[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 <[email protected]>
EdwardSnyder-NOAA · Mar 20, 2024 · 6010eff · 6010eff
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diff --git a/.github/workflows/python_tests.yaml b/.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: |

diff --git a/environment.yml b/environment.yml
@@ -5,4 +5,4 @@ channels:
 dependencies:
  - pylint=2.17*
  - pytest=7.2*
- - uwtools=1.0.0
+ - uwtools=2.1*
diff --git a/modulefiles/build_hera_gnu.lua b/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")

diff --git a/modulefiles/build_hera_intel.lua b/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"

diff --git a/parm/FV3.input.yml b/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
diff --git a/parm/fixed_files_mapping.yaml b/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"
- ]
-
 
  #
  #-----------------------------------------------------------------------