Update to brion 3.3.1 (#3)

* Use plain CMake (remove common/CMake dependency) * remove submodules * emSim 1.0.1
BlueBrain · Feb 1, 2021 · 6f0ee49 · 6f0ee49
1 parent 9b95b79
commit 6f0ee49
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Showing 15 changed files with 92 additions and 81 deletions.
diff --git a/.gitmodules b/.gitmodules
diff --git a/.gitsubprojects b/.gitsubprojects
diff --git a/CMake/common b/CMake/common
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -5,48 +5,26 @@
 # This file is part of EMSim <https://github.com/BlueBrain/EMSim>
 
 cmake_minimum_required(VERSION 3.1 FATAL_ERROR)
-project(EMSim VERSION 1.0.0)
+project(EMSim VERSION 1.0.1)
 set(EMSim_VERSION_ABI 1)
 
-if(NOT EXISTS ${CMAKE_SOURCE_DIR}/CMake/common/Common.cmake)
-  message(FATAL_ERROR "CMake/common missing, run: git submodule update --init")
-endif()
+set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
-list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/CMake
-                              ${CMAKE_SOURCE_DIR}/CMake/common)
+list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/CMake)
 
-set(EMSIM_LICENSE LGPL)
-set(EMSIM_DESCRIPTION "Electro-magnetic simulation software")
-set(COMMON_PROJECT_DOMAIN ch.epfl.bluebrain)
-set(EMSIM_DEB_DEPENDS libboost-program-options-dev libboost-test-dev libglm-dev)
+set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
 
-include(Common)
-
-common_find_package(Boost REQUIRED COMPONENTS unit_test_framework program_options)
-common_find_package(Brion REQUIRED)
-common_find_package_post()
+find_package(glm)
+find_package(Boost REQUIRED COMPONENTS program_options)
+find_package(Brion REQUIRED)
 
 set(ISPC_BINARY ispc)
-
 find_program(ISPC ispc)
-if(NOT ISPC)
-  set(ISPC_BINARY ${CMAKE_BINARY_DIR}/ispc-v1.9.2-linux/ispc)
-  if(NOT EXISTS ${ISPC_BINARY})
-    message("ispc not found. Trying to download... " ${ISPC_BINARY})
-    file(DOWNLOAD
-         https://github.com/ispc/ispc/releases/download/v1.9.2/ispc-v1.9.2b-linux.tar.gz
-         ${CMAKE_BINARY_DIR}/ispc-v1.9.2b-linux.tar.gz
-         SHOW_PROGRESS)
-    execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf ispc-v1.9.2b-linux.tar.gz
-                    WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
-  endif()
-endif()
-
-add_subdirectory(glm)
+
+enable_testing()
+
 add_subdirectory(apps)
 add_subdirectory(emSim)
 add_subdirectory(tests)
-
-set(CPACK_PACKAGE_DESCRIPTION_FILE "${PROJECT_SOURCE_DIR}/README.md")
-set(EMSIM_PACKAGE_DEB_DEPENDS libboost-program-options-dev libglm-dev)
-include(DoxygenRule)
diff --git a/apps/emsimLFP/CMakeLists.txt b/apps/emsimLFP/CMakeLists.txt
@@ -17,7 +17,10 @@
 # along with this library; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 
-set(EMSIM_SOURCES main.cpp)
-set(EMSIM_LINK_LIBRARIES PUBLIC boost_program_options EMSimCommon )
-
-common_application( emsim )
+add_executable(emsim main.cpp)
+target_link_libraries(emsim
+                      PUBLIC
+                          ${Boost_PROGRAM_OPTIONS_LIBRARY}
+                          EMSimCommon
+                      )
+install(TARGETS emsim RUNTIME DESTINATION ${CMAKE_INSTALL_FULL_BINDIR})
diff --git a/apps/emsimVSD/CMakeLists.txt b/apps/emsimVSD/CMakeLists.txt
@@ -17,7 +17,10 @@
 # along with this library; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 
-set(EMSIMVSD_SOURCES main.cpp)
-set(EMSIMVSD_LINK_LIBRARIES PUBLIC boost_program_options EMSimCommon )
-
-common_application( emsimVSD )
+add_executable(emsimVSD main.cpp)
+target_link_libraries(emsimVSD
+                      PUBLIC
+                          ${Boost_PROGRAM_OPTIONS_LIBRARY}
+                          EMSimCommon
+                      )
+install(TARGETS emsimVSD RUNTIME DESTINATION ${CMAKE_INSTALL_FULL_BINDIR})
diff --git a/emSim/CMakeLists.txt b/emSim/CMakeLists.txt
@@ -62,6 +62,33 @@ foreach(ISPC_FILE ${ISPC_FILES})
   list(APPEND EMSIMCOMMON_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/${ISPC_FILE}.o )
 endforeach()
 
