[develop] Use uwtools instead of set_namelist (ufs-community#1054)

Continues the integration of the uwtools package. In this PR, I've done the following:
 * Call the UW config tool instead of set_namelist using the uwtools CLI in bash scripts and API in Python scripts
 * Lint the ush/set_fv3nml*.py files
 * Update uwtools to the latest release version

---------

Co-authored-by: michael.lueken <Michael.Lueken@noaa.gov>

.github/workflows/python_tests.yaml

@@ -41,6 +41,8 @@ jobs:
           pylint --ignore-imports=yes tests/test_python/
           pylint ush/create_*.py
           pylint ush/generate_FV3LAM_wflow.py
+          pylint ush/set_fv3nml*.py
+          pylint ush/update_input_nml.py
 
       - name: Run python unittests
         run: |

environment.yml

@@ -5,4 +5,4 @@ channels:
 dependencies:
   - pylint=2.17*
   - pytest=7.2*
-  - uwtools=1.0.0
+  - uwtools=2.1*

modulefiles/build_hera_gnu.lua

@@ -5,10 +5,7 @@ the NOAA RDHPC machine Hera using GNU 9.2.0
 
 whatis([===[Loads libraries needed for building the UFS SRW App on Hera using GNU 9.2.0 ]===])
 
--- When Hera switches from CentOS to Rocky, replace line withh correct path to spack-stack
--- If you want to use Rocky OS now, use line below
---prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.0/envs/unified-env-rocky8/install/modulefiles/Core")
-prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.0/envs/unified-env-noavx512/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.0/envs/unified-env-rocky8/install/modulefiles/Core")
 prepend_path("MODULEPATH", "/scratch1/NCEPDEV/jcsda/jedipara/spack-stack/modulefiles")
 
 load("stack-gcc/9.2.0")

modulefiles/build_hera_intel.lua

@@ -8,10 +8,7 @@ whatis([===[Loads libraries needed for building the UFS SRW App on Hera ]===])
 prepend_path("MODULEPATH","/contrib/sutils/modulefiles")
 load("sutils")
 
--- When Hera switches from CentOS to Rocky, replace line withh correct path to spack-stack
--- If you want to use Rocky OS now, use line below
---prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.0/envs/unified-env-rocky8/install/modulefiles/Core")
-prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.0/envs/unified-env-noavx512/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.0/envs/unified-env-rocky8/install/modulefiles/Core")
 prepend_path("MODULEPATH", "/scratch1/NCEPDEV/jcsda/jedipara/spack-stack/modulefiles")
 
 stack_intel_ver=os.getenv("stack_intel_ver") or "2021.5.0"

parm/FV3.input.yml

@@ -4,12 +4,7 @@
 #   parm/input.nml.FV3
 #
 # to obtain the namelist for each physics suite that the SRW App can 
-# run with.  To build a namelist for one of these configurations, use 
-# the Python helper script 
-#
-#   ush/set_namelist.py
-#
-# and provide this file and the desired section via the -c option.
+# run with.
 
 
 FV3_RRFS_v1beta:
@@ -83,11 +78,11 @@ FV3_HRRR:
     <<: *RRFS_v1beta_phys
     cdmbgwd: [3.5, 1.0]
     do_mynnsfclay: True
-    do_sfcperts: !!python/none
+    do_sfcperts: null
     gwd_opt: 3
     do_gsl_drag_ss: True
     do_gsl_drag_tofd: True
-    do_gsl_drag_ls_bl: True 
+    do_gsl_drag_ls_bl: True
     iaer: 5111
     icliq_sw: 2
     iovr: 3
@@ -102,8 +97,8 @@ FV3_HRRR:
     mosaic_lu: 0
     mosaic_soil: 0
     thsfc_loc: False
-    nst_anl:
-    nstf_name:
+    nst_anl: null
+    nstf_name: null
 
