Merge pull request #1026 from GEOS-ESM/develop

Merge develop into main for 2.8.6 release
GEOS-ESM · Sep 13, 2021 · 5215b26 · 5215b26
2 parents 99d7b6e + 73ab621
commit 5215b26
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diff --git a/.github/workflows/release-tarball.yml b/.github/workflows/release-tarball.yml
@@ -0,0 +1,38 @@
+name: Create Complete Release Tarball
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+        with:
+          path: ${{ github.event.repository.name }}-${{ github.event.release.tag_name }}
+
+      - name: Checkout mepo
+        uses: actions/checkout@v2
+        with:
+          repository: GEOS-ESM/mepo
+          path: mepo
+
+      - name: Run mepo
+        run : |
+          cd ${GITHUB_WORKSPACE}/${{ github.event.repository.name }}-${{ github.event.release.tag_name }}
+          ${GITHUB_WORKSPACE}/mepo/mepo clone
+
+      - name: Create tarball
+        run: |
+          tar --exclude-vcs --exclude=.mepo -cf ${{ github.event.repository.name }}-${{ github.event.release.tag_name }}.COMPLETE.tar ${{ github.event.repository.name }}-${{ github.event.release.tag_name }}
+          xz -T6 ${{ github.event.repository.name }}-${{ github.event.release.tag_name }}.COMPLETE.tar
+
+      - name: Upload tarball
+        run: |
+          gh release upload ${{ github.event.release.tag_name }} ${{ github.event.repository.name }}-${{ github.event.release.tag_name }}.COMPLETE.tar.xz -R ${{ github.repository_owner }}/${{ github.event.repository.name }}
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,6 +15,28 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+## [2.8.6] - 2021-09-13
+
+### Added
+
+- Added the feature which can use nbits ( shave bit) in history binary output
+- Added script to automatically make a complete, mepo'd tarball on release
+
+### Changed
+
+- Refactored MAPL_Generic.F90 and MAPL_GenericCplComp.F90 from base to generic. This removes generic dependency from
+  base
+- Renamed MAPL_GenericCplComp.F90 to GenericCplComp.F90
+- Moved MAPL_ExtDataGridCompMod.F90, MAPL_OrbGridCompMod.F90, and MAPL_OrbGridComp.rc from base to gridcomps
+  subdirectories
+- Renamed Base.F90, Base_implementation.F90, and MAPL_Mod.F90 to Base_Base.F90, Base_Base_implementation.F90, and
+  Base.F90 respectively.
+
+### Fixed
+
+- Fixed issue #486. Empty state restarts will now be ignored (with warning) for writing (the code also protects reading, but the existing code already had a different protection)
+- Added default `CMAKE_BUILD_TYPE` for MAPL standalone. Defaults to `Release` build if not set on command line
+
 ## [2.8.5] - 2021-09-03
 
 ### Fixed

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -4,9 +4,18 @@ cmake_policy (SET CMP0054 NEW)
 
 project (
   MAPL
-  VERSION 2.8.5
+  VERSION 2.8.6
   LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
 
+# Set the default build type to release
+if (NOT CMAKE_BUILD_TYPE)
+  message (STATUS "Setting build type to 'Release' as none was specified.")
+  set (CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE)
+  # Set the possible values of build type for cmake-gui
+  set_property (CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
+    "Debug" "Release" "Aggressive")
+endif ()
+
 # mepo can now clone subrepos in three styles
 set (ESMA_CMAKE_DIRS
   ESMA_cmake

diff --git a/MAPL/CMakeLists.txt b/MAPL/CMakeLists.txt
@@ -3,7 +3,7 @@ esma_set_this()
 
 esma_add_library (${this}
   SRCS MAPL.F90
-  DEPENDENCIES MAPL.base MAPL.pfio MAPL_cfio_r4 MAPL.gridcomps
+  DEPENDENCIES MAPL.base MAPL.generic MAPL.pfio MAPL_cfio_r4 MAPL.gridcomps MAPL.orbit 
                esmf NetCDF::NetCDF_Fortran MPI::MPI_Fortran
                $<$<BOOL:${BUILD_WITH_FLAP}>:FLAP::FLAP>
   TYPE ${MAPL_LIBRARY_TYPE} 

diff --git a/MAPL/MAPL.F90 b/MAPL/MAPL.F90
@@ -1,10 +1,17 @@
 ! This module re-exports the public entities
 ! of the underlying packages.
 module MAPL
-   use MAPL_mod
+   use MAPLBase_mod
+   use MAPL_GenericMod
+   use MAPL_VarSpecMod
+   use MAPL_ExtDataGridCompMod, only: T_EXTDATA_STATE, EXTDATA_WRAP
    use ESMF_CFIOMod
    use pFIO
    use MAPL_GridCompsMod
    implicit none
 end module MAPL
+
+module MAPL_Mod
+   use MAPL
+end module MAPL_Mod
 
diff --git a/base/MAPL_Mod.F90 → base/Base.F90 b/base/MAPL_Mod.F90 → base/Base.F90
@@ -1,6 +1,6 @@
 
