Merge pull request #2031 from GEOS-ESM/develop

GitFlow: Merge Develop into main for 2.36.0 release

CHANGELOG.md

@@ -17,6 +17,23 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Deprecated
 
+## [2.36.0] - 2023-03-23
+
+### Added
+
+- Added config array overload to `MAPL_GetResource`
+- Implemented new generic XY grid factory to create regional grids on any input set of 2D lons and lats
+  - **NOTE**: This grid factory is experimental and the API may change or it might be superseded by another grid factory
+
+### Changed
+
+- Updated `components.yaml` to match GEOSgcm v10.25.1
+  - ESMA_env v4.8.0 → v4.9.1 (Move to Baselibs 7.8.1: ESMF v8.4.1)
+  - ESMA_cmake v3.24.0 → v3.28.0 (Detection of additional sites, updated Intel Fortran flags, updates for Python3 support)
+- Converted files in `Python/MAPL` to Python 3.
+  - **NOTE 1**: This will require changes to codes that call MAPL's Python layer.
+  - **NOTE 2**: If building with F2PY support, you will need to use ESMA_cmake v3.28.0 or later if using in a mixed Python 2/3 environment.
+
 ## [2.35.3] - 2023-03-17
 
 ### Fixed

CMakeLists.txt

@@ -4,7 +4,7 @@ cmake_policy (SET CMP0054 NEW)
 
 project (
   MAPL
-  VERSION 2.35.3
+  VERSION 2.36.0
   LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
 
 # Set the default build type to release

MAPL_cfio/CMakeLists.txt

@@ -57,9 +57,9 @@ endif ()
 
 if (USE_F2PY)
   if (precision STREQUAL "r4")
-    find_package(F2PY2)
-    if (F2PY2_FOUND)
-      esma_add_f2py2_module(ShaveMantissa_
+    find_package(F2PY3)
+    if (F2PY3_FOUND)
+      esma_add_f2py3_module(ShaveMantissa_
         SOURCES ShaveMantissa_py.F90 ShaveMantissa.c
         DESTINATION lib/Python/${this}
         INCLUDEDIRS ${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_BINARY_DIR}/lib ${include_${this}}

MAPL_cfio/shavemantissa.py

@@ -30,7 +30,7 @@ def shave(a,xbits=12,has_undef=0,undef=MISSING,chunksize=-1):
     a_shaved, rc = shave32(a,xbits,has_undef,undef,chunksize)
 
     if rc:
-        raise ValueError, 'shave: error on return from ShaveMantissa_.shave32: %d'%rc
+        raise ValueError('shave: error on return from ShaveMantissa_.shave32: %d'%rc)
 
     return a_shaved
 

Python/MAPL/__init__.py

@@ -11,7 +11,7 @@
   carried out by means of several *jobs* which are submitted through a
   queueing system such as PBS.
 
-job 
+job
   This package defines the base class *Job* which inherits from
   *Exp*. A *job* carries out a portion of the *experiment*,
   itself consisting of several *run* segments.
@@ -38,19 +38,10 @@
    |----------------------- Experiment ------------------------|
    |------ Job 1 ------|------ Job 2 ------|------ Job 3 ------|
    |- Run 1 -|- Run 2 -|- Run 3 -|- Run 4 -|- Run 5 -|- Run 6 -|
- 
+
 If each run segment is 2 weeks long, each job performs a 4 week
 integration, and the the whole experiment is about 3 month long.
 
 """
 
-__version__ = "0.1.2"
-
-from exp      import *
-from job      import *
-from run      import *
-from config   import *
-from history  import *
-from Date     import *
-from filelock import *
-
+__version__ = "1.0.0"

Python/MAPL/config.py

@@ -12,7 +12,7 @@
 import sys
 from types import *
 from datetime import datetime
-    
+
 class Config(object):
 
     def __init__(self,RcFiles,delim=':',Environ=True):
@@ -23,7 +23,7 @@ def __init__(self,RcFiles,delim=':',Environ=True):
         the current value of environment variables.
         """
 
