From 951d5a3f6052de96220c190280d6e20fb22ada46 Mon Sep 17 00:00:00 2001
From: Magnus Lundborg <lundborg.magnus@gmail.com>
Date: Tue, 14 Jan 2014 09:06:39 +0100
Subject: Use relative paths for includes.


diff --git a/CMakeLists.txt b/CMakeLists.txt
index 388d2af..a0f917d 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -9,7 +9,6 @@ endif()
 project(TNG_IO)
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
-include_directories(${CMAKE_CURRENT_SOURCE_DIR}/include)
 
 option(BUILD_SHARED_LIBS "Enable shared libraries" ON)
 
diff --git a/include/compression/fixpoint.h b/include/compression/fixpoint.h
index f448dbf..6be7482 100644
--- a/include/compression/fixpoint.h
+++ b/include/compression/fixpoint.h
@@ -11,7 +11,7 @@
 #ifndef FIXPOINT_H
 #define FIXPOINT_H
 
-#include "compression/my64bit.h"
+#include "../compression/my64bit.h"
 
 /* There are at least 32 bits available in a long. */
 typedef unsigned long fix_t;
diff --git a/include/compression/my64bit.h b/include/compression/my64bit.h
index 2959a8d..c17a4a9 100644
--- a/include/compression/my64bit.h
+++ b/include/compression/my64bit.h
@@ -18,7 +18,7 @@ typedef uint64_t my_uint64_t;
 #define HAVE64BIT
 #else /* USE_STD_INTTYPES */
 /* The USE_WINDOWS symbol should be automatically defined in tng_compress.h */
-#include "compression/tng_compress.h"
+#include "../compression/tng_compress.h"
 #ifdef USE_WINDOWS
 typedef __int64 my_int64_t;
 typedef unsigned __int64 my_uint64_t;
diff --git a/include/compression/warnmalloc.h b/include/compression/warnmalloc.h
index 46e7d52..4444271 100644
--- a/include/compression/warnmalloc.h
+++ b/include/compression/warnmalloc.h
@@ -12,7 +12,7 @@
 #ifndef WARNMALLOC_H
 #define WARNMALLOC_H
 
-#include "compression/tng_compress.h"
+#include "../compression/tng_compress.h"
 
 void DECLSPECDLLEXPORT *Ptngc_warnmalloc_x(size_t size, char *file, int line);
 
diff --git a/src/compression/bwlzh.c b/src/compression/bwlzh.c
index 517828c..de009d9 100644
--- a/src/compression/bwlzh.c
+++ b/src/compression/bwlzh.c
@@ -12,15 +12,15 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#include "compression/warnmalloc.h"
-#include "compression/tng_compress.h"
-#include "compression/bwlzh.h"
-#include "compression/dict.h"
-#include "compression/vals16.h"
-#include "compression/rle.h"
-#include "compression/mtf.h"
-#include "compression/bwt.h"
-#include "compression/lz77.h"
+#include "../../include/compression/warnmalloc.h"
+#include "../../include/compression/tng_compress.h"
+#include "../../include/compression/bwlzh.h"
+#include "../../include/compression/dict.h"
+#include "../../include/compression/vals16.h"
+#include "../../include/compression/rle.h"
+#include "../../include/compression/mtf.h"
+#include "../../include/compression/bwt.h"
+#include "../../include/compression/lz77.h"
 
 #if 0
 #define SHOWIT
diff --git a/src/compression/bwt.c b/src/compression/bwt.c
index 88eb444..66d3ecf 100644
--- a/src/compression/bwt.c
+++ b/src/compression/bwt.c
@@ -12,8 +12,8 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#include "compression/warnmalloc.h"
-#include "compression/bwt.h"
+#include "../../include/compression/warnmalloc.h"
+#include "../../include/compression/bwt.h"
 
 #if 0
 #define SHOWIT
diff --git a/src/compression/coder.c b/src/compression/coder.c
index 905e45d..cf89140 100644
--- a/src/compression/coder.c
+++ b/src/compression/coder.c
@@ -11,10 +11,10 @@
 
