want to refer to a specific version, follow the `Zenodo DOI 
 .. [1] Leppanen, J. et al. (2015) "The Serpent Monte Carlo code: Status,
     development and applications in 2013." Ann. Nucl. Energy, `82 (2015) 142-150
     <http://www.sciencedirect.com/science/article/pii/S0306454914004095>`_
 
+.. [2] https://github.com/CORE-GATECH-GROUP/serpent-tools/wiki/Publications-using-serpentTools
diff --git a/data/plut_xs0.m b/data/plut_xs0.m
@@ -191,6 +191,24 @@
 5.87774E+00 2.27284E-03 2.72848E+00 2.41217E+00 2.27284E-03 9.49498E-02 1.42231E-01 1.91357E-02 2.38983E-02 6.89030E-03 0.00000E+00 8.01346E-03 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 4.33261E-03 0.00000E+00 5.77543E-03 0.00000E+00 0.00000E+00 7.03469E-02 1.68538E-03 5.14204E-03 2.52079E-03 6.96677E-03 6.93165E-03 1.49274E-02 6.96715E-03 7.46602E-03 5.97098E-03 7.96117E-03 1.07498E-02 1.34154E-02 3.67423E-04 4.65750E-03 5.32589E-03 4.56426E-03 4.43752E-03 1.66154E-03 1.81176E-03 1.87937E-03 1.40625E-03 1.56047E-03 2.24766E-01 1.60937E-02 0.00000E+00 
 ];
 
+i82206_09c_bra_mt = [
+ 102 % (n,gamma)
+];
+
+i82206_09c_bra_f = [
+2.17000E-02 
+2.17000E-02 
+2.17000E-02 
+2.17000E-02 
+2.17000E-02 
+2.17000E-02 
+2.17000E-02 
+2.17000E-02 
+2.17000E-02 
+2.17000E-02 
+];
+
+
 i94239_03c_nu = [
 2.88002 0.00645 
 2.87172 0.00645 

diff --git a/docs/_templates/myclass.rst b/docs/_templates/myclass.rst
@@ -6,5 +6,3 @@
 
 .. autoclass:: {{ objname }}
     :members: 
-    :special-members:
-    :exclude-members: __init__
diff --git a/docs/changelog.rst b/docs/changelog.rst
@@ -6,6 +6,14 @@
 Changelog
 =========
 
+.. note::
+
+    Development will be limited to bug fixes for future 
+    ``0.9.x`` releases. Release ``0.10.0`` will introduce
+    new and improved parsers and containers alongside
+    existing structures. For more information, see
+    :ref:`data-model`
+
 .. _v0.10.0:
 
 0.10.0
@@ -17,10 +25,52 @@ Changelog
 * Installation also provides a ``serpentTools`` executable that
   can be used to access the :ref:`cli`
 
+.. _v0.9.3:
+
+:release-tag:`0.9.3`
+====================
+
+* Depletion data now exposed through attributes like
+  :attr:`~serpentTools.objects.DepletedMaterial.adens` - :pull:`390`
+* Generate a :class:`pandas.DataFrame` with depletion data using
+  :meth:`~serpentTools.objects.DepletedMaterial.toDataFrame`
+  - :pull:`391`
+* Dictionary-like item access and iteration for branching, detector,
+  history, depletion, and xsplot readers - :pull:`392`, :pull:`395`, :pull:`402`
+* Obtain data from :attr:`~serpentTools.ResultsReader.resdata` with
+  :meth:`~serpentTools.ResultsReader.__getitem__` and 
+  :meth:`~serpentTools.ResultsReader.get` - :pull:`392`
+* Modify plot legends for :meth:`serpentTools.objects.XSData.plot` for all
+  or some plotted MTs - :pull:`402`
+* Options for plotting sensitivity profiles against energies in MeV - :pull:`405`
+
+.. _v0.9.3-bug:
+
+Bug Fixes
+---------
+
+* Support ``xsplot`` files with branching fractions - :issue:`387`, :pull:`388`
+
+.. _v0.9.3-dep:
+
+Pending Deprecations
+--------------------
+
+* :attr:`serpentTools.DepletionReader.metadata`. Prefer attributes
+  like :attr:`~serpentTools.DepletionReader.zais`
+* :attr:`serpentTools.samplers.DepletionSampler.metadata`. Prefer
+  attributes like :attr:`~serpentTools.samplers.DepletionSampler.zais`
+* :meth:`serpentTools.BranchingReader.iterBranches`. Prefer
+  :meth:`~serpentTools.BranchingReader.items`
+* :attr:`serpentTools.XSPlotReader.metadata` and
+  :attr:`serpentTools.objects.XSData.metadata`. Prefer attributes like
+  :attr:`~serpentTools.XSPlotReader.majorant` or 
+  :attr:`~serpentTools.objects.XSData.energies` - :pull:`402`
+
 .. _v0.9.2:
 
-0.9.2
-=====
+:release-tag:`0.9.2`
+====================
 
 * Officially support installing under Python 3.8
 * Support for passing threshold values to hexagonal detector plots
@@ -34,7 +84,7 @@ Bug Fixes
 * Detector reader can handle sequential detectors with very similar
   names - :issue:`374`.
 * ``serpentTools`` doesn't make any modifications to the logging state,
-  other than introducing package-wide logger.
+  other than introducing package-wide logger - :pull:`380`
 * Colorbars for mesh plots are placed next to their corresponding
   plot, rather than near the last drawn plot - :issue:`372`
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -183,6 +183,9 @@
 
 autodoc_default_options = {
     'members': True,
+    'special-members': "__len__,__iter__,__contains__,__getitem__,__setitem__",
+    'exclude-members': '__init__',
+    'inherited-members': "serpentTools.objects.base.NamedObject,serpentTools.objects.base.BaseObject",
 }
 
 # -- Links to external documentation
@@ -191,6 +194,7 @@
     'matplotlib': ('https://matplotlib.org', None),
     'numpy': ('https://docs.scipy.org/doc/numpy/', None),
     'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
+    'pandas': ('https://pandas.pydata.org/docs', None),
 }
 
 # -- Prepend the following lines to each rst file generated

diff --git a/docs/containers.rst b/docs/containers.rst
@@ -64,6 +64,7 @@ Supporting Classes
     BranchContainer
     DepletedMaterial
     HomogUniv
+    UnivTuple
     XSData
 
 .. _api-xs:

diff --git a/docs/contributors.rst b/docs/contributors.rst
@@ -7,8 +7,9 @@ Developer Team
 Here are all the wonderful people that helped make this project happen
 
 * `Andrew Johnson <https://github.com/drewejohnson>`_
-* `Dr. Dan Kotlyar <https://github.com/CORE-GATECH>`_
+* `Dan Kotlyar <https://github.com/DanKotlyar>`_
 * `Stefano Terlizzi <https://github.com/sallustius>`_
 * `Gavin Ridley <https://github.com/gridley>`_
 * `Paul Romano <https://github.com/paulromano>`_
-
+* `Anton Travleev <https://github.com/travleev>`_
+* `@nicolaborate <https://github.com/nicoloabrate>`_