Build System Tweaks (BhallaLab#309)

* Fixes as suggested by PyLint. Added a target pylint in cmake file. * Do pylint testing on OSX. * Fixed import statement. * Fixed pylint errors, removed unneccessary file. * Test of available attributes in moose. * Install python-libsbml and pyneuroml on OSX before running pylint. * Removed temporary attributes from test. * plot_utils is not so important. It failes when python-tk not found. * Fixed boost segfault with dense solver. Also remove GSL specific attrib from the test. * Tweak to cmake on OSX. New clang-llvm compiler options added to ignore unused pragmas. Import hhfit only when required. * None of thest depends on matplotlib anymore. Added one more rdesineur tests from moose-examples scripts. * Fix travis: Install python-tk and python3-tk on travis. * TIDY UP: basecode and benchmarks can be built independantly. [skip ci] * Compiles as standalone. [skip ci] * One more directory is standalone. * Diffusion dir is standalone as well [skip ci] * hsolve built in isolation as well [skip ci] * ksolve is now tidied up [skip ci] * needs local testing now. * This passes locally with python3. * include_guard is not in cmake2.8. * More more fixes identified by clang-check. * Added Cell.cpp to build system. This class is probably broken but good to keep it included.
upibhalla · Oct 2, 2018 · d274993 · d274993
1 parent 88bcf07
commit d274993
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -66,15 +66,6 @@ add_custom_target(uninstall
 # This is for testing purpose.
 link_directories(${CMAKE_CURRENT_BINARY_DIR})
 
-################################# OS Specific ##################################
-message(STATUS "Operating system: ${CMAKE_SYSTEM_NAME}")
-if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
-    CMAKE_POLICY(SET CMP0042 NEW)
-    set(MACOSX TRUE)
-else()
-    set(MACOSX FALSE)
-endif()
-
 ################################ CMAKE OPTIONS ##################################
 option(WITH_NSDF            "Enable NSDF support. Requires hdf5" OFF )
 

diff --git a/CheckCXXCompiler.cmake b/CheckCXXCompiler.cmake
@@ -1,5 +1,8 @@
-########################### COMPILER MACROS #####################################
+if(COMPILER_IS_TESTED)
+    return()
+endif()
 
+########################### COMPILER MACROS #####################################
 include(CheckCXXCompilerFlag)
 CHECK_CXX_COMPILER_FLAG( "-std=c++11" COMPILER_SUPPORTS_CXX11 )
 CHECK_CXX_COMPILER_FLAG( "-std=c++0x" COMPILER_SUPPORTS_CXX0X )
@@ -34,12 +37,11 @@ if(COMPILER_SUPPORT_UNUSED_BUT_SET_VARIABLE_NO_WARN)
 endif(COMPILER_SUPPORT_UNUSED_BUT_SET_VARIABLE_NO_WARN)
 
 if(COMPILER_SUPPORTS_CXX11)
-    message(STATUS "Your compiler supports c++11 features. Enabling it")
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
     add_definitions( -DENABLE_CPP11 )
     if(APPLE)
         #set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++" )
-        message(STATUS "NOTE: Making clang to inline more aggresively" )
+        # message(STATUS "NOTE: Making clang to inline more aggresively" )
         add_definitions( -mllvm -inline-threshold=1000 )
     endif(APPLE)
 else(COMPILER_SUPPORTS_CXX11)
@@ -50,4 +52,4 @@ else(COMPILER_SUPPORTS_CXX11)
         ")
 endif(COMPILER_SUPPORTS_CXX11)
 
-
+set(COMPILER_IS_TESTED ON)
diff --git a/basecode/Cinfo.cpp b/basecode/Cinfo.cpp
@@ -202,14 +202,6 @@ const Cinfo* Cinfo::find( const string& name )
 	map<string, Cinfo*>::iterator i = cinfoMap().find(name);
 	if ( i != cinfoMap().end() )
 		return i->second;
-
-#ifdef  RESULT_CHECK
-        stringstream ss;
-        ss << "+ " << name << " not found. Available names are " << endl;
-        ss << mapToString<string, Cinfo*>( cinfoMap() );
-        dump(ss.str(), "DEBUG");
-#endif     /* -----  not RESULT_CHECK  ----- */
-
 	return 0;
 }
 

diff --git a/basecode/Eref.h b/basecode/Eref.h
@@ -10,19 +10,6 @@
 #ifndef _EREF_H
 #define _EREF_H
 
