Merge branch 'release/18.02.0'

HBPVIS · Feb 7, 2018 · c7fe9ee · c7fe9ee
2 parents aecc590 + cb8e039
commit c7fe9ee
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Showing 98 changed files with 4,285 additions and 1,042 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,4 @@
 build*
 BUILD*
 .dir-locals.el
+*.pyc
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,7 +1,7 @@
 #-------------------------------------------------------------------------------
 # nest in situ vis
 #
-# Copyright (c) 2017 RWTH Aachen University, Germany,
+# Copyright (c) 2017-2018 RWTH Aachen University, Germany,
 # Virtual Reality & Immersive Visualisation Group.
 #-------------------------------------------------------------------------------
 #                                  License
@@ -27,6 +27,15 @@ set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 set(CMAKE_CXX_STANDARD 17)
 
 find_package(Boost REQUIRED COMPONENTS python)
+find_library(Boost_PYTHON_NUMPY_LIBRARY
+  boost_numpy
+  PATHS ${Boost_LIBRARY_DIRS}
+  NO_DEFAULT_PATH
+  )
+set(Boost_LIBRARIES
+  ${Boost_LIBRARIES}
+  ${Boost_PYTHON_NUMPY_LIBRARY}
+  )
 
 find_package(PythonInterp)
 find_package(PythonLibs)
@@ -46,7 +55,7 @@ include(py.test)
 
 include(WarningLevels)
 
-find_package(conduit)
+find_package(Conduit)
 set_target_properties(conduit
   PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${CONDUIT_INCLUDE_DIRS}/..")
 

diff --git a/LICENSE b/LICENSE
@@ -1,7 +1,7 @@
 --------------------------------------------------------------------------------
  nest in situ vis
 
- Copyright (c) 2017 RWTH Aachen University, Germany,
+ Copyright (c) 2017-2018 RWTH Aachen University, Germany,
  Virtual Reality & Immersive Visualisation Group.
 --------------------------------------------------------------------------------
  Contact Information

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # nest in situ vis
 
-*nest in situ vis* is Copyright (c) 2017 RWTH Aachen University, Germany,
+*nest in situ vis* is Copyright (c) 2017-2018 RWTH Aachen University, Germany,
 Virtual Reality & Immersive Visualization Group.
 
 

diff --git a/cmake/ConfigureFiles.cmake b/cmake/ConfigureFiles.cmake
@@ -1,7 +1,7 @@
 #-------------------------------------------------------------------------------
 # nest in situ vis
 #
-# Copyright (c) 2017 RWTH Aachen University, Germany,
+# Copyright (c) 2017-2018 RWTH Aachen University, Germany,
 # Virtual Reality & Immersive Visualisation Group.
 #-------------------------------------------------------------------------------
 #                                  License

diff --git a/cmake/WarningLevels.cmake b/cmake/WarningLevels.cmake
@@ -1,7 +1,7 @@
 #-------------------------------------------------------------------------------
 # nest in situ vis
 #
-# Copyright (c) 2017 RWTH Aachen University, Germany,
+# Copyright (c) 2017-2018 RWTH Aachen University, Germany,
 # Virtual Reality & Immersive Visualisation Group.
 #-------------------------------------------------------------------------------
 #                                  License

diff --git a/cmake/catch.cmake b/cmake/catch.cmake
@@ -1,7 +1,7 @@
 #-------------------------------------------------------------------------------
 # nest in situ vis
 #
-# Copyright (c) 2017 RWTH Aachen University, Germany,
+# Copyright (c) 2017-2018 RWTH Aachen University, Germany,
 # Virtual Reality & Immersive Visualisation Group.
 #-------------------------------------------------------------------------------
 #                                  License
@@ -39,8 +39,14 @@ endfunction()
 
