[develop]: Remove shell workflow. (ufs-community#764)

* Bug fix with FIELD_TABLE_FN

* Modify crontab management, use config_defaults.sh.

* Add status badge.

* Update cheyenne crontab management.

* source lmod-setup

* Add main to set_predef_grid

* Bug fix in predef_grid

* Don't import dead params.

* Fix bug in resetting VERBOSE

* Minor fix in INI config.

* Construct var_defns components from dictionary.

* Allow also lower case variables to be exported.

* Updates to python workflow due to PR ufs-community#776

* Use python versions of link_fix and set_FV3_sfc in job script.

* Use python versions of create_diag/model.

* Some fixes addressing Christina's suggestions.

* Delete shell workflow

* Append pid to temp files.

* Update scripts to work with the latest hashes of UFS_UTILS and UPP (ufs-community#775)

* update input namelist of chgres_cube

* update diag_table templates

* update scripts

* back to original

* specify miniconda version on Jet

* Remove -S option from link_fix call.

* Fixes due to merge

* Cosmoetic changes.

Co-authored-by: Chan-Hoo.Jeon-NOAA <[email protected]>

README.md

@@ -1,3 +1,5 @@
+[![Python unittests](https://github.com/ufs-community/regional_workflow/actions/workflows/python_unittests.yaml/badge.svg)](https://github.com/ufs-community/regional_workflow/actions/workflows/python_unittests.yaml)
+
 # Regional Workflow
 
 **The regional workflow in this repository can no longer be run in a stand-alone configuration. To clone the end-to-end system, build the code, and run the workflow, see:**

scripts/exregional_make_grid.sh

@@ -17,8 +17,6 @@
 #-----------------------------------------------------------------------
 #
 . $USHDIR/make_grid_mosaic_file.sh
-. $USHDIR/link_fix.sh
-. $USHDIR/set_FV3nml_sfc_climo_filenames.sh
 #
 #-----------------------------------------------------------------------
 #
@@ -589,9 +587,9 @@ halo failed."
 #
 #-----------------------------------------------------------------------
 #
-link_fix \
-  verbose="$VERBOSE" \
-  file_group="grid" || \
+python3  $USHDIR/link_fix.py \
+  --path-to-defns ${GLOBAL_VAR_DEFNS_FP} \
+  --file-group "grid" || \
 print_err_msg_exit "\
 Call to function to create symlinks to the various grid and mosaic files
 failed."
@@ -607,7 +605,9 @@ failed."
 #
 #-----------------------------------------------------------------------
 #
-set_FV3nml_sfc_climo_filenames || print_err_msg_exit "\
+python3 $USHDIR/set_FV3nml_sfc_climo_filenames.py \
+  --path-to-defns ${GLOBAL_VAR_DEFNS_FP} \
+    || print_err_msg_exit "\
 Call to function to set surface climatology file names in the FV3 namelist
 file failed."
 #

scripts/exregional_make_orog.sh

@@ -12,14 +12,6 @@
 #
 #-----------------------------------------------------------------------
 #
-# Source other necessary files.
-#
-#-----------------------------------------------------------------------
-#
-. $USHDIR/link_fix.sh
-#
-#-----------------------------------------------------------------------
-#
 # Save current shell options (in a global array).  Then set new options
 # for this script/function.
 #
@@ -581,9 +573,9 @@ cd_vrfy -
 #
 #-----------------------------------------------------------------------
 #
-link_fix \
-  verbose="$VERBOSE" \
-  file_group="orog" || \
+python3  $USHDIR/link_fix.py \
+  --path-to-defns ${GLOBAL_VAR_DEFNS_FP} \
+  --file-group "orog" || \
 print_err_msg_exit "\
 Call to function to create links to orography files failed."
 #

scripts/exregional_make_sfc_climo.sh

@@ -12,14 +12,6 @@
 #
 #-----------------------------------------------------------------------
 #
-# Source other necessary files.
-#
-#-----------------------------------------------------------------------
-#
-. $USHDIR/link_fix.sh
-#
-#-----------------------------------------------------------------------
-#
 # Save current shell options (in a global array).  Then set new options
 # for this script/function.
 #
@@ -241,9 +233,9 @@ esac
 #
 #-----------------------------------------------------------------------
 #
-link_fix \
-  verbose="$VERBOSE" \
-  file_group="sfc_climo" || \
+python3  $USHDIR/link_fix.py \
+  --path-to-defns ${GLOBAL_VAR_DEFNS_FP} \
+  --file-group "sfc_climo" || \
 print_err_msg_exit "\
 Call to function to create links to surface climatology files failed."
 #

