Replace CDAT

setup.py

@@ -30,5 +30,10 @@ def package_files(directory, prefixes, extensions):
     python_requires=">=3.6",
     packages=find_packages(include=["zppy", "zppy.*"]),
     package_data={"": data_files},
-    entry_points={"console_scripts": ["zppy=zppy.__main__:main"]},
+    entry_points={
+        "console_scripts": [
+            "zppy=zppy.__main__:main",
+            "zppy_cdscan_replacement=zppy.__main__:zppy_cdscan_replacement",
+        ]
+    },
 )

zppy/__main__.py

@@ -3,8 +3,10 @@
 import importlib
 import io
 import os
+import sys
 from typing import List
 
+import pandas
 from configobj import ConfigObj
 from mache import MachineInfo
 from validate import Validator
@@ -246,3 +248,17 @@ def _validate_config(config):
         )
     else:
         print("Configuration file validation passed.")
+
+
+def zppy_cdscan_replacement():
+    output_file = sys.argv[1]
+    input_files = sys.argv[2:]
+    if len(input_files) == 1:
+        files = []
+        # Convert text file of files to a list of files.
+        with open(input_files[0]) as f:
+            for line in f:
+                files.append(line.strip())
+        input_files = files
+    dataframe = pandas.read_table(input_files)
+    dataframe.to_xml(output_file)

zppy/templates/e3sm_diags.bash

@@ -108,7 +108,7 @@ create_links_ts()
     # xml file will cover the whole period from year1 to year2
     xml_name=${v}_${begin_year}01_${end_year}12.xml
     export CDMS_NO_MPI=true
-    cdscan -x ${xml_name} -f ${v}_files.txt
+    zppy_cdscan_replacement ${xml_name} ${v}_files.txt
     if [ $? != 0 ]; then
       cd {{ scriptDir }}
       echo "ERROR (${error_num})" > {{ prefix }}.status
@@ -129,7 +129,7 @@ create_links_ts_rof()
   cd ${ts_rof_dir_destination}
   v="RIVER_DISCHARGE_OVER_LAND_LIQ"
   xml_name=${v}_${begin_year}01_${end_year}12.xml
-  cdscan -x ${xml_name} ${ts_rof_dir_source}/${v}_*.nc
+  zppy_cdscan_replacement ${xml_name} ${ts_rof_dir_source}/${v}_*.nc
   if [ $? != 0 ]; then
     cd {{ scriptDir }}
     echo "ERROR (${error_num})" > {{ prefix }}.status

zppy/templates/global_time_series.bash

@@ -42,7 +42,7 @@ use_atm={{ use_atm }}
 if [[ ${use_atm,,} == "true" ]]; then
     echo 'Create xml files for atm'
     cd ${case_dir}/post/atm/glb/ts/monthly/${ts_num_years}yr
-    cdscan -x glb.xml *.nc
+    zppy_cdscan_replacement glb.xml *.nc
     if [ $? != 0 ]; then
       cd {{ scriptDir }}
       echo 'ERROR (1)' > {{ prefix }}.status
@@ -54,7 +54,7 @@ use_lnd={{ use_lnd }}
 if [[ ${use_lnd,,} == "true" ]]; then
     echo 'Create xml files for lnd'
     cd ${case_dir}/post/lnd/glb/ts/monthly/${ts_num_years}yr
-    cdscan -x glb.xml *.nc
+    zppy_cdscan_replacement -x glb.xml *.nc
     if [ $? != 0 ]; then
       cd {{ scriptDir }}
       echo 'ERROR (2)' > {{ prefix }}.status
@@ -78,7 +78,7 @@ if [[ ${use_ocn,,} == "true" ]]; then
     echo 'Create xml for for ocn'
     export CDMS_NO_MPI=true
     cd ${case_dir}/post/ocn/glb/ts/monthly/${ts_num_years}yr
-    cdscan -x glb.xml mpaso.glb*.nc
+    zppy_cdscan_replacement glb.xml mpaso.glb*.nc
     if [ $? != 0 ]; then
       cd {{ scriptDir }}
       echo 'ERROR (4)' > {{ prefix }}.status

zppy/templates/readTS.py

@@ -1,13 +1,12 @@
-import cdms2
-import cdutil
+import xcdat
 
 
 class TS(object):
     def __init__(self, filename):
 
         self.filename = filename
 
-        self.f = cdms2.open(filename)
+        self.f = xcdat.open_dataset(filename)
 
     def __del__(self):
 
@@ -66,6 +65,6 @@ def globalAnnual(self, var):
             units = v.units
 
             # Annual average
-            v = cdutil.YEAR(v)
+            v = self.f.temporal.group_average(v, "year")
 
         return v, units