Merge branch 'develop' of git://github.com/cyclus/cycamore into develop

README.rst

@@ -99,34 +99,35 @@ in this guide:
   #. you have acquired the Cycamore source code from the 
      `Cycamore repo`_
   #. you have placed the Cycamore repository in .../cyclus/cycamore
-  #. you have a directory named .../cyclus/cycamore/build in which 
-     you plan to encapsulate all build-related files (they get in the
-     way otherwise)
-  #. you have installed Cyclopts using the CMAKE_INSTALL_PREFIX 
-     variable set to ../cyclus/install (see the `Cyclopts readme`_)
-  #. you have installed Cyclus using the CMAKE_INSTALL_PREFIX 
-     variable set to ../cyclus/install (see the `Cyclus readme`_)
+  #. you have installed Cyclopts in .../cyclus/install (see the `Cyclopts readme`_)
+  #. you have installed Cyclus  in .../cyclus/install (see the `Cyclus readme`_)
 
 Under these assumptions **and** if you used a package manager to 
 install coin-Cbc (i.e. it's installed in a standard location), the
 Cyclus building and installation process will look like:
 
 .. code-block:: bash
 
-    .../cyclus/cycamore$ cd build
-    .../cyclus/cycamore/build$ cmake ../src -DCMAKE_INSTALL_PREFIX=../../install -DCYCLOPTS_ROOT_DIR=../../install -DCYCLUS_ROOT_DIR=../../install
-    .../cyclus/cycamore/build$ make && make install
+    .../cyclus/cycamore$ python setup.py --prefix=../install --cyclus_root=../install --cyclopts_root=../install
 
 If you have installed coin-Cbc from source or otherwise have it 
-installed in a non-standard location, you should make use of the CMake
-COIN_ROOT_DIR variable. The otherwise identical process would look 
+installed in a non-standard location, you should make use of the
+``coinRoot`` flag. The otherwise identical process would look 
 like:
 
 .. code-block:: bash
 
-    .../cyclus/cycamore$ cd build
-    .../cyclus/cycamore/build$ cmake ../src -DCMAKE_INSTALL_PREFIX=../../install -DCYCLOPTS_ROOT_DIR=../../install -DCYCLUS_ROOT_DIR=../../install -DCOIN_ROOT_DIR=/the/path/to/coin/install 
-    .../cyclus/cycamore/build$ make && make install
+    .../cyclus/cycamore$ python setup.py --prefix=../install --coin_root=/path/to/coin --cyclus_root=../install --cyclopts_root=../install
+
+Additionally, if you have installed Boost from source or otherwise have it
+installed in a non-standard location, you should make use of the
+``boostRoot`` flag. The otherwise identical process would look
+like:
+
+.. code-block:: bash
+
+    .../cyclus/cycamore$ python setup.py --prefix=../install --coin_root=/path/to/coin --cyclus_root=../install --cyclopts_root=../install --boost_root=/path/to/boost
+
 
 .. _`CMake`: http://www.cmake.org
 .. _`apt-get`: http://linux.die.net/man/8/apt-get
@@ -200,12 +201,8 @@ Workflow Notes
         branch and then run the CycamoreUnitTestDriver (at the moment, ```make 
         test``` is insufficient). For example ::
 
-          mkdir build
           mkdir install
-          cd build
-          cmake ../src -DCMAKE_INSTALL_PREFIX=../install
-          make
-          make install
+          python setup.py --prefix=../install ...
           ../install/cycamore/bin/CycamoreUnitTestDriver
 
