merged ejh_docs_7

configure.ac

@@ -136,7 +136,7 @@ if test "x$enable_docs" = xyes; then
       AC_SUBST([FORTRAN_SRC_FILES], ["../src/flib"])
    else
       AC_SUBST([C_SRC_FILES], ["../src/clib/pio_nc.c ../src/clib/pio_nc4.c ../src/clib/pio_darray.c ../src/clib/pio_get_nc.c ../src/clib/pio_put_nc.c ../src/clib/pioc_support.c ../src/clib/pioc.c ../src/clib/pio_file.c ../src/clib/pio.h"])
-      AC_SUBST([FORTRAN_SRC_FILES], ["../src/flib"])
+      AC_SUBST([FORTRAN_SRC_FILES], ["../src/flib/piodarray.f90  ../src/flib/pio.F90  ../src/flib/pio_kinds.F90  ../src/flib/piolib_mod.f90  ../src/flib/pionfatt_mod.f90  ../src/flib/pio_nf.F90  ../src/flib/pionfget_mod.f90  ../src/flib/pionfput_mod.f90  ../src/flib/pio_support.F90  ../src/flib/pio_types.F90"])
 #      AC_SUBST([FORTRAN_SRC_FILES], ["../src/flib/pio_types.F90 ../src/flib/piodarray.F90 ../src/flib/piolib_mod.F90 ../src/flib/pio_nf.F90"])
    fi
    AC_CONFIG_FILES([doc/Doxyfile])

doc/source/api.txt

@@ -16,7 +16,7 @@
     - \ref PIO_read_darray
     - \ref PIO_write_darray
   \section utility Utility routines
-    - \ref PIO_set_hint
+    - \ref PIO_set_hint_grp
     - \ref PIO_setframe
     - \ref PIO_advanceframe
     - \ref PIO_setdebuglevel
@@ -41,7 +41,7 @@
     - \ref PIO_inq_attname
     - \ref PIO_inq_att
     - \ref PIO_inq_attlen
-    - \ref PIO_inq_var
+    - \ref PIO_inquire_variable
     - \ref PIO_inq_varid
     - \ref PIO_inq_varname
     - \ref PIO_inq_vartype

src/flib/Makefile.am

@@ -72,8 +72,26 @@ piolib_mod.mod pio.mod
 BUILT_SOURCES = $(MODFILES)
 include_HEADERS = $(MODFILES)
 
+# Doxygen does not cope well with pre-processor use in Fortran. So
+# create .f90 files from .F90 files by running the C
+# pre-processor. These will only be used by doxygen when --enable-docs
+# is used at configure.
+if BUILD_DOCS
+BUILT_SOURCES += piodarray.f90 piolib_mod.f90 pionfatt_mod.f90 pionfget_mod.f90 pionfput_mod.f90
+piodarray.f90: piodarray.F90
+	$(CC) -E $< > $@
+piolib_mod.f90: piolib_mod.F90
+	$(CC) -E $< > $@
+pionfatt_mod.f90: pionfatt_mod.F90
+	$(CC) -E $< > $@
+pionfget_mod.f90: pionfget_mod.F90
+	$(CC) -E $< > $@
+pionfput_mod.f90: pionfput_mod.F90
+	$(CC) -E $< > $@
+endif
+
 CLEANFILES = *.mod piodarray.F90 pionfatt_mod.F90 pionfget_mod.F90	\
-pionfput_mod.F90
+pionfput_mod.F90 *.f90
 
 EXTRA_DIST = CMakeLists.txt piodarray.F90.in pionfatt_mod.F90.in	\
 pionfget_mod.F90.in pionfput_mod.F90.in

src/flib/piolib_mod.F90

@@ -1,6 +1,4 @@
 #define __PIO_FILE__ "piolib_mod.f90"
-#define debug_rearr 0
-
 !>
 !! @file
 !! @brief Initialization Routines for PIO
@@ -437,7 +435,7 @@ end subroutine seterrorhandlingiosysid
 !>
 !! @public
 !! @ingroup PIO_initdecomp
-!! @brief Implements the @ref decomp_bc for PIO_initdecomp
+!! @brief Implements the block-cyclic decomposition for PIO_initdecomp
 !! @details  This provides the ability to describe a computational
 !! decomposition in PIO that has a block-cyclic form.  That is
 !! something that can be described using start and count arrays.
@@ -721,11 +719,12 @@ end subroutine initdecomp_1dof_nf_i8
 !>
 !! @public
 !! @ingroup PIO_initdecomp
-!! @brief Implements the @ref decomp_dof for PIO_initdecomp (previous name: \b initdecomp_1dof_nf_box)
+!! @brief Implements the degrees of freedom decomposition for
+!! PIO_initdecomp (previous name: \b initdecomp_1dof_nf_box)
 !! @details  This provides the ability to describe a computational
 !! decomposition in PIO using degrees of freedom method. This is
 !! a decomposition that can not be easily described using a start
-!! and count method (see @ref decomp_dof).
+!! and count method.
 !! Optional parameters for this subroutine allows for the specififcation of
 !! io decomposition using iostart and iocount arrays.  If iostart
 !! and iocount arrays are not specified by the user, and rearrangement
@@ -1151,7 +1150,7 @@ end subroutine init_intercom
 
 !>
 !! @public
-!! @defgroup PIO_set_hint  PIO_set_hint
+!! @defgroup PIO_set_hint_grp  PIO_set_hint
 !! @brief set file system hints using mpi_info_set
 !! @details This is a collective call which expects the following parameters:
 !! @param iosystem @copydoc io_desc_t

src/flib/pionfatt_mod.F90.in

@@ -337,7 +337,6 @@ contains
 
   end function put_att_1d_vid_{TYPE}
 
-
   !>
   !! @public
   !! @ingroup PIO_get_att