Merge branch 'source' of https://github.com/cyclus/cyclus.github.com …

…into source

.gitignore

@@ -4,4 +4,8 @@ build
 *~
 *.pyc
 gh-build
-source/arche/dbtypes.js
+source/arche/dbtypes.js
+source/user/CYCLUS_INSTALL.rst
+source/user/CYCAMORE_INSTALL.rst
+source/user/DEPENDENCIES.rst
+source/user/CYCAMORE_DEPS.rst

AUTHORS.rst

@@ -2,6 +2,8 @@ Robert Carlsen
 Robert Flanagan
 Matthew Gidden
 Katy Huff
+Meghan McGarry
+Baptiste Mouginot
 Arielle Opotowsky
 Olzhas Rakhimov
 Anthony Scopatz

LICENSE.rst

@@ -3,7 +3,7 @@ LICENSE
 *******
 ::
 
-    Copyright (c) 2010-2013, University of Wisconsin Computational Nuclear Engineering Research Group
+    Copyright (c) 2010-2016, University of Wisconsin Computational Nuclear Engineering Research Group
      All rights reserved.
     
     Redistribution and use in source and binary forms, with or without

Makefile

@@ -12,6 +12,9 @@ SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = ./gh-build
+GIT_BRANCH    = master
+GIT_FORK      = cyclus
+
 
 # Internal variables.
 PAPEROPT_a4     = -D latex_paper_size=a4
@@ -56,6 +59,11 @@ gh-clean gh-revert clean:
 	-rm -rf $(BUILDDIR)
 
 gh-preview html:
+	wget -nv https://raw.githubusercontent.com/${GIT_FORK}/cyclus/${GIT_BRANCH}/INSTALL.rst -O source/user/CYCLUS_INSTALL.rst
+	wget -nv https://raw.githubusercontent.com/${GIT_FORK}/cyclus/${GIT_BRANCH}/DEPENDENCIES.rst -O source/user/DEPENDENCIES.rst
+	wget -nv https://raw.githubusercontent.com/${GIT_FORK}/cycamore/${GIT_BRANCH}/INSTALL.rst -O source/user/CYCAMORE_INSTALL.rst
+	wget -nv https://raw.githubusercontent.com/${GIT_FORK}/cycamore/${GIT_BRANCH}/DEPENDENCIES.rst -O source/user/CYCAMORE_DEPS.rst
+
 	PYTHONDONTWRITEBYTECODE="TRUE" $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)
 	sed -i.bak 's/function top_offset([$$]node){ return [$$]node\[0\].getBoundingClientRect().top; }/function top_offset($$node){ return (typeof $$node[0] === "undefined") ? 0 : $$node[0].getBoundingClientRect().top; }/' ./gh-build/_static/cloud.js
 	sed -i.bak 's/  if (state == "collapsed"){/  if (typeof state === "undefined") {\n	var state = "uncollapsed";\n  };\n  if (state == "collapsed"){/' ./gh-build/_static/cloud.js

docker/fuelcycle.org-deps/Dockerfile

@@ -1,6 +1,8 @@
 
 FROM cyclus/cymetric
 
+RUN apt-get update
+RUN apt-get install -y --force-yes wget
 RUN apt-get install -y --force-yes python3-pip
 RUN pip3 install sphinx sphinxcontrib-bibtex
 RUN pip3 install cloud-sptheme==1.6

source/arche/cli.rst

@@ -2,7 +2,6 @@
 
 Archetype Command Line Interface
 =======================================
-
 There are a few archetype-specific |Cyclus| CLI commands that allow
 introspecting details of archetypes that |Cyclus| can find.  Most expose data
 that is automatically generated by the Cyclus preprocessor. For example,
@@ -39,15 +38,15 @@ To view a JSON structured output of all the data generated and collected from
       $ cyclus --agent-annotations :cycamore:Source
       {
        "all_parents": [
-        "cyclus::Agent", 
-        "cyclus::Facility", 
-        "cyclus::Ider", 
-        "cyclus::StateWrangler", 
-        "cyclus::TimeListener", 
-        "cyclus::Trader", 
-        "cyclus::toolkit::AgentManaged", 
+        "cyclus::Agent",
+        "cyclus::Facility",
+        "cyclus::Ider",
+        "cyclus::StateWrangler",
+        "cyclus::TimeListener",
+        "cyclus::Trader",
+        "cyclus::toolkit::AgentManaged",
         "cyclus::toolkit::CommodityProducer"
-       ], 
+       ],
        "doc": "This facility acts as a source of material with a fixed...
        ...
 
