Merge branch 'feature/aoloso/splitfield' into refactor/aoloso/replace…

…__RCplus_VERIFY_with__RC

.circleci/config.yml

@@ -21,7 +21,7 @@ bcs_version: &bcs_version v11.3.0
 tag_build_arg_name: &tag_build_arg_name maplversion
 
 orbs:
-  ci: geos-esm/circleci-tools@1
+  ci: geos-esm/circleci-tools@2
 
 workflows:
   build-and-test:
@@ -221,7 +221,7 @@ workflows:
     when:
       equal: [ "release", << pipeline.parameters.GHA_Event >> ]
     jobs:
-      - ci/publish-docker:
+      - ci/publish_docker:
           filters:
             tags:
               only: /^v.*$/
@@ -238,7 +238,7 @@ workflows:
           compiler_version: 2022.1.0
           image_name: geos-env
           tag_build_arg_name: *tag_build_arg_name
-      - ci/publish-docker:
+      - ci/publish_docker:
           filters:
             tags:
               only: /^v.*$/

.github/actions/deploy-ford-docs/action.yml

@@ -37,6 +37,10 @@ runs:
       run: ford --version
       shell: bash
 
+    - name: cpp version
+      run: cpp --version
+      shell: bash
+
     - name: Checkout gFTL
       uses: actions/checkout@v3
       with:

.github/workflows/validate_yaml_files.yml

@@ -24,7 +24,7 @@ jobs:
           format: colored
           config_file: .yamllint.yml
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: always()
         with:
           name: yamllint-logfile

CHANGELOG.md

@@ -17,18 +17,48 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Made changes to allocate fields to use farray instead of farrayPtr. This allows explicit specification of indexflag required by the new MAPL field split functionality. This functionality allows a clean way to create a new field from an exiting field where the new field is a 'slice' of the existing field with the slicing index being that of the trailing ungiridded dim of the existing field.
 - Replaced RC=STATUS plus `_VERIFY(RC)` in `Base_Base_implementation.F90` with just `_RC` in line with our new convention.
 - Updated CI to use ESMF 8.6.0 (Baselibs 7.16.0) and updated ESMF required version to 8.6.0
+- Swath grid step 1: allow for destroying and regenerating swath grid and regenerating regridder route handle, and creating
+  allocatable metadata in griddedIO. Modifications are made to GriddedIO.F90, MAPL_AbstractRegridder.F90, and MAPL_EsmfRegridder.F90.
+- Swath grid step 2: add control keywords for swath grid. Allow for filename template with `'*'` and DOY. Allow for missing obs files. Specify index_name_lon/lat, var_name_lon/lat/time, tunit, obs_file_begin/end/interval, Epoch and Epoch_init.
 - Update CI to Baselibs 7.17.0 (for future MAPL3 work) and the BCs v11.3.0 (to fix coupled run)
 - Update `components.yaml`
-  - ESMA_env v4.22.0 (Baselibs 7.15.1)
+  - ESMA_env v4.24.0 (Baselibs 7.17.0)
+- Update CI to use circleci-tools v2
+- Made changes to allocate fields to use farray instead of farrayPtr. This allows explicit specification of indexflag required by the new MAPL field split functionality. This functionality allows a clean way to create a new field from an exiting field where the new field is a 'slice' of the existing field with the slicing index being that of the trailing ungiridded dim of the existing field.
 
 ### Fixed
 
+- Fixed bug broken multi-step file output in History under certain template conditions
 - [#2433] Implemented workarounds for gfortran-13
+- Missing TARGET in GriddedIO - exposed runtime error when using NAG + debug.
 
 ### Removed
 
 ### Deprecated
 
+## [2.42.4] - 2023-12-10
+
+### Changed
+
+- Improved error message for missing labels in GridManager.
+
+### Fixed
+
+- Corrected some unit tests (and test utilities) to fix dangling pointers detected by NAG.  Most (possibly all) of these changes are already on release/MAPL-v3, but it was getting annoying to have NAG fail unit tests with develop branch.
+- Fix for CMake an Apple.  Needs to set `__DARWIN` as an fpp flag.  (Only used by NAG, but ...)
+
+## [2.42.3] - 2023-12-06
+
+### Fixed
+
+- `MAPL_Abort()` was passing an uninitialized integer to `MPI_Abort()` resulting in spurious false successes when running ctest.    Maybe was happening frequently, but CI would be blind to this.
+
+## [2.42.2] - 2023-12-05
+
+### Fixed
+
+- Corrected some unit tests (and test utilities) to fix dangling pointers detected by NAG.  Most (possibly all) of these changes are already on release/MAPL-v3, but it was getting annoying to have NAG fail unit tests with develop branch.
+
 ## [2.42.1] - 2023-11-20
 
