Changes all #include "esl_config.h" to #include <esl_config.h>

If you are using both a source tree and build tree(s), and you have
done a `configure` in both, build tree compilation includes the wrong
autoconf config.h file, from the source tree.

That's because having `#include "config.h"` in foo.c, with double
quotes, will attempt to find config.h in the directory that foo.c is
in (i.e. the source tree), before the -I include directory options are
checked.  Having `#include <config.h>`, with angle brackets, means
that only system include directories and directories explicitly listed
with -I will be searched. Directories are searched in the order of the
-I's on the cc compile line, so we put the build -I include directory
before the source.

This issue is unique to config.h files generated in the build tree by
./configure. All the other .h files are in the source tree.

I had never appreciated this difference between using quotes and angle
brackets, but it is indeed documented in the GNU autoconf manual, that
they recommend using angle brackets on #include <config.h> for exactly
this reason.

This fix replaces all #include "esl_config.h" with #include <esl_config.h>.

(xref SRE:2023/0807-h3-config-include-conflict)

documentation/codestyle.md

@@ -141,7 +141,7 @@ For example, this is the top of start of `esl_json`:
      *   www.json.org
      *   tools.ietf.org/html/rfc8259 
      */
-     #include "esl_config.h"
+     #include <esl_config.h>
 
 The short table of contents description lines are repeated in comments
 at the top of each section later in the file, facilitating
@@ -163,17 +163,23 @@ of external functions from the .c file.
 The first include is a project-wide configuration header named
 `<project_prefix>_config.h`.  It must be included first, because it
 may contain configuration constants that affect the behavior of other
-headers, even including system headers.  System headers come next,
-because they might contain configuration that affects our
-headers. Finally come our headers. I tend to group our headers
-together by project, and alphabetize them, but (aside from the
-project-wide config.h) our headers don't depend on any particular
+headers, even including system headers. It must be included with angle
+brackets, not double quotes, so compilation commands can control the
+order that -I include directories are searched (build tree first,
+source tree last), to assure that we don't erroneously use a stray
+previous config file in the source tree when we're building in a build
+tree.
+
+System headers come next, because they might contain configuration
+that affects our headers. Finally come our headers. I tend to group
+our headers together by project, and alphabetize them, but (aside from
+the project-wide config.h) our headers don't depend on any particular
 inclusion order.
 
 For example:
 