-set(EMSIMCOMMON_LINK_LIBRARIES PUBLIC Brion Brain  glm)
+set(EMSIM_INCLUDE_DIR ${PROJECT_SOURCE_DIR})
+
+add_library(EMSimCommon
+            SHARED
+                ${EMSIMCOMMON_PUBLIC_HEADERS}
+                ${EMSIMCOMMON_HEADERS}
+                ${EMSIMCOMMON_SOURCES}
+           )
+
+target_include_directories(EMSimCommon PUBLIC
+                           $<BUILD_INTERFACE:${EMSIM_INCLUDE_DIR}>
+                           $<INSTALL_INTERFACE:include>)
+target_include_directories(EMSimCommon PUBLIC
+                           $<BUILD_INTERFACE:${CMAKE_BINARY_DIR}/>
+                           $<INSTALL_INTERFACE:$/include>)
+target_include_directories(EMSimCommon SYSTEM PUBLIC ${Boost_INCLUDE_DIRS})
+
+target_link_libraries(EMSimCommon
+                      PUBLIC
+                          Brion
+                          Brain
+                          glm
+                      )
+
+install(TARGETS EMSimCommon
+   EXPORT EMSimCommon
+   LIBRARY
+      DESTINATION lib
+)
 
-common_library(EMSimCommon)
diff --git a/emSim/Events.h b/emSim/Events.h
@@ -23,8 +23,10 @@
 #include <cstddef>
 #include <cstdint>
 
+#define GLM_FORCE_CTOR_INIT
 #include <glm/glm.hpp>
 
+
 #include <emSim/helpers.h>
 
 namespace ems

diff --git a/emSim/EventsLoader.cpp b/emSim/EventsLoader.cpp
@@ -114,8 +114,8 @@ void EventsLoader::_computeStaticEventGeometry(
             {
                 auto pos = soma.getCentroid();
                 float radius = soma.getMeanRadius();
-                _events->addEvent(glm::vec3(pos.x(), pos.y(), pos.z()), radius);
-                _circuitAABB.add(glm::vec3(pos.x(), pos.y(), pos.z()), radius);
+                _events->addEvent(pos, radius);
+                _circuitAABB.add(pos, radius);
             }
             continue;
         }
@@ -136,10 +136,10 @@ void EventsLoader::_computeStaticEventGeometry(
 
         for (const auto& point : points)
         {
-            auto pos = point.get_sub_vector<3, 0>();
+            auto pos = glm::vec3(point);
             float radius = compartmentLength * .2f;
-            _events->addEvent(glm::vec3(pos.x(), pos.y(), pos.z()), radius);
-            _circuitAABB.add(glm::vec3(pos.x(), pos.y(), pos.z()), radius);
+            _events->addEvent(pos, radius);
+            _circuitAABB.add(pos, radius);
         }
     }
 }

diff --git a/emSim/SamplePoints.h b/emSim/SamplePoints.h
@@ -20,7 +20,9 @@
 #ifndef _SamplePoints_h_
 #define _SamplePoints_h_
 
+#define GLM_FORCE_CTOR_INIT
 #include <glm/glm.hpp>
+
 #include <string>
 #include <vector>
 