       - There are also a suite of sample input files 

setup.py

@@ -0,0 +1,99 @@
+import os
+import subprocess
+import shutil
+
+try:
+    import argparse as ap
+except ImportError:
+    import pyne._argparse as ap
+
+absexpanduser = lambda x: os.path.abspath(os.path.expanduser(x))
+
+def check_windows_cmake(cmake_cmd):
+    if os.name == 'nt':
+        files_on_path = set()
+        for p in os.environ['PATH'].split(';')[::-1]:
+            if os.path.exists(p):
+                files_on_path.update(os.listdir(p))
+        if 'cl.exe' in files_on_path:
+            pass
+        elif 'sh.exe' in files_on_path:
+            cmake_cmd += ['-G "MSYS Makefiles"']
+        elif 'gcc.exe' in files_on_path:
+            cmake_cmd += ['-G "MinGW Makefiles"']
+        cmake_cmd = ' '.join(cmake_cmd)
+
+def install_cycamore(args):
+    if not os.path.exists(args.build_dir):
+        os.mkdir(args.build_dir)
+    elif args.replace:
+        shutil.rmtree(args.build_dir)
+        os.mkdir(args.build_dir)
+
+    root_dir = os.path.split(__file__)[0]
+    src_dir = os.path.join(root_dir, 'src')
+    makefile = os.path.join(args.build_dir, 'Makefile')
+
+    if not os.path.exists(makefile):
+        cmake_cmd = ['cmake', absexpanduser(src_dir)]
+        if args.prefix:
+            cmake_cmd += ['-DCMAKE_INSTALL_PREFIX=' + absexpanduser(args.prefix)]
+        if args.cmake_prefix_path:
+            cmake_cmd += ['-DCMAKE_PREFIX_PATH=' + absexpanduser(args.cmake_prefix_path)]
+        if args.coin_root:
+            cmake_cmd += ['-DCOIN_ROOT_DIR=' + absexpanduser(args.coin_root)]
+        if args.boost_root:
+            cmake_cmd += ['-DBOOST_ROOT=' + absexpanduser(args.boost_root)]
+        if args.cyclopts_root:
+            cmake_cmd += ['-DCYCLOPTS_ROOT_DIR='+absexpanduser(args.cyclopts_root)]
+        if args.cyclus_root:
+            cmake_cmd += ['-DCYCLUS_ROOT_DIR='+absexpanduser(args.cyclus_root)]
+        check_windows_cmake(cmake_cmd)
+        rtn = subprocess.check_call(cmake_cmd, cwd=absexpanduser(args.build_dir), shell=(os.name=='nt'))
+
+    make_cmd = ['make']
+    if args.threads:
+        make_cmd += ['-j' + str(args.threads)]
+    make_cmd += ['install']
+    rtn = subprocess.check_call(make_cmd, cwd=absexpanduser(args.build_dir), shell=(os.name=='nt'))
+
+def main():
+
+    description = "A Cycamore installation helper script. "+\
+        "For more information, please see cyclus.github.com." 
+
+    parser = ap.ArgumentParser(description=description)
+
+    build_dir = 'where to place the build directory'
+    parser.add_argument('--build_dir', help=build_dir, default='build')
+
+    replace = 'whether or not to remove the build directory if it exists'
+    parser.add_argument('--replace', type=bool, help=replace, default=True)
+
+    threads = "the number of threads to use in the make step"
+    parser.add_argument('-j', '--threads', type=int, help=threads)
+
+    install = "the relative path to the installation directory"
+    parser.add_argument('--prefix', help=install)
+
+    coin = "the relative path to the Coin-OR libraries directory"
+    parser.add_argument('--coin_root', help=coin)
+
+    cyclopts = "the relative path to Cyclopts installation directory"
+    parser.add_argument('--cyclopts_root',help=cyclopts)
+
+    cyclus = "the relative path to Cyclus installation directory"
+    parser.add_argument('--cyclus_root',help=cyclus)
+
+    boost = "the relative path to the Boost libraries directory"
+    parser.add_argument('--boost_root', help=boost)
+
+    cmake_prefix_path = "the cmake prefix path for use with FIND_PACKAGE, " + \
+        "FIND_PATH, FIND_PROGRAM, or FIND_LIBRARY macros"
+    parser.add_argument('--cmake_prefix_path', help=cmake_prefix_path)
+
+
+    install_cycamore(parser.parse_args())
+
+if __name__ == "__main__":
+    main()

src/Models/Facility/BatchReactor/BatchReactorTests.cpp

@@ -61,7 +61,8 @@ void BatchReactorTest::initSrcFacility()
      << "  </commodity_production>"
      << "</start>";
 
