Remove gmxpreprocess from include path

One step closer to the final goal of only having src/ there.
This wasn't even necessary except for a few rare cases.
Also cleaned up the cppcheck rules slightly.

Change-Id: Ifc65fbb48699d0e4bb5c55b90a2c41b0255d353d

diff --git a/doxygen/codelayout.md b/doxygen/codelayout.md
index 45673206cef02235e8b164528605bb60c47f279c..24bb7ae0c5737ef0b47599658dbc5ebe7f78556f 100644 (file)
--- a/doxygen/codelayout.md
+++ b/doxygen/codelayout.md
@@ -90,8 +90,8 @@ that do not follow the above rules.  The installed headers for these are in
 directories and move code into proper modules.
 
 For similar historical reasons, the include path also includes
 directories and move code into proper modules.
 
 For similar historical reasons, the include path also includes

-`src/gromacs/legacyheaders/` and `src/gromacs/gmxpreprocess/` (the latter only
-for part of the source).  New code should not depend on these.
+`src/gromacs/legacyheaders/`.  It is preferred that new code does not depend on
+this.

 
 Documentation organization
 ==========================
 
 Documentation organization
 ==========================

diff --git a/src/gromacs/gmxana/legacytests/CMakeLists.txt b/src/gromacs/gmxana/legacytests/CMakeLists.txt
index bbefdc1f240c2e86c9ae80582fa85a466667a198..c1eaefff4d8176ca8cf917d1bd971fb285b45ab4 100644 (file)
--- a/src/gromacs/gmxana/legacytests/CMakeLists.txt
+++ b/src/gromacs/gmxana/legacytests/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
 #
 # This file is part of the GROMACS molecular simulation package.
 #

-# Copyright (c) 2013, by the GROMACS development team, led by
+# Copyright (c) 2013,2014, by the GROMACS development team, led by

 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.


@@ -35,8 +35,6 @@
 set(testname "LegacyToolsTests")
 set(exename "legacy-tools-test")
 
 set(testname "LegacyToolsTests")
 set(exename "legacy-tools-test")
 

-include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/gmxpreprocess)
-

 gmx_build_unit_test(
     ${testname}
     ${exename}
 gmx_build_unit_test(
     ${testname}
     ${exename}

diff --git a/src/gromacs/gmxpreprocess/tests/CMakeLists.txt b/src/gromacs/gmxpreprocess/tests/CMakeLists.txt
index f57c5414df372a963f06e7fc2b054f775f41699d..1e305476112dd49f78478a2a7e87e109118fcbd3 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/CMakeLists.txt
+++ b/src/gromacs/gmxpreprocess/tests/CMakeLists.txt
@@ -35,8 +35,6 @@
 set(testname "PreprocessingTests")
 set(exename "preprocessing-tools-test")
 
 set(testname "PreprocessingTests")
 set(exename "preprocessing-tools-test")
 

-#include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/gmxpreprocess)
-

 gmx_build_unit_test(
     ${testname}
     ${exename}
 gmx_build_unit_test(
     ${testname}
     ${exename}

diff --git a/src/programs/CMakeLists.txt b/src/programs/CMakeLists.txt
index 91e97d372e8458f6f5ff593051e473f40556e4b4..cf5ba06456941ac1d04712bd86bfcf90cab8d844 100644 (file)
--- a/src/programs/CMakeLists.txt
+++ b/src/programs/CMakeLists.txt
@@ -32,8 +32,6 @@
 # To help us fund GROMACS development, we humbly ask that you cite
 # the research papers on the package. Check out http://www.gromacs.org.
 
 # To help us fund GROMACS development, we humbly ask that you cite
 # the research papers on the package. Check out http://www.gromacs.org.
 

-include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/gmxpreprocess)
-

 file(GLOB MDRUN_SOURCES mdrun/*.c mdrun/*.cpp)
 # make an "object library" that we can re-use for multiple targets
 add_library(mdrun_objlib OBJECT ${MDRUN_SOURCES})
 file(GLOB MDRUN_SOURCES mdrun/*.c mdrun/*.cpp)
 # make an "object library" that we can re-use for multiple targets
 add_library(mdrun_objlib OBJECT ${MDRUN_SOURCES})

diff --git a/src/programs/mdrun/md.c b/src/programs/mdrun/md.c
index 65307a83330da131f0c4aeb5fa7999464121e4b2..2b9760ed659696c93f78c4dfb04b0e112de1df27 100644 (file)
--- a/src/programs/mdrun/md.c
+++ b/src/programs/mdrun/md.c
@@ -71,7 +71,7 @@
 #include "coulomb.h"
 #include "constr.h"
 #include "shellfc.h"
 #include "coulomb.h"
 #include "constr.h"
 #include "shellfc.h"