scripts/exregional_run_fcst.sh

@@ -9,16 +9,6 @@
 #
 . ${GLOBAL_VAR_DEFNS_FP}
 . $USHDIR/source_util_funcs.sh
-. $USHDIR/set_FV3nml_ens_stoch_seeds.sh
-#
-#-----------------------------------------------------------------------
-#
-# Source other necessary files.
-#
-#-----------------------------------------------------------------------
-#
-. $USHDIR/create_model_configure_file.sh
-. $USHDIR/create_diag_table_file.sh
 #
 #-----------------------------------------------------------------------
 #
@@ -446,7 +436,9 @@ fi
 
 if [ "${DO_ENSEMBLE}" = TRUE ] && ([ "${DO_SPP}" = TRUE ] || [ "${DO_SPPT}" = TRUE ] || [ "${DO_SHUM}" = TRUE ] \
    [ "${DO_SKEB}" = TRUE ] || [ "${DO_LSM_SPP}" =  TRUE ]); then
-  set_FV3nml_ens_stoch_seeds cdate="$cdate" || print_err_msg_exit "\
+  python3 $USHDIR/set_FV3nml_ens_stoch_seeds.py \
+      --path-to-defns ${GLOBAL_VAR_DEFNS_FP} \
+      --cdate "$cdate" || print_err_msg_exit "\
 Call to function to create the ensemble-based namelist for the current
 cycle's (cdate) run directory (run_dir) failed:
   cdate = \"${cdate}\"
@@ -464,12 +456,13 @@ fi
 #
 #-----------------------------------------------------------------------
 #
-create_model_configure_file \
-  cdate="$cdate" \
-  run_dir="${run_dir}" \
-  sub_hourly_post="${SUB_HOURLY_POST}" \
-  dt_subhourly_post_mnts="${DT_SUBHOURLY_POST_MNTS}" \
-  dt_atmos="${DT_ATMOS}" || print_err_msg_exit "\
+python3 $USHDIR/create_model_configure_file.py \
+  --path-to-defns ${GLOBAL_VAR_DEFNS_FP} \
+  --cdate "$cdate" \
+  --run-dir "${run_dir}" \
+  --sub-hourly-post "${SUB_HOURLY_POST}" \
+  --dt-subhourly-post-mnts "${DT_SUBHOURLY_POST_MNTS}" \
+  --dt-atmos "${DT_ATMOS}" || print_err_msg_exit "\
 Call to function to create a model configuration file for the current
 cycle's (cdate) run directory (run_dir) failed:
   cdate = \"${cdate}\"
@@ -482,8 +475,9 @@ cycle's (cdate) run directory (run_dir) failed:
 #
 #-----------------------------------------------------------------------
 #
-create_diag_table_file \
-  run_dir="${run_dir}" || print_err_msg_exit "\
+python3 $USHDIR/create_diag_table_file.py \
+  --path-to-defns ${GLOBAL_VAR_DEFNS_FP} \
+  --run-dir "${run_dir}" || print_err_msg_exit "\
 Call to function to create a diag table file for the current cycle's 
 (cdate) run directory (run_dir) failed:
   run_dir = \"${run_dir}\""

