Merge branch 'develop' into feature/msienkie/acars_divide_by_zero

.circleci/config.yml

@@ -1,10 +1,10 @@
 version: 2.1
 
 # Anchors to prevent forgetting to update a version
-baselibs_version: &baselibs_version v7.7.0
+baselibs_version: &baselibs_version v7.25.0
 
 orbs:
-  ci: geos-esm/circleci-tools@1
+  ci: geos-esm/circleci-tools@2
 
 workflows:
   build-test:

components.yaml

@@ -5,66 +5,91 @@ GEOSadas:
 env:
   local: ./@env
   remote: ../ESMA_env.git
-  tag: v4.9.1
+  tag: v4.29.1
   develop: main
 
 cmake:
   local: ./@cmake
   remote: ../ESMA_cmake.git
-  tag: v3.26.0
+  tag: v3.48.0
   develop: develop
 
 ecbuild:
   local: ./@cmake/@ecbuild
   remote: ../ecbuild.git
   tag: geos/v1.3.0
 
+crtm:
+  local: ./src/Shared/JCSDA_crtm/@crtm
+  remote: ../crtm.git
+  tag: geos/v2.4.1-jedi.1+1.1.0
+  develop: master
+
 NCEP_Shared:
   local: ./src/Shared/@NCEP_Shared
   remote: ../NCEP_Shared.git
   tag: v1.3.0
   develop: main
+  sparse: ./config/NCEP_Shared.sparse
 
 GMAO_Shared:
   local: ./src/Shared/@GMAO_Shared
   remote: ../GMAO_Shared.git
-  tag: v1.9.4
+  tag: g5.41.3
   develop: main
 
+GMAOpyobs:
+  local: ./src/Shared/@GMAO_Shared/@GMAO_pyobs
+  remote: ../GMAOpyobs.git
+  tag: v1.0.6
+  develop: develop
+
+AeroML:
+  local: ./src/Shared/@AeroML
+  remote: ../AeroML.git
+  tag: rt1.0.0-cak_tag0
+  develop: develop
+  sparse: ./config/AeroML.sparse
+
 GEOS_Util:
   local: ./src/Shared/@GMAO_Shared/@GEOS_Util
   remote: ../GEOS_Util.git
-  tag: v1.0.2
+  tag: rt-2.0.8+pr73
   develop: main
 
 MAPL:
   local: ./src/Shared/@MAPL
   remote: ../MAPL.git
-  tag: v2.35.2
+  tag: v2.47.1.2
   develop: develop
 
+GEOSldas_GridComp:
+  local: ./src/Components/@GEOSldas_GridComp
+  remote: ../GEOSldas_GridComp.git
+  tag: v1.0.2
+
 FMS:
   local: ./src/Shared/@FMS
   remote: ../FMS.git
-  tag: geos/2019.01.02+noaff.8
+  tag: geos/2019.01.02+noaff.10
   develop: geos/release/2019.01
 
 GEOSana_GridComp:
   local: ./src/Components/@GEOSana_GridComp
   remote: ../GEOSana_GridComp.git
-  branch: feature/mathomp4/extract-mksi
+  tag: g5.41.3
   develop: develop
 
 mksi:
-  local: ./src/Components/@GEOSana_GridComp/GEOSaana_GridComp/GSI_GridComp/@mksi
-  remote: ../GEOS_mksi.git
-  branch: develop
-  develop: develop
+   local: ./src/Components/@GEOSana_GridComp/GEOSaana_GridComp/GSI_GridComp/@mksi
+   remote: ../GEOS_mksi.git
+   tag: g5.41.2
+   develop: develop
 
 GEOSgcm_GridComp:
   local: ./src/Components/@GEOSgcm_GridComp
   remote: ../GEOSgcm_GridComp.git
-  tag: v1.17.4
+  tag: rt2.6.1.1
   sparse: ./config/GEOSgcm_GridComp.sparse
   develop: develop
 
@@ -77,25 +102,25 @@ g5pert:
 GEOSagcmPert_GridComp:
   local: ./src/Components/@GEOSagcmPert_GridComp
   remote: ../GEOSagcmPert_GridComp.git
-  tag: rt-GEOSagcmPert-g530-fix
+  tag: rt5.41.1
   develop: main
 
 FVdycoreCubed_GridComp:
   local: ./src/Components/@GEOSgcm_GridComp/GEOSagcm_GridComp/GEOSsuperdyn_GridComp/@FVdycoreCubed_GridComp
   remote: ../FVdycoreCubed_GridComp.git
-  tag: v1.12.1
+  tag: v2.11.1
   develop: develop
 
 fvdycore:
   local: ./src/Components/@GEOSgcm_GridComp/GEOSagcm_GridComp/GEOSsuperdyn_GridComp/@FVdycoreCubed_GridComp/@fvdycore
   remote: ../GFDL_atmos_cubed_sphere.git
-  tag: geos/v1.5.0
+  tag: geos/v2.9.0
   develop: geos/develop
 