-#include "compute_io.h"
+#include "gromacs/gmxpreprocess/compute_io.h"

 #include "checkpoint.h"
 #include "mtop_util.h"
 #include "sighandler.h"
 #include "checkpoint.h"
 #include "mtop_util.h"
 #include "sighandler.h"

diff --git a/src/programs/mdrun/membed.c b/src/programs/mdrun/membed.c
index a7b66b60fbda941d5fc59c3ae30eb614dc26ad40..5f64e5d84e29b97537d4f31c035ad263f0f0430e 100644 (file)
--- a/src/programs/mdrun/membed.c
+++ b/src/programs/mdrun/membed.c
@@ -56,7 +56,7 @@
 #include "membed.h"
 #include "pbc.h"
 #include "readinp.h"
 #include "membed.h"
 #include "pbc.h"
 #include "readinp.h"

-#include "readir.h"
+#include "gromacs/gmxpreprocess/readir.h"

 
 /* information about scaling center */
 typedef struct {
 
 /* information about scaling center */
 typedef struct {

diff --git a/src/programs/mdrun/runner.c b/src/programs/mdrun/runner.c
index add01471f37cb5e3493fef1a2f37fbb0ab25d053..f3d6ed3dda654263d791ee8584063fe3ec1b3027 100644 (file)
--- a/src/programs/mdrun/runner.c
+++ b/src/programs/mdrun/runner.c
@@ -72,7 +72,7 @@
 #include "txtdump.h"
 #include "gmx_detect_hardware.h"
 #include "gmx_omp_nthreads.h"
 #include "txtdump.h"
 #include "gmx_detect_hardware.h"
 #include "gmx_omp_nthreads.h"

-#include "calc_verletbuf.h"
+#include "gromacs/gmxpreprocess/calc_verletbuf.h"

 #include "gmx_fatal_collective.h"
 #include "membed.h"
 #include "macros.h"
 #include "gmx_fatal_collective.h"
 #include "membed.h"
 #include "macros.h"

diff --git a/src/programs/mdrun/tests/CMakeLists.txt b/src/programs/mdrun/tests/CMakeLists.txt
index 00acc25fc43ae8f7db6b769df5bf8e82512378e7..4da6ce4ac7ce1c88340c165a1b33fe861652c9a2 100644 (file)
--- a/src/programs/mdrun/tests/CMakeLists.txt
+++ b/src/programs/mdrun/tests/CMakeLists.txt
@@ -35,8 +35,6 @@
 set(testname "MdrunTests")
 set(exename "mdrun-test")
 
 set(testname "MdrunTests")
 set(exename "mdrun-test")
 

-include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/gmxpreprocess)
-

 gmx_build_unit_test(
     ${testname}
     ${exename}
 gmx_build_unit_test(
     ${testname}
     ${exename}

diff --git a/tests/CppCheck.cmake b/tests/CppCheck.cmake
index 918b6304d47e2dc53a9d2ccb87ba703e06a334bc..0e3aeab8f79e9652051acd52ecf959feeea0f7ed 100644 (file)
--- a/tests/CppCheck.cmake
+++ b/tests/CppCheck.cmake
@@ -74,8 +74,6 @@ if (CPPCHECK_EXECUTABLE AND UNIX)
         --quiet
         ${_outputopt})
     set(_c_flags
         --quiet
         ${_outputopt})
     set(_c_flags

-        -I src/gromacs/gmxpreprocess
-        -I src/programs/mdrun

         --suppress=variableScope
         --suppress=unnecessaryForwardDeclaration
         --suppress=unusedVariable
         --suppress=variableScope
         --suppress=unnecessaryForwardDeclaration
         --suppress=unusedVariable


@@ -84,7 +82,7 @@ if (CPPCHECK_EXECUTABLE AND UNIX)
         --suppress=invalidscanf
         --suppress=sizeofCalculation
         --suppress=missingInclude:src/programs/mdrun/gmx_gpu_utils/gmx_gpu_utils.cu
         --suppress=invalidscanf
         --suppress=sizeofCalculation
         --suppress=missingInclude:src/programs/mdrun/gmx_gpu_utils/gmx_gpu_utils.cu

-       --suppress=*:src/external/Random123-1.08/include/Random123/features/compilerfeatures.h
+        --suppress=*:src/external/Random123-1.08/include/Random123/features/compilerfeatures.h

         --inline-suppr)
     set(_cxx_flags
         -D__cplusplus
         --inline-suppr)
     set(_cxx_flags
         -D__cplusplus