Merge branch 'v1.5.0-release'

.gitignore

@@ -32,3 +32,10 @@ src/pyne_decay.cc
 src/hdf5_back.cc
 share/dbtypes.json
 tests/db.h5
+cyclus/cpp_typesystem.pxd
+cyclus/typesystem.pxd
+cyclus/typesystem.pyx
+tests/libcyclus-orig.h5
+tests/libcyclus-orig.sqlite
+tests/libcyclus-test.h5
+tests/libcyclus-test.sqlite

CMakeLists.txt

@@ -40,7 +40,7 @@ IF(NOT CYCLUS_DOC_ONLY)
                     RESULT_VARIABLE res_var)
 
     IF(NOT "${res_var}" STREQUAL "0")
-      message(FATAL_ERROR "fetching decay source code failed, res_var = '${res_var}'")
+        message(FATAL_ERROR "fetching decay source code failed, res_var = '${res_var}'")
     ENDIF()
 
     ##############################################################################################
@@ -57,6 +57,7 @@ IF(NOT CYCLUS_DOC_ONLY)
     SET(CYCLUS_TEST_DIR "${PROJECT_SOURCE_DIR}/tests")
     SET(CYCLUS_AGENTS_DIR "${PROJECT_SOURCE_DIR}/agents")
     SET(CYCLUS_CMAKE_DIR "${PROJECT_SOURCE_DIR}/cmake")
+    SET(CYCLUS_PYSOURCE_DIR "${PROJECT_SOURCE_DIR}/cyclus")
 
     # set cycpp var
     SET(CYCPP "${CYCLUS_CLI_DIR}/cycpp.py")
@@ -134,14 +135,17 @@ IF(NOT CYCLUS_DOC_ONLY)
     MESSAGE("-- Dependency Root Dir (DEPS_ROOT_DIR): ${DEPS_ROOT_DIR}")
     if (DEPS_ROOT_DIR)
         SET(DEPS_HINTS HINTS "${DEPS_ROOT_DIR}")
+        SET(DEPS_BIN_HINTS ${DEPS_HINTS} "${DEPS_ROOT_DIR}/bin")
         SET(DEPS_LIB_HINTS ${DEPS_HINTS} "${DEPS_ROOT_DIR}/lib")
         SET(DEPS_INCLUDE_HINTS HINTS "${DEPS_ROOT_DIR}/include")
     else (DEPS_ROOT_DIR)
         SET(DEPS_HINTS)
+        SET(DEPS_bin_HINTS)
         SET(DEPS_LIB_HINTS)
         SET(DEPS_INCLUDE_HINTS)
     endif (DEPS_ROOT_DIR)
     MESSAGE("-- Dependency Hints (DEPS_HINTS): ${DEPS_HINTS}")
+    MESSAGE("-- Dependency Binary Hints (DEPS_BIN_HINTS): ${DEPS_BIN_HINTS}")
     MESSAGE("-- Dependency Library Hints (DEPS_LIB_HINTS): ${DEPS_LIB_HINTS}")
     MESSAGE("-- Dependency Include Hints (DEPS_INCLUDE_HINTS): ${DEPS_INCLUDE_HINTS}")
 
@@ -251,6 +255,40 @@ IF(NOT CYCLUS_DOC_ONLY)
         set(LIBS ${LIBS} ${ICUUC_LIBRARIES})
     ENDIF(ICUUC_LIBRARIES)
 
