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