 #include <stdio.h>
 #include <stdlib.h>
-#include "compression/tng_compress.h"
-#include "compression/bwlzh.h"
-#include "compression/coder.h"
-#include "compression/warnmalloc.h"
+#include "../../include/compression/tng_compress.h"
+#include "../../include/compression/bwlzh.h"
+#include "../../include/compression/coder.h"
+#include "../../include/compression/warnmalloc.h"
 
 #ifndef USE_WINDOWS
 #if defined(WIN32) || defined(_WIN32) || defined(WIN64) || defined(_WIN64)
diff --git a/src/compression/dict.c b/src/compression/dict.c
index 5fb3c01..24e6ae7 100644
--- a/src/compression/dict.c
+++ b/src/compression/dict.c
@@ -10,7 +10,7 @@
 
 
 #include <string.h>
-#include "compression/dict.h"
+#include "../../include/compression/dict.h"
 
 void Ptngc_comp_canonical_dict(unsigned int *dict, int *ndict)
 {
diff --git a/src/compression/fixpoint.c b/src/compression/fixpoint.c
index 696cf48..17fe6e8 100644
--- a/src/compression/fixpoint.c
+++ b/src/compression/fixpoint.c
@@ -10,7 +10,7 @@
 
 #include <stdio.h>
 #include <math.h>
-#include "compression/fixpoint.h"
+#include "../../include/compression/fixpoint.h"
 
 #define MAX32BIT 4294967295UL
 #define MAX31BIT 2147483647UL
diff --git a/src/compression/huffman.c b/src/compression/huffman.c
index bda2126..2abcbcf 100644
--- a/src/compression/huffman.c
+++ b/src/compression/huffman.c
@@ -12,9 +12,9 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#include "compression/warnmalloc.h"
-#include "compression/merge_sort.h"
-#include "compression/huffman.h"
+#include "../../include/compression/warnmalloc.h"
+#include "../../include/compression/merge_sort.h"
+#include "../../include/compression/huffman.h"
 
 #define MAX_HUFFMAN_LEN 31
 
diff --git a/src/compression/huffmem.c b/src/compression/huffmem.c
index 249fa54..183eff1 100644
--- a/src/compression/huffmem.c
+++ b/src/compression/huffmem.c
@@ -11,13 +11,13 @@
 
 #include <stdio.h>
 #include <stdlib.h>
-#include "compression/warnmalloc.h"
-#include "compression/tng_compress.h"
-#include "compression/bwlzh.h"
-#include "compression/huffman.h"
-#include "compression/dict.h"
-#include "compression/rle.h"
-#include "compression/vals16.h"
+#include "../../include/compression/warnmalloc.h"
+#include "../../include/compression/tng_compress.h"
+#include "../../include/compression/bwlzh.h"
+#include "../../include/compression/huffman.h"
+#include "../../include/compression/dict.h"
+#include "../../include/compression/rle.h"
+#include "../../include/compression/vals16.h"
 
 int Ptngc_comp_huff_buflen(int nvals)
 {
diff --git a/src/compression/lz77.c b/src/compression/lz77.c
index 51dd301..17b147c 100644
--- a/src/compression/lz77.c
+++ b/src/compression/lz77.c
@@ -12,9 +12,9 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#include "compression/warnmalloc.h"
-#include "compression/bwt.h"
-#include "compression/lz77.h"
+#include "../../include/compression/warnmalloc.h"
+#include "../../include/compression/bwt.h"
+#include "../../include/compression/lz77.h"
 
 /* This is a simple Lempel-Ziv-77 compressor. It has not been set up
    to remove every possible repeating pattern, but it might be better
diff --git a/src/compression/merge_sort.c b/src/compression/merge_sort.c
index 04c20ad..7cb9837 100644
--- a/src/compression/merge_sort.c
+++ b/src/compression/merge_sort.c
@@ -12,8 +12,8 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#include "compression/warnmalloc.h"
-#include "compression/merge_sort.h"
+#include "../../include/compression/warnmalloc.h"
+#include "../../include/compression/merge_sort.h"
 
 static void ms_inner(void *base, size_t size,
              size_t start, size_t end,
diff --git a/src/compression/mtf.c b/src/compression/mtf.c
index 5f96d62..d6eaf30 100644
--- a/src/compression/mtf.c
+++ b/src/compression/mtf.c
@@ -10,8 +10,8 @@
 
