Merge branch 'data_yaml_updates' of github.com:uramirez8707/FMS into …

…yaml_ready

.github/workflows/github_autotools_gnu.yml

@@ -4,6 +4,11 @@ name: Build libFMS test with autotools
 
 on: [push, pull_request]
 
+# cancel running jobs if theres a newer push
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ubuntu-latest
@@ -22,7 +27,7 @@ jobs:
         SKIP_TESTS: "test_yaml_parser.5" # temporary till fixes are in
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
     - name: Prepare GNU autoconf for build
       run: autoreconf -if
     - name: Configure the build

.github/workflows/github_autotools_intel.yml

@@ -1,4 +1,10 @@
 on: pull_request
+
+# cancel running jobs if theres a newer push
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   intel-autotools:
     runs-on: ubuntu-latest
@@ -47,7 +53,7 @@ jobs:
         ./configure --prefix=/libs
         make -j install && cd
     - name: checkout
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
     - name: Configure
       run: autoreconf -if ./configure.ac && ./configure --with-yaml
     - name: Compile

.github/workflows/github_cmake_gnu.yml

@@ -2,6 +2,11 @@ name: Build libFMS with cmake
 
 on: [push, pull_request]
 
+# cancel running jobs if theres a newer push
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ubuntu-latest
@@ -16,7 +21,7 @@ jobs:
         CMAKE_FLAGS: "${{ matrix.omp-flags }} ${{ matrix.io-flag  }} ${{ matrix.libyaml-flag }} -D64BIT=on"
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
     - name: Generate makefiles with CMake
       run: cmake $CMAKE_FLAGS .
     - name: Build the library

.github/workflows/github_coupler_gnu.yml

@@ -1,6 +1,11 @@
 name: Test coupler build
 on: [pull_request]
 
+# cancel running jobs if theres a newer push
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   coupler-build:
     runs-on: ubuntu-latest
@@ -17,11 +22,11 @@ jobs:
         LDFLAGS: '-L/opt/view/lib'
     steps:
     - name: Checkout FMS
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         path: FMS
     - name: Checkout FMScoupler
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         repository: 'NOAA-GFDL/FMScoupler'
         path: FMScoupler

.github/workflows/github_doc_site.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Setup repo
         run: | # do autotool's job for substitutes since we don't need a full build environement
           mkdir gen_docs

.github/workflows/github_linter.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Run Lint
         uses: NOAA-GFDL/simple_lint@f5aa1fe976bd4c231db0536ba00cbfdc26708253
         with:

.github/workflows/version.yml

@@ -7,7 +7,7 @@ jobs:
   add-dev-to-version:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Append version with dev
       run: sed -i '/20[0-9][0-9]\.[0-9][0-9]/ s/]/-dev]/' configure.ac
     - name: Create pull request

CMakeLists.txt

@@ -349,7 +349,7 @@ foreach(kind ${kinds})
   if ( CMAKE_Fortran_COMPILER_VERSION MATCHES "1[0-9]\.[0-9]*\.[0-9]*" AND CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
     if(MPI_C_COMPILER MATCHES ".*mpich.*" )
       message(STATUS "Adding -fallow-argument-mismatch flag to compile with GCC >=10 and MPICH")
-      set_target_properties(${libTgt}_f PROPERTIES COMPILE_FLAGS "-fallow-argument-mismatch -w")
+      target_compile_options(${libTgt}_f PRIVATE "-fallow-argument-mismatch;-w")
     endif()
   endif()
 

Makefile.am

@@ -79,15 +79,15 @@ pkgconfigdir = $(libdir)/pkgconfig
 pkgconfig_DATA = FMS.pc
 
 ## Build libFMS module
-AM_CPPFLAGS = -I${top_srcdir}/include -I${top_srcdir}/mpp/include
+AM_CPPFLAGS = -I${top_srcdir}/include
 AM_FCFLAGS = $(FC_MODINC). $(FC_MODOUT)$(MODDIR)
 
 noinst_LTLIBRARIES = libFMS_mod.la
 libFMS_mod_la_SOURCES = libFMS.F90
 
 fms.$(FC_MODEXT): .mods/*_mod.$(FC_MODEXT)
 
-nodist_include_HEADERS = libFMS_mod.la
+nodist_include_HEADERS = .mods/fms.$(FC_MODEXT)
 
 include $(top_srcdir)/mkmods.mk
 
@@ -130,3 +130,20 @@ else
 clean-local:
 	-rm -rf .mods
 endif
+
+install-data-hook:
+	@echo ''
+	@echo '+-------------------------------------------------------------+'
+	@echo '| Congratulations! You have successfully installed the FMS    |'
+	@echo '| Fortran library.                                            |'
+	@echo '|                                                             |'
+	@echo '| After the installed include and link paths have been        |'
+	@echo '| specified, code using FMS should be compiled using the      |'
+	@echo '| "-lFMS" flag.                                               |'
+	@echo '|                                                             |'
+	@echo '| FMS is developed and maintained at the GFDL publicly on     |'
+	@echo '| Github. To report an issue or view available documentation, |'
+	@echo '| please see our page: https://www.github.com/NOAA-GFDL/FMS   |'
+	@echo '+-------------------------------------------------------------+'
+	@echo ''
+