+    #
+    # Cython & Python Bindings
+    #
+    # Use new Python library finder
+    find_package(PythonInterp)
+    find_package(PythonLibs)
+    message("-- PYTHON_EXECUTABLE: ${PYTHON_EXECUTABLE}")
+
+    # Include the CMake script UseCython.cmake.  This defines add_cython_module().
+    # Instruction for use can be found at the top of cmake/UseCython.cmake.
+
+    FIND_PACKAGE(Cython)
+    message("-- Found Cython: ${Cython_FOUND}")
+    if(Cython_FOUND)
+        include(UseCython)
+        execute_process(COMMAND "${CYTHON_EXECUTABLE}" "-V"
+                        ERROR_VARIABLE CYTHON_VERSION
+                        ERROR_STRIP_TRAILING_WHITESPACE)
+        message(STATUS "Cython Version: ${CYTHON_VERSION}")
+
+        find_package(Numpy REQUIRED)
+        find_package(Jinja2 REQUIRED)
+
+        # With CMake, a clean separation can be made between the source tree and the
+        # build tree.  When all source is compiled, as with pure C/C++, the source is
+        # no-longer needed in the build tree.  However, with pure *.py source, the
+        # source is processed directly.  To handle this, we reproduce the availability
+        # of the source files in the build tree.
+        add_custom_target(ReplicatePythonSourceTree ALL "${CMAKE_COMMAND}" -P
+            "${CMAKE_CURRENT_SOURCE_DIR}/cmake/ReplicatePythonSourceTree.cmake"
+            "${CMAKE_CURRENT_BINARY_DIR}"
+            WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}")
+    endif(Cython_FOUND)
+
     ##############################################################################################
     #################################### end find libraries ######################################
     ##############################################################################################
@@ -270,7 +308,9 @@ IF(NOT CYCLUS_DOC_ONLY)
         "${HDF5_INCLUDE_DIRS}"
         "${Boost_INCLUDE_DIR}"
         "${COIN_INCLUDE_DIRS}")
-
+    if(Cython_FOUND)
+        INCLUDE_DIRECTORIES("${NUMPY_INCLUDE_DIRS}")
+    endif(Cython_FOUND)
     # set core version, one way or the other
     IF(NOT "${CORE_VERSION}" STREQUAL "")
         SET(core_version "${CORE_VERSION}")
@@ -280,23 +320,27 @@ IF(NOT CYCLUS_DOC_ONLY)
                         OUTPUT_STRIP_TRAILING_WHITESPACE)
     ENDIF(NOT "${CORE_VERSION}" STREQUAL "")
     IF("${core_version}" STREQUAL "")
-      MESSAGE(WARNING "Unable to read current core version, falling back to previous version. Core version will be set to -1")
-      SET(core_version "-1")
+        MESSAGE(WARNING "Unable to read current core version, falling back to previous version. Core version will be set to -1")
+        SET(core_version "-1")
     ENDIF()
-    MESSAGE("-- core version set to: ${core_version}")
+    SET(ENV{CYCLUS_CORE_VERSION} "${core_version}")
+    MESSAGE("-- core version ($CYCLUS_CORE_VERSION) set to: ${core_version}")
 
     ADD_SUBDIRECTORY("${CYCLUS_SHARE_DIR}")
     ADD_SUBDIRECTORY("${CYCLUS_SOURCE_DIR}")
     ADD_SUBDIRECTORY("${CYCLUS_TEST_DIR}")
     ADD_SUBDIRECTORY("${CYCLUS_AGENTS_DIR}")
     ADD_SUBDIRECTORY("${CYCLUS_CLI_DIR}")
     ADD_SUBDIRECTORY("${CYCLUS_CMAKE_DIR}")
+    if(Cython_FOUND)
+        ADD_SUBDIRECTORY("${CYCLUS_PYSOURCE_DIR}")
+    endif(Cython_FOUND)
 
     ##############################################################################################
     ####################################### end includes #########################################
     ##############################################################################################
 
-    ################# stub files #################################################################
+    ################# custom install files #######################################################
     INSTALL(
         FILES
         stubs/CMakeLists.txt
@@ -325,6 +369,12 @@ IF(NOT CYCLUS_DOC_ONLY)
         DESTINATION share/cyclus/stubs/src
         COMPONENT stubs
         )
+
+    if(Cython_FOUND)
+        set(pyinstallscript "${CMAKE_CURRENT_BINARY_DIR}/cmake/SetupPyInstall.cmake")
+        configure_file(cmake/SetupPyInstall.cmake.in ${pyinstallscript} @ONLY)
+        install(SCRIPT ${pyinstallscript})
+    endif(Cython_FOUND)
     ##############################################################################################
     ################################## begin uninstall target ####################################
     ##############################################################################################

DEPENDENCIES.rst

@@ -37,7 +37,7 @@ Package                Minimum Version
 
 .. website_include_end
 
-On some platforms, such as Ubuntu 14.04, the following are also necessary:
+On some platforms, such as Ubuntu 16.04, the following are also necessary:
 
 ====================   ==================
 Package                Minimum Version
@@ -54,12 +54,20 @@ And a few optional dependencies:
 Package                Minimum Version
 ====================   ==================
 doxygen (for docs)     1.7.6.1
-tcmalloc (for speed)   any?
+tcmalloc (for speed)   any
+Cython                 0.13.1
+Python (dev version)   2.7 or 3.3+
+Jinja2                 any
+NumPy                  1.9+
+Pandas                 any
 ====================   ==================
 
 *Note that the Debian/Ubuntu package ``libtcmalloc`` is NOT discovered correctly
 by our build system.  Instead use ``libgoogle-perftools-dev``.*
 
+*Also note that the development version of Python, Jinja2, NumPy, and Pandas are
+only needed if Cython is installed.*
+
 ***********************
 Installing Dependencies
 ***********************
@@ -73,7 +81,7 @@ Installing Dependencies (Linux and Unix)
 This guide assumes that the user has root access (to issue ``sudo`` commands) and
 access to a package manager or has some other suitable method of automatically
 installing established libraries. This process was tested using a fresh install
-of Ubuntu versions 14.04 and 16.04, using ``apt-get`` as the package
+of Ubuntu versions 16.04, using ``apt-get`` as the package
 manager (scroll down further for Mac OSX instructions).
 
