Switch from MpasConfigParser to tranche

The main advantage of tranche is just that it's a standalone
repo so packages can use it without needing MPAS-Tools but it
also provides more testing and some additional functionality
beyond the MpasConfigParser like interpolation of enviornment
variables.

Author: xylar

docs/tutorials/dev_add_task.rst

@@ -610,13 +610,13 @@ renaming the task are:
 
         Parameters
         ----------
-        config : mpas_tools.config.MpasConfigParser
+        config : tranche.Tranche
             Configuration options
 
         mpas_climatology_task : mpas_analysis.shared.climatology.MpasClimatologyTask
             The task that produced the climatology to be remapped and plotted
 
-        control_config : mpas_tools.config.MpasConfigParser, optional
+        control_config : tranche.Tranche, optional
             Configuration options for a control run (if any)
         """
 
@@ -1197,13 +1197,13 @@ described in this tutorial:
 
             Parameters
             ----------
-            config : mpas_tools.config.MpasConfigParser
+            config : tranche.Tranche
                 Configuration options
 
             mpas_climatology_task : mpas_analysis.shared.climatology.MpasClimatologyTask
                 The task that produced the climatology to be remapped and plotted
 
-            control_config : mpas_tools.config.MpasConfigParser, optional
+            control_config : tranche.Tranche, optional
                 Configuration options for a control run (if any)
             """
 

docs/tutorials/dev_understand_a_task.rst

@@ -242,7 +242,7 @@ super class's ``__init__()`` method:
 
         Parameters
         ----------
-        config : mpas_tools.config.MpasConfigParser
+        config : tranche.Tranche
             Configuration options
 
         mpas_climatology_task : mpas_analysis.shared.climatology.MpasClimatologyTask
@@ -252,7 +252,7 @@ super class's ``__init__()`` method:
             The task that produced the climatology from the first year to be
             remapped and then subtracted from the main climatology
 
-        control_config : mpas_tools.config.MpasConfigParser, optional
+        control_config : tranche.Tranche, optional
             Configuration options for a control run (if any)
         """
 
@@ -303,7 +303,7 @@ find something unexpected:
 
         depth_ranges = config.getexpression('climatologyMapOHCAnomaly',
                                             'depthRanges',
-                                            use_numpyfunc=True)
+                                            allow_numpy=True)
 
 By default, these config options look like this:
 
@@ -904,7 +904,7 @@ here is the full analysis task as described in this tutorial:
 
             Parameters
             ----------
-            config : mpas_tools.config.MpasConfigParser
+            config : tranche.Tranche
                 Configuration options
 
             mpas_climatology_task : mpas_analysis.shared.climatology.MpasClimatologyTask
@@ -914,7 +914,7 @@ here is the full analysis task as described in this tutorial:
                 The task that produced the climatology from the first year to be
                 remapped and then subtracted from the main climatology
 
-            control_config : mpas_tools.config.MpasConfigParser, optional
+            control_config : tranche.Tranche, optional
                 Configuration options for a control run (if any)
             """
 
@@ -946,7 +946,7 @@ here is the full analysis task as described in this tutorial:
 
             depth_ranges = config.getexpression('climatologyMapOHCAnomaly',
                                                 'depthRanges',
-                                                use_numpyfunc=True)
+                                                allow_numpy=True)
 
             mpas_field_name = 'deltaOHC'
 

mpas_analysis/__main__.py

@@ -37,7 +37,7 @@
 
 from mache import discover_machine, MachineInfo
 
-from mpas_tools.config import MpasConfigParser
+from tranche import Tranche
 
 from mpas_analysis.shared.analysis_task import AnalysisFormatter
 
@@ -70,7 +70,7 @@ def update_time_bounds_in_config(config):
 
     Parameters
     ----------
-    config : mpas_tools.config.MpasConfigParser
+    config : tranche.Tranche
         contains config options
 
     """
@@ -88,10 +88,10 @@ def build_analysis_list(config, controlConfig):
 
