more documentation changes

rfiorella · May 31, 2019 · 866608a · 866608a
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diff --git a/doc/Doxyfile.in b/doc/Doxyfile.in
@@ -771,8 +771,8 @@ WARN_LOGFILE           = doxywarn.log
 INPUT                  = @CMAKE_CURRENT_SOURCE_DIR@/../doc/source \
                          @CMAKE_CURRENT_SOURCE_DIR@/../examples/c \
                          @CMAKE_CURRENT_SOURCE_DIR@/../examples/f03 \
-			 @C_SRC_FILES@ \
-			 @FORTRAN_SRC_FILES@
+			 @FORTRAN_SRC_FILES@ \
+			 @C_SRC_FILES@ 
 
 
 # This tag can be used to specify the character encoding of the source files

diff --git a/doc/source/api.txt b/doc/source/api.txt
@@ -1,57 +1,42 @@
  /*!  \page api PIO Fortran Interface
   This is a list of all user interface routines:
 
-  \section api_system PIO startup and shutdown routines
-     - \ref PIO_init
-     - \ref PIO_finalize
-  \section api_fileops PIO file Operations
-     - \ref PIO_openfile
-     - \ref PIO_createfile
-     - \ref PIO_syncfile
-     - \ref PIO_closefile
-  \section api_decomp PIO decomposition routines
-    - \ref PIO_initdecomp
-    - \ref PIO_freedecomp
-  \section readwrite Reading and Writing distributed variables
-    - \ref PIO_read_darray
-    - \ref PIO_write_darray
-  \section utility Utility routines
-    - \ref PIO_set_hint
-    - \ref PIO_setframe
-    - \ref PIO_advanceframe
-    - \ref PIO_setdebuglevel
-    - \ref PIO_seterrorhandling
-    - \ref PIO_get_local_array_size
+  \section api_system PIO Startup and Shutdown
+    - \ref PIO_init
+    - \ref PIO_finalize
     - \ref PIO_getnumiotasks
     - \ref PIO_set_blocksize
-  \section netcdf NetCDF format specific routines 
-     Also see: http://www.unidata.ucar.edu/software/netcdf/docs/
-     \subsection putget Reading/Writing netcdf metadata  
-         - \ref PIO_get_att
-         - \ref PIO_put_att
-         - \ref PIO_get_var
-         - \ref PIO_put_var
-     \subsection utilnc Netcdf utility routines
+    - \ref PIO_set_hint
+  \section api_fileops File Operations
+    - \ref PIO_openfile
+    - \ref PIO_createfile
+    - \ref PIO_syncfile
     - \ref PIO_enddef
-    - \ref PIO_redef
-    - \ref PIO_def_dim 
-    - \ref PIO_def_var
-     \subsection inqnc NetCDF file inquiry routines
+    - \ref PIO_closefile
+  \section inqnc Inquiry
     - \ref PIO_inquire
-    - \ref PIO_inq_attname
-    - \ref PIO_inq_att
-    - \ref PIO_inq_attlen
-    - \ref PIO_inquire_variable
-    - \ref PIO_inq_varid
-    - \ref PIO_inq_varname
-    - \ref PIO_inq_vartype
-    - \ref PIO_inq_varndims
-    - \ref PIO_inq_vardimid
-    - \ref PIO_inq_varnatts
-    - \ref PIO_inq_ndims
-    - \ref PIO_inq_nvars
-    - \ref PIO_inq_natts
-    - \ref PIO_inquire_variable
     - \ref PIO_inquire_dimension
+    - \ref PIO_inquire_variable
+    - \ref PIO_inq_att
+  \section metadata Defining Metadata
+    - \ref PIO_def_dim 
+    - \ref PIO_def_var
+    - \ref PIO_get_att
+    - \ref PIO_put_att
+  \section api_decomp Distributed Arrays
+    - \ref PIO_initdecomp
+    - \ref PIO_freedecomp
+    - \ref PIO_setframe
+    - \ref PIO_read_darray
+    - \ref PIO_write_darray
+    - \ref PIO_get_local_array_size
+  \section standard_arrays Standard Arrays
+    - \ref PIO_get_var
+    - \ref PIO_put_var
+  \section utility Errors
+    - \ref PIO_seterrorhandling
+    - \ref PIO_setdebuglevel
+
+Also see: http://www.unidata.ucar.edu/software/netcdf/docs/
 
 */
diff --git a/src/clib/pio_get_nc.c b/src/clib/pio_get_nc.c
@@ -12,7 +12,7 @@
 #include <pio_internal.h>
 
 /**
- * @addtogroup PIO_get_var_c Get Data from a Variable
+ * @addtogroup PIO_get_var_c Get Data from a Variable in C
  * @{
  */
 

diff --git a/src/clib/pio_nc.c b/src/clib/pio_nc.c
@@ -2632,7 +2632,8 @@ PIOc_inq_var_fill(int ncid, int varid, int *no_fill, void *fill_valuep)
 }
 
 /**
- * @addtogroup PIO_get_att_c Get Attribute Values
+ * @addtogroup PIO_get_att_c Get Attribute Values in C
+ * Get the values stored in an attribute.
  * @{
  */
 
@@ -2924,7 +2925,8 @@ PIOc_get_att_float(int ncid, int varid, const char *name, float *ip)
  */
 
 /**
- * @addtogroup PIO_put_att_c Write an Attribute
+ * @addtogroup PIO_put_att_c Write an Attribute in C
+ * Create an attribute.
  * @{
  */
 

diff --git a/src/clib/pio_put_nc.c b/src/clib/pio_put_nc.c
@@ -11,7 +11,7 @@
 #include <pio_internal.h>
 
 /**
- * @addtogroup PIO_put_var_c Write Data to a Variable
+ * @addtogroup PIO_put_var_c Write Data to a Variable in C
  * @{
  */
 

diff --git a/src/clib/pioc.c b/src/clib/pioc.c
@@ -11,7 +11,7 @@
 #include <pio_internal.h>
 
 /**
- * @defgroup PIO_init_c Initialize the IO System
+ * @defgroup PIO_init_c Initialize the IO System in C
  * Initialize the IOSystem, including specifying number of IO and
  * computation tasks.
  *

diff --git a/src/flib/pio.F90 b/src/flib/pio.F90
@@ -5,8 +5,8 @@
 !<
 
 !>
-!! @defgroup PIO_set_blocksize PIO_set_blocksize
-!! Set the box rearranger blocksize.
+!! @defgroup PIO_set_blocksize Box Rearranger Settings
+!! Set the box rearranger blocksize in Fortran.
 
 module pio
 ! Package all exposed variables and functions under one roof
-Original file line number
+Diff line change
@@ Expand Up / @@ -12,7 +12,7 @@ @@
     #include <pio_internal.h>
     /**
-     * @addtogroup PIO_get_var_c Get Data from a Variable
+     * @addtogroup PIO_get_var_c Get Data from a Variable in C
      * @{
      */
@@ Expand Down @@