tests/WE2E/get_WE2Etest_names_subdirs_descs.sh

@@ -438,9 +438,6 @@ function get_WE2Etest_names_subdirs_descs() {
 #
   ushdir=$( readlink -f "$WE2Edir/../../ush" )
   . $ushdir/constants.sh
-  . $ushdir/set_predef_grid_params.sh
-  . $ushdir/set_gridparams_GFDLgrid.sh
-  . $ushdir/set_gridparams_ESGgrid.sh
 #
 #-----------------------------------------------------------------------
 #
@@ -1220,70 +1217,16 @@ ${test_desc}${stripped_line} "
 # parameters.  The way the latter are obtained depends on whether or not
 # a predefined grid is being used.
 #
-# If using a predefined grid, call the set_predef_grid_params() function
-# to get the grid parameters.
-#
-      if [ ! -z "${PREDEF_GRID_NAME}" ]; then
-#
-# Note:
-# Can set "quilting" to "FALSE" in the following argument list because
-# the write-component parameters are not needed below; only those of the
-# native grid are needed.
-#
-        set_predef_grid_params \
-          predef_grid_name="${PREDEF_GRID_NAME}" \
-          quilting="FALSE" \
-          outvarname_grid_gen_method="grid_gen_method" \
-          outvarname_esggrid_lon_ctr="esggrid_lon_ctr" \
-          outvarname_esggrid_lat_ctr="esggrid_lat_ctr" \
-          outvarname_esggrid_delx="esggrid_delx" \
-          outvarname_esggrid_dely="esggrid_dely" \
-          outvarname_esggrid_nx="esggrid_nx" \
-          outvarname_esggrid_ny="esggrid_ny" \
-          outvarname_esggrid_pazi="esggrid_pazi" \
-          outvarname_esggrid_wide_halo_width="esggrid_wide_halo_width" \
-          outvarname_gfdlgrid_lon_t6_ctr="gfdlgrid_lon_t6_ctr" \
-          outvarname_gfdlgrid_lat_t6_ctr="gfdlgrid_lat_t6_ctr" \
-          outvarname_gfdlgrid_stretch_fac="gfdlgrid_stretch_fac" \
-          outvarname_gfdlgrid_num_cells="gfdlgrid_num_cells" \
-          outvarname_gfdlgrid_refine_ratio="gfdlgrid_refine_ratio" \
-          outvarname_gfdlgrid_istart_of_rgnl_dom_on_t6g="gfdlgrid_istart_of_rgnl_dom_on_t6g" \
-          outvarname_gfdlgrid_iend_of_rgnl_dom_on_t6g="gfdlgrid_iend_of_rgnl_dom_on_t6g" \
-          outvarname_gfdlgrid_jstart_of_rgnl_dom_on_t6g="gfdlgrid_jstart_of_rgnl_dom_on_t6g" \
-          outvarname_gfdlgrid_jend_of_rgnl_dom_on_t6g="gfdlgrid_jend_of_rgnl_dom_on_t6g" \
-          outvarname_dt_atmos="dta"
-#
-# If using a custom grid, the test's configuration file should contain 
-# the grid parameters.  Source this file and set the values of the grid
-# parameters it contains to local variables.
-#
-      else
-
-        . ./${config_fn}
-        grid_gen_method="${GRID_GEN_METHOD}"
-        if [ "${grid_gen_method}" = "GFDLgrid" ]; then
-          gfdlgrid_lon_t6_ctr="${GFDLgrid_LON_T6_CTR}"
-          gfdlgrid_lat_t6_ctr="${GFDLgrid_LAT_T6_CTR}"
-          gfdlgrid_num_cells="${GFDLgrid_NUM_CELLS}"
-          gfdlgrid_stretch_fac="${GFDLgrid_STRETCH_FAC}"
-          gfdlgrid_refine_ratio="${GFDLgrid_REFINE_RATIO}"
-          gfdlgrid_istart_of_rgnl_dom_on_t6g="${GFDLgrid_ISTART_OF_RGNL_DOM_ON_T6G}"
-          gfdlgrid_iend_of_rgnl_dom_on_t6g="${GFDLgrid_IEND_OF_RGNL_DOM_ON_T6G}"
-          gfdlgrid_jstart_of_rgnl_dom_on_t6g="${GFDLgrid_JSTART_OF_RGNL_DOM_ON_T6G}"
-          gfdlgrid_jend_of_rgnl_dom_on_t6g="${GFDLgrid_JEND_OF_RGNL_DOM_ON_T6G}"
-        elif [ "${grid_gen_method}" = "ESGgrid" ]; then
-          esggrid_lon_ctr="${ESGgrid_LON_CTR}"
-          esggrid_lat_ctr="${ESGgrid_LAT_CTR}"
-          esggrid_delx="${ESGgrid_DELX}"
-          esggrid_dely="${ESGgrid_DELY}"
-          esggrid_nx="${ESGgrid_NX}"
-          esggrid_ny="${ESGgrid_NY}"
-          esggrid_pazi="${ESGgrid_PAZI}"
-          esggrid_wide_halo_width="${ESGgrid_WIDE_HALO_WIDTH}"
-        fi
-        dta="${DT_ATMOS}"
+params=$(\
+  PREDEF_GRID_NAME="${PREDEF_GRID_NAME}" \
+  QUILTING="FALSE" \
+  RADIUS_EARTH=${RADIUS_EARTH} \
+  DEGS_PER_RADIAN=${DEGS_PER_RADIAN} \
+  NH4=${NH4} \
+    $ushdir/calculate_cost.py -c "${test_configs_basedir}/$subdir/${config_fn}")
+
+read dta nxny dta_r nxny_r <<< "${params}"
 
