From: Teemu Murtola <teemu.murtola@gmail.com>
Date: Mon, 24 Mar 2014 15:44:30 +0000 (+0200)
Subject: Remove gmxpreprocess from include path
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=13350954cdd1daa2f1b9034d12a7aabc6920508d;p=alexxy%2Fgromacs.git

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 45673206ce..24bb7ae0c5 100644
--- 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
-`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
 ==========================
diff --git a/src/gromacs/gmxana/legacytests/CMakeLists.txt b/src/gromacs/gmxana/legacytests/CMakeLists.txt
index bbefdc1f24..c1eaefff4d 100644
--- 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.
 #
-# 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.
@@ -35,8 +35,6 @@
 set(testname "LegacyToolsTests")
 set(exename "legacy-tools-test")
 
-include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/gmxpreprocess)
-
 gmx_build_unit_test(
     ${testname}
     ${exename}
diff --git a/src/gromacs/gmxpreprocess/tests/CMakeLists.txt b/src/gromacs/gmxpreprocess/tests/CMakeLists.txt
index f57c5414df..1e30547611 100644
--- 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")
 
-#include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/gmxpreprocess)
-
 gmx_build_unit_test(
     ${testname}
     ${exename}
diff --git a/src/programs/CMakeLists.txt b/src/programs/CMakeLists.txt
index 91e97d372e..cf5ba06456 100644
--- 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.
 
-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})
diff --git a/src/programs/mdrun/md.c b/src/programs/mdrun/md.c
index 65307a8333..2b9760ed65 100644
--- 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 "compute_io.h"
+#include "gromacs/gmxpreprocess/compute_io.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 a7b66b60fb..5f64e5d84e 100644
--- 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 "readir.h"
+#include "gromacs/gmxpreprocess/readir.h"
 
 /* information about scaling center */
 typedef struct {
diff --git a/src/programs/mdrun/runner.c b/src/programs/mdrun/runner.c
index add01471f3..f3d6ed3dda 100644
--- 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 "calc_verletbuf.h"
+#include "gromacs/gmxpreprocess/calc_verletbuf.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 00acc25fc4..4da6ce4ac7 100644
--- 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")
 
-include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/gmxpreprocess)
-
 gmx_build_unit_test(
     ${testname}
     ${exename}
diff --git a/tests/CppCheck.cmake b/tests/CppCheck.cmake
index 918b6304d4..0e3aeab8f7 100644
--- a/tests/CppCheck.cmake
+++ b/tests/CppCheck.cmake
@@ -74,8 +74,6 @@ if (CPPCHECK_EXECUTABLE AND UNIX)
         --quiet
         ${_outputopt})
     set(_c_flags
-        -I src/gromacs/gmxpreprocess
-        -I src/programs/mdrun
         --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=*: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