@@ -69,26 +68,33 @@ And to list all archetypes inside a particular library:
 
 Archetype Versioning
 --------------------
-
 The ``cyclus::Agent`` class exposes a ``version()`` member function which can be
-queried with the |Cyclus| CLI. For example, 
+queried with the |Cyclus| CLI. For example,
 
-  .. code-block:: bash
+.. code-block:: bash
 
-      $ cyclus --agent-version :agents:Source
-      1.3.1-7-g9a2c9c9
+    $ cyclus --agent-version :agents:Source
+    1.3.1-7-g9a2c9c9
 
 This is generated from some ``git`` version control information. You can make
 your own version tag information for some archetype like
 
+**C++:**
+
+.. code-block:: c++
 
-  .. code-block:: c++
+    virtual std::string version() { return "My Version"; }
 
-      virtual std::string version() { return "My Version"; }
+**Python:**
+
+.. code-block:: Python
+
+    def version(self):
+        return "My Version"
 
 and then access the version with
 
-  .. code-block:: bash
+.. code-block:: bash
 
-      $ cyclus --agent-version my/path:my_library:MyArchetype
-      My Version
+    $ cyclus --agent-version my/path:my_library:MyArchetype
+    My Version

source/arche/custom_tables.rst

@@ -1,11 +1,12 @@
-
 Custom Database Tables
 =======================
 
 Agents are allowed to write their own custom output into the database during
 simulations.  The interface for recording this data is accessible through the
 agent's :term:`context`.  Data may be logged via the Context::NewDatum function:
 
+**C++:**
+
 .. code-block:: c++
 
   MyReactor::Tick() {
@@ -22,17 +23,38 @@ agent's :term:`context`.  Data may be logged via the Context::NewDatum function:
     ...
   }
 
+**Python:**
+
+.. code-block:: python
+
+    from cyclus.agents import Facility
+    import cyclus.typesystem as ts
+
+    class MyReactor(Facility):
+
+        def tick(self):
+            ...
+            d = self.context.new_datum("MyReactorData")
+            d.add_val("AgentID", self.id, type=ts.INT)
+            d.add_val("Time", self.context.time, type=ts.INT)
+            d.add_val("WaterUsage", self.monthl_water, type=ts.DOUBLE)
+            d.add_val("OperatingCost", self.monthly_op_cost, type=ts.DOUBLE)
+            d.record()
+            ...
+
 This would create a table in the output database named "MyReactorData". The
 table would get a new row entry every time step with four columns named
-"AgentID", "Time", "WaterUsage" and "OperatingCost".  ``AddVal`` calls can be chained
-any number of times for an arbitrary number of columns.  ``Record`` must be
+"AgentID", "Time", "WaterUsage" and "OperatingCost".  "Add value" calls can be chained
+any number of times for an arbitrary number of columns.  Record must be
 called once for each datum after all values have been added.  Any custom
 tables created in this manner will appear in the output database alongside the
 |cyclus| core tables.  Because there may be several agent instances of a
 single agent class, tables should generally include a column that adds their
 ID; and for similar reasons, it is often desirable to include the simulation
 time as a column in these tables:
 
+**C++:**
+
 .. code-block:: c++
 
     context()->NewDatum("MyReactorData")
@@ -41,6 +63,16 @@ time as a column in these tables:
              ->AddVal(...
              ...
 