 
-module MAPL_Mod
+module MAPLBase_Mod
 
   use ESMFL_Mod         !  Stopgap
   use MAPL_ExceptionHandling
@@ -11,8 +11,6 @@ module MAPL_Mod
   use MAPL_IOMod
   use MAPL_CFIOMod
   use MAPL_CommsMod
-  use MAPL_GenericMod
-  use MAPL_VarSpecMod
 ! For temporary backward compatibility after Constants Library
   use MAPL_ConstantsMod
   use MAPL_ConstantsMod, only: MAPL_PI_R8
@@ -31,7 +29,6 @@ module MAPL_Mod
   use MAPL_MemUtilsMod
   use MAPL_HashMod
   use MAPL_LoadBalanceMod
-  use MAPL_ExtDataGridCompMod, only : T_EXTDATA_STATE, EXTDATA_WRAP
   use MAPL_AbstractGridFactoryMod
   use MAPL_AbstractRegridderMod
   use MAPL_RegridderManagerMod
@@ -60,4 +57,4 @@ module MAPL_Mod
   use MAPL_ServerManager
   logical, save, private :: mapl_is_initialized = .false.
 
-end module MAPL_Mod
+end module MAPLBase_Mod
diff --git a/base/Base/Base.F90 → base/Base/Base_Base.F90 b/base/Base/Base.F90 → base/Base/Base_Base.F90
@@ -805,7 +805,7 @@ end module MAPL_Base
 module MAPL_BaseMod
   use MAPL_Base
   use MAPL_RangeMod, only:   MAPL_Range
-  use MaplGeneric, only: MAPL_GridGet, MAPL_DistGridGet, MAPL_GetImsJms, MAPL_GridHasDE
+  use mapl_MaplGrid, only: MAPL_GridGet, MAPL_DistGridGet, MAPL_GetImsJms, MAPL_GridHasDE
   use MAPL_Constants
 
 

diff --git a/base/Base/Base_implementation.F90 → base/Base/Base_Base_implementation.F90 b/base/Base/Base_implementation.F90 → base/Base/Base_Base_implementation.F90
@@ -13,7 +13,7 @@
   use MAPL_Constants
   use MAPL_RangeMod
   use MAPL_SphericalGeometry
-  use MaplGeneric, only: MAPL_GridGet, MAPL_DistGridGet, MAPL_GetImsJms, MAPL_GridHasDE
+  use mapl_MaplGrid, only: MAPL_GridGet, MAPL_DistGridGet, MAPL_GetImsJms, MAPL_GridHasDE
   use MAPL_ExceptionHandling
   implicit NONE
 