-#ifdef  CYMOOSE
-
-#include <iostream>
-#include <vector>
-using namespace std;
-
-class Element;
-class Id;
-class ObjId;
-class MsgDigest;
-
-#endif     /* -----  CYMOOSE  ----- */
-
 class Eref
 {
 public:

diff --git a/basecode/SrcFinfo.h b/basecode/SrcFinfo.h
@@ -9,13 +9,6 @@
 #ifndef _SRC_FINFO_H
 #define _SRC_FINFO_H
 
-#ifdef  CYMOOSE
-
-#include "../basecode/Finfo.h"
-#include "../basecode/header.h"
-
-#endif     /* -----  CYMOOSE  ----- */
-
 /**
  * This set of classes define Message Sources. Their main job is to supply
  * a type-safe send operation, and to provide typechecking for it.

diff --git a/basecode/main.cpp b/basecode/main.cpp
@@ -10,18 +10,10 @@
 #include "header.h"
 #include "SparseMatrix.h"
 
-#ifndef WIN32
-#include <sys/time.h>
-#else
 #include <time.h>
-#endif
 #include <math.h>
 #include <queue>
-#ifdef WIN32
-#include "../external/xgetopt/XGetopt.h"
-#else
 #include <unistd.h> // for getopt
-#endif
 #include "../scheduling/Clock.h"
 #include "../msg/DiagonalMsg.h"
 #include "../msg/SparseMsg.h"
@@ -93,12 +85,6 @@ extern void mooseBenchmarks( unsigned int option );
 unsigned int getNumCores()
 {
     unsigned int numCPU = 0;
-#ifdef WIN_32
-    SYSTEM_INFO sysinfo;
-    GetSystemInfo( &sysinfo );
-
-    numCPU = sysinfo.dwNumberOfProcessors;
-#endif
 
 #ifdef LINUX
     numCPU = sysconf( _SC_NPROCESSORS_ONLN );

diff --git a/benchmarks/CMakeLists.txt b/benchmarks/CMakeLists.txt
@@ -1,5 +1,7 @@
-include_directories(../msg)
-include_directories(../basecode)
+cmake_minimum_required(VERSION 2.8)
+
+include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake )
+
 add_library(benchmarks
     benchmarks.cpp
     kineticMarks.cpp

diff --git a/benchmarks/kineticMarks.cpp b/benchmarks/kineticMarks.cpp
@@ -7,7 +7,7 @@
 ** See the file COPYING.LIB for the full notice.
 **********************************************************************/
 
-#include "header.h"
+#include "../basecode/header.h"
 #include "../shell/Shell.h"
 
 /// Small model, long runtime.

diff --git a/biophysics/CMakeLists.txt b/biophysics/CMakeLists.txt
@@ -1,53 +1,53 @@
-include_directories(../basecode ../synapse ../utility ../)
-include_directories(../external/muparser/include)
+cmake_minimum_required(VERSION 2.8)
+include(${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake)
 
 if(WITH_GSL)
     include_directories(${GSL_INCLUDE_DIRS})
 endif(WITH_GSL)
 
