Cmor bite wrapup

fre/cmor/README.md

@@ -29,18 +29,39 @@ this subtool's help, and command-specific `run` help:
 
 
 # subtool command-specific help, e.g. for run
-> fre cmor run --help
-    Usage: fre cmor run [OPTIONS]
-
-      Rewrite climate model output
-
-    Options:
-      -d, --indir TEXT         Input directory  [required]
-      -l, --varlist TEXT       Variable list  [required]
-      -r, --table_config TEXT  Table configuration  [required]
-      -p, --exp_config TEXT    Experiment configuration  [required]
-      -o, --outdir TEXT        Output directory  [required]
-      --help                   Show this message and exit.
+> fre cmor run --help                        
+Usage: fre cmor run [OPTIONS]                                                 
+
+  Rewrite climate model output files with CMIP-compliant metadata for down-   
+  stream publishing                                                           
+
+Options:                                                                      
+  -d, --indir TEXT         directory containing netCDF files. keys specified  
+                           in json_var_list are local variable names used for 
+                           targeting specific files in this directory         
+                           [required]                                         
+  -l, --varlist TEXT       path pointing to a json file containing directory  
+                           of key/value pairs. the keys are the 'local' names 
+                           used in the filename, and the values pointed to by 
+                           those keys are strings representing the name of the
+                           variable contained in targeted files. the key and  
+                           value are often the same, but it is not required.  
+                           [required]                                         
+  -r, --table_config TEXT  json file containing CMIP-compliant per-           
+                           variable/metadata for specific MIP table. The MIP  
+                           table can generally be identified by the specific  
+                           filename (e.g. 'Omon')  [required]                 
+  -p, --exp_config TEXT    json file containing metadata dictionary for       
+                           CMORization. this metadata is effectively appended 
+                           to the final output file's header  [required]      
+  -o, --outdir TEXT        directory root that will contain the full output   
+                           and output directory structure generated by the    
+                           cmor module upon request.  [required]              
+  -v, --opt_var_name TEXT  optional, specify a variable name to specifically  
+                           process only filenames matching that variable name.
+                           I.e., this string help target local_vars, not      
+                           target_vars.                                       
+  --help                   Show this message and exit.                        
 ```