 
-    #include "h4_config.h"
+    #include <h4_config.h>
 
     #include <stdio.h>
     #include <stdlib.h>
@@ -199,7 +205,7 @@ included once during compilation, regardless of the order of
 ```
 #ifndef eslJSON_INCLUDED
 #define eslJSON_INCLUDED
-#include "esl_config.h"
+#include <esl_config.h>
 
  /* ...contents here... */
 

easel.c

@@ -14,7 +14,7 @@
  *   11. Test driver.
  *   12. Examples. 
  */
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdio.h>
 #include <stdlib.h>

easel.h

@@ -16,7 +16,7 @@
  */
 #ifndef eslEASEL_INCLUDED
 #define eslEASEL_INCLUDED
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdlib.h>
 #include <stdio.h>		/* for FILE */

esl_alloc.c

@@ -9,7 +9,7 @@
  *    4. Unit tests
  *    5. Test driver
  */
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdio.h>
 #include <stdlib.h>

esl_alphabet.c

@@ -7,7 +7,7 @@
  *    5. Test driver.
  *    6. Examples.
  */
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdlib.h>
 #include <string.h>

esl_alphabet.h

@@ -2,7 +2,7 @@
  */
 #ifndef eslALPHABET_INCLUDED
 #define eslALPHABET_INCLUDED
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <ctype.h>		/* isascii() */
 #include "easel.h"

esl_arr2.c

@@ -1,4 +1,4 @@
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdlib.h>
 #include <string.h>

esl_arr3.c

@@ -1,4 +1,4 @@
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdlib.h>
 #include <string.h>

esl_avx.c

@@ -15,7 +15,7 @@
  * about empty translation units and no symbols, and dummy drivers
  * that do nothing but declare success.
  */
-#include "esl_config.h"
+#include <esl_config.h>
 #ifdef eslENABLE_AVX
 
 #include <stdio.h>
@@ -43,7 +43,7 @@ esl_avx_dump_256i_hex4(__m256i v)
  *****************************************************************/
 #ifdef eslAVX_BENCHMARK
 
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdio.h>
 #include <string.h>
@@ -200,7 +200,7 @@ utest_hmax_epi16(ESL_RANDOMNESS *rng)
  *****************************************************************/
 
 #ifdef eslAVX_TESTDRIVE
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdio.h>
 #include <math.h>

esl_avx.h

@@ -11,7 +11,7 @@
  */
 #ifndef eslAVX_INCLUDED
 #define eslAVX_INCLUDED
-#include "esl_config.h"
+#include <esl_config.h>
 #ifdef  eslENABLE_AVX
 
 #include "easel.h"

esl_avx512.c

@@ -14,7 +14,7 @@
  * about empty translation units and no symbols, and dummy drivers
  * that do nothing but declare success.
  */
-#include "esl_config.h"
+#include <esl_config.h>
 #ifdef eslENABLE_AVX512
 
 #include <stdio.h>
@@ -110,7 +110,7 @@ utest_hmax_epi16(ESL_RANDOMNESS *rng)
  *****************************************************************/
 
 #ifdef eslAVX512_TESTDRIVE
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdio.h>
 #include <math.h>

esl_avx512.h

@@ -10,7 +10,7 @@
  */
 #ifndef eslAVX512_INCLUDED
 #define eslAVX512_INCLUDED
-#include "esl_config.h"
+#include <esl_config.h>
 #ifdef  eslENABLE_AVX512 
 
 #include "easel.h"

esl_bitfield.c

@@ -5,7 +5,7 @@
  *   2. Unit tests
  *   3. Test driver
  */
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <string.h>
 

esl_bitfield.h

@@ -1,6 +1,6 @@
 #ifndef eslBITFIELD_INCLUDED
 #define eslBITFIELD_INCLUDED
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include "easel.h"
 

esl_buffer.c

@@ -17,7 +17,7 @@
 /*::cexcerpt::header_example::end::*/
 
 /*::cexcerpt::include_example::begin::*/
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdio.h>
 #include <stdlib.h>
@@ -1889,7 +1889,7 @@ buffer_counttok(ESL_BUFFER *bf, const char *sep, esl_pos_t *ret_nc)
 /* compile: gcc -g -Wall -I. -L. -o esl_buffer_benchmark -DeslBUFFER_BENCHMARK esl_buffer.c -leasel -lm
  * run:     ./esl_buffer_benchmark
  */
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdio.h>
 #include <fcntl.h>
@@ -2783,7 +2783,7 @@ utest_halfnewline(void)
  *  (gcov): gcc -g -Wall -fprofile-arcs -ftest-coverage -I. -L. -o esl_buffer_utest -DeslBUFFER_TESTDRIVE esl_buffer.c -leasel -lm
  * run:     ./esl_buffer_utest
  */
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdio.h>
 

esl_buffer.h

@@ -2,7 +2,7 @@
  */
 #ifndef eslBUFFER_INCLUDED
 #define eslBUFFER_INCLUDED