 set(BIOPHYSICS_SRCS
-	IntFire.cpp
-	SpikeGen.cpp
-        RandSpike.cpp
-	CompartmentDataHolder.cpp
-	CompartmentBase.cpp
-	Compartment.cpp
-	SymCompartment.cpp
-        GapJunction.cpp
-	ChanBase.cpp
-        ChanCommon.cpp
-	HHChannel.cpp
-        HHChannelBase.cpp
-        HHChannel2D.cpp
-	HHGate.cpp
-	HHGate2D.cpp
-	HHChannel2D.cpp
-        CaConcBase.cpp
-	CaConc.cpp
-	MgBlock.cpp
-        Nernst.cpp
-	Neuron.cpp
-	ReadCell.cpp
-        SwcSegment.cpp
-        ReadSwc.cpp
-	SynChan.cpp
-        NMDAChan.cpp
-	testBiophysics.cpp
-	IzhikevichNrn.cpp
-	DifShellBase.cpp
-	DifShell.cpp
-	DifBufferBase.cpp
-	DifBuffer.cpp
-	MMPump.cpp
-	Leakage.cpp
-	VectorTable.cpp
-	MarkovRateTable.cpp
-	MarkovChannel.cpp
-	MatrixOps.cpp
-	MarkovSolverBase.cpp
-	MarkovSolver.cpp
-	VClamp.cpp
-        Spine.cpp
+    IntFire.cpp
+    SpikeGen.cpp
+    RandSpike.cpp
+    CompartmentDataHolder.cpp
+    CompartmentBase.cpp
+    Compartment.cpp
+    SymCompartment.cpp
+    GapJunction.cpp
+    ChanBase.cpp
+    ChanCommon.cpp
+    HHChannel.cpp
+    HHChannelBase.cpp
+    HHChannel2D.cpp
+    HHGate.cpp
+    HHGate2D.cpp
+    HHChannel2D.cpp
+    CaConcBase.cpp
+    CaConc.cpp
+    MgBlock.cpp
+    Nernst.cpp
+    Neuron.cpp
+    ReadCell.cpp
+    SwcSegment.cpp
+    ReadSwc.cpp
+    SynChan.cpp
+    NMDAChan.cpp
+    testBiophysics.cpp
+    IzhikevichNrn.cpp
+    DifShellBase.cpp
+    DifShell.cpp
+    DifBufferBase.cpp
+    DifBuffer.cpp
+    MMPump.cpp
+    Leakage.cpp
+    VectorTable.cpp
+    MarkovRateTable.cpp
+    MarkovChannel.cpp
+    MatrixOps.cpp
+    MarkovSolverBase.cpp
+    MarkovSolver.cpp
+    VClamp.cpp
+    Spine.cpp
     )
 
 if(WITH_GSL)

diff --git a/biophysics/CaConc.cpp b/biophysics/CaConc.cpp
@@ -7,8 +7,7 @@
 ** See the file COPYING.LIB for the full notice.
 **********************************************************************/
 
-// #include <cfloat>
-#include "header.h"
+#include "../basecode/header.h"
 #include "CaConcBase.h"
 #include "CaConc.h"
 

diff --git a/biophysics/CaConcBase.cpp b/biophysics/CaConcBase.cpp
@@ -8,8 +8,8 @@
  **********************************************************************/
 
 // #include <cfloat>
-#include "header.h"
-#include "ElementValueFinfo.h"
+#include "../basecode/header.h"
+#include "../basecode/ElementValueFinfo.h"
 #include "CaConcBase.h"
 
 ///////////////////////////////////////////////////////

diff --git a/biophysics/ChanBase.cpp b/biophysics/ChanBase.cpp
@@ -7,8 +7,8 @@
 ** See the file COPYING.LIB for the full notice.
 **********************************************************************/
 
-#include "header.h"
-#include "ElementValueFinfo.h"
+#include "../basecode/header.h"
+#include "../basecode/ElementValueFinfo.h"
 #include "ChanBase.h"
 
 SrcFinfo1< double >* ChanBase::permeability()

diff --git a/biophysics/ChanCommon.cpp b/biophysics/ChanCommon.cpp
@@ -7,7 +7,7 @@
 ** See the file COPYING.LIB for the full notice.
 **********************************************************************/
 
-#include "header.h"
+#include "../basecode/header.h"
 #include "ChanBase.h"
 #include "ChanCommon.h"
 

diff --git a/biophysics/CompartmentBase.cpp b/biophysics/CompartmentBase.cpp
@@ -7,8 +7,8 @@
 ** See the file COPYING.LIB for the full notice.
 **********************************************************************/
 