 GEOSchem_GridComp:
   local: ./src/Components/@GEOSgcm_GridComp/GEOSagcm_GridComp/GEOSphysics_GridComp/@GEOSchem_GridComp
   remote: ../GEOSchem_GridComp.git
-  tag: v1.12.0
+  tag: v1.14.0
   develop: develop
 
 HEMCO:
@@ -113,7 +138,7 @@ geos-chem:
 GOCART:
   local: ./src/Components/@GEOSgcm_GridComp/GEOSagcm_GridComp/GEOSphysics_GridComp/@GEOSchem_GridComp/@GOCART
   remote: ../GOCART.git
-  tag: v2.1.2
+  tag: sdr_v2.2.1.2
   develop: develop
 
 QuickChem:
@@ -125,13 +150,13 @@ QuickChem:
 TR:
   local: ./src/Components/@GEOSgcm_GridComp/GEOSagcm_GridComp/GEOSphysics_GridComp/@GEOSchem_GridComp/@TR
   remote: ../TR.git
-  tag: v1.0.0
+  tag: v1.2.0
   develop: develop
 
 GMI:
   local: ./src/Components/@GEOSgcm_GridComp/GEOSagcm_GridComp/GEOSphysics_GridComp/@GEOSchem_GridComp/@GMI
   remote: ../GMI.git
-  tag: v1.0.0
+  tag: v1.3.0
   develop: develop
 
 StratChem:
@@ -143,7 +168,7 @@ StratChem:
 GEOS_OceanGridComp:
   local: ./src/Components/@GEOSgcm_GridComp/GEOSogcm_GridComp/@GEOS_OceanGridComp
   remote: ../GEOS_OceanGridComp.git
-  tag: v1.2.1
+  tag: v2.1.6
   develop: develop
 
 mom:
@@ -155,16 +180,27 @@ mom:
 mom6:
   local: ./src/Components/@GEOSgcm_GridComp/GEOSogcm_GridComp/@GEOS_OceanGridComp/MOM6_GEOSPlug/@mom6
   remote: ../MOM6.git
-  tag: geos/v2.1.0
+  tag: geos/v3.1
   develop: main
   recurse_submodules: true
 
+mit:
+  local: ./src/Components/@GEOSgcm_GridComp/GEOSogcm_GridComp/@GEOS_OceanGridComp/MIT_GEOS5PlugMod/@mit
+  remote: ../MITgcm.git
+  tag: checkpoint68o
+
 cice6:
   local: ./src/Components/@GEOSgcm_GridComp/GEOSogcm_GridComp/GEOSseaice_GridComp/CICE_GEOSPlug/@cice6
   remote: ../CICE.git
-  tag: geos/v0.0.1
-  develop: geos/main
-  recurse_submodules: true
+  tag: geos/v0.2.0
+  develop: geos/develop
+  ignore_submodules: true
+
+icepack:
+  local: ./src/Components/@GEOSgcm_GridComp/GEOSogcm_GridComp/GEOSseaice_GridComp/CICE_GEOSPlug/@cice6/icepack
+  remote: ../Icepack.git
+  tag: geos/v0.3.0
+  develop: geos/develop
 
 sis2:
   local: ./src/Components/@GEOSgcm_GridComp/GEOSogcm_GridComp/GEOSseaice_GridComp/CICE_GEOSPlug/@sis2
@@ -175,20 +211,32 @@ sis2:
 GEOSradiation_GridComp:
   local: ./src/Components/@GEOSgcm_GridComp/GEOSagcm_GridComp/GEOSphysics_GridComp/@GEOSradiation_GridComp
   remote: ../GEOSradiation_GridComp.git
-  tag: v1.2.0
+  tag: v1.8.0
   develop: develop
 
 RRTMGP:
   local: ./src/Components/@GEOSgcm_GridComp/GEOSagcm_GridComp/GEOSphysics_GridComp/@GEOSradiation_GridComp/GEOS_RadiationShared/@RRTMGP
   remote: ../rte-rrtmgp.git
-  tag: geos/v1.5+1.0.0
+  tag: geos/v1.7+1.0.0
   develop: geos/develop
   sparse: ./config/RRTMGP.sparse
 