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdio.h>
 

esl_cluster.c

@@ -6,7 +6,7 @@
  *     3. Test driver
  *     4. Example
  */
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdlib.h>
 
@@ -240,7 +240,7 @@ utest_singlelinkage(double *testdata, int n, double threshold, int *correct_assi
 #ifdef eslCLUSTER_TESTDRIVE
 /* gcc -g -Wall -o test -I. -L. -DeslCLUSTER_TESTDRIVE esl_cluster.c -leasel -lm
  */
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdio.h>
 #include <math.h>
@@ -286,7 +286,7 @@ main(int argc, char **argv)
 #ifdef eslCLUSTER_EXAMPLE
 /*::cexcerpt::cluster_example::begin::*/
 /* gcc -g -Wall -o example -I. -L. -DeslCLUSTER_EXAMPLE esl_cluster.c easel.c -lm  */
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdio.h>
 #include <stdlib.h>

esl_cluster.h

@@ -4,7 +4,7 @@
  */
 #ifndef eslCLUSTER_INCLUDED
 #define eslCLUSTER_INCLUDED
-#include "esl_config.h"
+#include <esl_config.h>
 
 extern int esl_cluster_SingleLinkage(const void *base, size_t n, size_t size, 
 				     int (*linkfunc)(const void *, const void *, const void *, int *), const void *param,

esl_composition.c

@@ -1,4 +1,4 @@
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include "easel.h"
 #include "esl_composition.h"

esl_composition.h

@@ -1,4 +1,4 @@
-#include "esl_config.h"
+#include <esl_config.h>
 
 extern int  esl_composition_BL62(double *f);
 extern int  esl_composition_WAG (double *f);

esl_cpu.c

@@ -12,7 +12,7 @@
  *   https://software.intel.com/en-us/articles/how-to-detect-knl-instruction-support
  *   https://en.wikipedia.org/wiki/CPUID
  */
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdlib.h>
 #include <stdint.h>
@@ -454,7 +454,7 @@ main(int argc, char **argv)
  *****************************************************************/
 #ifdef eslCPU_EXAMPLE
 
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include "easel.h"
 #include "esl_cpu.h"

esl_dirichlet.c

@@ -11,7 +11,7 @@
  *   esl_mixdchlet : mixture Dirichlets
  *   esl_gamma:      Gamma densities
  */
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <assert.h>
 #include <stdlib.h>

esl_dirichlet.h

@@ -5,7 +5,7 @@
  */
 #ifndef eslDIRICHLET_INCLUDED
 #define eslDIRICHLET_INCLUDED
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include "esl_random.h"      
 #include "esl_fileparser.h"  // Parameter input from file

esl_distance.c

@@ -11,7 +11,7 @@
  *    8. Test driver.
  *    9. Example.
  */
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <ctype.h>
 #include <string.h>

esl_distance.h

@@ -5,7 +5,7 @@
  */
 #ifndef eslDISTANCE_INCLUDED
 #define eslDISTANCE_INCLUDED
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include "easel.h"		
 #include "esl_alphabet.h"	

esl_dmatrix.c

@@ -20,7 +20,7 @@
  *   - eventually probably want additional matrix types
  *   - unit tests poor 
  */
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdio.h>
 #include <stdlib.h>

esl_dmatrix.h

@@ -4,7 +4,7 @@
  */
 #ifndef eslDMATRIX_INCLUDED
 #define eslDMATRIX_INCLUDED
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdio.h>
 

esl_dsqdata.c

@@ -32,7 +32,7 @@
  *   8. Test driver
  *   9. Examples
  */
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdio.h>
 #include <string.h>

esl_dsqdata.h

@@ -2,7 +2,7 @@
  */
 #ifndef eslDSQDATA_INCLUDED
 #define eslDSQDATA_INCLUDED
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdio.h>
 #include <stdint.h>

esl_exponential.c

@@ -18,7 +18,7 @@
  *      on failure due to small n. Compare esl_gumbel. xref J12/93.
  *      SRE, Wed Nov 27 11:03:07 2013
  */
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdio.h>
 #include <math.h>

esl_exponential.h

@@ -4,7 +4,7 @@
  */
 #ifndef eslEXPONENTIAL_INCLUDED
 #define eslEXPONENTIAL_INCLUDED
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include "esl_histogram.h"
 #include "esl_random.h"

esl_fileparser.c

@@ -7,7 +7,7 @@
  *    4. Test driver.
  *    5. Examples.
  */
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdlib.h>
 #include <stdio.h>

esl_fileparser.h

@@ -2,7 +2,7 @@
  */
 #ifndef eslFILEPARSER_INCLUDED
 #define eslFILEPARSER_INCLUDED
-#include "esl_config.h"
+#include <esl_config.h>
 
 #include <stdio.h>
 #include "easel.h"