-#include "header.h"
-#include "ElementValueFinfo.h"
+#include "../basecode/header.h"
+#include "../basecode/ElementValueFinfo.h"
 #include "CompartmentBase.h"
 #include "CompartmentDataHolder.h"
 #include "../shell/Wildcard.h"

diff --git a/biophysics/CompartmentDataHolder.cpp b/biophysics/CompartmentDataHolder.cpp
@@ -6,7 +6,7 @@
 ** GNU Lesser General Public License version 2.1
 ** See the file COPYING.LIB for the full notice.
 **********************************************************************/
-#include "header.h"
+#include "../basecode/header.h"
 #include "CompartmentBase.h"
 #include "CompartmentDataHolder.h"
 // static func

diff --git a/biophysics/DifBuffer.cpp b/biophysics/DifBuffer.cpp
@@ -45,10 +45,10 @@
 
 // Code:
 
-#include "header.h"
+#include "../basecode/header.h"
 #include "DifBufferBase.h"
 #include "DifBuffer.h"
-#include "ElementValueFinfo.h"
+#include "../basecode/ElementValueFinfo.h"
 #include "../utility/numutil.h"
 #include <cmath>
 const double DifBuffer::EPSILON = 1.0e-10;

diff --git a/biophysics/DifBufferBase.cpp b/biophysics/DifBufferBase.cpp
@@ -1,6 +1,6 @@
-#include "header.h"
+#include "../basecode/header.h"
 #include "DifBufferBase.h"
-#include "ElementValueFinfo.h"
+#include "../basecode/ElementValueFinfo.h"
 #include "../utility/numutil.h"
 #include <cmath>
 

diff --git a/biophysics/DifShell.cpp b/biophysics/DifShell.cpp
@@ -8,7 +8,7 @@
  ** See the file COPYING.LIB for the full notice.
  **********************************************************************/
 
-#include "header.h"
+#include "../basecode/header.h"
 #include "DifShellBase.h"
 #include "DifShell.h"
 

diff --git a/biophysics/DifShellBase.cpp b/biophysics/DifShellBase.cpp
@@ -8,9 +8,9 @@
  ** See the file COPYING.LIB for the full notice.
  ****/
 
-#include "header.h"
+#include "../basecode/header.h"
 #include "DifShellBase.h"
-#include "ElementValueFinfo.h"
+#include "../basecode/ElementValueFinfo.h"
 
 SrcFinfo1< double >* DifShellBase::concentrationOut()
 {

diff --git a/biophysics/GapJunction.cpp b/biophysics/GapJunction.cpp
@@ -45,7 +45,7 @@
 
 // Code:
 
-#include "header.h"
+#include "../basecode/header.h"
 #include "GapJunction.h"
 
 static SrcFinfo2< double, double >* channel1Out()

diff --git a/biophysics/HHChannel.cpp b/biophysics/HHChannel.cpp
@@ -7,8 +7,8 @@
 ** See the file COPYING.LIB for the full notice.
 **********************************************************************/
 
-#include "header.h"
-#include "ElementValueFinfo.h"
+#include "../basecode/header.h"
+#include "../basecode/ElementValueFinfo.h"
 #include "HHGate.h"
 #include "ChanBase.h"
 #include "ChanCommon.h"

diff --git a/biophysics/HHChannel2D.cpp b/biophysics/HHChannel2D.cpp
@@ -7,8 +7,8 @@
 ** See the file COPYING.LIB for the full notice.
 **********************************************************************/
 
-#include "header.h"
-#include "ElementValueFinfo.h"
+#include "../basecode/header.h"
+#include "../basecode/ElementValueFinfo.h"
 #include "../builtins/Interpol2D.h"
 #include "ChanBase.h"
 #include "ChanCommon.h"

diff --git a/biophysics/HHChannelBase.cpp b/biophysics/HHChannelBase.cpp
@@ -7,8 +7,8 @@
 ** See the file COPYING.LIB for the full notice.
 **********************************************************************/
 
-#include "header.h"
-#include "ElementValueFinfo.h"
+#include "../basecode/header.h"
+#include "../basecode/ElementValueFinfo.h"
 #include "HHGate.h"
 #include "ChanBase.h"
 #include "HHChannelBase.h"