GEOS-ESM · danholdaway · Aug 10, 2023 · Mar 14, 2023 · Mar 22, 2023 · Mar 23, 2023
@@ -8,5 +8,5 @@ defaults:
     shell: bash
 
 jobs:
-  run-discover-nightly:
-    uses: GEOS-ESM/CI-workflows/.github/workflows/swell-discover-nightly.yml@main
+  run-tier1-apps-discover:
+    uses: GEOS-ESM/CI-workflows/.github/workflows/swell-tier1_application_discover.yml@feature/ufo_tests
@@ -12,5 +12,5 @@ defaults:
     shell: bash
 
 jobs:
-  run-discover-nightly:
-    uses: GEOS-ESM/CI-workflows/.github/workflows/swell-discover-nightly.yml@main
+  run-tier2-apps-discover:
+    uses: GEOS-ESM/CI-workflows/.github/workflows/swell-tier2_application_discover.yml@feature/ufo_tests
diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,7 @@
 # System files
 *.swp
 *DS_Store*
+._*
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

diff --git a/README.md b/README.md
@@ -15,7 +15,7 @@
 
 ### Licence:
 
-(C) Copyright 2021-2022 United States Government as represented by the Administrator of the National
+(C) Copyright 2021- United States Government as represented by the Administrator of the National
 Aeronautics and Space Administration. All Rights Reserved.
 
 [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)

diff --git a/requirements-standalone.txt b/requirements-standalone.txt
@@ -0,0 +1,12 @@
+click>=8.1.5
+jinja2>=3.1.2
+pyyaml>=6.0
+pycodestyle>=2.10.0
+pandas>=1.4.0
+isodate>=0.5.4
+f90nml>=1.4.3
+questionary>=1.10.0
+flake8>=6.0.0
+netCDF4
+xarray
+matplotlib
diff --git a/requirements.txt b/requirements.txt
@@ -1,7 +1,7 @@
 click>=8.1.5
 jinja2>=3.1.2
 pyyaml>=6.0
-pycodestyle>=2.8.0
+pycodestyle==2.8.0
 pandas>=1.4.0
 isodate>=0.5.4
 f90nml>=1.4.3

diff --git a/src/swell/__init__.py b/src/swell/__init__.py
@@ -9,4 +9,4 @@
 repo_directory = os.path.dirname(__file__)
 
