Merge pull request #291 from GEOS-ESM/feature/mathomp4/remap-argparse

Convert remap_restart to use argparse

CHANGELOG.md

@@ -15,13 +15,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Removed
 
-## [1.6.3] - 2022-12-07
+## [1.6.3] - 2022-12-08
 
 ### Changed
 
 - Moved to GitHub Actions for label enforcement
 - Updated CircleCI to Baselibs 7.7.0
 - Set default data ocean to be `CS` at C90+ resolution in `remap_restarts.py`
+- Updated `remap_restarts.py` to use argparse
 
 ### Fixed
 

GEOS_Util/post/remap_restart/.gitignore

@@ -0,0 +1 @@
+/__pycache__/

GEOS_Util/post/remap_restart/remap_restarts.py

@@ -3,91 +3,101 @@
 # source install/bin/g5_modules
 #
 # Newer GEOS code should load a module with GEOSpyD Python3 if not run:
-#   module load python/GEOSpyD/Min4.10.3_py3.9
+#   module load python/GEOSpyD/Min4.11.0_py3.9
 #
 
-import sys, getopt
+import sys
+import argparse
+import textwrap
 import ruamel.yaml
 import questionary
 from remap_utils import *
-from remap_questions import get_config_from_questionary 
+from remap_questions import get_config_from_questionary
 from remap_params import *
 from remap_upper import *
 from remap_lake_landice_saltwater import *
 from remap_analysis  import *
 from remap_catchANDcn  import *
 
-def main(argv):
+# Define the argument parser
+def parse_args():
+
+    program_description = textwrap.dedent(f'''
+      USAGE:
+
+      There are three ways to use this script to remap restarts.
+
+      1. Use an existing config file to remap:
+           ./remap_restarts.py -c my_config.yaml
+
+      2. Use questionary to convert template remap_params.tpl to
+         remap_params.yaml and then remap:
+           ./remap_restarts.py
+
+      3. Use command line to input a flattened yaml file:
+           ./remap_restarts.py -o input:air:drymass=1 input:air:hydrostatic=0 ...
+
+      NOTE: Each individual script can be executed independently
+        1. remap_questions.py generates raw_answer.yaml
+        2. remap_params.py uses raw_answer.yaml and remap_params.tpl as inputs and generates remap_params.yaml
+        3. remap_upper.py uses remap_params.yaml as input for remapping
+        4. remap_lake_landice_saltwater.py uses remap_params.yaml as input for remapping
+        5. remap_catchANDcn.py uses remap_params.yaml as input for remapping
+        6. remap_analysis.py uses remap_params.yaml as input for remapping
+    ''')
+
+    parser = argparse.ArgumentParser(description='Remap restarts',epilog=program_description,formatter_class=argparse.RawDescriptionHelpFormatter)
+    # define a mutually exclusive group of arguments
+    group = parser.add_mutually_exclusive_group()
+    group.add_argument('-c', '--config_file', help='YAML config file')
+    group.add_argument('-o', '--flattened_yaml', help='Flattened YAML config', metavar='input:air:drymass=1 input:air:hydrostatic=0 ...')
+
+    # Parse using parse_known_args so we can pass the rest to the remap scripts
+    # If config_file is used, then extra_args will be empty
+    # If flattened_yaml is used, then extra_args will be populated
+    args, extra_args = parser.parse_known_args()
+    return args, extra_args
+
+def main():
 
   question_flag = False
-  cmd2yaml_flag = False
-  yaml_flag     = False
   config        = ''
 
-  try:
-    opts, args = getopt.getopt(argv,"hc:o", ['config_file='])
-  except getopt.GetoptError:
-    print('Usage: remap_restarts.py -c remap_params.yaml or ./remap_restarts.py or ./remap_restarts.py -o key=value ....')
-    sys.exit('command line error')
-  for opt, arg in opts:
-    if opt == '-h':
-      print('''\nThere are two ways to use this script to remap restarts. \n 
-              1) Use an exsiting config file to remap: \n
-                ./remap_restarts.py -c my_config.yaml \n \n
-              2) Use questionary to convert template remap_params.tpl to \n
-                 remap_params.yaml and then remap. \n
-                ./remap_restarts.py \n
-              3) Use command line to input a flattened yaml file: \n
-                ./remap_restarts.py -o input:air:drymass=1 input:air:hydrostatic=0 ... 
-              \nHelp message: \n
-              1) Each individual script can be executed independently
-              2) remap_questions.py generates raw_answer.yaml
-              3) remap_params.py uses raw_answer.yaml and remap_params.tpl as inputs and generates remap_params.yaml
-              4) remap_upper.py uses remap_params.yaml as input for remapping
-              5) remap_lake_landice_saltwater.py uses remap_params.yaml as input for remapping
-              6) remap_catchANDcn.py uses remap_params.yaml as input for remapping
-              7) remap_analysis.py uses remap_params.yaml as input for remapping ''')
-      sys.exit(0)
-    if opt in("-c", "--config_file"):
-      config_yaml = arg
-      yaml_flag = True
-
-    if opt == '-o':
-      print("\n Use command line to input a flattened yaml config file \n")
-      cmd2yaml_flag = True
-      config_yaml = 'remap_params.yaml'
-
-  if yaml_flag :
-     config  = yaml_to_config(config_yaml)
+  # Parse the command line arguments from parse_args() capturing the arguments and the rest
+  command_line_args, extra_args = parse_args()
+  config_yaml = command_line_args.config_file
+  flattened_yaml = command_line_args.flattened_yaml
 
-  if cmd2yaml_flag :
-     config  = args_to_config(args)
+  if config_yaml:
+      config = yaml_to_config(config_yaml)
+  elif flattened_yaml:
+      config_yaml = 'remap_params.yaml'
+      config  = args_to_config(extra_args)
+  else:
+      raw_config = get_config_from_questionary()
+      params = remap_params(raw_config)
+      config = params.config
+      question_flag = True
+      config_yaml = 'remap_params.yaml'
 
-  if not ( yaml_flag or cmd2yaml_flag) :
-     raw_config = get_config_from_questionary()
-     params = remap_params(raw_config)
-     config = params.config
-     question_flag = True  
-     config_yaml = 'remap_params.yaml'
-
   print('\n')
   print_config(config)
-  
+
   questions = [
         {
             "type": "confirm",
             "name": "Continue",
             "message": "Above is the YAML config file, would you like to continue?",
             "default": True
-        },]  
+        },]
   answer = questionary.prompt(questions)
 
   if not answer['Continue'] :
      print("\nYou answered not to continue, exiting.\n")
      sys.exit(0)
- 
-  if yaml_flag     or question_flag :  write_cmd(config)
-  if cmd2yaml_flag or question_flag :  config_to_yaml(config, config_yaml)
+
+  if config_yaml or question_flag: write_cmd(config)
+  if flattened_yaml or question_flag: config_to_yaml(config, config_yaml)
 
   # upper air
   upper = upperair(params_file=config_yaml)
@@ -106,5 +116,5 @@ def main(argv):
   ana.remap()
 
 if __name__ == '__main__' :
-  main(sys.argv[1:])
+  main()