 ### Fixed

CMakeLists.txt

@@ -8,7 +8,7 @@ endif ()
 
 project (
   MAPL
-  VERSION 2.42.1
+  VERSION 2.42.4
   LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
 
 # Set the possible values of build type for cmake-gui
@@ -225,6 +225,9 @@ include(CheckCompilerCapabilities)
 if(SUPPORT_FOR_MPI_IERROR_KEYWORD)
   add_compile_definitions(SUPPORT_FOR_MPI_IERROR_KEYWORD)
 endif()
+if (APPLE)
+  add_compile_definitions("-D__DARWIN")
+endif()
 
 add_subdirectory (pfio)
 add_subdirectory (profiler)

base/CMakeLists.txt

@@ -32,7 +32,7 @@ set (srcs
   MAPL_IO.F90
   MAPL_LatLonGridFactory.F90          MAPL_TransposeRegridder.F90
   MAPL_Comms.F90                        MAPL_LatLonToLatLonRegridder.F90    MAPL_TripolarGridFactory.F90
-  MAPL_LlcGridFactory.F90
+  MAPL_LlcGridFactory.F90               MAPL_SwathGridFactory.F90
   MAPL_Config.F90                       MAPL_LocStreamMod.F90
   MAPL_ConservativeRegridder.F90        MAPL_MaxMinMod.F90                  MAPL_VerticalInterpMod.F90
   MAPL_CubedSphereGridFactory.F90       MAPL_MemUtils.F90                   MAPL_VerticalMethods.F90
@@ -55,7 +55,7 @@ set (srcs
   MAPL_Resource.F90
   MAPL_XYGridFactory.F90
   MAPL_NetCDF.F90                       Plain_netCDF_Time.F90
-  MAPL_DateTime_Parsing_ESMF.F90
+  MAPL_DateTime_Parsing_ESMF.F90	MAPL_ObsUtil.F90
   # Orphaned program: should not be in this library.
   # tstqsat.F90
   )

base/MAPL_AbstractGridFactory.F90

@@ -82,6 +82,11 @@ module MAPL_AbstractGridFactoryMod
       procedure(get_file_format_vars), deferred :: get_file_format_vars
       procedure(decomps_are_equal), deferred :: decomps_are_equal
       procedure(physical_params_are_equal), deferred :: physical_params_are_equal
+
+      procedure :: get_xy_subset
+      procedure :: get_xy_mask
+      procedure :: destroy
+      procedure :: get_obs_time
    end type AbstractGridFactory
 
    abstract interface
@@ -238,6 +243,7 @@ function generate_file_reference3D(this,fpointer,metadata) result(ref)
          type(FileMetadata), intent(in), optional :: metaData
       end function generate_file_reference3D
 
+
    end interface
 
    character(len=*), parameter :: MOD_NAME = 'MAPL_AbstractGridFactory::'
@@ -1030,5 +1036,49 @@ function get_grid(this, unusable, rc) result(grid)
       end if
 
    end function get_grid
-
+
+
+   ! This procedure should only be called for time dependent grids.
+   ! A default implementation is to fail for other grid types, so we do not 
+   ! have to explicitly add methods to all of the existing subclasses.  
+   subroutine get_xy_subset(this, interval, xy_subset, rc)
+      class(AbstractGridFactory), intent(in) :: this
+      type(ESMF_Time), intent(in) :: interval(2)
+      integer, intent(out) :: xy_subset(2,2)
+      integer, optional, intent(out) :: rc
+      integer :: status
+
+      _RETURN(_FAILURE)
+    end subroutine get_xy_subset
+
+   subroutine get_xy_mask(this, interval, xy_mask, rc)
+      class(AbstractGridFactory), intent(inout) :: this
+      type(ESMF_Time), intent(in) :: interval(2)
+      integer, allocatable, intent(out) :: xy_mask(:,:)
+      integer, optional, intent(out) :: rc
+      integer :: status
+
+      _RETURN(_FAILURE)
+    end subroutine get_xy_mask
+
+   ! Probably don't need to do anything more for subclasses unless they have
+   ! other objects that don't finalize well.  (NetCDF, ESMF, MPI, ...)
+   subroutine destroy(this, rc)
+      class(AbstractGridFactory), intent(inout) :: this
+      integer, optional, intent(out) :: rc
+      integer :: status
+
+      call ESMF_GridDestroy(this%grid, noGarbage=.true., _RC)      
+      _RETURN(_SUCCESS)
+   end subroutine destroy
+
+   subroutine get_obs_time(this, grid, obs_time,  rc)
+     class(AbstractGridFactory), intent(inout) :: this
+     type (ESMF_Grid), intent(in) :: grid
+     real(ESMF_KIND_R4), intent(out) :: obs_time(:,:)
+     integer, optional, intent(out) :: rc
+
+     _RETURN(_SUCCESS)
+   end subroutine get_obs_time
+
 end module MAPL_AbstractGridFactoryMod

base/MAPL_AbstractRegridder.F90

@@ -8,6 +8,7 @@ module MAPL_AbstractRegridderMod
    use ESMF
    use MAPL_MemUtilsMod
    use MAPL_ExceptionHandling
+   use MAPL_RegridderSpecRouteHandleMap
    use, intrinsic :: iso_fortran_env, only: REAL32, REAL64
    implicit none
    private
@@ -92,6 +93,9 @@ module MAPL_AbstractRegridderMod
       procedure :: has_undef_value
       procedure :: get_regrid_method
 
