Merge branch 'develop' into feature/land_snodl

NOAA-EMC · Jul 5, 2023 · 9b74ec2 · 9b74ec2
2 parents 64040a2 + 6f48fd2
commit 9b74ec2
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Showing 8 changed files with 46 additions and 73 deletions.
diff --git a/parm/aero/berror/staticb_bump.yaml b/parm/aero/berror/staticb_bump.yaml
diff --git a/parm/aero/berror/staticb_bump_aero.yaml b/parm/aero/berror/staticb_bump_aero.yaml
@@ -0,0 +1,23 @@
+covariance model: SABER
+saber central block:
+  saber block name: BUMP_NICAS
+  read:
+    io:
+      data directory: &staticb_aero_dir $(DATA)/berror
+      files prefix: 'nicas_aero'
+    drivers:
+      multivariate strategy: univariate
+      read local nicas: true
+  saber outer blocks:
+  - saber block name: StdDev
+    read: 
+      model file: 
+        datetime: '2016-06-30T00:00:00Z'
+        set datetime on read: true
+        filetype: fms restart
+        psinfile: true
+        datapath: Data/staticb_aero/
+        filename_core: 20160630.000000.stddev.fv_core.res.nc
+        filename_trcr: 20160630.000000.stddev.fv_tracer.res.nc
+        filename_cplr: 20160630.000000.stddev.coupler.res
+        date: '2016-06-30T00:00:00Z'
diff --git a/scripts/exgdas_global_marine_analysis_bmat.sh b/scripts/exgdas_global_marine_analysis_bmat.sh
@@ -134,7 +134,7 @@ if false; then
     # TODO: resurect this section when making use of bump 3D in the static B, skip for now
     yaml_bump2d=soca_bump2d.yaml
     clean_yaml $yaml_bump2d
-    $APRUN_OCNANAL $JEDI_BIN/soca_error_covariance_training.x $yaml_bump2d 2>$yaml_bump2d.err
+    $APRUN_OCNANAL $JEDI_BIN/soca_error_covariance_toolbox.x $yaml_bump2d 2>$yaml_bump2d.err
     export err=$?; err_chk
     if [ $err -gt 0  ]; then
         exit $err
@@ -144,7 +144,7 @@ if false; then
     yaml_list=`ls soca_bump3d_*.yaml`
     for yaml in $yaml_list; do
         clean_yaml $yaml
-        $APRUN_OCNANAL $JEDI_BIN/soca_error_covariance_training.x $yaml 2>$yaml.err
+        $APRUN_OCNANAL $JEDI_BIN/soca_error_covariance_toolbox.x $yaml 2>$yaml.err
         export err=$?; err_chk
         if [ $err -gt 0  ]; then
             exit $err
@@ -156,7 +156,7 @@ fi
 ################################################################################
 # Compute convolution coefs for L
 clean_yaml soca_bump_loc.yaml
-$APRUN_OCNANAL $JEDI_BIN/soca_error_covariance_training.x soca_bump_loc.yaml
+$APRUN_OCNANAL $JEDI_BIN/soca_error_covariance_toolbox.x soca_bump_loc.yaml
 export err=$?; err_chk
 if [ $err -gt 0  ]; then
     exit $err

