Add Python Script to Translate Increments

.github/workflows/pynorms.yaml

@@ -1,5 +1,5 @@
 name: Check Python Coding Norms
-on: [push, pull_request]
+on: [push]
 
 jobs:
   check_pynorms:

.github/workflows/unittests.yaml

@@ -1,5 +1,5 @@
 name: Run Unit Tests
-on: [push, pull_request]
+on: [pull_request]
 
 jobs:
   ctests:
@@ -8,6 +8,12 @@ jobs:
 
     steps:
 
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip
+        pip install pycodestyle
+        pip install netCDF4
+
     - name: Checkout
       uses: actions/checkout@v2
       with:
@@ -41,3 +47,4 @@ jobs:
       run: |
         cd $GITHUB_WORKSPACE/build
         ctest --output-on-failure
+

CMakeLists.txt

@@ -3,7 +3,7 @@
 # ------------------------------------------------------------------------- #
 
 # Check for minimim cmake requirement
-cmake_minimum_required( VERSION 3.12 FATAL_ERROR )
+cmake_minimum_required( VERSION 3.20 FATAL_ERROR )
 
 find_package(ecbuild 3.5 REQUIRED HINTS ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/../ecbuild)
 

test/CMakeLists.txt

@@ -1,3 +1,41 @@
-add_test(NAME test_check_yaml_keys
+##### get test data from EMC FTP server
+# set URL and hash
+set(URL "https://ftp.emc.ncep.noaa.gov/static_files/public/GDASApp")
+set(SHA "75c4ce84028956c1ce050e07f70abc25c540492c3e1a40f6fa56d35182322e8e")
+string(SUBSTRING ${SHA} 0 6 SHORTSHA)
+set(TAR "gdasapp-fix-${SHORTSHA}.tgz")
+# download test files
+file(DOWNLOAD
+  ${URL}/${TAR}
+  ${CMAKE_CURRENT_BINARY_DIR}/${TAR}
+  INACTIVITY_TIMEOUT 30
+  TIMEOUT 90
+  SHOW_PROGRESS
+  STATUS status
+  EXPECTED_HASH SHA256=${SHA}
+  )
+# Extract downloaded tarball.
+file(ARCHIVE_EXTRACT INPUT ${TAR})
+
+# list of test files to install
+list(APPEND test_data
+  ${CMAKE_CURRENT_BINARY_DIR}/testdata/atminc_compress.nc4
+)
+
+# install
+install(FILES ${test_data}
+        DESTINATION "test/testdata")
+
+##### unit tests
+# test for python coding norms
+add_test(NAME GDASApp_check_python_norms
+         COMMAND pycodestyle -v --config ./.pycodestyle .
+         WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
+# test for ush/check_yaml_keys.py
+add_test(NAME GDASApp_check_yaml_keys
          COMMAND ${Python3_EXECUTABLE} ${PROJECT_SOURCE_DIR}/ush/check_yaml_keys.py ${PROJECT_SOURCE_DIR}/test/testinput/check_yaml_keys_ref.yaml ${PROJECT_SOURCE_DIR}/test/testinput/check_yaml_keys_test.yaml
          WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/)
+# test for ush/jediinc2fv3.py
+add_test(NAME GDASApp_jedi_increment_to_fv3
+         COMMAND ${Python3_EXECUTABLE} ${PROJECT_SOURCE_DIR}/ush/jediinc2fv3.py ${PROJECT_BINARY_DIR}/test/testdata/atminc_compress.nc4 ${PROJECT_BINARY_DIR}/test/testdata/fv_increment.nc 
+         WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/)

ush/jediinc2fv3.py

@@ -0,0 +1,77 @@
+#!/usr/bin/env python3
+# translate FV3-JEDI increment to FV3 readable format
+import argparse
+import netCDF4 as nc
+import numpy as np
+import os
+
+vardict = {
+    'ua': 'u_inc',
+    'va': 'v_inc',
+    'delp': 'delp_inc',
+    'DELP': 'delp_inc',
+    'delz': 'delz_inc',
+    'T': 'T_inc',
+    'sphum': 'sphum_inc',
+    'liq_wat': 'liq_wat_inc',
+    'o3mr': 'o3mr_inc',
+    'ice_wat': 'icmr_inc',
+    'lat': 'lat',
+    'lon': 'lon',
+}
+
+
+def jedi_inc_to_fv3(FV3JEDIinc, FV3inc):
+    # open netCDF files
+    try:
+        with nc.Dataset(FV3JEDIinc) as ncin, nc.Dataset(FV3inc, "w", format="NETCDF4") as ncout:
+            # copy over dimensions
+            for name, dimension in ncin.dimensions.items():
+                if name == 'time':
+                    continue
+                elif name == 'edge':
+                    nameout = 'ilev'
+                else:
+                    nameout = name
+                ncout.createDimension(nameout,
+                                      (len(dimension) if not dimension.isunlimited() else None))
+            # some global attributes
+            ncout.source = 'jediinc2fv3.py'
+            ncout.comment = 'Increment produced by FV3-JEDI and modified for use by FV3 read'
+            # create all the dummy vertical coordinate variables
+            nlevs = len(ncin.dimensions['lev'])
+            pfull = range(1, nlevs+1)
+            phalf = range(1, nlevs+2)
+            levvar = ncout.createVariable('lev', 'f4', ('lev'))
+            levvar[:] = pfull
+            pfullvar = ncout.createVariable('pfull', 'f4', ('lev'))
+            pfullvar[:] = pfull
+            ilevvar = ncout.createVariable('ilev', 'f4', ('ilev'))
+            ilevvar[:] = phalf
+            hyaivar = ncout.createVariable('hyai', 'f4', ('ilev'))
+            hyaivar[:] = phalf
+            hybivar = ncout.createVariable('hybi', 'f4', ('ilev'))
+            hybivar[:] = phalf
+            # rename and change dimensionality of fields
+            for name, variable in ncin.variables.items():
+                if len(variable.dimensions) == 4:
+                    dimsout = variable.dimensions[1:]
+                else:
+                    dimsout = variable.dimensions
+                if name in vardict:
+                    x = ncout.createVariable(vardict[name], 'f4', dimsout)
+                    if len(variable.dimensions) == 4:
+                        ncout[vardict[name]][:] = ncin[name][0, ...]
+                    else:
+                        ncout[vardict[name]][:] = ncin[name][:]
+    except FileNotFoundError as e:
+        print(e)
+        raise
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('FV3JEDIincrement', type=str, help='Input FV3-JEDI LatLon Increment File')
+    parser.add_argument('FV3increment', type=str, help='Output FV3 Increment File')
+    args = parser.parse_args()
+    jedi_inc_to_fv3(args.FV3JEDIincrement, args.FV3increment)