update environment variables in EOF_500hpa ncl files (#603)

fix file formatting
change axis def to uppercase in pod settings file

diagnostics/EOF_500hPa/EOF_500hPa.py

@@ -1,70 +1,73 @@
 # This file is part of the EOF_500hPa module of the MDTF code package (see LICENSE.txt)
 
-#============================================================
+# ============================================================
 # EOF of 500hPa Height Diagnostics
 # Sample code to call NCL from python 
-#============================================================
+# ============================================================
 
 import os
 import subprocess
 import time
 
-#============================================================
+
+# ============================================================
 # generate_ncl_plots - call a nclPlotFile via subprocess call
-#============================================================
+# ============================================================
+
+
 def generate_ncl_plots(nclPlotFile):
     """generate_plots_call - call a nclPlotFile via subprocess call
    
     Arguments:
     nclPlotFile (string) - full path to ncl plotting file name
     """
     # check if the nclPlotFile exists - 
-    # don't exit if it does not exists just print a warning.
+    # don't exit if it does not exist just print a warning.
     try:
         pipe = subprocess.Popen(['ncl {0}'.format(nclPlotFile)], shell=True, stdout=subprocess.PIPE)
         output = pipe.communicate()[0].decode()
-        print('NCL routine {0} \n {1}'.format(nclPlotFile,output))            
+        print('NCL routine {0} \n {1}'.format(nclPlotFile, output))
         while pipe.poll() is None:
             time.sleep(0.5)
     except OSError as e:
-        print('WARNING',e.errno,e.strerror)
+        print('WARNING', e.errno, e.strerror)
 
     return 0
 
-print("Entered "+__file__)
+
+print("Entered " + __file__)
 filename1 = os.environ["ZG_FILE"]
 filename2a = os.environ["ZG_HYBRID_SIGMA_FILE"]
 filename2b = os.environ["PS_FILE"]
-print("Looking for "+filename1)
-if not os.path.isfile( filename1 ):
-    print("ERROR missing file "+filename1)
+print("Looking for " + filename1)
+if not os.path.isfile(filename1):
+    print("ERROR missing file " + filename1)
     os.environ['USE_HYBRID_SIGMA'] = "1"
-print("Looking for "+filename2a)
-if not os.path.isfile( filename2a ):
-    print("ERROR missing file "+filename2a)
+print("Looking for " + filename2a)
+if not os.path.isfile(filename2a):
+    print("ERROR missing file " + filename2a)
     os.environ['USE_HYBRID_SIGMA'] = "0"
-print("Looking for "+filename2b)
-if not os.path.isfile( filename2b ):
-    print("ERROR missing file "+filename2b)
-
+print("Looking for " + filename2b)
+if not os.path.isfile(filename2b):
+    print("ERROR missing file " + filename2b)
 
 if os.path.isfile(filename1) \
-    or (os.path.isfile(filename2a) and os.path.isfile(filename2b)):
-    print("height and surface pressure files found") 
+        or (os.path.isfile(filename2a) and os.path.isfile(filename2b)):
+    print("height and surface pressure files found")
     print("computing EOF of geopotential height anomalies of 500 hPa")
 
-#============================================================
-# Call NCL code here
-#============================================================
+    # ============================================================
+    # Call NCL code here
+    # ============================================================
     print("COMPUTING ANOMALIES")
-    generate_ncl_plots(os.environ["POD_HOME"]+"/compute_anomalies.ncl")
+    generate_ncl_plots(os.environ["POD_HOME"] + "/compute_anomalies.ncl")
 
     print(" N ATLANTIC EOF PLOT")
-    generate_ncl_plots(os.environ["POD_HOME"]+"/eof_natlantic.ncl")
+    generate_ncl_plots(os.environ["POD_HOME"] + "/eof_natlantic.ncl")
 
     print(" N PACIFIC EOF PLOT")
-    generate_ncl_plots(os.environ["POD_HOME"]+"/eof_npacific.ncl")
+    generate_ncl_plots(os.environ["POD_HOME"] + "/eof_npacific.ncl")
 
 
 else:
-    print("height and surface pressure files NOT found, skip EOF of geopotential height anomalies of 500 hPa")        
+    print("height and surface pressure files NOT found, skip EOF of geopotential height anomalies of 500 hPa")

diagnostics/EOF_500hPa/compute_anomalies.ncl

@@ -7,10 +7,10 @@ begin
 
 setfileoption("nc", "Format", getenv("MDTF_NC_FORMAT"))
 
-wk_dir = getenv("WK_DIR")
+wk_dir = getenv("WORK_DIR")
 casename = getenv("CASENAME")
-yr1 = getenv("FIRSTYR")
-yr2 = getenv("LASTYR")
+yr1 = getenv("startdate")
+yr2 = getenv("enddate")
 date_off = getenv("date_int_offset")
 use_hybrid_sigma = (getenv("USE_HYBRID_SIGMA").eq."1")
 

diagnostics/EOF_500hPa/eof_natlantic.ncl

@@ -9,10 +9,10 @@ load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/contributed.ncl"
 setfileoption("nc", "Format", getenv("MDTF_NC_FORMAT"))
 
 begin
-yr1 = getenv("FIRSTYR")
-yr2 = getenv("LASTYR")
+yr1 = getenv("startdate")
+yr2 = getenv("enddate")
 rgb = getenv("RGB")
-wk_dir = getenv("WK_DIR")
+wk_dir = getenv("WORK_DIR")
 casename = getenv("CASENAME")
 
 firstyr = stringtointeger(yr1)

diagnostics/EOF_500hPa/eof_npacific.ncl

@@ -8,10 +8,10 @@ load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/contributed.ncl"
 setfileoption("nc", "Format", getenv("MDTF_NC_FORMAT"))
 
 begin
-yr1 = getenv("FIRSTYR")
-yr2 = getenv("LASTYR")
+yr1 = getenv("startdate")
+yr2 = getenv("enddate")
 rgb = getenv("RGB")
-wk_dir = getenv("WK_DIR")
+wk_dir = getenv("WORK_DIR")
 casename = getenv("CASENAME")
 
 firstyr = stringtointeger(yr1)

diagnostics/EOF_500hPa/settings.jsonc

@@ -31,7 +31,7 @@
     "lon": {
              "standard_name": "longitude",
              "units": "degrees_east",
-             "axis": "x"
+             "axis": "X"
            },
     "plev": {
       "standard_name": "air_pressure",