diff --git a/base/CMakeLists.txt b/base/CMakeLists.txt
@@ -16,12 +16,12 @@ set (srcs
   RegridderTypeSpec.F90                 RegridderSpec.F90                   RegridderSpecRouteHandleMap.F90
   RegridMethods.F90                     HorizontalFluxRegridder.F90
   MAPL_FractionalRegridder.F90          MAPL_RegridderTypeSpecRegridderMap.F90
-  ESMF_CFIOPtrVectorMod.F90             MAPL_GenericCplComp.F90             MAPL_RegridderVector.F90
-  ESMFL_Mod.F90                         MAPL_Generic.F90                    MAPL_SatVapor.F90
+  ESMF_CFIOPtrVectorMod.F90             MAPL_RegridderVector.F90
+  ESMFL_Mod.F90                         MAPL_SatVapor.F90
   FileMetadataUtilities.F90             MAPL_GetLatLonCoord.F90             MAPL_SimpleAlarm.F90
   FileMetadataUtilitiesVector.F90       MAPL_GridManager.F90                MAPL_SimpleBundleMod.F90
   MAPL_AbstractGridFactory.F90          MAPL_GridSpec.F90                   MAPL_StringGridFactoryMap.F90
-  MAPL_GridType.F90                     MAPL_StringGridMap.F90
+  MAPL_GridType.F90                     MAPL_StringGridMap.F90              MaplGrid.F90
   MAPL_AbstractRegridder.F90                      
   MAPL_StringRouteHandleMap.F90
   MAPL_IdentityRegridder.F90            MAPL_stubs.F90
@@ -34,20 +34,19 @@ set (srcs
   MAPL_Config.F90                       MAPL_LocStreamMod.F90
   MAPL_ConservativeRegridder.F90        MAPL_MaxMinMod.F90                  MAPL_VerticalInterpMod.F90
   MAPL_CubedSphereGridFactory.F90       MAPL_MemUtils.F90                   MAPL_VerticalMethods.F90
-  MAPL_DefGridName.F90                  MAPL_Mod.F90                        MAPL_VotingRegridder.F90
+  MAPL_DefGridName.F90                  Base.F90                        MAPL_VotingRegridder.F90
   MAPL_EsmfRegridder.F90                MAPL_NewArthParser.F90              
   MAPL_ESMFTimeVectorMod.F90            MAPL_newCFIO.F90                    Regrid_Functions_Mod.F90
   MAPL_EtaHybridVerticalCoordinate.F90  MAPL_newCFIOitem.F90                
   MAPL_ExtDataCollection.F90            MAPL_NominalOrbitsMod.F90           
   MAPL_ExtDataCollectionManager.F90                 
-  MAPL_ExtDataGridCompMod.F90           MAPL_OrbGridCompMod.F90
   MAPL_LocStreamFactoryMod.F90          MAPL_LocstreamRegridder.F90
   MAPL_ExternalGridFactory.F90
   ServerManager.F90 ApplicationSupport.F90 
   regex_module.F90 StringTemplate.F90 MAPL_SphericalGeometry.F90  FieldBundleWrite.F90 FieldBundleRead.F90
   regex_F.c
   c_mapl_locstream_F.c  getrss.c  memuse.c
-  Base/Base.F90 Base/Base_implementation.F90
+  Base/Base_Base.F90 Base/Base_Base_implementation.F90
 
   # Orphaned program: should not be in this library.
   # tstqsat.F90
@@ -59,7 +58,7 @@ endif()
 
 esma_add_library(
   ${this} SRCS ${srcs}
-  DEPENDENCIES MAPL.generic MAPL.shared MAPL.constants MAPL.profiler MAPL.pfio MAPL_cfio_r4 PFLOGGER::pflogger GFTL_SHARED::gftl-shared
+  DEPENDENCIES MAPL.shared MAPL.constants MAPL.profiler MAPL.pfio MAPL_cfio_r4 PFLOGGER::pflogger GFTL_SHARED::gftl-shared
                esmf NetCDF::NetCDF_Fortran MPI::MPI_Fortran
   TYPE ${MAPL_LIBRARY_TYPE})
 

diff --git a/base/MAPL_TimeMethods.F90 b/base/MAPL_TimeMethods.F90
@@ -2,7 +2,6 @@
 
 module MAPL_TimeDataMod
   use ESMF
-  use MAPL_GenericMod
   use MAPL_BaseMod
   use pFIO
   use MAPL_ExceptionHandling

diff --git a/base/MAPL_VerticalMethods.F90 b/base/MAPL_VerticalMethods.F90
@@ -2,7 +2,6 @@
 
 module MAPL_VerticalDataMod
   use ESMF
-  use MAPL_GenericMod
   use MAPL_BaseMod
   use pFIO
   use MAPL_AbstractRegridderMod

diff --git a/base/MAPL_newCFIO.F90 b/base/MAPL_newCFIO.F90
@@ -6,7 +6,6 @@ module MAPL_newCFIOMod
   use MAPL_AbstractGridFactoryMod
   use MAPL_AbstractRegridderMod
   use MAPL_GridManagerMod
-  use MAPL_GenericMod
   use MAPL_BaseMod
   use MAPL_NewRegridderManager
   use MAPL_RegridMethods

diff --git a/generic/MaplGrid.F90 → base/MaplGrid.F90 b/generic/MaplGrid.F90 → base/MaplGrid.F90
@@ -135,7 +135,7 @@ subroutine set(this, grid, unusable, rc)
     this%NY0 = this%MYID/this%NX + 1
 
 
-    lgr => logging%get_logger('MAPL.GENERIC')
+    lgr => logging%get_logger('MAPL.BASE')
     call lgr%debug("grid global max= [%3(i0,:,',')~]", WrapArray(counts))
     call lgr%debug(" NX: %i0 ;   NY: %i0", this%nx, this%ny)
     call lgr%debug("NX0: %i0 ;  NY0: %i0", this%nx0, this%ny0)

diff --git a/base/TeX/MAPL_CapIntro.tex b/base/TeX/MAPL_CapIntro.tex
@@ -42,7 +42,7 @@
 
  Program Main
 
-   use MAPL_Mod
+   use MAPLBase_Mod
    use GEOS_AgcmSimpleGridCompMod, only:  ROOT_SetServices => SetServices
 
    implicit none

diff --git a/base/TeX/MAPL_Intro.tex b/base/TeX/MAPL_Intro.tex
@@ -805,7 +805,7 @@ \subsubsection{Example 1: Using the Generic Component}
   Program Example1
 
     use ESMF
-    use MAPL_Mod, only: SetServices => MAPL_GenericSetServices
+    use MAPLBase_Mod, only: SetServices => MAPL_GenericSetServices
 
     type(ESMF_GridComp)    :: GC
     type(ESMF_State)       :: Import, Export
@@ -901,7 +901,7 @@ \subsubsection{Example 2: HelloWorldMod}
     ! We always have this preamble
     !-----------------------------
     use ESMF
-    use MAPL_Mod
+    use MAPLBase_Mod
 
     implicit none
 

diff --git a/base/tests/CMakeLists.txt b/base/tests/CMakeLists.txt
@@ -13,7 +13,6 @@ set (TEST_SRCS
     Test_LatLon_Corners.pf
     Test_MAPL_Config.pf
     test_DirPath.pf
-    Test_VarSpec.pf
   )
 
 # SRCS are mostly mocks to facilitate tests

diff --git a/base/tests/Test_CFIO_Bundle.pf b/base/tests/Test_CFIO_Bundle.pf
@@ -6,7 +6,7 @@
 module Test_CFIO_Bundle
    use pfunit
    use ESMF
-   use MAPL_Mod
+   use MAPLBase_Mod
    use ESMF_TestCase_Mod
    use ESMF_TestMethod_mod
    implicit none

diff --git a/base/tests/utCFIO_Bundle.F90 b/base/tests/utCFIO_Bundle.F90
@@ -7,7 +7,7 @@
    Program utCFIO
 
    use ESMF
-   use MAPL_Mod
+   use MAPLBase_Mod
 
    implicit NONE
 

diff --git a/base/tests/ut_ExtData.F90 b/base/tests/ut_ExtData.F90
@@ -57,7 +57,7 @@ MODULE RUTMod
 ! !USES:
 !
    USE ESMF_Mod
-   USE MAPL_Mod
+   USE MAPLBase_Mod
 
    use MAPL_ExtDataGridCompMod, only: ExtData_SetServices => SetServices
 
@@ -352,7 +352,7 @@ end module RUTMod
 
 Program ut_ExtData
 
-   use MAPL_Mod
+   use MAPLBase_Mod
 
    use RUTMod,                  only: ROOT_SetServices    => SetServices
    use MAPL_ExtDataGridCompMod, only: ExtData_SetServices => SetServices

diff --git a/base/tstqsat.F90 b/base/tstqsat.F90
@@ -1,6 +1,6 @@
 
 
-use MAPL_Mod
+use MAPLBase_Mod
 
 
 integer i,l

diff --git a/generic/CMakeLists.txt b/generic/CMakeLists.txt
@@ -21,21 +21,24 @@ set (srcs
   MAPL_VarSpecMod.F90
   StateSpecification.F90
   ComponentSpecification.F90
-  
+
   BaseFrameworkComponent.F90
   MaplGenericComponent.F90
 
-  MaplGrid.F90
-  
+  GenericCplComp.F90
+
   MaplGeneric.F90
+
+  MAPL_Generic.F90
+
   )
 if (BUILD_WITH_PFLOGGER)
   find_package(PFLOGGER REQUIRED)
 endif ()
 find_package(GFTL REQUIRED)
 find_package(GFTL_SHARED REQUIRED)
 
-esma_add_library(${this} SRCS ${srcs} DEPENDENCIES MAPL.shared PFLOGGER::pflogger GFTL_SHARED::gftl-shared GFTL::gftl TYPE ${MAPL_LIBRARY_TYPE})
+esma_add_library(${this} SRCS ${srcs} DEPENDENCIES MAPL.shared MAPL.profiler MAPL.base PFLOGGER::pflogger GFTL_SHARED::gftl-shared GFTL::gftl TYPE ${MAPL_LIBRARY_TYPE})
 target_include_directories (${this} PUBLIC
   $<BUILD_INTERFACE:${MAPL_SOURCE_DIR}/include>)
 target_link_libraries (${this} PUBLIC esmf NetCDF::NetCDF_Fortran)

diff --git a/base/MAPL_GenericCplComp.F90 → generic/GenericCplComp.F90 b/base/MAPL_GenericCplComp.F90 → generic/GenericCplComp.F90