 function(ADD_TEST_CATCH_INTERNAL_
     NAME SOURCES HEADERS INCLUDE_DIRECTORIES LINK_LIBRARIES PATH_TO_ADD)
+  STRING(REGEX REPLACE
+    "^__" ""
+    NAME "${NAME}"
+    )
   add_executable(${NAME} ${SOURCES} ${HEADERS})
-  target_include_directories(${NAME} PRIVATE ${INCLUDE_DIRECTORIES})
+  target_include_directories(${NAME}
+    PRIVATE ${INCLUDE_DIRECTORIES}
+    )
   target_link_libraries(${NAME} ${LINK_LIBRARIES})
   add_test(NAME ${NAME} COMMAND ${NAME})
   set_warning_levels_RWTH(${NAME})
@@ -83,13 +89,22 @@ function(ADD_TEST_CATCH)
 
   # add test for each test source file
   foreach(TEST_SOURCE_FILE ${ADD_TEST_CATCH_SOURCES})
+    get_filename_component(TEST_SUBDIR ${TEST_SOURCE_FILE} DIRECTORY)
+    STRING(REGEX REPLACE
+      "^${CMAKE_CURRENT_SOURCE_DIR}" ""
+      TEST_SUBDIR "${TEST_SUBDIR}"
+      )
+    STRING(REGEX REPLACE
+      "[/|\\]" "__"
+      TEST_SUBDIR "${TEST_SUBDIR}"
+      )
     get_filename_component(TEST_NAME ${TEST_SOURCE_FILE} NAME_WE)
-    ADD_TEST_CATCH_INTERNAL_("${TEST_NAME}"
+    ADD_TEST_CATCH_INTERNAL_("${TEST_SUBDIR}__${TEST_NAME}"
       "${TEST_SOURCE_FILE}"
       ""
       "${ADD_TEST_CATCH_INCLUDE_DIRECTORIES}"
       "${ADD_TEST_CATCH_LINK_LIBRARIES};${ADD_TEST_CATCH_NAME}_catch_main"
       "${ADD_TEST_CATCH_PATH_TO_ADD}"
-    )
+      )
   endforeach()
 endfunction()
diff --git a/cmake/cpplint.cmake b/cmake/cpplint.cmake
@@ -1,7 +1,7 @@
 #-------------------------------------------------------------------------------
 # nest in situ vis
 #
-# Copyright (c) 2017 RWTH Aachen University, Germany,
+# Copyright (c) 2017-2018 RWTH Aachen University, Germany,
 # Virtual Reality & Immersive Visualisation Group.
 #-------------------------------------------------------------------------------
 #                                  License
@@ -27,7 +27,7 @@ if(NOT PYTHON_EXECUTABLE)
         CMake will not generate the project without it. ")
 endif()
 
-find_file(CPPLINT_COMMAND cpplint.py
+find_file(CPPLINT_COMMAND cpplint.py cpplint
   PATHS $ENV{PATH} $ENV{CPPLINT_DIR}
 )
 if(NOT CPPLINT_COMMAND)

diff --git a/cmake/niv-config.cmake.in b/cmake/niv-config.cmake.in
@@ -1,7 +1,7 @@
 #-------------------------------------------------------------------------------
 # nest in situ vis
 #
-# Copyright (c) 2017 RWTH Aachen University, Germany,
+# Copyright (c) 2017-2018 RWTH Aachen University, Germany,
 # Virtual Reality & Immersive Visualisation Group.
 #-------------------------------------------------------------------------------
 #                                  License

diff --git a/cmake/py.test.cmake b/cmake/py.test.cmake
@@ -1,7 +1,7 @@
 #-------------------------------------------------------------------------------
 # nest in situ vis
 #
-# Copyright (c) 2017 RWTH Aachen University, Germany,
+# Copyright (c) 2017-2018 RWTH Aachen University, Germany,
 # Virtual Reality & Immersive Visualisation Group.
 #-------------------------------------------------------------------------------
 #                                  License
@@ -27,15 +27,15 @@ if(NOT PYTHON_EXECUTABLE)
         CMake will not generate the project without it. ")
 endif()
 
