more pylint cleanup!

more snake case enforcement.
variables appearing unused to pylint b.c. of click conventions ignored in more places
some unnecessary returns/passes/if-else conditions removed/rewritten
a doc string here and there

fre/app/__init__.py

@@ -1,5 +1,5 @@
 ''' for fre.app imports '''
-from .maskAtmosPlevel import maskAtmosPlevel_subtool
+from .mask_atmos_plevel import mask_atmos_plevel_subtool
 from .freapp import app_cli
 
-__all__ = ["maskAtmosPlevel_subtool", "app_cli"]
+__all__ = ["mask_atmos_plevel_subtool", "app_cli"]

fre/app/freapp.py

@@ -5,7 +5,7 @@
 
 import click
 
-from .maskAtmosPlevel import maskAtmosPlevel_subtool
+from .mask_atmos_plevel import mask_atmos_plevel_subtool
 from .generate_time_averages.generate_time_averages import generate
 
 @click.group(help=click.style(" - access fre app subcommands", fg=(250,154,90)))
@@ -29,7 +29,7 @@ def app_cli():
 def mask_atmos_plevel(context, infile, outfile, psfile):
     # pylint: disable=unused-argument
     """Mask out pressure level diagnostic output below land surface"""
-    context.forward(maskAtmosPlevel_subtool)
+    context.forward(mask_atmos_plevel_subtool)
 
 
 @app_cli.command()

fre/catalog/frecatalog.py

@@ -1,5 +1,9 @@
+'''
+entry point for fre catalog subcommands
+'''
+
 import click
-import catalogbuilder
+#import catalogbuilder
 from catalogbuilder.scripts import gen_intake_gfdl
 from catalogbuilder.scripts import test_catalog
 
@@ -33,7 +37,8 @@ def builder(context, input_path = None, output_path = None, config = None, filte
 @catalog_cli.command()
 @click.argument('json_path', nargs = 1 , required = True)
 @click.argument('json_template_path', nargs = 1 , required = False)
-@click.option('-tf', '--test-failure', is_flag=True, default = False, help="Errors are only printed. Program will not exit.")
+@click.option('-tf', '--test-failure', is_flag=True, default = False,
+              help="Errors are only printed. Program will not exit.")
 @click.pass_context
 def validate(context, json_path, json_template_path, test_failure):
     # pylint: disable=unused-argument

fre/check/frecheck.py

@@ -1,4 +1,7 @@
+''' fre check '''
+
 import click
+
 from .frecheckexample import check_test_function
 
 @click.group(help=click.style(" - access fre check subcommands", fg=(162,91,232)))
@@ -9,6 +12,7 @@ def check_cli():
 @click.option('--uppercase', '-u', is_flag=True, help = 'Print statement in uppercase.')
 @click.pass_context
 def function(context, uppercase):
+    # pylint: disable=unused-argument
     """ - Execute fre check test """
     context.forward(check_test_function)
 

fre/check/frecheckexample.py

@@ -7,7 +7,7 @@
 import click
 
 @click.command()
-def check_test_function(uppercase):
+def check_test_function(uppercase=None):
     """Execute fre list testfunction2."""
     statement = "testingtestingtestingtesting"
     if uppercase:

fre/cmor/frecmor.py

@@ -1,4 +1,7 @@
+''' fre cmor '''
+
 import click
+
 from .CMORmixer import cmor_run_subtool
 
 @click.group(help=click.style(" - access fre cmor subcommands", fg=(232,91,204)))
@@ -28,6 +31,7 @@ def cmor_cli():
               required=True)
 @click.pass_context
 def run(context, indir, outdir, varlist, table_config, exp_config):
+    # pylint: disable=unused-argument
     """Rewrite climate model output"""
     context.forward(cmor_run_subtool)
 

fre/list/frelist.py

@@ -1,14 +1,18 @@
+''' fre list '''
+
 import click
+
 from .frelistexample import list_test_function
 
 @click.group(help=click.style(" - access fre list subcommands", fg=(232,204,91)))
 def list_cli():
-    pass
+    ''' entry point to fre list click commands '''
 
 @list_cli.command()
 @click.option('--uppercase', '-u', is_flag=True, help = 'Print statement in uppercase.')
 @click.pass_context
 def function(context, uppercase):
+    # pylint: disable=unused-argument
     """ - Execute fre list test """
     context.forward(list_test_function)
 

fre/list/frelistexample.py

@@ -7,7 +7,7 @@
 import click
 
 @click.command()
-def list_test_function(uppercase):
+def list_test_function(uppercase=None):
     """Execute fre list testfunction2."""
     statement = "testingtestingtestingtesting"
     if uppercase: