Merge pull request #2504 from GEOS-ESM/develop

GitFlow: Merge develop into main for release

.circleci/config.yml

@@ -16,12 +16,12 @@ parameters:
 
 # Anchors to prevent forgetting to update a version
 os_version: &os_version ubuntu20
-baselibs_version: &baselibs_version v7.14.0
+baselibs_version: &baselibs_version v7.17.0
 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/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

.github/workflows/workflow.yml

@@ -17,7 +17,7 @@ jobs:
     name: Build and Test MAPL GNU
     runs-on: ubuntu-latest
     container:
-      image: gmao/ubuntu20-geos-env-mkl:v7.14.0-openmpi_4.1.4-gcc_12.1.0
+      image: gmao/ubuntu20-geos-env-mkl:v7.17.0-openmpi_4.1.4-gcc_12.1.0
       # Per https://github.com/actions/virtual-environments/issues/1445#issuecomment-713861495
       # It seems like we might not need secrets on GitHub Actions which is good for forked
       # pull requests
@@ -77,7 +77,7 @@ jobs:
     name: Build and Test MAPL Intel
     runs-on: ubuntu-latest
     container:
-      image: gmao/ubuntu20-geos-env:v7.14.0-intelmpi_2021.6.0-intel_2022.1.0
+      image: gmao/ubuntu20-geos-env:v7.17.0-intelmpi_2021.6.0-intel_2022.1.0
       # Per https://github.com/actions/virtual-environments/issues/1445#issuecomment-713861495
       # It seems like we might not need secrets on GitHub Actions which is good for forked
       # pull requests

CHANGELOG.md

@@ -17,6 +17,34 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Deprecated
 
+## [2.43.0] - 2023-12-21
+
+### Added
+
+- Station sampler: add support to Global Historical Climatology Network Daily (GHCN-D)
+- Add to trajectory sampler DEFINE_OBS_PLATFORM for reading multiple IODA files. To do this, we add union_platform function for observation.
+- New directory (`docs/tutorial/grid_comps/automatic_code_generator`) containing an example showing how to automatically generate the source code using the `MAPL_GridCompSpecs_ACG.py` tool.
+- Added/modified a few _ASSERT calls in ExtData, to better explain what is wrong in .yaml file
+
+### Changed
+
+- Change the verification of the grid in MAPL_GetGlobalHorzIJIndex to avoid collective call
+- 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 DOY. Allow for missing obs files. User needs to 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 v4.24.0 (Baselibs 7.17.0)
+- Update CI to use circleci-tools v2
+- Changed the Python MAPL `__init__.py` file to restore behavior from pre-Python3 transition where we did `from foo import *`. Also fix up other Python2 code to Python3.
+
+### 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.
+- Allow ExtData2G to be built as SHARED or STATIC
+
 ## [2.42.4] - 2023-12-10
 
 ### Changed

CMakeLists.txt

@@ -8,7 +8,7 @@ endif ()
 
 project (
   MAPL
-  VERSION 2.42.4
+  VERSION 2.43.0
   LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
 
 # Set the possible values of build type for cmake-gui
@@ -207,6 +207,11 @@ endif ()
 
 add_definitions(-Dsys${CMAKE_SYSTEM_NAME})
 
+# Support for automated code generation
+include(mapl_acg)
+include(mapl_create_stub_component)
+add_subdirectory (Apps)
+
 # Special case - MAPL_cfio is built twice with two different precisions.
 add_subdirectory (MAPL_cfio MAPL_cfio_r4)
 add_subdirectory (MAPL_cfio MAPL_cfio_r8)
@@ -245,12 +250,6 @@ if (PFUNIT_FOUND)
   add_subdirectory (pfunit EXCLUDE_FROM_ALL)
 endif ()
 
-
-# Support for automated code generation
-include(mapl_acg)
-include(mapl_create_stub_component)
-add_subdirectory (Apps)
-
 add_subdirectory (Tests)
 
