Merge branch 'develop' into feature/wcoss2_spack-stack

NOAA-EMC · Jan 10, 2025 · e24acb5 · e24acb5
2 parents ea28e5e + 614c7b6
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diff --git a/sorc/fv3-jedi b/sorc/fv3-jedi
diff --git a/sorc/ioda b/sorc/ioda
diff --git a/sorc/iodaconv b/sorc/iodaconv
diff --git a/sorc/oops b/sorc/oops
diff --git a/sorc/saber b/sorc/saber
diff --git a/sorc/soca b/sorc/soca
diff --git a/sorc/ufo b/sorc/ufo
+117 −9		src/fv3jedi/Geometry/fv3jedi_geom_mod.f90
+4 −2		src/fv3jedi/IO/CubeSphereHistory/fv3jedi_io_cube_sphere_history_mod.f90
+11 −3		src/fv3jedi/IO/Utils/IOBase.h
+10 −3		src/fv3jedi/Increment/Increment.h
+1 −1		src/fv3jedi/LinearVariableChange/Analysis2Model/LinVarChaA2M.cc
+0 −1		src/fv3jedi/LinearVariableChange/Analysis2Model/LinVarChaA2M.h
+7 −7		src/fv3jedi/LinearVariableChange/Base/LinearVariableChangeBase.h
+1 −1		src/fv3jedi/LinearVariableChange/Control2Analysis/LinVarChaC2A.cc
+0 −1		src/fv3jedi/LinearVariableChange/Control2Analysis/LinVarChaC2A.h
+0 −1		src/fv3jedi/LinearVariableChange/LinearVariableChange.h
+1 −1		src/fv3jedi/LinearVariableChange/Model2GeoVaLs/LinVarChaModel2GeoVaLs.cc
+0 −1		src/fv3jedi/LinearVariableChange/Model2GeoVaLs/LinVarChaModel2GeoVaLs.h
+10 −3		src/fv3jedi/State/State.h
+1 −1		src/fv3jedi/Utilities/fv3jedi_tile_comms_mod.f90
+0 −1		src/fv3jedi/VariableChange/Analysis2Model/VarChaA2M.cc
+0 −1		src/fv3jedi/VariableChange/Analysis2Model/VarChaA2M.h
+7 −5		src/fv3jedi/VariableChange/Base/VariableChangeBase.h
+0 −1		src/fv3jedi/VariableChange/ColdStartWinds/VarChaColdStartWinds.cc
+0 −1		src/fv3jedi/VariableChange/ColdStartWinds/VarChaColdStartWinds.h
+0 −1		src/fv3jedi/VariableChange/Control2Analysis/VarChaC2A.cc
+0 −1		src/fv3jedi/VariableChange/Control2Analysis/VarChaC2A.h
+0 −1		src/fv3jedi/VariableChange/Model2GeoVaLs/VarChaModel2GeoVaLs.cc
+0 −1		src/fv3jedi/VariableChange/Model2GeoVaLs/VarChaModel2GeoVaLs.h
+0 −1		src/fv3jedi/VariableChange/VariableChange.cc
+0 −1		src/fv3jedi/VariableChange/VertRemap/VarChaVertRemap.cc
+0 −1		src/fv3jedi/VariableChange/VertRemap/VarChaVertRemap.h
+6 −0		src/mains/CMakeLists.txt
+18 −0		src/mains/fv3jediProcessPerts.cc
+11 −0		test/CMakeLists.txt
+6 −2		test/testinput/4dvar_append_obs.yaml
+1 −0		test/testinput/forecast_ufs_1.yaml
+1 −0		test/testinput/forecast_ufs_2.yaml
+142 −0		test/testinput/processperts_gfs.yaml
+26 −26		test/testoutput/4dvar_append_obs.ref
+140 −0		test/testoutput/processperts_gfs.ref
+1 −3		share/ioda/yaml/iodatest_odb_groundgps.yaml
+2 −5		share/ioda/yaml/odb_default_name_map.yaml
+2 −5		share/ioda/yaml/odb_gnssro_name_map.yaml