 
 #include <stdlib.h>
-#include "compression/warnmalloc.h"
-#include "compression/mtf.h"
+#include "../../include/compression/warnmalloc.h"
+#include "../../include/compression/mtf.h"
 
 /* "Partial" MTF. Byte based. */
 /* Move to front coding.
diff --git a/src/compression/rle.c b/src/compression/rle.c
index 9663534..adaee65 100644
--- a/src/compression/rle.c
+++ b/src/compression/rle.c
@@ -9,7 +9,7 @@
  */
 
 
-#include "compression/rle.h"
+#include "../../include/compression/rle.h"
 
 static void add_rle(unsigned int *rle,
                     int v,int nsim,
diff --git a/src/compression/tng_compress.c b/src/compression/tng_compress.c
index 3a378d1..6174e8f 100644
--- a/src/compression/tng_compress.c
+++ b/src/compression/tng_compress.c
@@ -11,9 +11,9 @@
 #include <stdlib.h>
 #include <string.h>
 #include <math.h>
-#include "compression/tng_compress.h"
-#include "compression/coder.h"
-#include "compression/fixpoint.h"
+#include "../../include/compression/tng_compress.h"
+#include "../../include/compression/coder.h"
+#include "../../include/compression/fixpoint.h"
 
 /* Please see tng_compress.h for info on how to call these routines. */
 
diff --git a/src/compression/vals16.c b/src/compression/vals16.c
index ab65953..c4ed635 100644
--- a/src/compression/vals16.c
+++ b/src/compression/vals16.c
@@ -9,7 +9,7 @@
  */
 
 
-#include "compression/vals16.h"
+#include "../../include/compression/vals16.h"
 
 /* Coding 32 bit ints in sequences of 16 bit ints. Worst case
    the output is 3*nvals long. */
diff --git a/src/compression/warnmalloc.c b/src/compression/warnmalloc.c
index c05be20..36f0d9f 100644
--- a/src/compression/warnmalloc.c
+++ b/src/compression/warnmalloc.c
@@ -11,8 +11,8 @@
 
 #include <stdio.h>
 #include <stdlib.h>
-#include "compression/tng_compress.h"
-#include "compression/warnmalloc.h"
+#include "../../include/compression/tng_compress.h"
+#include "../../include/compression/warnmalloc.h"
 
 void DECLSPECDLLEXPORT *Ptngc_warnmalloc_x(size_t size, char *file, int line)
 {
diff --git a/src/compression/widemuldiv.c b/src/compression/widemuldiv.c
index 3c2ac79..7d03c57 100644
--- a/src/compression/widemuldiv.c
+++ b/src/compression/widemuldiv.c
@@ -12,15 +12,15 @@
 #include <stdio.h>
 #include <stdlib.h>
 
-#include "compression/tng_compress.h"
+#include "../../include/compression/tng_compress.h"
 
 /* 64 bit integers are not required in this part of the program. But
    they improve the running speed if present. If 64 bit integers are
    available define the symbol HAVE64BIT. It should get automatically
    defined by the defines in my64bit.h */
-#include "compression/my64bit.h"
+#include "../../include/compression/my64bit.h"
 
-#include "compression/widemuldiv.h"
+#include "../../include/compression/widemuldiv.h"
 
 #ifndef TRAJNG_X86_GCC_INLINE_MULDIV
 #if defined(__GNUC__) && defined(__i386__)
diff --git a/src/compression/xtc2.c b/src/compression/xtc2.c
index b39db79..bbd45e9 100644
--- a/src/compression/xtc2.c
+++ b/src/compression/xtc2.c
@@ -19,9 +19,9 @@
 #include <stdlib.h>
 #include <string.h>
 #include <math.h>
-#include "compression/coder.h"
-#include "compression/widemuldiv.h"
-#include "compression/warnmalloc.h"
+#include "../../include/compression/coder.h"
+#include "../../include/compression/widemuldiv.h"
+#include "../../include/compression/warnmalloc.h"
 
