Clean up imports

Previous commit let us call MARBL_generate_diagnostics_file.py from command
line, but caused problems when importing generate_diagnostics_file() into a
python script. This clean-up allows both use-cases.

Also, I renamed diag_mode_opts() -> valid_diag_modes() because that seems like
a more descriptive name.

MARBL_tools/MARBL_generate_diagnostics_file.py

@@ -45,13 +45,13 @@
   -a, --append          Append to existing diagnostics file (default: False)
 """
 
-import MARBL_utils
 #######################################
 
 def generate_diagnostics_file(MARBL_diagnostics, diagnostics_file_out, diag_mode="full", append=False):
     """ Produce a list of MARBL diagnostic frequencies and operators from a JSON parameter file
     """
 
+    from MARBL_tools import valid_diag_modes
     import logging
     logger = logging.getLogger(__name__)
 
@@ -85,7 +85,7 @@ def generate_diagnostics_file(MARBL_diagnostics, diagnostics_file_out, diag_mode
     # is also a dictionary containing frequency and operator information. Note that
     # string values of frequency and operator are converted to lists of len 1 when the
     # JSON file that generates this list is processed
-    diag_mode_opts = MARBL_utils.diag_mode_opts()
+    diag_mode_opts = valid_diag_modes()
     diag_mode_in = diag_mode_opts.index(diag_mode)
     for diag_name in sorted(MARBL_diagnostics.diagnostics_dict.keys()):
         frequencies = MARBL_diagnostics.diagnostics_dict[diag_name]['frequency']
@@ -107,6 +107,7 @@ def _parse_args(marbl_root):
     """
 
     import argparse
+    from MARBL_tools import valid_diag_modes
 
     parser = argparse.ArgumentParser(description="Generate a MARBL settings file from a JSON file",
                                      formatter_class=argparse.ArgumentDefaultsHelpFormatter)
@@ -144,7 +145,7 @@ def _parse_args(marbl_root):
 
     # Diagnostic mode (level of output to include)
     parser.add_argument('-m', '--diag-mode', action='store', dest='diag_mode', default='full',
-                        choices=MARBL_utils.diag_mode_opts(),
+                        choices=valid_diag_modes(),
                         help='Level of output to include')
 
     # Append to existing diagnostics file?

MARBL_tools/MARBL_utils.py

@@ -8,7 +8,7 @@
 #                            PUBLIC MODULE METHODS                             #
 ################################################################################
 
-def diag_mode_opts():
+def valid_diag_modes():
     """ Return ordered list of the valid values for diag_mode.
         (Ordered list => selecting diag mode includes variables)
     """
@@ -98,7 +98,7 @@ def diagnostics_dictionary_is_consistent(DiagsDict):
            ii.  If they are all lists, must be same length
         5. Allowable frequencies are never, low, medium, and high
         6. Allowable operators are instantaneous, average, minimum, and maximum
-        7. Allowable diag_modes are defined in diag_mode_opts()
+        7. Allowable diag_modes are defined in valid_diag_modes()
     """
 
     import logging
@@ -157,11 +157,11 @@ def diagnostics_dictionary_is_consistent(DiagsDict):
 
         # 5. Allowable frequencies are never, low, medium, and high
         # 6. Allowable operators are instantaneous, average, minimum, and maximum
-        # 7. Allowable diag_modes are defined in diag_mode_opts()
+        # 7. Allowable diag_modes are defined in valid_diag_modes()
         #    * "none" should not appear in the dictionary
         ok_freqs = ['never', 'low', 'medium', 'high']
         ok_ops = ['instantaneous', 'average', 'minimum', 'maximum']
-        ok_dms = diag_mode_opts()[1:] # do not include 'none' in ok_dms
+        ok_dms = valid_diag_modes()[1:] # do not include 'none' in ok_dms
         invalid_freq_op_dm = False
         if not isinstance(diag_dict['frequency'], dict):
             if isinstance(diag_dict['frequency'], list):

MARBL_tools/__init__.py

@@ -4,6 +4,7 @@
 from .MARBL_diagnostics_file_class import MARBL_diagnostics_class
 from .MARBL_utils import settings_dictionary_is_consistent
 from .MARBL_utils import diagnostics_dictionary_is_consistent
+from .MARBL_utils import valid_diag_modes
 from .MARBL_share import abort
 from .MARBL_share import LogFormatter
 from .MARBL_share import sort