+2 −5		share/ioda/yaml/odb_gnssro_profile_name_map.yaml
+2 −5		share/ioda/yaml/odb_surface_name_map.yaml
+2 −5		share/ioda/yaml/odb_surfacesst_name_map.yaml
+372 −237		src/ObsSpace.cc
+23 −4		src/ObsSpace.h
+7 −1		src/ObsSpaceParameters.h
+1 −0		src/containers/ColumnMetadatum.cpp
+1 −0		src/containers/Constants.h
+3 −0		src/containers/Data.cpp
+3 −0		src/containers/Datum.cpp
+28 −0		src/containers/FrameCols.cpp
+7 −0		src/containers/FrameCols.h
+17 −0		src/containers/FrameColsData.cpp
+23 −0		src/containers/FrameRows.cpp
+7 −0		src/containers/FrameRows.h
+19 −0		src/containers/Functions.cpp
+30 −0		src/containers/FunctionsCols.cpp
+4 −0		src/containers/FunctionsRows.cpp
+11 −0		src/containers/IFrame.h
+1 −1		src/core/IodaUtils.cc
+7 −1		src/engines/ioda/CMakeLists.txt
+82 −0		src/engines/ioda/include/ioda/Engines/ODC/ComplementarityInfo.h
+0 −19		src/engines/ioda/include/ioda/Engines/ODC/DataFromSQL.h
+39 −0		src/engines/ioda/include/ioda/Engines/ODC/ObsGroupTransform.h
+1 −1		src/engines/ioda/include/ioda/Engines/ODC/ObsGroupTransformFactory.h
+89 −0		src/engines/ioda/include/ioda/Engines/ODC/OdbColumnUtils.h
+37 −0		src/engines/ioda/include/ioda/Engines/ODC/OdbConstants.h
+36 −0		src/engines/ioda/include/ioda/Engines/ODC/ParsedColumnExpression.h
+1 −1		src/engines/ioda/include/ioda/Engines/ODC/VariableCreator.h
+0 −27		src/engines/ioda/include/ioda/Layout.h
+0 −33		src/engines/ioda/include/ioda/Misc/MergeMethods.h
+0 −15		src/engines/ioda/include/ioda/Variables/Has_Variables.h
+120 −0		src/engines/ioda/src/ioda/Engines/ODC/ComplementarityInfo.cpp
+1 −1		src/engines/ioda/src/ioda/Engines/ODC/DataFromSQL.cpp
+182 −240		src/engines/ioda/src/ioda/Engines/ODC/ODC.cpp
+94 −1		src/engines/ioda/src/ioda/Engines/ODC/ObsGroupTransform.cpp
+141 −0		src/engines/ioda/src/ioda/Engines/ODC/OdbColumnUtils.cpp
+51 −0		src/engines/ioda/src/ioda/Engines/ODC/ParsedColumnExpression.cpp
+1 −0		src/engines/ioda/src/ioda/Engines/ODC/VariableCreator.cpp
+1 −0		src/engines/ioda/src/ioda/Engines/ODC/VariableReader.cpp
+0 −133		src/engines/ioda/src/ioda/Has_Variables.cpp
+0 −22		src/engines/ioda/src/ioda/Layouts/Layout.cpp
+1 −86		src/engines/ioda/src/ioda/Layouts/Layout_ObsGroup_ODB.cpp
+0 −19		src/engines/ioda/src/ioda/Layouts/Layout_ObsGroup_ODB.h
+0 −18		src/engines/ioda/src/ioda/Layouts/Layout_ObsGroup_ODB_Params.h
+1 −2		src/engines/test/ioda/CMakeLists.txt
+0 −28		src/engines/test/ioda/layouts/CMakeLists.txt
+0 −5		src/engines/test/ioda/layouts/odb_concat_name_map.yaml
+0 −5		src/engines/test/ioda/layouts/odb_matchinginputoutput_name_map.yaml