-        if type(RcFiles) is StringType:
+        if isinstance(RcFiles, str):
             Files = ( RcFiles, ) # in case a single file is given
         else:
             Files = RcFiles     # more often, a List/Tuple of RC files
@@ -39,22 +39,22 @@ def __init__(self,RcFiles,delim=':',Environ=True):
                     if value is not None:
                         value = string.Template(value).safe_substitute(os.environ)
                 if name:
-                    self.Rc[name] = {  'value': value, 
-                                     'comment': comment, 
+                    self.Rc[name] = {  'value': value,
+                                     'comment': comment,
                                         'flag': 0}
-                    
+
     def __call__(self,name,value=None):
         """Either get or set a resource depending on whether *value* is given"""
         if value == None:
             if self.Rc.__contains__(name):
                 return self.Rc[name]['value']
         else:
             if self.Rc.__contains__(name):
-                self.Rc[name]['value'] = value 
+                self.Rc[name]['value'] = value
                 self.Rc[name]['flag'] = 1
                 return self.Rc[name]['value']
         return None
-        
+
     get = __call__
 
     def set(self,name,value):
@@ -65,7 +65,7 @@ def save(self,rcfile=None):
         if rcfile is None:
             f = sys.stdout
         else:
-            f = open(rcfile,'w') 
+            f = open(rcfile,'w')
         for line in self.Lines:
             line = line.rstrip()
             name, value, comment = _parseLine(line,self.delim)
@@ -76,16 +76,16 @@ def save(self,rcfile=None):
                     else:
                         comment = ''
                     value = self.Rc[name]['value']
-                    print >>f, name + self.delim+' ' + str(value) + comment # this line has been edited
+                    print(name + self.delim+' ' + str(value) + comment, file=f) # this line has been edited
                 else:
-                    print >>f, line
+                    print(line, file=f)
             else:
-                print >>f, line
+                print(line, file=f)
         f.close()
-       
+
     def upd(self,dict):
         pass
-         
+
     def interp(self,str,outFile=None,**kws):
         """
         Use the resource values for $-substitution (a.k.a.
@@ -108,7 +108,7 @@ def interpFile(self,template,outFile,**kws):
         for tmpl in Tmpl:
             Text.append(self.interpStr(tmpl,**kws))
         open(outFile,"w").writelines(Text)
-                    
+
     def interpStr(self,template,strict=False):
         """
         Replace occurences of resource variables in the
@@ -149,21 +149,21 @@ def setenv(self,Only=None):
         Use resources to set environment variables. Option,
         one can provide a list of strings (*Only*) with those
         resources to be turned into environment variables.
-        """ 
+        """
         for name in self.Rc:
             if Only is None:
                 os.environ[name] = self.Rc[name]['value']
             elif name in Only:
                 os.environ[name] = self.Rc[name]['value']
- 
+
     def keys(self):
-        """ 
+        """
         Return list of resource names.
         """
-        return self.Rc.keys()
+        return list(self.Rc.keys())
 
     def values(self):
-        """ 
+        """
         Return list of resource names.
         """
         vals = []
@@ -216,7 +216,7 @@ def strTemplate(templ,expid=None,nymd=None,nhms=None,
 
        dtime ---  python datetime
 
-    Unlike GrADS, notice that seconds are expanded using the %S2 token. 
+    Unlike GrADS, notice that seconds are expanded using the %S2 token.
     Input date/time can be either strings or integers.
 
     Examples:
@@ -229,9 +229,9 @@ def strTemplate(templ,expid=None,nymd=None,nhms=None,
 
     """
 
-    MMM = ( 'jan', 'feb', 'mar', 'apr', 'may', 'jun', 
-            'jul', 'aug', 'sep', 'oct', 'nov', 'dec' ) 
-    
+    MMM = ( 'jan', 'feb', 'mar', 'apr', 'may', 'jun',
+            'jul', 'aug', 'sep', 'oct', 'nov', 'dec' )
+
     str_ = templ[:]
 
     if dtime is not None:
@@ -254,24 +254,24 @@ def strTemplate(templ,expid=None,nymd=None,nhms=None,
         m = (nhms - h * 10000)/100
         s = nhms - (10000*h + 100*m)
 