 # Set the version for swell
-__version__ = '1.5.0'
+__version__ = '1.6.0'
diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/analysis.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/analysis.yaml
@@ -0,0 +1,6 @@
+filetype: cube sphere history
+provider: geos
+datapath: '{{cycle_dir}}'
+filename: '{{experiment_id}}.analysis.%yyyy%mm%dd_%hh%MM%ssz.nc4'
+first: PT0H
+frequency: PT1H
diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/background.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/background.yaml
@@ -4,7 +4,7 @@ provider: geos
 datapath: ''
 filenames: ['{{cycle_dir}}/bkg.%yyyy%mm%ddT%hh%MM%ssZ.nc4',
             '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/bkg/geos.crtmsrf.{{horizontal_resolution}}.nc4']
-state variables: [u,v,ua,va,t,delp,q,qi,ql,qr,qs,o3ppmv,phis,
+state variables: [u,v,ua,va,t,delp,ps,q,qi,ql,qr,qs,o3ppmv,phis,
                   qls,qcn,cfcn,frocean,frland,varflt,ustar,bstar,
                   zpbl,cm,ct,cq,kcbl,tsm,khl,khu,frlake,frseaice,vtype,
                   stype,vfrac,sheleg,ts,soilt,soilm,u10m,v10m]
diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/background_error.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/background_error.yaml
@@ -0,0 +1,28 @@
+covariance model: SABER
+saber central block:
+  saber block name: gsi covariance
+  read:
+    gsi akbk: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fv3files/akbk{{vertical_resolution}}.nc4'
+    gsi error covariance file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/gsibec/gsibec_coefficients_c{{horizontal_resolution}}.nc4'
+    gsi berror namelist file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/gsibec/gsibec_configuration_c{{horizontal_resolution}}.nml'
+    processor layout x direction: {{gsibec_npx_proc}}
+    processor layout y direction: {{gsibec_npy_proc}}
+    debugging mode: false
+saber outer blocks:
+- saber block name: gsi interpolation to model grid
+  state variables to inverse: &bvars [eastward_wind,northward_wind,air_temperature,surface_pressure,
+                                      specific_humidity,cloud_liquid_ice,cloud_liquid_water,
+                                      mole_fraction_of_ozone_in_air,
+                                      skin_temperature,
+                                      fraction_of_ocean,fraction_of_lake,fraction_of_ice,
+                                      sfc_geopotential_height_times_grav]
+  gsi akbk: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fv3files/akbk{{vertical_resolution}}.nc4'
+  gsi error covariance file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/gsibec/gsibec_coefficients_c{{horizontal_resolution}}.nc4'
+  gsi berror namelist file: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/gsibec/gsibec_configuration_c{{horizontal_resolution}}.nml'
+  processor layout x direction: {{gsibec_npx_proc}}
+  processor layout y direction: {{gsibec_npy_proc}}
+  debugging mode: false
+linear variable change:
+  linear variable change name: Control2Analysis
+  input variables: *bvars
+  output variables: {{analysis_variables}}
diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/geometry_inner.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/geometry_inner.yaml
@@ -0,0 +1,9 @@
+fms initialization:
+  namelist filename: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fv3files/fmsmpp.nml'
+  field table filename: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fv3files/field_table_gmao'
+akbk: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fv3files/akbk{{vertical_resolution}}.nc4'
+layout: [{{npx_proc}},{{npy_proc}}]
+npx: {{horizontal_resolution}}
+npy: {{horizontal_resolution}}
+npz: {{vertical_resolution}}
+field metadata override: '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fieldmetadata/geos.yaml'
diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/pseudo-model.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/pseudo-model.yaml
@@ -5,6 +5,3 @@ provider: geos
 datapath: ''
 filenames: ['{{cycle_dir}}/bkg.%yyyy%mm%ddT%hh%MM%ssZ.nc4',
             '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/bkg/geos.crtmsrf.{{horizontal_resolution}}.nc4']
-model variables: [u,v,ua,va,t,delp,q,qi,ql,qr,qs,o3ppmv,phis,qls,qcn,cfcn,frocean,frland,varflt,ustar,
-                  bstar,zpbl,cm,ct,cq,kcbl,tsm,khl,khu,frlake,frseaice,vtype,stype,vfrac,sheleg,
-                  ts,soilt,soilm,u10m,v10m]
diff --git a/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/stage.yaml b/src/swell/configuration/jedi/interfaces/geos_atmosphere/model/stage.yaml
@@ -3,3 +3,5 @@
       - ['{{swell_static_files}}/jedi/interfaces/geos_atmosphere/GEOS_CRTM_Surface/geos.crtmsrf.{{horizontal_resolution}}.nc4', '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/bkg/']
       - ['{{experiment_root}}/{{experiment_id}}/jedi_bundle/source/fv3-jedi/test/Data/fieldmetadata/*', '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fieldmetadata/']
       - ['{{experiment_root}}/{{experiment_id}}/jedi_bundle/source/fv3-jedi/test/Data/fv3files/*', '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/fv3files/']
+      - ['{{swell_static_files}}/jedi/interfaces/geos_atmosphere/gsibec/gsibec_coefficients_c{{horizontal_resolution}}.nc4', '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/gsibec/']
+      - ['{{swell_static_files}}/jedi/interfaces/geos_atmosphere/gsibec/gsibec_configuration_c{{horizontal_resolution}}.nml', '{{experiment_root}}/{{experiment_id}}/stage/fv3-jedi/geos_atmosphere/gsibec/']