     Parameters
     ----------
-    config : mpas_tools.config.MpasConfigParser
+    config : tranche.Tranche
         contains config options
 
-    controlConfig : mpas_tools.config.MpasConfigParser or None
+    controlConfig : tranche.Tranche or None
         contains config options for a control run, or ``None`` if no config
         file for a control run was specified
 
@@ -588,7 +588,7 @@ def update_generate(config, generate):
 
     Parameters
     ----------
-    config : mpas_tools.config.MpasConfigParser
+    config : tranche.Tranche
         contains config options
 
     generate : str
@@ -615,7 +615,7 @@ def run_analysis(config, analyses):
 
     Parameters
     ----------
-    config : mpas_tools.config.MpasConfigParser
+    config : tranche.Tranche
         contains config options
 
     analyses : OrderedDict of ``AnalysisTask`` objects
@@ -869,7 +869,7 @@ def build_config(user_config_file, shared_configs, machine_info):
     if not os.path.exists(user_config_file):
         raise OSError(f'A config file {user_config_file} was specified but '
                       f'the file does not exist')
-    config = MpasConfigParser()
+    config = Tranche()
     for config_file in shared_configs:
         if config_file.endswith('.py'):
             # we'll skip config options set in python files
@@ -1053,7 +1053,7 @@ def main():
         parser.print_help()
         sys.exit(0)
 
-    config = MpasConfigParser()
+    config = Tranche()
 
     # add default.cfg to cover default not included in the config files
     # provided on the command line

mpas_analysis/analysis_task_template.py

@@ -84,7 +84,7 @@ class MyTask(AnalysisTask):
     #    python class start with the argument self, which is not included in
     #    the list of arguments when you call a method of an object (because it
     #    is always included automatically).
-    # config is an mpas_tools.config.MpasConfigParser object that can be used
+    # config is an tranche.Tranche object that can be used
     #    to get configuration options stored in default.cfg or a custom config
     #    file specific to a given simulation.  See examples below or in
     #    existing analysis tasks.
@@ -103,7 +103,7 @@ def __init__(self, config, prerequsiteTask, myArg='myDefaultValue'):
 
         Parameters
         ----------
-        config :  mpas_tools.config.MpasConfigParser
+        config :  tranche.Tranche
             Contains configuration options
 
         prerequsiteTask : ``AnotherTaskClass``

mpas_analysis/ocean/antship_transects.py

@@ -34,14 +34,14 @@ def __init__(self, config, mpasClimatologyTask, controlConfig=None):
 
         Parameters
         ----------
-        config : mpas_tools.config.MpasConfigParser
+        config : tranche.Tranche
             Configuration options
 
         mpasClimatologyTask : ``MpasClimatologyTask``
             The task that produced the climatology to be remapped and plotted
             as a transect
 
-        controlconfig : mpas_tools.config.MpasConfigParser, optional
+        controlconfig : tranche.Tranche, optional
             Configuration options for a control run (if any)
         """
         # Authors
@@ -69,7 +69,7 @@ def __init__(self, config, mpasClimatologyTask, controlConfig=None):
             verticalComparisonGrid = None
         else:
             verticalComparisonGrid = config.getexpression(
-                sectionName, 'verticalComparisonGrid', use_numpyfunc=True)
+                sectionName, 'verticalComparisonGrid', allow_numpy=True)
 
         verticalBounds = config.getexpression(sectionName, 'verticalBounds')
 

mpas_analysis/ocean/climatology_map_antarctic_melt.py

@@ -50,7 +50,7 @@ def __init__(self, config, mpasClimatologyTask, regionMasksTask,
 
         Parameters
         ----------
-        config : mpas_tools.config.MpasConfigParser
+        config : tranche.Tranche
             Configuration options
 
         mpasClimatologyTask : ``MpasClimatologyTask``
@@ -59,7 +59,7 @@ def __init__(self, config, mpasClimatologyTask, regionMasksTask,
         regionMasksTask : ``ComputeRegionMasks``
             A task for computing region masks
 