-    if expid is not None: 
+    if expid is not None:
         str_ = str_.replace('%s',expid)
-    if yy is not None: 
+    if yy is not None:
         y2 = yy%100
         str_ = str_.replace('%y4',str(yy))
         str_ = str_.replace('%y2',"%02d"%y2)
-    if mm is not None: 
+    if mm is not None:
         mm = int(mm)
         mmm = MMM[mm-1]
         str_ = str_.replace('%m2',"%02d"%mm)
         str_ = str_.replace('%m3',mmm)
-    if dd is not None: 
+    if dd is not None:
         str_ = str_.replace('%d2',"%02d"%int(dd))
-    if h  is not None: 
+    if h  is not None:
         str_ = str_.replace('%h2',"%02d"%int(h))
-    if m  is not None: 
+    if m  is not None:
         str_ = str_.replace('%n2',"%02d"%int(m))
-    if s  is not None: 
+    if s  is not None:
         str_ = str_.replace('%S2',"%02d"%int(s))
 
     return str_
@@ -284,14 +284,14 @@ def strTemplate(templ,expid=None,nymd=None,nhms=None,
 def _ut_strTemplate():
 
 
-    
+
     templ = "%s.aer_f.eta.%m3%y2.%y4%m2%d2_%h2:%n2:%S2z.nc"
 
     expid = "e0054A"
     yy = "2008"
     mm = "10"
     dd = "30"
-    
+
     h = "1"
     m = "30"
     s = "47"
@@ -301,20 +301,20 @@ def _ut_strTemplate():
     nymd = int(yy) * 10000 + int(mm)*100 + int(dd)
     nhms = int(h) * 10000 + int(m) * 100 + int(s)
 
-    print "Template: "+templ
-    print strTemplate(templ)
-    print strTemplate(templ,expid=expid)
-    print strTemplate(templ,expid=expid,yy=2008)
-    print strTemplate(templ,expid=expid,yy=2008,mm=mm)
-    print strTemplate(templ,expid=expid,yy=2008,mm=mm,dd=dd)
-    print strTemplate(templ,expid=expid,yy=2008,mm=mm,dd=dd,h=h)
-    print strTemplate(templ,expid=expid,yy=2008,mm=mm,dd=dd,h=h,m=m,s=s)
-    print strTemplate(templ,expid=expid,nymd=nymd)
-    print strTemplate(templ,expid=expid,nymd=nymd,nhms=nhms)
-    print strTemplate(templ,expid=expid,dtime=dtime)
+    print("Template: "+templ)
+    print(strTemplate(templ))
+    print(strTemplate(templ,expid=expid))
+    print(strTemplate(templ,expid=expid,yy=2008))
+    print(strTemplate(templ,expid=expid,yy=2008,mm=mm))
+    print(strTemplate(templ,expid=expid,yy=2008,mm=mm,dd=dd))
+    print(strTemplate(templ,expid=expid,yy=2008,mm=mm,dd=dd,h=h))
+    print(strTemplate(templ,expid=expid,yy=2008,mm=mm,dd=dd,h=h,m=m,s=s))
+    print(strTemplate(templ,expid=expid,nymd=nymd))
+    print(strTemplate(templ,expid=expid,nymd=nymd,nhms=nhms))
+    print(strTemplate(templ,expid=expid,dtime=dtime))
 
 if __name__ == "__main__":
     cf = Config('test.rc', delim=' = ')
-    
+
 #    _ut_strTemplate()
 

README.md

@@ -13,27 +13,27 @@ MAPL is a foundation layer of the GEOS architecture, whose original purpose is t
 
 MAPL has 10 primary subdirectories for Fortran source code:
 