+0 −5		src/engines/test/ioda/layouts/odb_verticalreference_name_map.yaml
+0 −55		src/engines/test/ioda/layouts/test-layoutobsgroup.cpp
+0 −94		src/engines/test/ioda/layouts/test-layoutodb.cpp
+0 −5		src/engines/test/ioda/variables/CMakeLists.txt
+0 −13		src/engines/test/ioda/variables/hasvariables_stitching_map.yaml
+0 −155		src/engines/test/ioda/variables/test_stitchcomplementaryvariables.cpp
+121 −9		src/mains/filterObs/filterObs.hpp
+43 −9		test/CMakeLists.txt
+0 −24		test/ioda/ObsSpace.h
+1 −2		test/ioda/ObsSpaceAppend.h
+19 −0		test/mains/TestIodaObsSpaceOSDF.cc
+28 −0		test/testinput/iodatest_filter_obs_amsua.yaml
+27 −0		test/testinput/iodatest_filter_obs_sondes.yaml
+36 −0		test/testinput/iodatest_obsspace.yaml
+6 −6		test/testinput/iodatest_obsspace_append.yaml
+4 −4		test/testinput/iodatest_obsspace_append_mpi.yaml
+0 −119		test/testinput/iodatest_obsspace_dataframe_flag.yaml
+37 −0		test/testinput/iodatest_obsspace_out_odc.yaml
+35 −0		test/testinput/iodatest_obsspace_out_odc_readbackin.yaml
+2 −1		src/gnssro/CMakeLists.txt
+516 −0		src/gnssro/gnss_tec_ground_based.py
+1 −0		src/hdf5/CMakeLists.txt
+445 −0		src/hdf5/ozone_product_2ioda.py
+232 −82		src/hdf5/tropics_2ioda.py
+28 −1		test/CMakeLists.txt
+3 −0		test/testinput/V8PRO-EDR_v3r3_j01_s202202142345436_e202202142346211_c202202150032490.nc
+683 −0		test/testinput/tec_groundBased_TENET_20201001T00Z.tec
+3 −0		test/testoutput/20220214T21Z_PT6H_ozonecolumn_omps_n20.sample.nc4
+3 −0		test/testoutput/obs.20201001T000000Z_PT1M_tec_groundbased.nc4
+15 −2		l95/src/lorenz95/ObsData1D.h
+2 −2		l95/src/lorenz95/ObsTable.cc
+1 −1		l95/src/lorenz95/ObsTable.h
+8 −0		l95/src/lorenz95/ObsVec1D.cc
+3 −0		l95/src/lorenz95/ObsVec1D.h
+14 −2		qg/model/ObsDataQG.h
+2 −2		qg/model/ObsSpaceQG.cc
+1 −1		qg/model/ObsSpaceQG.h
+8 −0		qg/model/ObsVecQG.cc
+4 −1		qg/model/ObsVecQG.h
+0 −4		src/CMakeLists.txt
+28 −1		src/oops/assimilation/CostFct3DVar.h
+38 −3		src/oops/assimilation/CostFct4DEnsVar.h
+37 −3		src/oops/assimilation/CostFct4DVar.h
+29 −1		src/oops/assimilation/CostFctFGAT.h
+38 −2		src/oops/assimilation/CostFctWeak.h
+2 −12		src/oops/assimilation/CostFunction.h
+10 −0		src/oops/assimilation/CostJb3D.h
+10 −0		src/oops/assimilation/CostJb4D.h
+10 −0		src/oops/assimilation/CostJbJq.h
+3 −0		src/oops/assimilation/CostJbState.h
+34 −13		src/oops/assimilation/CostJbTotal.h
+23 −5		src/oops/assimilation/CostJcDFI.h
+10 −21		src/oops/assimilation/CostJo.h
+3 −0		src/oops/assimilation/CostTermBase.h
+2 −2		src/oops/assimilation/IncrementalAssimilation.h
+1 −0		src/oops/base/GetValuePosts.h