 # @env will exist here if MAPL is built as itself but not as part of, say, GEOSgcm

Python/MAPL/Date.py

@@ -149,7 +149,7 @@ def copy(self):
     def __iter__(self):
         return self
 
-    def next(self):
+    def __next__(self):
         #Last day of the month.
         if self.day == NumberDaysMonth(self.month, self.year):
             self.day = 1
@@ -230,7 +230,7 @@ def __add__(self, n):
             #Convert back to date format.
             return DateFromJDNumber(temp)
         else:
-            raise TypeError, "%s is not an integer." % str(n)
+            raise TypeError("%s is not an integer." % str(n))
 
     def __sub__(self, date):
         """Returns the (signed) difference of days between the dates."""
@@ -253,7 +253,7 @@ def __sub__(self, date):
                         ret += NumberDaysYear(year)
                     return ret
         else:
-            raise TypeError, "%s is neither an integer nor a Date." % str(date)
+            raise TypeError("%s is neither an integer nor a Date." % str(date))
 
     #Adding an integer is "commutative".
     def __radd__(self, n):
@@ -283,7 +283,7 @@ def ToCOMTime(self):
 def DateFromJDNumber(n):
     """Returns a date corresponding to the given Julian day number."""
     if not isinstance(n, int):
-        raise TypeError, "%s is not an integer." % str(n)
+        raise TypeError("%s is not an integer." % str(n))
 
     a = n + 32044
     b = (4*a + 3)//146097
@@ -320,21 +320,21 @@ def strpdate(s):
     temp = Date()
     curr_month = temp.month
     while temp.month == curr_month:
-        print temp
-        temp.next()
+        print(temp)
+        next(temp)
 
-    print "\n"
+    print("\n")
 
     #How many days until the end of the year?
     temp = Date()
     temp.day, temp.month = 1, 1
     curr_year = temp.year
     while temp.year == curr_year:
-        print "%s is %d days away from the end of the year." % (str(temp),
-                                                                temp.DaysToEndYear())
+        print("%s is %d days away from the end of the year." % (str(temp),
+                                                                temp.DaysToEndYear()))
         temp += NumberDaysMonth(temp.month)
 
-    print "\n"
+    print("\n")
 
     #Playing with __sub__.
     temp = Date()
@@ -344,11 +344,11 @@ def strpdate(s):
         temp_list.append(temp)
         temp += NumberDaysMonth(temp.month)
     for elem in temp_list:
-        print "%s differs %d days from current date: %s" % (str(elem),
+        print("%s differs %d days from current date: %s" % (str(elem),
                                                             elem - Date(),
-                                                            str(Date()))
+                                                            str(Date())))
 
-    print "\n"
+    print("\n")
 
     #Swapping arguments works?
-    print 23 + Date()
+    print(23 + Date())

Python/MAPL/__init__.py

@@ -45,3 +45,11 @@
 """
 
 __version__ = "1.0.0"
+
+from .exp      import *
+from .job      import *
+from .run      import *
+from .config   import *
+from .history  import *
+from .Date     import *
+from .filelock import *

Python/MAPL/exp.py

@@ -35,7 +35,7 @@ def __del__(self):
         self.submit()  # resubmit itsef
 
     def submit(self):
-        raise NotImplementedError, "Not implemented yet"
+        raise NotImplementedError("Not implemented yet")
 
 
 #                   --------------
@@ -74,15 +74,15 @@ def setup(inConfigFiles=None):
     os.mkdir(tmpdir)
     os.chdir(tmpdir)
     if os.system(cmd):
-       raise IOerror, "red_ma.pl did not complete successfully"
+       raise IOerror("red_ma.pl did not complete successfully")
 
 #   Resources as specified by user
 #   ------------------------------
     cf = Config(ConfigFiles)
 
 #   Setup directory tree
 #   --------------------
-    for dir in  cf.regex('Dir$').values():
+    for dir in  list(cf.regex('Dir$').values()):
         os.mkdir(dir)
 
 #   Populate Resources

Python/MAPL/history.py

@@ -2,7 +2,7 @@
 A special class for handling history resources.
 """
 