-      fi
 #
 # Save the value of dta (which is just dt_atmos) in an array.  The single 
 # quote at the beginning forces Google Sheets to interpret this quantity 
@@ -1292,49 +1235,9 @@ ${test_desc}${stripped_line} "
 #
       prim_test_dt_atmos+=( "'${dta}" )
 #
-# The way the number of grid points in the horizontal directions (nx and
-# ny) are calculated depends on the method used to generate the grid as 
-# well as the grid parameters for that method.
-#
-      if [ "${grid_gen_method}" = "GFDLgrid" ]; then
-#
-# Note:
-# The workflow generation mode (run_envir) can be set to "community" here
-# since this does not affect the values of nx and ny.
-#
-        set_gridparams_GFDLgrid \
-          lon_of_t6_ctr="${gfdlgrid_lon_t6_ctr}" \
-          lat_of_t6_ctr="${gfdlgrid_lat_t6_ctr}" \
-          res_of_t6g="${gfdlgrid_num_cells}" \
-          stretch_factor="${gfdlgrid_stretch_fac}" \
-          refine_ratio_t6g_to_t7g="${gfdlgrid_refine_ratio}" \
-          istart_of_t7_on_t6g="${gfdlgrid_istart_of_rgnl_dom_on_t6g}" \
-          iend_of_t7_on_t6g="${gfdlgrid_iend_of_rgnl_dom_on_t6g}" \
-          jstart_of_t7_on_t6g="${gfdlgrid_jstart_of_rgnl_dom_on_t6g}" \
-          jend_of_t7_on_t6g="${gfdlgrid_jend_of_rgnl_dom_on_t6g}" \
-          verbose="$verbose" \
-          outvarname_nx_of_t7_on_t7g="nx" \
-          outvarname_ny_of_t7_on_t7g="ny"
-
-      elif [ "${grid_gen_method}" = "ESGgrid" ]; then
-
-        set_gridparams_ESGgrid \
-          lon_ctr="${esggrid_lon_ctr}" \
-          lat_ctr="${esggrid_lat_ctr}" \
-          nx="${esggrid_nx}" \
-          ny="${esggrid_ny}" \
-          pazi="${esggrid_pazi}" \
-          halo_width="${esggrid_wide_halo_width}" \
-          delx="${esggrid_delx}" \
-          dely="${esggrid_dely}" \
-          outvarname_nx="nx" \
-          outvarname_ny="ny"
-
-      fi
-#
 # Calculate the total number of horizontal grid points.
 #
-      num_grid_pts=$(( nx*ny ))
+      num_grid_pts=$nxny
 #
 # Calculate the number of time steps for the test.  Note that FCST_LEN_HRS 
 # is in units of hours while dta is in units of seconds.  Also, the factor
@@ -1348,30 +1251,6 @@ ${test_desc}${stripped_line} "
 #
       ac=$(( num_grid_pts*num_time_steps*nf ))
 #
-# Unset all grid paramters so that they are not accidentally reused for
-# the next test.
-#
-      unset gfdlgrid_lon_t6_ctr \
-            gfdlgrid_lat_t6_ctr \
-            gfdlgrid_num_cells \
-            gfdlgrid_stretch_fac \
-            gfdlgrid_refine_ratio \
-            gfdlgrid_istart_of_rgnl_dom_on_t6g \
-            gfdlgrid_iend_of_rgnl_dom_on_t6g \
-            gfdlgrid_jstart_of_rgnl_dom_on_t6g \
-            gfdlgrid_jend_of_rgnl_dom_on_t6g \
-            esggrid_lon_ctr \
-            esggrid_lat_ctr \
-            esggrid_nx \
-            esggrid_ny \
-            esggrid_pazi \
-            esggrid_wide_halo_width \
-            esggrid_delx \
-            esggrid_dely \
-            dta \
-            nx \
-            ny
-#
 # Save the absolute cost for this test in the array that will eventually
 # contain the relative cost.  The values in this array will be divided
 # by abs_cost_ref later below to obtain relative costs.
@@ -1397,16 +1276,9 @@ ${test_desc}${stripped_line} "
 #
 #-----------------------------------------------------------------------
 #
-    set_predef_grid_params \
-      predef_grid_name="RRFS_CONUS_25km" \
-      quilting="FALSE" \
-      outvarname_esggrid_nx="nx" \
-      outvarname_esggrid_ny="ny" \
-      outvarname_dt_atmos="dta"
-
-    num_grid_pts=$(( nx*ny ))
+    num_grid_pts=$nxny_r
     fcst_len_hrs="6"
-    num_time_steps=$(( (fcst_len_hrs*3600 + dta - 1)/dta ))
+    num_time_steps=$(( (fcst_len_hrs*3600 + dta_r - 1)/dta_r ))
     abs_cost_ref=$(( num_grid_pts*num_time_steps ))
 
     for (( i=0; i<=$((num_prim_tests-1)); i++ )); do

tests/WE2E/run_WE2E_tests.sh

@@ -1281,7 +1281,7 @@ exist or is not a directory:
 #
 #-----------------------------------------------------------------------
 #
-  $ushdir/generate_FV3LAM_wflow.sh || \
+  $ushdir/generate_FV3LAM_wflow.py || \
     print_err_msg_exit "\
 Could not generate an experiment for the test specified by test_name:
   test_name = \"${test_name}\""

tests/WE2E/setup_WE2E_tests.sh

@@ -79,6 +79,7 @@ exec_subdir='bin_intel/bin'
 env_path="${SRW_APP_DIR}/modulefiles"
 env_file="wflow_${machine}"
 echo "-- Load environment =>" $env_file
+source ${SRW_APP_DIR}/etc/lmod-setup.sh ${machine}
 module use ${env_path}
 module load ${env_file}
 conda activate regional_workflow