Inputs with marshmallow release 3

README.md

@@ -14,13 +14,6 @@ OR pass a json_dictionary directly into the module with the parameters defined
 
 AND/OR pass parameters via the command line, in a way that will override the input_json or the json_dictionary given.
 
-## Upgrading to version 2.0
-The major change in argschema 2.0 is becoming
-compatible with marshmallow 3, which changes
-many of the ways your schemas and schema modifications work.  Some noteable differences  are that schemas are strict now by default, so tossing keys in your outputs or inputs that were ignored and stripped before now throw errors unless  
-def
-Please read this document for more guidance
-https://marshmallow.readthedocs.io/en/stable/upgrading.html
 
 ## Level of Support
 We are planning on occasional updating this tool with no fixed schedule. Community involvement is encouraged through both issues and pull requests.  Please make pull requests against the dev branch, as we will test changes there before merging into master.
@@ -75,7 +68,7 @@ You start building some code in an ipython notebook to play around with a new id
 
 It's a mess, and you know you should migrate your code over to a module that you can call from other programs or notebooks.  You start collecting your input variables to the top of the notebook and make yourself a wrapper function that you can call.  However, now your mistake in filename typing is a disaster because the file doesn't exist, and your code doesn't check for the existence of the file until quite late. You start implementing some input validation checks to avoid this problem.
 
-Now you start wanting to integrate this code with other things, including elements that aren't in python.  You decide that you need to have a command line module that executes the code, because then you can use other tools to stitch together your processing, like maybe some shell scripts or docker run commands.  You implement an argparse set of inputs and default values that make your python program a self-contained program, with some help documentation.  Along the way, you have to refactor the parsed argparse variables into your function and strip out your old hacky validation code to avoid maintaining two versions of validation in the future.
+Now you start wanting to integrate this code with other things, including elements that aren't in python.  You decide that you need to have a command line module that executes the code, because then you can use other tools to stitch together your processing, like maybe some shell scripts or docker run commands.  You implement an argparse set of inputs and default values that make your python program a self-contained program, with some helpful documentation.  Along the way, you have to refactor the parsed argparse variables into your function and strip out your old hacky validation code to avoid maintaining two versions of validation in the future.
 
 This module starts becoming useful enough that you want to integrate it into more complex modules.  You end up copying and pasting various argparse lines over to other modules, and then 5 other modules.  Later you decide to change your original module a little bit, and you have a nightmare of code replace to fix up the other modules to mirror this phenomenon.. you kick yourself for not having thought this through more clearly.
 
@@ -85,5 +78,25 @@ If you had only designed things from the beginning to allow for each of these us
 
 This is what argschema is designed to do.
 
+
+## Upgrading to version 3.0
+The major change in argschema 3.0 is introducing a more generalized interface for reading and writing dictionaries, referred to as ArgSource and ArgSink.  One can define customized classes that read dictionaries from any source you can code, such as making a database call,  reading from a web service, reading a yaml file, etc.  Argschema isn't just for json anymore.  Similarly you can now dynamically tell your ArgSchemaParser to write output to an Argsink, which might write to a database, a webservice, or a messaging service.  This enables those integrating modules into larger workflow management solutions more flexibility in wiring up your python modules to those systems.
+
+It also removes features that were marked previously as deprecated. 
+
+Notably parsing List arguments with --listarg a b c, which instead should be called as --listarg a,b,c.  In other words cli_as_single_argument = False is no longer an option. 
+
+It also removes the old names JsonModule, ModuleParameters, which are now ArgSchemaParser and ArgSchema respectively.
+
+The field OptionList has been removed. The same functionality can be accomplished with the keyword, validate=mm.validate.OneOf([a,b,c...]) in the field definition.
+
+## Upgrading to version 2.0
+The major change in argschema 2.0 is becoming
+compatible with marshmallow 3, which changes
+many of the ways your schemas and schema modifications work.  Some noteable differences are that schemas are strict now by default, so tossing keys in your outputs or inputs that were ignored and stripped before now throw errors. 
+
+Please read this document for more guidance
+https://marshmallow.readthedocs.io/en/stable/upgrading.html
+
 Copyright 2017 Allen Institute
 

argschema/__init__.py

@@ -1,8 +1,7 @@
 '''argschema: flexible definition, validation and setting of parameters'''
-from .fields import InputFile, InputDir, OutputFile, OptionList # noQA:F401
-from .schemas import ArgSchema # noQA:F401
-from .argschema_parser import ArgSchemaParser # noQA:F401
-from .deprecated import JsonModule, ModuleParameters # noQA:F401
+from argschema.fields import InputFile, InputDir, OutputFile # noQA:F401
+from argschema.schemas import ArgSchema # noQA:F401
+from argschema.argschema_parser import ArgSchemaParser # noQA:F401
 
 __version__ = "3.0.1"