Yaml Parser (#858)

Adds fortran wrappers to libyaml, enabled via the -Duse_yaml macro
Adds unit test to test if the parser is working/crashing as expected
Adds an option, --with-yaml to autotools that checks that the environment is set up correctly and adds the -Duse_yaml macro to your compilation.
Implements the parser to read data_table.yaml and tests this using an ongrid data_override test

Makefile.am

@@ -42,6 +42,7 @@ SUBDIRS = \
   fms2_io \
   mosaic2 \
   fms \
+  parser \
   affinity \
   mosaic \
   time_manager \

configure.ac

@@ -67,6 +67,12 @@ AC_ARG_WITH([mpi],
 AS_IF([test ${with_mpi:-yes} = yes],
   [with_mpi=yes],
   [with_mpi=no])
+AC_ARG_WITH([yaml],
+  [AS_HELP_STRING([--with-yaml],
+    [Build with YAML support.  This option will be ignored if --disable-fortran-flag-setting is also given. (Default no)])])
+AS_IF([test ${with_yaml:-no} = no],
+  [with_yaml=no],
+  [with_yaml=yes])
 AC_ARG_ENABLE([setting-flags],
   [AS_HELP_STRING([--enable-setting-flags],
     [Allow configure to set some compiler flags.  Disabling this will also disable any other --with or --enable options that set flags, and will only use user-provided falgs. (Default yes)])])
@@ -122,6 +128,19 @@ if test $with_mpi = yes; then
   AC_CHECK_FUNC([MPI_Init], [], [AC_MSG_ERROR([Can't find the MPI C library.  Set CC/LDFLAGS/LIBS])])
 fi
 
+# Require yaml
+if test $with_yaml = yes; then
+  AC_CHECK_HEADERS([yaml.h], [], [AC_MSG_ERROR(["Can't find the libYAML C header file.  Set CC/CPPFLAGS/CFLAGS"])])
+  AC_SEARCH_LIBS([yaml_parser_initialize], [yaml], [], [AC_MSG_ERROR(["Can't find the libYAML C library.  Set CC/LDFLAGS/LIBS"])])
+
+  #If the test pass, define use_yaml macro
+  AC_DEFINE([use_yaml], [1], [This is required to use yaml parser])
+
+  AM_CONDITIONAL([SKIP_PARSER_TESTS], false )
+else
+  AM_CONDITIONAL([SKIP_PARSER_TESTS], true )
+fi
+
 # Require netCDF
 AC_CHECK_HEADERS([netcdf.h], [], [AC_MSG_ERROR([Can't find the netCDF C header file.  Set CPPFLAGS/CFLAGS])])
 AC_SEARCH_LIBS([nc_create], [netcdf], [], [AC_MSG_ERROR([Can't find the netCDF C library.  Set LDFLAGS/LIBS])])
@@ -337,6 +356,7 @@ AC_CONFIG_FILES([
   random_numbers/Makefile
   libFMS/Makefile
   docs/Makefile
+  parser/Makefile
   test_fms/test_common.sh
   test_fms/Makefile
   test_fms/diag_manager/Makefile
@@ -357,6 +377,7 @@ AC_CONFIG_FILES([
   test_fms/mosaic/Makefile
   test_fms/affinity/Makefile
   test_fms/coupler/Makefile
+  test_fms/parser/Makefile
   FMS.pc
   ])
 

docs/Doxyfile.in

@@ -2033,7 +2033,7 @@ INCLUDE_FILE_PATTERNS  = *.inc
 # recursively expanded use the := operator instead of the = operator.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-PREDEFINED             =
+PREDEFINED             =  use_yaml
 
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
 # tag can be used to specify a list of macro names that should be expanded. The

docs/grouping.h

@@ -114,6 +114,10 @@
  *
  */
 
+/** @defgroup parser Parser
+ *
+ */
+
 /** @defgroup platform Platform
  *
  */

fms/fms.F90

@@ -839,7 +839,7 @@ function fms_c2f_string (cstring) result(fstring)
 
  allocate(character(len=length) :: fstring) !> Set the length of fstring
 fstring = string_buffer
-
+ deallocate(string_buffer)
 end function fms_c2f_string
 !#######################################################################
 !> @brief Prints to the log file (or a specified unit) the version id string and

libFMS/Makefile.am

@@ -62,6 +62,7 @@ libFMS_la_LIBADD += $(top_builddir)/tracer_manager/libtracer_manager.la
 libFMS_la_LIBADD += $(top_builddir)/random_numbers/librandom_numbers.la
 libFMS_la_LIBADD += $(top_builddir)/diag_integral/libdiag_integral.la
 libFMS_la_LIBADD += $(top_builddir)/sat_vapor_pres/libsat_vapor_pres.la
+libFMS_la_LIBADD += $(top_builddir)/parser/libparser.la
 libFMS_la_LIBADD += $(top_builddir)/libFMS_mod.la
 
 # At least one source file must be included to please Automake.

parser/Makefile.am

@@ -0,0 +1,42 @@
+#***********************************************************************
+#*                   GNU Lesser General Public License
+#*
+#* This file is part of the GFDL Flexible Modeling System (FMS).
+#*
+#* FMS is free software: you can redistribute it and/or modify it under
+#* the terms of the GNU Lesser General Public License as published by
+#* the Free Software Foundation, either version 3 of the License, or (at
+#* your option) any later version.
+#*
+#* FMS is distributed in the hope that it will be useful, but WITHOUT
+#* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+#* FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+#* for more details.
+#*
+#* You should have received a copy of the GNU Lesser General Public
+#* License along with FMS.  If not, see <http://www.gnu.org/licenses/>.
+#***********************************************************************
+
+# This is an automake file for the constants directory of the FMS
+# package.
+
+# Ed Hartnett 2/22/19
+
+# Include .h and .mod files.
+AM_CPPFLAGS = -I$(top_srcdir)/include
+AM_FCFLAGS = $(FC_MODINC). $(FC_MODOUT)$(MODDIR)
+
+# Build this uninstalled convenience library.
+noinst_LTLIBRARIES = libparser.la
+
+# The convenience library depends on its source.
+libparser_la_SOURCES = \
+  yaml_parser.F90 \
+  yaml_parser_binding.c
+
+MODFILES = \
+  yaml_parser_mod.$(FC_MODEXT)
+BUILT_SOURCES = $(MODFILES)
+nodist_include_HEADERS = $(MODFILES)
+
+include $(top_srcdir)/mkmods.mk