-        controlConfig : mpas_tools.config.MpasConfigParser
+        controlConfig : tranche.Tranche
             Configuration options for a control run
         """
         # Authors
@@ -460,7 +460,7 @@ def __init__(self, parentTask, mpasClimatologyTask, controlConfig,
         mpasClimatologyTask : ``MpasClimatologyTask``
             The task that produced the climatology to be remapped and plotted
 
-        controlConfig : mpas_tools.config.MpasConfigParser
+        controlConfig : tranche.Tranche
             Configuration options for a control run (if any)
 
         regionMasksTask : ``ComputeRegionMasks``

mpas_analysis/ocean/climatology_map_argo.py

@@ -49,13 +49,13 @@ def __init__(self, config, mpasClimatologyTask,
 
         Parameters
         ----------
-        config : mpas_tools.config.MpasConfigParser
+        config : tranche.Tranche
             Configuration options
 
         mpasClimatologyTask : ``MpasClimatologyTask``
             The task that produced the climatology to be remapped and plotted
 
-        controlconfig : mpas_tools.config.MpasConfigParser, optional
+        controlconfig : tranche.Tranche, optional
             Configuration options for a control run (if any)
         """
         # Authors
@@ -189,13 +189,13 @@ def __init__(self, config, mpasClimatologyTask,
 
         Parameters
         ----------
-        config : mpas_tools.config.MpasConfigParser
+        config : tranche.Tranche
             Configuration options
 
         mpasClimatologyTask : ``MpasClimatologyTask``
             The task that produced the climatology to be remapped and plotted
 
-        controlconfig : mpas_tools.config.MpasConfigParser, optional
+        controlconfig : tranche.Tranche, optional
             Configuration options for a control run (if any)
         """
         # Authors

mpas_analysis/ocean/climatology_map_bgc.py

@@ -37,13 +37,13 @@ def __init__(self, config, mpasClimatologyTask, controlConfig=None):
 
         Parameters
         ----------
-        config : mpas_tools.config.MpasConfigParser
+        config : tranche.Tranche
             Configuration options
 
         mpasClimatologyTask : ``MpasClimatologyTask``
             The task that produced the climatology to be remapped and plotted
 
-        controlconfig : mpas_tools.config.MpasConfigParser, optional
+        controlconfig : tranche.Tranche, optional
             Configuration options for a control run (if any)
 
         Authors

mpas_analysis/ocean/climatology_map_bsf.py

@@ -40,13 +40,13 @@ def __init__(self, config, mpas_climatology_task, control_config=None):
 
         Parameters
         ----------
-        config : mpas_tools.config.MpasConfigParser
+        config : tranche.Tranche
             Configuration options
 
         mpas_climatology_task : mpas_analysis.shared.climatology.MpasClimatologyTask
             The task that produced the climatology to be remapped and plotted
 
-        control_config : mpas_tools.config.MpasConfigParser, optional
+        control_config : tranche.Tranche, optional
             Configuration options for a control run (if any)
         """  # noqa: E501
         field_name = 'barotropicStreamfunction'
@@ -64,7 +64,7 @@ def __init__(self, config, mpas_climatology_task, control_config=None):
         seasons = config.getexpression(section_name, 'seasons')
         depth_ranges = config.getexpression(section_name,
                                             'depthRanges',
-                                            use_numpyfunc=True)
+                                            allow_numpy=True)
         if len(seasons) == 0:
             raise ValueError(f'config section {section_name} does not contain '
                              f'valid list of seasons')

mpas_analysis/ocean/climatology_map_custom.py

@@ -39,13 +39,13 @@ def __init__(self, config, mpasClimatologyTask, controlConfig=None):
 
         Parameters
         ----------
-        config : mpas_tools.config.MpasConfigParser
+        config : tranche.Tranche
             Configuration options
 
         mpasClimatologyTask : ``MpasClimatologyTask``
             The task that produced the climatology to be remapped and plotted
 
-        controlconfig : mpas_tools.config.MpasConfigParser, optional
+        controlconfig : tranche.Tranche, optional
             Configuration options for a control run (if any)
         """