 FV3_RAP:
   fv_core_nml:
@@ -112,7 +107,7 @@ FV3_RAP:
     <<: *RRFS_v1beta_phys
     cdmbgwd: [3.5, 1.0]
     do_mynnsfclay: True
-    do_sfcperts: !!python/none
+    do_sfcperts: null
     gwd_opt: 3
     do_gsl_drag_ss: True
     do_gsl_drag_tofd: True
@@ -140,40 +135,40 @@ FV3_GFS_2017_gfdlmp:
     k_split: 6
     n_split: 6
     nord: 2
-    nord_zs_filter: !!python/none
+    nord_zs_filter: null
     range_warn: False
     vtdm4: 0.075
   gfs_physics_nml: &gfs_2017_gfdlmp_phys
     avg_max_length: 3600.0
-    bl_mynn_tkeadvect: !!python/none
-    bl_mynn_edmf: !!python/none
-    bl_mynn_edmf_mom: !!python/none
+    bl_mynn_tkeadvect: null
+    bl_mynn_edmf: null
+    bl_mynn_edmf_mom: null
     cdmbgwd: [3.5, 0.01]
-    cplflx: !!python/none
+    cplflx: null
     do_deep: False
-    do_mynnedmf: !!python/none
-    do_mynnsfclay: !!python/none
+    do_mynnedmf: null
+    do_mynnsfclay: null
     fhcyc: 0.0
     fhlwr: 3600.0
     fhswr: 3600.0
     hybedmf: True
-    icloud_bl: !!python/none
+    icloud_bl: null
     imfdeepcnv: 2
     imfshalcnv: 2
     imp_physics: 11
     lgfdlmprad: True
-    lheatstrg: !!python/none
-    lndp_type: !!python/none
-    lsm: !!python/none
-    lsoil: !!python/none
-    lsoil_lsm: !!python/none
-    ltaerosol: !!python/none
-    n_var_lndp: !!python/none
+    lheatstrg: null
+    lndp_type: null
+    lsm: null
+    lsoil: null
+    lsoil_lsm: null
+    ltaerosol: null
+    n_var_lndp: null
     oz_phys: True
     oz_phys_2015: False
-    satmedmf: !!python/none
+    satmedmf: null
     shal_cnv: True
-    ttendlim: !!python/none
+    ttendlim: null
   gfdl_cloud_microphysics_nml: &gfs_gfdl_cloud_mp
     c_cracw: 0.8
     c_paut: 0.5
@@ -272,7 +267,7 @@ FV3_GFS_v15p2:
     kord_wz: 9
     n_split: 8
     n_sponge: 30
-    nord_zs_filter: !!python/none
+    nord_zs_filter: null
     nudge_qv: True
     range_warn: False
     rf_cutoff: 750.0
@@ -283,29 +278,29 @@ FV3_GFS_v15p2:
     tau_l2v: 225.0
     tau_v2l: 150.0
   gfs_physics_nml: &gfs_v15_gfs_physics
-    bl_mynn_edmf: !!python/none
-    bl_mynn_edmf_mom: !!python/none
-    bl_mynn_tkeadvect: !!python/none
+    bl_mynn_edmf: null
+    bl_mynn_edmf_mom: null
+    bl_mynn_tkeadvect: null
     cnvcld: True
     cnvgwd: True    
-    cplflx: !!python/none
+    cplflx: null
     do_myjpbl: False
     do_myjsfc: False
-    do_mynnedmf: !!python/none
-    do_mynnsfclay: !!python/none
+    do_mynnedmf: null
+    do_mynnsfclay: null
     do_tofd: False
     do_ugwp: False
     do_ysu: False
     fhcyc: 0.0
     fhlwr: 3600.0
     fhswr: 3600.0
     hybedmf: True
-    iau_delthrs: !!python/none
-    iaufhrs: !!python/none
+    iau_delthrs: null
+    iaufhrs: null
     imfdeepcnv: 2
     imfshalcnv: 2
     imp_physics: 11
-    icloud_bl: !!python/none
+    icloud_bl: null
     iopt_alb: 2
     iopt_btr: 1
     iopt_crs: 1
@@ -321,28 +316,28 @@ FV3_GFS_v15p2:
     iopt_trs: 2
     ldiag_ugwp: False
     lgfdlmprad: True
-    lradar: !!python/none
+    lradar: null
     lsm: 1
-    lsoil: !!python/none
-    lsoil_lsm: !!python/none
-    ltaerosol: !!python/none
+    lsoil: null
+    lsoil_lsm: null
+    ltaerosol: null
     shal_cnv: True
     shinhong: False
-    ttendlim: !!python/none
+    ttendlim: null
     xkzm_h: 1.0
     xkzm_m: 1.0
     xkzminv: 0.3
   namsfc:
     landice: True
     ldebug: False
-  surf_map_nml:
+  surf_map_nml: null
 