+**Python:**
+
+.. code-block:: python
+
+    d = self.context.new_datum("MyReactorData")
+    d.add_val("AgentID", self.id, type=ts.INT)
+    d.add_val("Time", self.context.time, type=ts.INT)
+    d.add_val(...
+    ...
+
 Datums with the same table name must have the same schema (e.g. same field
 names and value types). It is the responsibility of the developer to
 enforce this in their code.
@@ -53,8 +85,8 @@ enforce this in their code.
    use. For information on which c++ types the backends support, you can check
    :doc:`here <dbtypes>`.
 
-.. note:: If you require a datatype that isn't currently supported, please 
-          ask the kernel developers and they will help as soon as possible. 
+.. note:: If you require a datatype that isn't currently supported, please
+          ask the kernel developers and they will help as soon as possible.
 
 Table Data Shapes
 ------------------
@@ -70,6 +102,8 @@ vector indicates variable length also.  It is an error to pass in a shape
 vector with the wrong rank (number of elements) for that type.  An example of
 using the shape vector follows:
 
+**C++:**
+
 .. code-block:: c++
 
     std::vector<std::string> colors;
@@ -84,15 +118,27 @@ using the shape vector follows:
     context()->NewDatum("DecorPreferences")
              ->AddVal("AgentID", id())
              ->AddVal("Time", context()->time())
-             ->AddVal("FavoritColors", colors, shape)
+             ->AddVal("FavoriteColors", colors, shape)
              ->Record();
 
+**Python:**
+
+.. code-block:: c++
+
+    colors = ["green", "blue", "chartreuse"]
+    shape = [5, 8]
+    d = self.context.new_datum("DecorPreferences")
+    d.add_val("AgentID", self.id, type=ts.INT)
+    d.add_val("Time", self.context.time, type=ts.INT)
+    d.add_val("FavoriteColors", colors, shape, ts.VECTOR_STRING)
+    d.record()
+
 In the example above, the "chartreuse" color is longer than the 8 characters
 specified in the shape.  So it will be truncated to "chartreu" in the
 database. Shape vectors should generally be stored as class member variables
 to avoid excessive memory [de]allocation and should be set correctly from
 construction to destruction of your agent.
-    
+
 Reserved Table Names
 ---------------------
 

source/arche/cycpp.rst

@@ -126,6 +126,11 @@ contains a listing of all special keys and their meanings.
                  post-process.
     default      The default value for this variable that is used if otherwise 
                  unspecified. The value must match the type of the variable.
+    internal     ``True`` if this state variable is only for
+                 archetype-internal usage.  Although the variable will still
+                 be persisted in the database and initialized normally (e.g.
+                 with any default), it will not be included in the XML schema
+                 or input file.
     shape        The shape of a variable length datatypes. If present this must
                  be a list of integers whose length (rank) makes sense for this
                  type. Specifying positive values will (depending on the 

source/arche/dbtypes.rst

@@ -3,8 +3,8 @@
 Database Types
 ==============
 
-Here is a listing of all supported data types that the various backends have 
-implemented, by |cyclus| version number. If your agents need a type that is not 
+Here is a listing of all supported data types that the various backends have
+implemented, by |cyclus| version number. If your agents need a type that is not
 yet supported, please let us know and we'll get to it as soon as possible!
 