-from config import *
+from .config import *
 
 class History(Config):
 
@@ -35,15 +35,14 @@ def arc(self,outFile):
         *.temkplate resources.
         """
         dict = self.regex('template$')
-        Tmpl = [str.replace("'","").replace(",","") for str in dict.values()]
-        Coll = [ str.split('.')[0].replace(",","")  for str in dict.keys()  ]
+        Tmpl = [str.replace("'","").replace(",","") for str in list(dict.values())]
+        Coll = [ str.split('.')[0].replace(",","")  for str in list(dict.keys())  ]
         Arch = [str.replace("'","").replace(",","") \
-                for str in self.regex('archive$').values()]
+                for str in list(self.regex('archive$').values())]
 
         if len(Tmpl) != len(Arch):
-            raise IOError,\
-            "There are %d template resources but only %d archive resources."\
-            %(len(Tmpl),len(Arch))
+            raise IOError("There are %d template resources but only %d archive resources."\
+            %(len(Tmpl),len(Arch)))
 
         header = '# PESTO resource for History Collections ' + \
                  '(automatically generated - do not edit)'

Python/MAPL/job.py

@@ -11,8 +11,8 @@
 
 """
 
-import Abstract
-from exp import Exp
+from . import Abstract
+from .exp import Exp
 
 class Job(Exp):
 
@@ -72,13 +72,13 @@ def __del__(self):
 #                         -----------------
 
     def getResources(self):
-        raise NotImplementedError, "Not implemented yet"
+        raise NotImplementedError("Not implemented yet")
 
     def getRecyclables(self):
-        raise NotImplementedError, "Not implemented yet"
+        raise NotImplementedError("Not implemented yet")
 
     def putRecyclables(self):
-        raise NotImplementedError, "Not implemented yet"
+        raise NotImplementedError("Not implemented yet")
 
 
 #                         ----------------

Python/MAPL/run.py

@@ -5,7 +5,7 @@
 
 """
 
-from job import Job
+from .job import Job
 
 class Run(Job):
 

base/Base/Base_Base_implementation.F90

@@ -3210,17 +3210,19 @@ function grid_is_ok(grid) result(OK)
        type(ESMF_Grid), intent(inout) :: grid
        logical :: OK
        integer :: I1, I2, J1, J2, j
-       real(ESMF_KIND_R8), allocatable :: corner_lons(:,:), corner_lats(:,:)
+       real(ESMF_KIND_R8), pointer :: corner_lons(:,:), corner_lats(:,:)
        real(ESMF_KIND_R8) :: accurate_lat, accurate_lon
        real :: tolerance
 
        tolerance = epsilon(1.0)
        call MAPL_GridGetInterior(grid,I1,I2,J1,J2)
        OK = .true.
        ! check the edge of face 1 along longitude
-       allocate(corner_lons(I2-I1+2, J2-J1+2))
-       allocate(corner_lats(I2-I1+2, J2-J1+2))
-       call MAPL_GridGetCorners(Grid,corner_lons,corner_lats)
+       call ESMF_GridGetCoord(grid,localDE=0,coordDim=1,staggerloc=ESMF_STAGGERLOC_CORNER, &
+            farrayPtr=corner_lons, rc=status)
+       call ESMF_GridGetCoord(grid,localDE=0,coordDim=2,staggerloc=ESMF_STAGGERLOC_CORNER, &
+            farrayPtr=corner_lats, rc=status)
+
        if ( I1 ==1 .and. J2<=IM_WORLD ) then
           if (J1 == 1) then
             accurate_lon = 1.750d0*MAPL_PI_R8 - shift
@@ -3233,7 +3235,7 @@ function grid_is_ok(grid) result(OK)
             endif
           endif
 
-          do j = J1, J2+1
+          do j = J1+1, J2
              accurate_lat = -alpha + (j-1)*dalpha
              if ( abs(accurate_lat - corner_lats(1,j-J1+1)) > 5.0*tolerance) then
                 print*, "accurate_lat: ", accurate_lat

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
   )