 The command to install a dependency takes the form of:
@@ -106,19 +114,56 @@ and (optionally):
 #. libblas-dev
 #. liblapack-dev
 #. libgoogle-perftools-dev
+#. python-dev    or  python3-dev
+#. python-tables or  python3-tables
+#. python-pandas or  python3-pandas
+#. python-numpy  or  python3-numpy
+#. python-nose   or  python3-nose
+#. python-jinja2 or  python3-jinja2
+#. cython        or  cython3       
 
 For example, in order to install libxml++ (and libxml2) on your system, type:
 
 .. code-block:: bash
 
   sudo apt-get install libxml++2.6-dev
 
-If you'd prefer to copy/paste, the following line will install all *Cyclus*
-dependencies:
+If you'd prefer to copy/paste, the following line will install all **required**
+*Cyclus* dependencies:
+
+.. code-block:: bash
+
+   sudo apt-get install -y cmake make libboost-all-dev libxml2-dev libxml++2.6-dev \
+   libsqlite3-dev libhdf5-serial-dev libbz2-dev coinor-libcbc-dev coinor-libcoinutils-dev \
+   coinor-libosi-dev coinor-libclp-dev coinor-libcgl-dev
+
+And to install all *Cyclus* dependencies (**required and optional**):
+
+- if using python 2.x:
+
+.. code-block:: bash
+
+   sudo apt-get install -y cmake make libboost-all-dev libxml2-dev libxml++2.6-dev \
+   libsqlite3-dev libhdf5-serial-dev libbz2-dev coinor-libcbc-dev coinor-libcoinutils-dev \
+   coinor-libosi-dev coinor-libclp-dev coinor-libcgl-dev libblas-dev liblapack-dev g++ \
+   libgoogle-perftools-dev python-dev python-tables python-pandas python-numpy python-nose \
+   python-jinja2 cython
+
+- if using python 3.x:
+
+.. code-block:: bash
+
+   sudo apt-get install -y cmake make libboost-all-dev libxml2-dev libxml++2.6-dev \
+   libsqlite3-dev libhdf5-serial-dev libbz2-dev coinor-libcbc-dev coinor-libcoinutils-dev \
+   coinor-libosi-dev coinor-libclp-dev coinor-libcgl-dev libblas-dev liblapack-dev g++ \
+   libgoogle-perftools-dev python3-dev python3-tables python3-pandas python3-numpy python3-nose \
+   python3-jinja2 cython3
+
+To determine which version of Python is already installed on your computer, run:
 
 .. code-block:: bash
 
-   sudo apt-get install -y cmake make libboost-all-dev libxml2-dev libxml++2.6-dev libsqlite3-dev libhdf5-serial-dev libbz2-dev coinor-libcbc-dev coinor-libcoinutils-dev coinor-libosi-dev coinor-libclp-dev coinor-libcgl-dev libblas-dev liblapack-dev g++ libgoogle-perftools-dev
+   python -V
 
 Boost Note
 ^^^^^^^^^^
@@ -173,9 +218,9 @@ required library package names is:
 
 Then install Coin-Cbc from source. They can be downloaded to any directory on
 your computer:
-   
+
 **Coin-Cbc**: Download and build using the svn command in the terminal:
-   
+
 .. code-block:: bash
 
   svn co https://projects.coin-or.org/svn/Cbc/stable/2.8 Coin-Cbc

INSTALL.rst

@@ -56,6 +56,15 @@ You need to add ``~/.local/bin`` to the front of your ``$PATH``:
   echo 'export PATH="$HOME/.local/bin:$PATH' >> ~/.bashrc
   source ~/.bashrc
 
+On MacOSX you also need to add ~/.local/lib/pythonX.Y/site-packages to your
+``$PYTHONPATH``:
+
+.. code-block:: bash
+
+  echo "export PYTHONPATH=\"\$HOME/.local/lib/python`python -c 'import sys; \
+  print(".".join(map(str, sys.version_info[:2])))'`/site-packages:\$PYTHONPATH\"" >> ~/.bashrc
+  source ~/.bashrc
+
 .. website_include_end
 
 .. website_custom_start

README.rst

@@ -83,8 +83,10 @@ on the source code from github is fairly straightforward:
 - to install Cyclus locally (in ``~/.local/``) just run: ``python install.py``
   from the ``cyclus`` folder,
 