 FV3_GFS_v15_thompson_mynn_lam3km:
   atmos_model_nml:
     avg_max_length: 3600.0
   fv_core_nml:
     agrid_vel_rst: True
-    full_zs_filter: !!python/none
+    full_zs_filter: null
     n_sponge: 9
     npz_type: ''
     rf_fast: False
@@ -382,20 +377,20 @@ FV3_GFS_v15_thompson_mynn_lam3km:
     iopt_snf: 4
     iopt_stc: 1
     iopt_tbot: 2
-    iopt_trs: !!python/none
+    iopt_trs: null
     iovr: 3
     ldiag_ugwp: False
     lgfdlmprad: False
     lsm: 1
-    lsoil: !!python/none
-    lsoil_lsm: !!python/none
+    lsoil: null
+    lsoil_lsm: null
     ltaerosol: False    
     print_diff_pgr: True
-    sfclay_compute_flux: !!python/none
+    sfclay_compute_flux: null
     xkzminv: 0.3
     xkzm_m: 1.0
     xkzm_h: 1.0
-  surf_map_nml: !!python/none
+  surf_map_nml: null
 
 FV3_GFS_v16:
   cires_ugwp_nml:
@@ -419,7 +414,7 @@ FV3_GFS_v16:
     na_init: 0
     nudge_dz: False
     res_latlon_dynamics: ''
-    rf_fast: !!python/none
+    rf_fast: null
     tau: 10.0
   gfdl_cloud_microphysics_nml:
     <<: *gfs_gfdl_cloud_mp
@@ -431,10 +426,10 @@ FV3_GFS_v16:
   gfs_physics_nml:
     <<: *gfs_v15_gfs_physics
     cdmbgwd: [4.0, 0.15, 1.0, 1.0]
-    do_myjpbl: !!python/none
-    do_myjsfc: !!python/none
+    do_myjpbl: null
+    do_myjsfc: null
     do_tofd: True
-    do_ysu: !!python/none
+    do_ysu: null
     hybedmf: False
     iaer: 5111
     icliq_sw: 2
@@ -443,23 +438,23 @@ FV3_GFS_v16:
     isatmedmf: 1
     lgfdlmprad: True
     lheatstrg: True
-    lndp_type: !!python/none
+    lndp_type: null
     lsoil: 4
-    n_var_lndp: !!python/none
+    n_var_lndp: null
     prautco: [0.00015, 0.00015]
     psautco: [0.0008, 0.0005]
     satmedmf: True
-    shinhong: !!python/none
-    xkzminv: !!python/none
-    xkzm_m: !!python/none
-    xkzm_h: !!python/none
+    shinhong: null
+    xkzminv: null
+    xkzm_m: null
+    xkzm_h: null
   mpp_io_nml:
     deflate_level: 1
     shuffle: 1
   namsfc:
     landice: True
     ldebug: False
-  surf_map_nml: !!python/none
+  surf_map_nml: null
 
 FV3_GFS_v17_p8:
   cires_ugwp_nml:
@@ -485,7 +480,7 @@ FV3_GFS_v17_p8:
     nord: 1
     nudge_dz: False
     res_latlon_dynamics: ''
-    rf_fast: !!python/none
+    rf_fast: null
     tau: 10.0
   gfs_physics_nml:
     cdmbgwd: [4.0, 0.05, 1.0, 1.0]
@@ -548,6 +543,4 @@ FV3_GFS_v17_p8:
   mpp_io_nml:
     deflate_level: 1
     shuffle: 1
-  namsfc:
-  surf_map_nml: !!python/none
-
+  surf_map_nml: null

parm/fixed_files_mapping.yaml

@@ -139,35 +139,6 @@ fixed_files:
   !join_str ["FNSMCC | ",*FNSMCC],
   !join_str ["FNMSKH | ",*FNMSKH]
   ]
-  #"FNZORC | $FNZORC",
-
-  #
-  #-----------------------------------------------------------------------
-  #
-  # FV3_NML_VARNAME_TO_SFC_CLIMO_FIELD_MAPPING:
-  # This array is used to set some of the namelist variables in the forecast 
-  # model's namelist file that represent the relative or absolute paths of 
-  # various fixed files (the first column of the array, where columns are 
-  # delineated by the pipe symbol "|") to the full paths to surface climatology 
-  # files (on the native FV3-LAM grid) in the FIXlam directory derived from 
-  # the corresponding surface climatology fields (the second column of the 
-  # array).
-  #
-  #-----------------------------------------------------------------------
-  #
-  FV3_NML_VARNAME_TO_SFC_CLIMO_FIELD_MAPPING: [
-  "FNALBC  | snowfree_albedo",
-  "FNALBC2 | facsf",
-  "FNTG3C  | substrate_temperature",
-  "FNVEGC  | vegetation_greenness",
-  "FNVETC  | vegetation_type",
-  "FNSOTC  | soil_type",
-  "FNVMNC  | vegetation_greenness",
-  "FNVMXC  | vegetation_greenness",
-  "FNSLPC  | slope_type",
-  "FNABSC  | maximum_snow_albedo"
-  ]
-
 
   #
   #-----------------------------------------------------------------------