data_override/include/data_override.inc

@@ -44,8 +44,9 @@ use mpp_domains_mod, only : domainUG, mpp_pass_SG_to_UG, mpp_get_UG_SG_domain, N
 use time_manager_mod, only: time_type
 use fms2_io_mod,     only : FmsNetcdfFile_t, open_file, close_file, &
                             read_data, fms2_io_init, variable_exists, &
-                            get_mosaic_tile_file
+                            get_mosaic_tile_file, file_exists
 use get_grid_version_mod, only: get_grid_version_1, get_grid_version_2
+use fms_string_utils_mod, only: string
 
 implicit none
 private
@@ -201,18 +202,26 @@ end if
 
 #ifdef use_yaml
     if (use_data_table_yaml) then
+       if (file_exists("data_table")) &
+         call mpp_error(FATAL, "You cannot have the legacy data_table if use_data_table_yaml=.true.")
        call read_table_yaml(data_table)
     else
+       if (file_exists("data_table.yaml"))&
+         call mpp_error(FATAL, "You cannot have the yaml data_table if use_data_table_yaml=.false.")
        allocate(data_table(max_table))
        do i = 1, max_table
           data_table(i) = default_table
        enddo
        call read_table(data_table)
     end if
 #else
+    if (file_exists("data_table.yaml"))&
+         call mpp_error(FATAL, "You cannot have the yaml data_table if use_data_table_yaml=.false.")
+
     if (use_data_table_yaml) then
-       call mpp_error(FATAL, "compilation error, need to compile with `-Duse_yaml`")
+       call mpp_error(FATAL, "You cannot have use_data_table_yaml=.true. without compiling with -Duse_yaml")
     else
+
        allocate(data_table(max_table))
        do i = 1, max_table
           data_table(i) = default_table
@@ -491,8 +500,9 @@ subroutine read_table(data_table)
 end subroutine read_table
 
 #ifdef use_yaml
+!> @brief Read and parse the data_table.yaml
 subroutine read_table_yaml(data_table)
-    type(data_type), dimension(:), allocatable, intent(out) :: data_table
+    type(data_type), dimension(:), allocatable, intent(out) :: data_table !< Contents of the data_table.yaml
 
     integer, allocatable :: entry_id(:)
     integer :: nentries
@@ -511,6 +521,7 @@ subroutine read_table_yaml(data_table)
 
       do i = 1, nentries
          call get_value_from_key(file_id, entry_id(i), "gridname", data_table(i)%gridname)
+         call check_for_valid_gridname(data_table(i)%gridname)
          call get_value_from_key(file_id, entry_id(i), "fieldname_code", data_table(i)%fieldname_code)
 
          data_table(i)%fieldname_file = ""
@@ -524,28 +535,98 @@ subroutine read_table_yaml(data_table)
          data_table(i)%interpol_method = "none"
          call get_value_from_key(file_id, entry_id(i), "interpol_method", data_table(i)%interpol_method, &
            & is_optional=.true.)
+         call check_interpol_method(data_table(i)%interpol_method, data_table(i)%file_name, &
+            data_table(i)%fieldname_file)
 
          call get_value_from_key(file_id, entry_id(i), "factor", data_table(i)%factor)
+         buffer = ""
          call get_value_from_key(file_id, entry_id(i), "region_type", buffer, is_optional=.true.)
-
-         if(trim(buffer) == "inside_region" ) then
-            data_table(i)%region_type = INSIDE_REGION
-         else if( trim(buffer) == "outside_region" ) then
-            data_table(i)%region_type = OUTSIDE_REGION
-         else
-            data_table(i)%region_type = NO_REGION
-         endif
-
-         call get_value_from_key(file_id, entry_id(i), "lon_start", data_table(i)%lon_start, is_optional=.true.)
-         call get_value_from_key(file_id, entry_id(i), "lon_end", data_table(i)%lon_end, is_optional=.true.)
-         call get_value_from_key(file_id, entry_id(i), "lat_start", data_table(i)%lat_start, is_optional=.true.)
-         call get_value_from_key(file_id, entry_id(i), "lat_end", data_table(i)%lat_end, is_optional=.true.)
-
+         call check_and_set_region_type(buffer, data_table(i)%region_type)
+
+        if (data_table(i)%region_type .ne. NO_REGION) then
+          call get_value_from_key(file_id, entry_id(i), "lon_start", data_table(i)%lon_start, is_optional=.true.)
+          call get_value_from_key(file_id, entry_id(i), "lon_end", data_table(i)%lon_end, is_optional=.true.)
+          call get_value_from_key(file_id, entry_id(i), "lat_start", data_table(i)%lat_start, is_optional=.true.)
+          call get_value_from_key(file_id, entry_id(i), "lat_end", data_table(i)%lat_end, is_optional=.true.)
+          call check_valid_lat_lon(data_table(i)%lon_start, data_table(i)%lon_end, &
+            data_table(i)%lat_start, data_table(i)%lat_end)
+        endif
       end do
 