diff --git a/emSim/VSDLoader.cpp b/emSim/VSDLoader.cpp
@@ -19,8 +19,6 @@
 
 #include <iostream>
 
-#include <servus/servus.h>
-
 #include <emSim/VSDLoader.h>
 
 namespace ems
@@ -41,9 +39,10 @@ VSDLoader::VSDLoader(const VSDParams& params)
     _circuit.reset(new brain::Circuit(_bc));
     _gids = params.target.empty() ? _circuit->getRandomGIDs(params.fraction)
                                   : _circuit->getRandomGIDs(params.fraction, params.target);
-    auto reportSource = _bc.getReportSource(params.reportVoltage);
-    _reportVoltage.reset(new brion::CompartmentReport(reportSource, brion::MODE_READ, _gids));
-    _reportArea.reset(new brion::CompartmentReport(servus::URI(params.reportArea), brion::MODE_READ, _gids));
+    auto reportSourceVoltage = _bc.getReportSource(params.reportVoltage);
+    _reportVoltage.reset(new brion::CompartmentReport(reportSourceVoltage, brion::MODE_READ, _gids));
+    auto reportSourceArea = _bc.getReportSource(params.reportArea);
+    _reportArea.reset(new brion::CompartmentReport(reportSourceArea, brion::MODE_READ, _gids));
 
     const uint32_t timeStepMultiplier = params.timeStep / _reportVoltage->getTimestep() + 0.5f;
     _dt = timeStepMultiplier * _reportVoltage->getTimestep();
@@ -183,10 +182,9 @@ void VSDLoader::_computeStaticEventGeometry(const FlatInverseMapping& mapping,
             const auto& soma = morphology.getSoma();
             const auto pos = soma.getCentroid();
             const float radius = soma.getMeanRadius();
-            _circuitAABB.add(glm::vec3(pos.x(), pos.y(), pos.z()),
-                             radius);            
+            _circuitAABB.add(pos, radius);            
             for (uint16_t k = 0; k != compartments; ++k)
-                positions.push_back(glm::vec3(pos.x(), pos.y(), pos.z()));
+                positions.push_back(pos);
 
             continue;
         }
@@ -210,10 +208,10 @@ void VSDLoader::_computeStaticEventGeometry(const FlatInverseMapping& mapping,
 	assert(compartments == points.size());
         for (const auto& point : points)
         {
-            auto pos = point.get_sub_vector<3, 0>();
+            auto pos = glm::vec3(point);
             float radius = compartmentLength * .2f;
-            positions.push_back(glm::vec3(pos.x(), pos.y(), pos.z()));
-            _circuitAABB.add(glm::vec3(pos.x(), pos.y(), pos.z()), radius);
+            positions.push_back(pos);
+            _circuitAABB.add(pos, radius);
         }
     }
 }

diff --git a/emSim/Volume.h b/emSim/Volume.h
@@ -19,8 +19,9 @@
 
 #ifndef _Volume_h_
 #define _Volume_h_
-
+#define GLM_FORCE_CTOR_INIT
 #include <glm/glm.hpp>
+
 #include <string>
 #include <vector>
 

diff --git a/emSim/helpers.h b/emSim/helpers.h
@@ -24,6 +24,7 @@
 #include <memory>
 #include <sstream>
 
+#define GLM_FORCE_CTOR_INIT
 #include <glm/glm.hpp>
 
 namespace ems

diff --git a/glm b/glm
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
@@ -1,14 +1,20 @@
-# Copyright (c) BBP/EPFL 2011-2017, Stefan.Eilemann@epfl.ch
-# Change this number when adding tests to force a CMake run: 1
+## Copyright (c) BBP/EPFL 2011-2017, Stefan.Eilemann@epfl.ch
 
-# Includes the install_files function below
-include(InstallFiles)
+find_package(Boost REQUIRED COMPONENTS unit_test_framework)
 
-# TEST_LIBRARIES variable is used by the CommonCTest.cmake script to link against the given libraries
-set(TEST_LIBRARIES ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY} EMSimCommon)
+set(TESTS_SRC
+    samplePoints.cpp
+    volume.cpp
+)
 
-# CommonCTest, in the current folder recursively compiles targets for *.cpp files using TEST_LIBRARIES
-include(CommonCTest)
+foreach(FILE ${TESTS_SRC})
+    get_filename_component(NAME ${FILE} NAME_WE)
+    add_executable(${NAME} ${FILE})
 
-# Installs the compiled tests ${TEST_FILES} into the examples directory
-install_files(share/EMSim/tests FILES ${TEST_FILES} COMPONENT examples)
+    target_link_libraries(${NAME}
+        PRIVATE
+        ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}
+        EMSimCommon
+        )
+    add_test(NAME ${NAME} COMMAND ${NAME})
+endforeach()