 /* Generated by gen_magic.py */
 #define MAX_MAGIC  92
diff --git a/src/compression/xtc3.c b/src/compression/xtc3.c
index 942839d..95483b3 100644
--- a/src/compression/xtc3.c
+++ b/src/compression/xtc3.c
@@ -23,9 +23,9 @@
 #include <stdlib.h>
 #include <string.h>
 #include <math.h>
-#include "compression/warnmalloc.h"
-#include "compression/widemuldiv.h"
-#include "compression/bwlzh.h"
+#include "../../include/compression/warnmalloc.h"
+#include "../../include/compression/widemuldiv.h"
+#include "../../include/compression/bwlzh.h"
 
 static const double iflipgaincheck=0.89089871814033927; /*  1./(2**(1./6)) */
 
diff --git a/src/lib/md5.c b/src/lib/md5.c
index bd11de3..ea8bb37 100644
--- a/src/lib/md5.c
+++ b/src/lib/md5.c
@@ -75,7 +75,7 @@
   1999-05-03 lpd Original version.
  */
 
-#include "md5.h"
+#include "../../include/md5.h"
 #include <string.h>
 
 #undef BYTE_ORDER	/* 1 = big-endian, -1 = little-endian, 0 = unknown */
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c
index a9e1520..8e1e7ed 100644
--- a/src/lib/tng_io.c
+++ b/src/lib/tng_io.c
@@ -24,9 +24,9 @@
 #include <zlib.h>
 #endif
 
-#include "tng_io.h"
-#include "md5.h"
-#include "compression/tng_compress.h"
+#include "../../include/tng_io.h"
+#include "../../include/md5.h"
+#include "../../include/compression/tng_compress.h"
 
 
 struct tng_bond {
diff --git a/src/lib/tng_io_fortran.c b/src/lib/tng_io_fortran.c
index 9c3e551..f6101be 100644
--- a/src/lib/tng_io_fortran.c
+++ b/src/lib/tng_io_fortran.c
@@ -11,7 +11,7 @@
  * modify it under the terms of the Revised BSD License.
  */
 
-#include "tng_io.h"
+#include "../../include/tng_io.h"
 
 /* The following is for calling the library from fortran */
 
diff --git a/src/tests/tng_io_read_pos.c b/src/tests/tng_io_read_pos.c
index 3ff7660..079cad7 100644
--- a/src/tests/tng_io_read_pos.c
+++ b/src/tests/tng_io_read_pos.c
@@ -17,7 +17,7 @@
 
 #include <stdlib.h>
 #include <stdio.h>
-#include "tng_io.h"
+#include "../../include/tng_io.h"
 
 int main(int argc, char **argv)
 {
diff --git a/src/tests/tng_io_read_pos_util.c b/src/tests/tng_io_read_pos_util.c
index 6dd6524..64df9df 100644
--- a/src/tests/tng_io_read_pos_util.c
+++ b/src/tests/tng_io_read_pos_util.c
@@ -19,7 +19,7 @@
 
 #include <stdlib.h>
 #include <stdio.h>
-#include "tng_io.h"
+#include "../../include/tng_io.h"
 
 int main(int argc, char **argv)
 {
diff --git a/src/tests/tng_io_testing.c b/src/tests/tng_io_testing.c
index 3899b15..8d8a68a 100644
--- a/src/tests/tng_io_testing.c
+++ b/src/tests/tng_io_testing.c
@@ -17,7 +17,7 @@
 
 #include <stdlib.h>
 #include <string.h>
-#include "tng_io.h"
+#include "../../include/tng_io.h"
 
 static tng_function_status tng_test_setup_molecules(tng_trajectory_t traj)
 {
diff --git a/src/tests/tng_parallel_read.c b/src/tests/tng_parallel_read.c
index 598d42a..95d1c9a 100644
--- a/src/tests/tng_parallel_read.c
+++ b/src/tests/tng_parallel_read.c
@@ -15,7 +15,7 @@
 
 #include <stdlib.h>
 #include <stdio.h>
-#include "tng_io.h"
+#include "../../include/tng_io.h"
 
 
 /* N.B. this code is for testing parallel reading of trajectory frame sets. The
-- 
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