+14 −2		src/oops/base/GetValues.h
+7 −13		src/oops/base/IncrementEnsemble.h
+8 −5		src/oops/base/ObsSpaces.h
+9 −0		src/oops/base/Observations.h
+14 −0		src/oops/base/Observer.h
+14 −0		src/oops/base/Observers.h
+1 −0		src/oops/base/StateEnsemble.h
+0 −32		src/oops/base/WriteParametersBase.cc
+0 −84		src/oops/base/WriteParametersBase.h
+1 −68		src/oops/interface/Increment.h
+16 −0		src/oops/interface/ObsDataVector.h
+4 −0		src/oops/interface/ObsDataVector_head.h
+3 −3		src/oops/interface/ObsSpace.h
+12 −0		src/oops/interface/ObsVector.h
+11 −57		src/oops/runs/AddIncrement.h
+9 −15		src/oops/runs/ConvertIncrement.h
+1 −3		src/oops/runs/ConvertToStructuredGrid.h
+1 −3		src/oops/runs/DiffStates.h
+2 −3		src/oops/runs/EnsMeanAndVariance.h
+15 −17		src/oops/runs/LocalEnsembleDA.h
+5 −10		src/oops/runs/RescaleEnsPerts.h
+4 −6		src/oops/runs/SqrtOfVertLoc.h
+28 −0		src/oops/util/TimeWindow.cc
+10 −3		src/oops/util/TimeWindow.h
+0 −54		src/oops/util/parameters/HasReadParameters_.h
+0 −54		src/oops/util/parameters/HasWriteParameters_.h
+8 −3		quench/src/LinearVariableChangeParameters.h
+9 −5		quench/src/VariableChangeParameters.h
+3 −7		src/saber/oops/ProcessPerts.h
+1 −1		src/saber/oops/Utilities.h
+1 −0		src/saber/spectralb/spectralbParameters.h
+2 −2		test/testdata/gauss_state.nc
+6 −7		src/soca/LinearVariableChange/Base/LinearVariableChangeBase.h
+6 −5		src/soca/LinearVariableChange/LinearVariableChange.h
+5 −4		src/soca/VariableChange/Base/VariableChangeBase.h
+4 −1		src/soca/VariableChange/Soca2Cice/Soca2Cice.F90
+19 −4		src/soca/VariableChange/Soca2Cice/Soca2Cice.cc
+7 −0		src/soca/VariableChange/Soca2Cice/Soca2Cice.h
+11 −11		src/soca/VariableChange/Soca2Cice/soca_ciceutils_mod.F90
+94 −80		src/soca/VariableChange/Soca2Cice/soca_soca2cice_mod.F90
+2 −4		src/soca/VariableChange/VariableChange.h
+6 −6		test/testref/convertstate_soca2cice.test
+2 −0		src/ufo/filters/CMakeLists.txt
+54 −17		src/ufo/filters/PrintFilterData.cc
+435 −0		src/ufo/filters/obsfunctions/StableLayersCloudTopPressure.cc
+160 −0		src/ufo/filters/obsfunctions/StableLayersCloudTopPressure.h
+16 −0		src/ufo/operators/crtm/ufo_crtm_utils_mod.F90
+11 −6		src/ufo/utils/Constants.h
+1 −0		test/CMakeLists.txt
+20 −0		test/testinput/unit_tests/filters/CMakeLists.txt
+10 −1		test/testinput/unit_tests/filters/obsfunctions/CMakeLists.txt
+92 −0		test/testinput/unit_tests/filters/obsfunctions/function_cloudtoppressure.yaml
+38 −0		test/testinput/unit_tests/filters/print_filter_data_time_window_selection.yaml
+383 −0		test/testref/unit_tests/filters/print_filter_data_time_window_selection.ref