Clean up misc pages in sidebar, fix version num

.github/workflows/update_docs.yml

@@ -16,7 +16,7 @@ jobs:
           sed -i 's/@abs_top_srcdir@/./' gen_docs/Doxyfile
           # grab version number from configure.ac
           export ver=`awk '/AC_INIT/{getline;print}' configure.ac | cut -d "[" -f2 | cut -d "]" -f1`
-          sed -i 's/@PACKAGE_VERSION@/"$ver"/' gen_docs/Doxyfile
+          sed -i 's/@PACKAGE_VERSION@/"$(ver)"/' gen_docs/Doxyfile
       - name: Run Doxygen
         uses: mattnotmitt/doxygen-action@v1
         with:

CHANGELOG.md

@@ -1,3 +1,4 @@
+@ingroup misc
 # ChangeLog
 All notable changes to this project will be documented in this file.
 

CMAKE_INSTRUCTIONS.md

@@ -1,3 +1,4 @@
+@ingroup misc
 # Instructions for building FMS with cmake
 
 ## 1. Environment Variables

CODE_OF_CONDUCT.md

@@ -1,3 +1,4 @@
+@ingroup misc
 # Code of Conduct
 
 ## Our Pledge

CODE_STYLE.md

@@ -1,3 +1,4 @@
+@ingroup misc
 # Coding Style
 
 ## General

CONTRIBUTING.md

@@ -1,3 +1,4 @@
+@ingroup misc
 # Contributing To libFMS
 
 Thank you for taking time to contribute.

INSTALL.md

@@ -1,3 +1,4 @@
+@ingroup misc
 # libFMS Installation
 
 ## External Requirements

LICENSE.md

@@ -1,3 +1,4 @@
+@ingroup misc
 ### GNU LESSER GENERAL PUBLIC LICENSE
 
 Version 3, 29 June 2007

README.md

@@ -1,3 +1,4 @@
+@ingroup misc
 # Modeling Framework: Flexible Modeling System (FMS)
 
 Today’s climate models simulate highly complex systems. In response to

amip_interp/amip_interp.rey_oi.txt

@@ -1,6 +1,6 @@
 /** @file
- *  @brief Information about optimum interpolation through amip_interp
  *  @ingroup amip_interp
+ *  @brief Information about optimum interpolation through amip_interp
  */ 
 (This file was edited for the Flexible Modeling System on July 26, 1999)
 

astronomy/astronomy.F90

@@ -71,6 +71,7 @@ module astronomy_mod
               astronomy_end, universal_time, orbital_time
 
 !> @page diurnal_solar diurnal_solar Interface
+!> @ingroup astronomy_mod
 !!
 !! ~~~~~~~~~~{.f90}
 !! call diurnal_solar (lat, lon, time, cosz, fracday, rrsun, dt_time)
@@ -244,7 +245,7 @@ module astronomy_mod
 end interface
 
 !> @page get_period get_period Interface
-!!
+!! Example usage:
 !! ~~~~~~~~~~{.f90}
 !! call get_period (period)
 !! ~~~~~~~~~~
@@ -263,7 +264,7 @@ module astronomy_mod
 end interface
 
 !> @page set_period set_period Interface
-!!
+!! Example usage:
 !! ~~~~~~~~~~{.f90}
 !! call set_period (period_in)
 !! ~~~~~~~~~~
@@ -290,7 +291,7 @@ module astronomy_mod
 !             universal_time ! called from  diurnal_solar:
 
 !> @page half_day half_day Interface
-!!
+!! Example usage:
 !! ~~~~~~~~~~{.f90}
 !! half_day (latitude, dec) result (h)
 !! ~~~~~~~~~~
@@ -411,6 +412,7 @@ subroutine astronomy_init (latb, lonb)
       if (module_is_initialized) return
 
 !-------------------------------------------------------------------
+!>    This routine will:
 !>    Verify that modules used by this module have been initialized.
 !-------------------------------------------------------------------
       call fms_init

docs/grouping.h

@@ -131,3 +131,6 @@
  *
  */
 
+/** @defgroup misc General Project Documents 
+ *  @brief Documentation files not pertaining to specific modules
+ */

docs/landingPage.md

@@ -2,10 +2,10 @@
 
 This is the documentation homepage for the Flexible Modeling System(FMS), a software environment built for supporting atmospheric, oceanic, and climate system models on high-end computing architectures.
 
-For more general information on FMS, it's uses, scope, and licensing, please see the project's 
+For more general information on FMS, it's uses, scope, and licensing, please see the project's
 description page [here](README.md).
 
-For documentation on the FMS codebase, a top level view of all modules by subdirectory can be 
-found in the 'Modules' section in the sidebar, or linked [here](modules.html).
+For documentation on the FMS codebase, a top level view of all modules by subdirectory can be
+found in the 'Modules' section in the sidebar, or linked [**here**](modules.html).
 
-All project code and contributing information can be found at [github.com/NOAA-GFDL/FMS].
+All project code and contributing information can be found at <https://github.com/NOAA-GFDL/FMS>

drifters/README.md

@@ -1,3 +1,4 @@
+@ingroup drifters
 # Drifters
 
 [email protected]

libFMS.F90

@@ -16,17 +16,13 @@
 !* You should have received a copy of the GNU Lesser General Public
 !* License along with FMS.  If not, see <http://www.gnu.org/licenses/>.
 !***********************************************************************
-!> @file
+!> @defgroup FMS FMS
+!> @ingroup libfms
+!> @brief A convenience module to use any FMS routines, functions, values
+!> @author Ryan Mulhall
+!
+!> @date 2/2021
 !
-!> @author
-!> Ryan Mulhall
-!>
-!> @date
-!> 2/2021
-!>
-!> @brief
-!> A convenience file to use any FMS routines, functions, values
-!>
 !> Imports all supported FMS modules so that any public interfaces,
 !! variables or routines can be used via this module. Excludes mpp_io modules
 !! and routines. Overloaded type operators/assignments cannot be imported individually
@@ -50,6 +46,12 @@
 !! this module is provided in the [supported_interfaces.md](../../supported_interfaces.md)
 !! file.
 
+!> @file
+!> @ingroup libfms
+!> @brief File for @ref FMS Global Module
+
+!> @addtogroup FMS
+!> @{
 module fms
 
   !> import each FMS module's public routines/functions, interfaces, and variables
@@ -421,3 +423,5 @@ module fms
   implicit none
 
 end module fms
+!> @}
+! close documentation grouping

supported_interfaces.md

@@ -1,3 +1,4 @@
+@ingroup libfms
 # Supported Public Interfaces for FMS
 
 List of supported public interfaces and associated types meant for external use through the 'fms' module.