 **Description of fields:**
@@ -29,7 +29,7 @@ yet supported, please let us know and we'll get to it as soon as possible!
 
     <style>
     p {
-      font-size: 100%; 
+      font-size: 100%;
     }
 
     img {
@@ -52,7 +52,7 @@ yet supported, please let us know and we'll get to it as soon as possible!
     var dbdata = []
     $.getJSON("/arche/dbtypes.json", function(json) {
         dbdata = json;
-    
+
         function setupPivot(input){
           input.callbacks = {afterUpdateResults: function(){
             $('#results > table').dataTable({
@@ -72,16 +72,16 @@ yet supported, please let us know and we'll get to it as soon as possible!
             fields =[{name: 'id',         type: 'integer', filterable: true},
                      {name: 'name',       type: 'string',  filterable: true,
                       displayFunction: function(value){
-                        return '<div style="font-family:Courier,monospace;">' + 
+                        return '<div style="font-family:Courier,monospace;">' +
                                value + '</div>';}},
                      {name: "C++ type",   type: 'string',  filterable: true,
                       displayFunction: function(value){
-                        return '<div style="font-family:Courier,monospace;">' + 
+                        return '<div style="font-family:Courier,monospace;">' +
                                value + '</div>';}},
                      {name: 'shape rank', type: 'integer', filterable: true},
-                     {name: 'backend',    type: 'string',  filterable: true, 
+                     {name: 'backend',    type: 'string',  filterable: true,
                       columnLabelable: true},
-                     {name: 'version',    type: 'string',  filterable: true, 
+                     {name: 'version',    type: 'string',  filterable: true,
                       columnLabelable: true},
                      {name: 'supported',  type: 'integer', filterable: true,
                       rowLabelable: true, summarizable: 'sum',
@@ -90,15 +90,15 @@ yet supported, please let us know and we'll get to it as soon as possible!
                           return '<div style="text-align:center;' +
                                  'background-color:#c8e8b0">Yes</div>';
                         else
-                          return '<div style="text-align:center;' + 
+                          return '<div style="text-align:center;' +
                                  'background-color:#fcf1df">No</div>';
                         }
                       }
                      ];
 
             setupPivot({json: dbdata, fields: fields,
-                        filters: {version: "v1.2"}, 
-                        rowLabels: ["C++ type"], 
+                        filters: {version: "v1.2"},
+                        rowLabels: ["C++ type"],
                         columnLabels: ["backend"],
                         summaries: ["supported_sum"]});
 

source/arche/decay.rst

@@ -2,7 +2,6 @@
 
 Radioactive Decay in |Cyclus|
 =============================
-
 .. warning:: Decay in |cyclus| is experimental.
 
 Radioactive decay of a group of isotopes over time can be described by the
@@ -28,7 +27,6 @@ is explained in more detail below.
 
 The Uniformization Method
 -------------------------
-
 The Uniformization Method is essentially a modification of the truncated Taylor
 Series expansion of the matrix exponential solution, which can be described by
 the following summation:
@@ -51,7 +49,7 @@ The first step in applying the uniformization technique is to define
 element of `A`:
 
 .. math::
-  
+
    \alpha=max_i\left | {a_i}_i \right |
 
 Then, given `alpha`, the next step is to redefine the matrix
@@ -114,15 +112,15 @@ in an even lower maximum time scale.
 References
 ----------
 
-  #. Cleve Moler and Charles van Loan, "Nineteen Dubious Ways to Compute the
-     Exponential of a Matrix, Twenty-Five Years Later," *SIAM Review*, *45*,
-     3-49 (2003)
+#. Cleve Moler and Charles van Loan, "Nineteen Dubious Ways to Compute the
+   Exponential of a Matrix, Twenty-Five Years Later," *SIAM Review*, *45*,
+   3-49 (2003)
+
+#. Erwin Muller, Frederik Reitsma and Paulus P. Kruger, "A Stable Nuclide
+   Transmutation Procedure Free of Numerical Roundoff," *PHYSOR 2006*, September
+   10-14, Vancouver, Canada (2006)
 
-  #. Erwin Muller, Frederik Reitsma and Paulus P. Kruger, "A Stable Nuclide
-     Transmutation Procedure Free of Numerical Roundoff," *PHYSOR 2006*, September
-     10-14, Vancouver, Canada (2006)
+#. R. B. Sidje and W. J. Stewart, "A numerical study of large sparse matrix
+   exponentials arising in Markov chains," *Computational Statistics & Data
+   Analysis*, *29*, 345-368 (1999)
 
-  #. R. B. Sidje and W. J. Stewart, "A numerical study of large sparse matrix
-     exponentials arising in Markov chains," *Computational Statistics & Data
-     Analysis*, *29*, 345-368 (1999)
-