     end if
     table_size = nentries !< Because one variable is not enough
 end subroutine read_table_yaml
+
+!> @brief Check if a grid name is valid, crashes if it is not
+subroutine check_for_valid_gridname(gridname)
+   character(len=*), intent(in) :: gridname !< Gridname
+
+   select case(trim(gridname))
+   case ("OCN", "ATM", "LND", "ICE")
+   case default
+      call mpp_error(FATAL, trim(gridname)//" is not a valid gridname. "//&
+         "The acceptable values are OCN ATM LND and ICE. Check your data_table.yaml")
+   end select
+end subroutine check_for_valid_gridname
+
+!> @brief Check if the interpol method is correct, crashes if it is not
+subroutine check_interpol_method(interp_method, filename, fieldname)
+   character(len=*), intent(in) :: interp_method !< The interpo_method
+   character(len=*), intent(in) :: filename      !< The filename
+   character(len=*), intent(in) :: fieldname     !< The fieldname in the file
+
+   select case(trim(interp_method))
+   case ("bicubic", "bilinear")
+      if (trim(filename) .eq. "" .or. trim(fieldname) .eq. "") call mpp_error(FATAL, &
+         "The file_name and the fieldname_file must be set if using the bicubic or bilinear interpolation method."//&
+         " Check your data_table.yaml")
+   case ("none")
+      if (trim(filename) .ne. "" ) then
+         if (trim(fieldname) .eq. "") call mpp_error(FATAL, &
+            "If the interpol_method is none and file_name is specified (ongrid case), "//&
+            "you must also specify the fieldname_file")
+      endif
+   case default
+      call mpp_error(FATAL, trim(interp_method)//" is not a valid interp method. "//&
+         "The acceptable values are bilinear and bicubic")
+   end select
+end subroutine check_interpol_method
+
+!> @brief Check if a region_type is valid, crashes if it is not. Otherwise it sets the
+!! correct integer parameter.
+subroutine check_and_set_region_type(region_type_str, region_type_int)
+   character(len=*), intent(in)  :: region_type_str !< The region type as defined in the data.yaml
+   integer,          intent(out) :: region_type_int !< The region type as an integer parameter
+
+   select case(trim(region_type_str))
+   case ("inside_region")
+      region_type_int = INSIDE_REGION
+   case ("outside_region")
+      region_type_int = OUTSIDE_REGION
+   case ("")
+      region_type_int = NO_REGION
+   case default
+      call mpp_error(FATAL, trim(region_type_str)//" is not a valid region type. "//&
+         "The acceptable values are inside_region and outside_regioon. Check your data_table.yaml")
+   end select
+end subroutine check_and_set_region_type
+
+!> @brief Check if a region lon_start, lon_end, lat_start and lat_end is valid.
+!! Crashes if it is not.
+subroutine check_valid_lat_lon(lon_start, lon_end, lat_start, lat_end)
+   real(FMS_DATA_OVERRIDE_KIND_), intent(in) :: lon_start !< Starting longitude of the data_override region
+   real(FMS_DATA_OVERRIDE_KIND_), intent(in) :: lon_end   !< Ending longitude of the data_override region
+   real(FMS_DATA_OVERRIDE_KIND_), intent(in) :: lat_start !< Starting lattiude of the data_override region
+   real(FMS_DATA_OVERRIDE_KIND_), intent(in) :: lat_end   !< Ending lattiude of the data_override region
+
+   if (lon_start > lon_end) call mpp_error(FATAL, &
+      "lon_start:"//string(lon_start)//" is greater than lon_end"//string(lon_end)//&
+      ". Check your data_table.yaml.")
+
+   if (lat_start > lat_end) call mpp_error(FATAL, &
+      "lat_start:"//string(lat_start)//" is greater than lat_end:"//string(lat_end)//&
+      ". Check your data_table.yaml.")
+end subroutine check_valid_lat_lon
 #endif
 
 subroutine DATA_OVERRIDE_UNSET_ATM_

test_fms/data_override/Makefile.am

@@ -71,10 +71,10 @@ TESTS_ENVIRONMENT= test_input_path="@TEST_INPUT_PATH@" \
                    parser_skip=${skipflag}
 
 # Run the test program.
-TESTS = test_data_override2.sh
+TESTS = test_data_override2.sh test_data_override_init.sh
 
 # Include these files with the distribution.
-EXTRA_DIST = test_data_override2.sh
+EXTRA_DIST = test_data_override2.sh test_data_override_init.sh
 
 # Clean up
-CLEANFILES = input.nml *.nc* *.out diag_table data_table data_table.yaml INPUT/* *.dpi *.spi *.dyn *.spl
+CLEANFILES = input.nml *.nc* *.out diag_table data_table data_table.yaml INPUT/* *.dpi *.spi *.dyn *.spl *-files/*