-  XMLParser parser(ss);
+  XMLParser parser;
+  parser.init(ss);
   XMLQueryEngine* engine = new XMLQueryEngine(parser);
   src_facility = new BatchReactor();
   src_facility->initModuleMembers(engine);

src/Models/Facility/EnrichmentFacility/EnrichmentFacilityTests.cpp

@@ -71,7 +71,8 @@ void EnrichmentFacilityTest::initFacility()
      << "  </output>"
      << "</start>";
 
-  XMLParser parser(ss);
+  XMLParser parser;
+  parser.init(ss);
   XMLQueryEngine* engine = new XMLQueryEngine(parser);
 
   EXPECT_NO_THROW(src_facility->initModuleMembers(engine));

src/Models/Facility/SinkFacility/SinkFacility.rng

@@ -5,7 +5,9 @@ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes">
      <element name="SinkFacility"> 
        <element name ="input">
          <element name = "commodities">
-           <ref name="incommodity"/>
+           <oneOrMore>
+             <ref name="incommodity"/>
+           </oneOrMore>
          </element>         
           <optional>
            <ref name="input_capacity"/>

src/Models/Facility/SourceFacility/SourceFacility.cpp

@@ -42,10 +42,16 @@ void SourceFacility::initModuleMembers(QueryEngine* qe) {
   setCommodity(data);
   Commodity commod(data);
   CommodityProducer::addCommodity(commod);
-
-  data = output->getElementContent("output_capacity"); 
-  CommodityProducer::setCapacity(commod,lexical_cast<double>(data));
-  setCapacity(lexical_cast<double>(data));  
+
+  double val = numeric_limits<double>::max();
+  try
+  {
+    data = output->getElementContent("output_capacity"); 
+    val = lexical_cast<double>(data); // overwrite default if given a value
+  }
+  catch (CycNullQueryException e) {}
+  CommodityProducer::setCapacity(commod, val);
+  setCapacity(val);  
 
   try
     {

src/Models/Facility/SourceFacility/SourceFacility.rng

@@ -5,7 +5,9 @@ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes">
      <element name="SourceFacility"> 
        <element name ="output">
          <ref name="outcommodity"/>
-         <ref name="output_capacity"/>
+         <optional>
+           <ref name="output_capacity"/>
+         </optional>
          <optional>
            <ref name="inventorysize"/>
          </optional>

src/Models/Facility/StorageFacility/StorageFacility.h → src/Models/Facility/deprecated/StorageFacility/StorageFacility.h

@@ -87,6 +87,7 @@ class StorageFacility : public FacilityModel
   /* --- */
 
   /* --- Transaction Methods --- */  
+
   /**
      Transacted resources are extracted through this method 
       
@@ -109,6 +110,17 @@ class StorageFacility : public FacilityModel
      When the facility receives a message, execute any transaction 
    */
   virtual void receiveMessage(msg_ptr msg);
+
+ protected:
+  /**
+     builds a transaction 
+   */
+  Transaction buildTransaction();
+
+  /**
+     sends a transaction as an offer 
+   */
+  void sendOffer(Transaction trans);
   /* --- */
 
   /* --- StorageFacility Methods --- */

src/Models/Inst/ManagerInst/ManagerInst.h

@@ -53,7 +53,6 @@ class ManagerInst : public InstModel,
   /**
      write information about a commodity producer to a stream
      @param producer the producer
-     @param stream the stream
    */
   void writeProducerInformation(SupplyDemand::CommodityProducer* producer);
 };

src/Models/Region/GrowthRegion/GrowthRegionTests.cpp

@@ -5,6 +5,7 @@
 
 #include "Commodity.h"
 #include "XMLQueryEngine.h"
+#include "XMLParser.h"
 
 #include <sstream>
 
@@ -53,7 +54,8 @@ void GrowthRegionTests::initRegion()
      << "  </commodity>"
      << "</start>";
 
-  XMLParser parser(ss);
+  XMLParser parser;
+  parser.init(ss);
   XMLQueryEngine* engine = new XMLQueryEngine(parser);
   region->initModuleMembers(engine);
   delete engine;