-- finally, add the following Cyclus installation path (``~/.local/cyclus``) to
+- finally, add the following Cyclus installation path (``~/.local/bin``) to
   the **front** on your ``$PATH``.
+- additionnaly if you are using MacOSX, also add
+  ``~/.local/lib/pythonX.Y/site-packages`` to your ``$PYTHONPATH``
 
 For more detailed installation procedure, and/or custom installation please
 refer to the `INSTALLATION guide <INSTALL.rst>`_.

circle.yml

@@ -26,10 +26,7 @@ deployment:
       - docker tag cyclus/cyclus:latest cyclus/cyclus:stable # creation
       - docker push cyclus/cyclus:stable # push to docker depot
       ## DEB GENERATION
-        #ubuntu 14.04
-      - docker/deb-ci/build_upload_deb.sh 14 :
-          timeout: 1200 # set 20 minute timeout (to avoid CI to fail)
-          # Ubuntu 16.04
+      # Ubuntu 16.04
       - docker/deb-ci/build_upload_deb.sh 16 :
           timeout: 1200 # set 20 minute timeout (to avoid CI to fail)
         ## END DEB GENERATION

cli/cycpp.py

@@ -492,6 +492,7 @@ def transform_pass2(self, statement, sep):
         annotations['type'] = state.canonize_type(vtype, vname,
                                                   statement=statement)
         annotations['index'] = len(state.context[classname]['vars'])
+        annotations['shape'] = state.canonize_shape(annotations)
         state.context[classname]['vars'][vname] = annotations
         if 'alias' in annotations:
             alias = annotations['alias']
@@ -813,12 +814,58 @@ def canonize_type(self, t, name="<member variable>", statement=None):
                     p=pformat(self.supported_types))
                 raise TypeError(msg)
         return t
-
+    
     def _canonize_targs(self, newtname, targs):
         newt = [newtname]
         newt += [self.canonize_type(targ) for targ in targs]
         return tuple(newt)
 
+    def canonize_shape(self, ann_dict):
+        """This canonizes a shape. We take a look at the current shape, and 
+        standardize its format if necessary. We append -1's to the shape if 
+        its length does not match our expected length. Returns the new shape
+        or raises an error if the given shape was longer than expected.
+        """
+        type_canon = ann_dict['type']
+        try: 
+            current_shape = ann_dict['shape']
+        except KeyError:
+            ann_dict['shape'] = None
+            current_shape = ann_dict['shape']
+        new_shape = []
+        # Flatten list dimensions
+        if isinstance(type_canon, str):
+            result = [type_canon]
+        else:
+            result = list(type_canon)
+            i = 0
+            while i < len(result):
+                if isinstance(result[i], str):
+                    i += 1
+                else:
+                    temp = result[i][1:]
+                    i += 1
+                    for j in range(len(temp)):
+                        result.insert(i+j, temp[j])
+        expected_shape_length = len(result)
+        # Shape wasn't given.
+        if current_shape is None:
+            new_shape = [-1] * expected_shape_length
+        # Shape is correct as is.
+        elif len(current_shape) == expected_shape_length:
+            new_shape = current_shape
+        # Shape is too short.
+        elif len(current_shape) < expected_shape_length:    
+            diff = expected_shape_length - len(current_shape)
+            new_shape = current_shape.extend([-1] * diff)
+        # Shape is too long- we throw an error.
+        elif len(current_shape) > expected_shape_length:
+            err_string = ("Shape array for type {t} is not formatted correctly."
+                          " Expected length {length} or less.")
+            raise ValueError(err_string.format(t=str(type_canon), 
+                                               length=str(expected_shape_length)))
+        return new_shape
+
     def canonize_class(self, cls, _usens=True):
         """This canonizes a classname.  The class name need not be the current
         class whose scope we are in, but may be any class whatsoever. Returns

cmake/CMakeLists.txt

@@ -1,18 +1,6 @@
-INSTALL(
-    FILES 
-        FindCOIN.cmake
-        FindCyclus.cmake
-        FindGlib.cmake
-        FindGlibmm.cmake
-        FindHDF5.cmake
-        FindLibXML++.cmake
-        FindSigC++.cmake
-        FindSqlite3.cmake
-        FindTcmalloc.cmake
-        LibFindMacros.cmake
-        UseCyclus.cmake
-	cmake_uninstall.cmake.in
-    DESTINATION share/cyclus/cmake
-    COMPONENT core
-    )
+file(GLOB find_use_files "*.cmake")
+INSTALL(FILES ${find_use_files} cmake_uninstall.cmake.in
+        DESTINATION share/cyclus/cmake
+        COMPONENT core
+        )