+ww3:
+  local: ./src/Components/@GEOSgcm_GridComp/GEOSwgcm_GridComp/GEOSwavewatch_GridComp/@ww3
+  remote: ../WW3.git
+  tag: v6.07.1-geos-r2
+  develop: geos/develop
+
+umwm:
+  local: ./src/Components/@GEOSgcm_GridComp/GEOSwgcm_GridComp/GEOSumwm_GridComp/@umwm
+  remote: ../umwm.git
+  tag: v2.0.0-geos-r1
+  develop: geos
+
 GEOSgcm_App:
   local: ./src/Applications/@GEOSgcm_App
   remote: ../GEOSgcm_App.git
-  tag: v1.9.4
+  tag: g5.41.0
   develop: develop
 
 Ocean-LETKF:

config/AeroML.sparse

@@ -0,0 +1,5 @@
+/*
+!/src/eNNR
+!/src/NNR
+!/src/Shared
+!/Cmakelists.txt

config/NCEP_Shared.sparse

@@ -0,0 +1,2 @@
+/*
+!/NCEP_crtm

src/Applications/CMakeLists.txt

@@ -9,5 +9,6 @@ esma_add_subdirectories(
   MKIAU_App
   GMAO_Etc
   @CPLFCST_Etc
+  SABER_App
   )
 

src/Applications/GAAS_App/aeronet_all.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 """
 Splits AERONET into synoptic chunks.
 """
@@ -17,7 +17,7 @@ def makethis_dir(path):
     if path != '':
         rc = os.system('mkdir -p '+path)
         if rc:
-            raise IOError, "could not create directory "+path
+            raise IOError("could not create directory "+path)
 
 if __name__ == "__main__":
 
@@ -28,16 +28,16 @@ def makethis_dir(path):
     onehour = timedelta(seconds=60*60)
 
     if len(sys.argv)<2:
-        print "Usage:"
-        print "        aeronet4_all.py  year1 [year2]"
+        print("Usage:")
+        print("        aeronet4_all.py  year1 [year2]")
         sys.exit(1)
     else:
         y1 = sys.argv[1]
         if len(sys.argv)>2:
             y2 = sys.argv[2]
         else:
             y2 = y1
-        Years = range(int(y1),int(y2)+1)
+        Years = list(range(int(y1),int(y2)+1))
 
     # Loop over years
     # ---------------
@@ -49,7 +49,7 @@ def makethis_dir(path):
 
             today = tyme0 + (doy-1) * oneday
 
-            print 'Day: ', today
+            print('Day: ', today)
 
             # Read AERONET for this day
             # -------------------------

src/Applications/GAAS_App/ana_aod.j.tmpl

@@ -42,7 +42,7 @@ setenv nymd           >>>NYMD<<<
 cd $AODWORK
 ls
 
-setenv PYTHONPATH $FVROOT/lib/Python
+setenv PYTHONPATH $FVROOT/lib/Python:$FVROOT/lib/Python/pyobs:$FVROOT/lib/Python/pyods
 setenv PSAS_NUM_MPI 1 # $NCPUS_AOD
 
 set aod_modis_pcf = $AODWORK/modis_l2a.pcf

src/Applications/GAAS_App/aod_data.py

@@ -1,15 +1,15 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import os, sys
 
 def aod_type(dataID, stdoutFLG=True):
     """
+    input_parameters
+     => dataID: label used to identify data set in the obsys_rc file
+     => stdoutFLG: set to False, if calling directly from Python code
+
     purpose
     Identify AOD data type
 
-    input parameters
-     => dataID: label used to identify data set in the obsys_rc file
-     => stdoutFLG: if True, then print result to STDOUT before returning it
-
     return value
      => aod_type_val: AOD data type
     """
@@ -49,12 +49,13 @@ def aod_type(dataID, stdoutFLG=True):
 #.......................................................................
 def aod_filter(classlist_string, stdoutFLG=True):
     """
-    purpose: remove excess AOD data sets from obsclass list.
+    input_parameters
+     => classlist_string: AOD obsclass list (separated by commas, no spaces)
+     => stdoutFLG: set to False, if calling directly from Python code
+
+    purpose: remove duplicate AOD data sets from obsclass list
 
-    input parameters
-     => classlist_string: AOD obsclass list (string with labels separated by
-                          commas, no spaces)
-     => stdoutFLG: if True, then print result to STDOUT before returning it
+    NOTE: THIS ROUTINE DOES NOT CHECK DATA AVAILABILITY
 
     return value
      => newlist_string: filtered obsclass list string
@@ -114,8 +115,8 @@ def aod_filter(classlist_string, stdoutFLG=True):
 
     if len(sys.argv) < 2:
         scriptname = os.path.basename(sys.argv[0])
-        print("\n    usage: {0} routineName routineParams".format(scriptname))
-        print( "     routineName options = {0}\n".format(routineList.keys()))
+        print(("\n    usage: {0} routineName routineParams".format(scriptname)))
+        print(( "     routineName options = {0}\n".format(routineList.keys())))
         exit()
 
     routineName = sys.argv[1]