+      procedure :: destroy
+      procedure :: destroy_route_handle
+
    end type AbstractRegridder
 
 
@@ -1006,4 +1010,21 @@ integer function get_regrid_method(this) result(method)
       method = this%spec%regrid_method
    end function get_regrid_method
 
+
+   subroutine destroy(this, rc)
+      class(AbstractRegridder), intent(inout) :: this
+      integer, optional, intent(out) :: rc
+      integer :: status
+
+      _RETURN(_SUCCESS)
+   end subroutine destroy
+
+   subroutine destroy_route_handle(this, kind, rc)
+      class(AbstractRegridder), intent(inout) :: this
+      type(ESMF_TypeKind_Flag), intent(in) :: kind
+      integer, optional, intent(out) :: rc
+
+      _RETURN(_SUCCESS)
+   end subroutine destroy_route_handle
+
 end module MAPL_AbstractRegridderMod

base/MAPL_Config.F90

@@ -72,14 +72,15 @@ function MAPL_ConfigCreate(unusable, rc) result(config)
 #endif
       character, parameter :: NUL = achar(00)   !! what it says
 
-      _UNUSED_DUMMY(unusable)
       config = ESMF_ConfigCreate(rc=rc)
       config%cptr%buffer(1:1) = EOL
       config%cptr%buffer(2:2) = EOB
       config%cptr%nbuf = 2
       config%cptr%next_line = 1
       config%cptr%value_begin = 1
 
+      _RETURN(_SUCCESS)
+      _UNUSED_DUMMY(unusable)
    end function MAPL_ConfigCreate
 
 !------------------------------------------------------------------------------

base/MAPL_EsmfRegridder.F90

@@ -53,6 +53,8 @@ module MAPL_EsmfRegridderMod
       procedure :: do_regrid
       procedure :: create_route_handle
       procedure :: select_route_handle
+      procedure :: destroy
+      procedure :: destroy_route_handle
 
    end type EsmfRegridder
 
@@ -1600,4 +1602,54 @@ function select_route_handle(this, kind, do_transpose, rc) result(route_handle)
 
    end function select_route_handle
 
+   subroutine destroy(this, rc)
+      class(EsmfRegridder), intent(inout) :: this
+      integer, optional, intent(out) :: rc
+      integer :: status
+
+      call this%destroy_route_handle(ESMF_TYPEKIND_R4, _RC)
+
+      _RETURN(_SUCCESS)
+   end subroutine destroy
+
+
+   subroutine destroy_route_handle(this, kind, rc)
+      class(EsmfRegridder), intent(inout) :: this
+      type(ESMF_TypeKind_Flag), intent(in) :: kind
+      integer, optional, intent(out) :: rc
+
+     type (RegridderSpec) :: spec
+     type(ESMF_RouteHandle) :: dummy_rh
+     type(RegridderSpecRouteHandleMap), pointer :: route_handles, transpose_route_handles
+     type(ESMF_RouteHandle) :: route_handle
+     type(RegridderSpecRouteHandleMapIterator) :: iter
+     integer :: status
+
+     if (kind == ESMF_TYPEKIND_R4) then
+        route_handles => route_handles_r4
+        transpose_route_handles => transpose_route_handles_r4
+     else if(kind == ESMF_TYPEKIND_R8) then
+        route_handles => route_handles_r8
+        transpose_route_handles => transpose_route_handles_r8
+     else
+        _FAIL('unsupported type kind (must be R4 or R8)')
+     end if
+
+     spec = this%get_spec()
+
+     _ASSERT(route_handles%count(spec) == 1, 'Did not find this spec in route handle table.')
+     route_handle = route_handles%at(spec)
+     call ESMF_RouteHandleDestroy(route_handle, noGarbage=.true.,_RC)
+     iter = route_handles%find(spec)
+     call route_handles%erase(iter)
+
+     _ASSERT(transpose_route_handles%count(spec) == 1, 'Did not find this spec in route handle table.')
+     route_handle = transpose_route_handles%at(spec)
+     call ESMF_RouteHandleDestroy(route_handle, noGarbage=.true., _RC)
+     iter = transpose_route_handles%find(spec)
+     call transpose_route_handles%erase(iter)
+
+      _RETURN(_SUCCESS)
+   end subroutine destroy_route_handle
+
 end module MAPL_EsmfRegridderMod