-find_file(PY_TEST_COMMAND py.test
+find_file(PY_TEST_COMMAND py.test pytest
   PATHS $ENV{PATH} $ENV{PY_TEST_DIR}
 )
 if(NOT PY_TEST_COMMAND)
   message(SEND_ERROR
     " ERROR: Could not find py.test.
         Having py.test is a mandatory requirement.
         CMake will not generate the project without it.
-        Add its location to the environments variables PATH or CPPLINT_DIR.")
+        Add its location to the environments variables PATH or PY_TEST_DIR.")
 endif()
 
 function(ADD_TEST_PY_TEST)

diff --git a/cmake/suppress_warnings.hpp.in b/cmake/suppress_warnings.hpp.in
@@ -1,7 +1,7 @@
 //------------------------------------------------------------------------------
 // nest in situ vis
 //
-// Copyright (c) 2017 RWTH Aachen University, Germany,
+// Copyright (c) 2017-2018 RWTH Aachen University, Germany,
 // Virtual Reality & Immersive Visualisation Group.
 //------------------------------------------------------------------------------
 //                                 License
@@ -22,23 +22,58 @@
 #ifndef NEST_IN_SITU_VIS_SUPPRESS_WARNINGS_
 #define NEST_IN_SITU_VIS_SUPPRESS_WARNINGS_
 
+// clang-format off
 #if defined __clang__
-#define SUPPRESS_WARNINGS_BEGIN                           \
-  _Pragma("clang diagnostic push")                        \
-      _Pragma("clang diagnostic ignored \"-Wall\"")       \
-          _Pragma("clang diagnostic ignored \"-Wextra\"") \
-              _Pragma("clang diagnostic ignored \"-Wc++98-compat-pedantic\"")
+#define SUPPRESS_WARNINGS_BEGIN                                                \
+  _Pragma("clang diagnostic push")                                             \
+  _Pragma("clang diagnostic ignored \"-Wall\"")                                \
+  _Pragma("clang diagnostic ignored \"-Wextra\"")                              \
+  _Pragma("clang diagnostic ignored \"-Wc++98-compat-pedantic\"")              \
+  _Pragma("clang diagnostic ignored \"-Wundefined-func-template\"")            \
+  _Pragma("clang diagnostic ignored \"-Wold-style-cast\"")                     \
+  _Pragma("clang diagnostic ignored \"-Wreserved-id-macro\"")                  \
+  _Pragma("clang diagnostic ignored \"-Wdocumentation-unknown-command\"")      \
+  _Pragma("clang diagnostic ignored \"-Wdeprecated-dynamic-exception-spec\"")  \
+  _Pragma("clang diagnostic ignored \"-Wpadded\"")                             \
+  _Pragma("clang diagnostic ignored \"-Wdocumentation\"")                      \
+  _Pragma("clang diagnostic ignored \"-Wswitch-enum\"")                        \
+  _Pragma("clang diagnostic ignored \"-Wextra-semi\"")                         \
+  _Pragma("clang diagnostic ignored \"-Wundef\"")                              \
+  _Pragma("clang diagnostic ignored \"-Wcovered-switch-default\"")             \
+  _Pragma("clang diagnostic ignored \"-Wglobal-constructors\"")                \
+  _Pragma("clang diagnostic ignored \"-Wdeprecated\"")                         \
+  _Pragma("clang diagnostic ignored \"-Wmissing-noreturn\"")                   \
+  _Pragma("clang diagnostic ignored \"-Wdouble-promotion\"")                   \
+  _Pragma("clang diagnostic ignored \"-Wdouble-promotion\"")                   \
+  _Pragma("clang diagnostic ignored \"-Wdisabled-macro-expansion\"")           \
+  _Pragma("clang diagnostic ignored \"-Wsign-conversion\"")                    \
+  _Pragma("clang diagnostic ignored \"-Wcomma\"")                              \
+  _Pragma("clang diagnostic ignored \"-Wconversion\"")                         \
+  _Pragma("clang diagnostic ignored \"-Wshadow\"")                             \
+  _Pragma("clang diagnostic ignored \"-Wexit-time-destructors\"")              \
+  _Pragma("clang diagnostic ignored \"-Wcast-align\"")
+// clang-format on
+
+#define SUPPRESS_WARNINGS_BEGIN_PADDED \
+  _Pragma("clang diagnostic push")     \
+      _Pragma("clang diagnostic ignored \"-Wpadded\"")
+
 #define SUPPRESS_WARNINGS_END _Pragma("clang diagnostic pop")
 