-1. shared - low level utilities that are used throughout the remainder of MAPL.
-2. profiler - time and memory profiling utility
-3. pfio - high-performance client-server I/O layer
-5. base (formerly MAPL_Base) - legacy core of MAPL.   This layer will gradually evaporate under further refactoring.
-6. generic (under construction) - new home for MAPL extension of ESMF framework.
-7. oomph - next gen generic will eventually disappear
-8. gridcomps - Cap, History, and ExtData gridcomps used by all GEOS configurations.
-9. MAPL_cfio - this is a deprecated lower-level I/O layer that is generally replaced by GMAO_pFIO.    Not all of the strings have been cut yet.  Sometime soon, this directory will be eliminated.
-10. griddedio - layer between ESMF container and pfio library
+1. **shared** - low level utilities that are used throughout the remainder of MAPL.
+2. **profiler** - time and memory profiling utility
+3. [**pfio**](https://github.com/GEOS-ESM/MAPL/tree/main/pfio) - high-performance client-server I/O layer
+5. **base** (formerly MAPL_Base) - legacy core of MAPL.   This layer will gradually evaporate under further refactoring.
+6. **generic** (under construction) - new home for MAPL extension of ESMF framework.
+7. **oomph** - next gen generic will eventually disappear
+8. **gridcomps** - Cap, [History](https://github.com/GEOS-ESM/MAPL/tree/main/gridcomps/History), and [ExtData](https://github.com/GEOS-ESM/MAPL/tree/main/gridcomps/ExtData2G) gridcomps used by all GEOS configurations.
+9. **MAPL_cfio** - this is a deprecated lower-level I/O layer that is generally replaced by GMAO_pFIO.    Not all of the strings have been cut yet.  Sometime soon, this directory will be eliminated.
+10. **griddedio** - layer between ESMF container and pfio library
 
 
 MAPL also has a variety of other auxiliary directories:
 
-1. include - include files used by external gridded components.
-2. Apps - various Python and Perl scripts used by gridded components.
-3. Python - beginnings of a run-time scripting framework for GEOS configurations
-4. cmake - CMake build macros
-5. MAPL_pFUnit - implements extensions of pFUnit unit testing framework that enable unit tests of grid comp run methods.   This layer should eventually be migrated into pFUnit itself.
-6. Tests - miscellaneous standalone drivers.
-7. pflogger_stub - workaround for apps that wish to avoid a dependency on pFlogger
-8. pfunit - pFUnit (unit testing framework) extensions for ESMF components
+1. **include** - include files used by external gridded components.
+2. **Apps** - various Python and Perl scripts used by gridded components.
+3. **Python** - beginnings of a run-time scripting framework for GEOS configurations
+4. **cmake** - CMake build macros
+5. **MAPL_pFUnit** - implements extensions of pFUnit unit testing framework that enable unit tests of grid comp run methods.   This layer should eventually be migrated into pFUnit itself.
+6. **Tests** - miscellaneous standalone drivers.
+7. **pflogger_stub** - workaround for apps that wish to avoid a dependency on pFlogger
+8. **pfunit** - pFUnit (unit testing framework) extensions for ESMF components
 
 ## Contributing
 

base/CMakeLists.txt

@@ -54,6 +54,7 @@ set (srcs
   MAPL_ISO8601_DateTime_ESMF.F90
   FieldUtilities.F90
   MAPL_Resource.F90
+  MAPL_XYGridFactory.F90
   # Orphaned program: should not be in this library.
   # tstqsat.F90
   )

base/MAPL_GridManager.F90

@@ -120,6 +120,7 @@ subroutine initialize_prototypes(this, unusable, rc)
       use MAPL_TripolarGridFactoryMod, only: TripolarGridFactory
       use MAPL_LlcGridFactoryMod, only: LlcGridFactory
       use MAPL_ExternalGridFactoryMod, only: ExternalGridFactory
+      use MAPL_XYGridFactoryMod, only: XYGridFactory
 
       class (GridManager), intent(inout) :: this
       class (KeywordEnforcer), optional, intent(in) :: unusable
@@ -131,6 +132,7 @@ subroutine initialize_prototypes(this, unusable, rc)
       type (TripolarGridFactory) :: tripolar_factory
       type (LlcGridFactory) :: llc_factory
       type (ExternalGridFactory) :: external_factory
+      type (XYGridFactory) :: xy_factory
 
       ! This is a local variable to prevent the subroutine from running
       ! initialiazation twice. Calling functions have their own local variables
@@ -148,6 +150,7 @@ subroutine initialize_prototypes(this, unusable, rc)
          call this%prototypes%insert('Tripolar',  tripolar_factory)
          call this%prototypes%insert('llc',  llc_factory)
          call this%prototypes%insert('External', external_factory)
+         call this%prototypes%insert('XY', xy_factory)
          initialized = .true. 
       end if