diff --git a/test/atm/global-workflow/CMakeLists.txt b/test/atm/global-workflow/CMakeLists.txt
@@ -59,3 +59,14 @@ add_test(NAME test_gdasapp_atm_jjob_ens_final
   COMMAND ${PROJECT_SOURCE_DIR}/test/atm/global-workflow/jjob_ens_final.sh
           ${PROJECT_BINARY_DIR} ${PROJECT_SOURCE_DIR}
   WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/atm/global-workflow/testrun)
+
+# python fix
+  set_tests_properties(
+      test_gdasapp_run_jedi_exe_3dhofx
+      test_gdasapp_run_jedi_exe_3dvar
+      test_gdasapp_run_jedi_exe_3denvar
+      test_gdasapp_run_jedi_exe_letkf
+      PROPERTIES
+          ENVIRONMENT "PYTHONPATH=${PROJECT_BINARY_DIR}/lib/python${Python3_VERSION_MAJOR}.${Python3_VERSION_MINOR}:$ENV{PYTHONPATH}"
+  )
+
diff --git a/test/genYAML_prep_aero.sh b/test/genYAML_prep_aero.sh
@@ -6,7 +6,7 @@ cat > testoutput/genYAML_example_aero.yaml << EOF
 template: ${srcdir}/parm/aero/variational/3dvar_gfs_aero.yaml
 output: ${bindir}/test/testoutput/genYAML_output_3dvar_gfs_aero.yaml
 config:
-  BERROR_YAML: \${PARMgfs}/aero/berror/staticb_bump.yaml
+  BERROR_YAML: \${PARMgfs}/aero/berror/staticb_bump_aero.yaml
   OBS_YAML_DIR: \${PARMgfs}/aero/obs/config
   COMPONENT: chem 
   layout_x: '8'

diff --git a/test/land/test_imsproc.sh b/test/land/test_imsproc.sh
@@ -56,7 +56,7 @@ done
 ulimit -Ss unlimited
 ${EXECDIR}/calcfIMS.exe
 
-export PYTHONPATH=$PYTHONPATH:${project_source_dir}/iodaconv/src/:${project_source_dir}/build/lib/python${Python3_VERSION_MAJOR}.${Python3_VERSION_MINOR}/pyioda/
+export PYTHONPATH=$PYTHONPATH:${project_source_dir}/iodaconv/src/:${project_source_dir}/build/lib/python${Python3_VERSION_MAJOR}.${Python3_VERSION_MINOR}
 IMS_IODA=${EXECDIR}/imsfv3_scf2ioda.py
 
 echo 'do_landDA: calling ioda converter'

diff --git a/test/soca/gw/CMakeLists.txt b/test/soca/gw/CMakeLists.txt
@@ -27,7 +27,7 @@ add_test(NAME test_gdasapp_soca_concatioda
          WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/soca/gw/concatioda)
        set_tests_properties(test_gdasapp_soca_concatioda
       PROPERTIES
-      ENVIRONMENT "PYTHONPATH=${PROJECT_BINARY_DIR}/ush:$ENV{PYTHONPATH}")
+      ENVIRONMENT "PYTHONPATH=${PROJECT_BINARY_DIR}/ush:${PROJECT_BINARY_DIR}/lib/python${Python3_VERSION_MAJOR}.${Python3_VERSION_MINOR}:$ENV{PYTHONPATH}")
 
 # Clean-up
 add_test(NAME test_gdasapp_soca_run_clean
@@ -58,6 +58,10 @@ foreach(jjob ${jjob_list})
          -y ${PROJECT_BINARY_DIR}/test/soca/gw/testrun/run_jjobs_${jjob}.yaml
          ${setup}
     WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/soca/gw/testrun)
+  set_tests_properties(${test_name}
+    PROPERTIES
+    ENVIRONMENT "PYTHONPATH=${PROJECT_BINARY_DIR}/lib/python${Python3_VERSION_MAJOR}.${Python3_VERSION_MINOR}:$ENV{PYTHONPATH}")
+
 
   set(setup "--skip") # Only run the setup of the first test, if not, it will hang
                       # waiting for standard input from setup_expt.py

diff --git a/ush/ufsda/soca_utils.py b/ush/ufsda/soca_utils.py
@@ -18,8 +18,8 @@
 pyiodaconv_lib = Path(os.path.join(jedilib, 'pyiodaconv')).resolve()
 sys.path.append(str(pyioda_lib))
 sys.path.append(str(pyiodaconv_lib))
-import ioda_conv_engines as iconv
-from orddicts import DefaultOrderedDict
+import pyiodaconv.ioda_conv_engines as iconv
+from pyiodaconv.orddicts import DefaultOrderedDict
 
 __all__ = ['concatenate_ioda']