 #elif defined _MSC_VER
 #define NOMINMAX
 #define SUPPRESS_WARNINGS_BEGIN __pragma(warning(push, 0));
+#define SUPPRESS_WARNINGS_BEGIN_PADDED
+
 #define SUPPRESS_WARNINGS_END __pragma(warning(pop));
 
 #elif defined __GNUC__
 #define SUPPRESS_WARNINGS_BEGIN                                              \
   _Pragma("GCC diagnostic push") _Pragma("GCC diagnostic ignored \"-Wall\"") \
-      _Pragma("GCC diagnostic ignored \"-Wextra\"")
+      _Pragma("GCC diagnostic ignored \"-Wextra\"")                          \
+          _Pragma("GCC diagnostic ignored \"-Wunused-local-typedefs\"")      \
+              _Pragma("GCC diagnostic ignored \"-Wdeprecated-declarations\"")
+#define SUPPRESS_WARNINGS_BEGIN_PADDED
 #define SUPPRESS_WARNINGS_END _Pragma("GCC diagnostic pop")
 
 #endif

diff --git a/demo/CMakeLists.txt b/demo/CMakeLists.txt
@@ -1,7 +1,7 @@
 #-------------------------------------------------------------------------------
 # nest in situ vis
 #
-# Copyright (c) 2017 RWTH Aachen University, Germany,
+# Copyright (c) 2017-2018 RWTH Aachen University, Germany,
 # Virtual Reality & Immersive Visualisation Group.
 #-------------------------------------------------------------------------------
 #                                  License
@@ -20,3 +20,4 @@
 #-------------------------------------------------------------------------------
 
 add_subdirectory(nest_python_vis)
+add_subdirectory(brunel_example)
diff --git a/demo/brunel_example/CMakeLists.txt b/demo/brunel_example/CMakeLists.txt
@@ -0,0 +1,39 @@
+#-------------------------------------------------------------------------------
+# nest in situ vis
+#
+# Copyright (c) 2017-2018 RWTH Aachen University, Germany,
+# Virtual Reality & Immersive Visualisation Group.
+#-------------------------------------------------------------------------------
+#                                  License
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#-------------------------------------------------------------------------------
+
+set(NEST_PYTHON_VIS_SOURCE nest_python_vis.py)
+set(NEST_SIM_SOURCE nest_sim.py)
+
+if(NOT CMAKE_MAKE_PROGRAM STREQUAL "/usr/bin/xcodebuild")
+
+file(GENERATE OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/run_vis.sh
+  CONTENT "PYTHONPATH=$<TARGET_FILE_DIR:pyniv>:$<TARGET_FILE_DIR:pytest_utilities> ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/${NEST_PYTHON_VIS_SOURCE}"
+  )
+
+set(NEST_DIR
+  CACHE PATH "Path to installed nest")
+file(GENERATE OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/run_sim.sh
+  CONTENT
+"source ${NEST_DIR}/bin/nest_vars.sh
+PYTHONPATH=$<TARGET_FILE_DIR:pyniv>:$PYTHONPATH ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/${NEST_SIM_SOURCE}"
+  )
+
+endif()