fix: added map definition to the config.yaml so that we know which maps are expected for the phenotype. It is still possible to run one of them using the -t option but they must be specified the config file. This means a user can run acmc phen map and all the required codes are created. It also reduces the chance of inconsistency between the map files generated between versions. It does not remove it entirely because it is still possible for a user to only run with a subset of the coding types but that should be discouraged. We retain the option for phenottype development because you might not want to run everything all of the time due the time it takes. Closes #40.

refactor: converted all examples to yaml and added test for config2. Updated readme. Fixed but in diff that assumed all csv files in map directory where map files when some where error files if no codes exists, moved error files to errors directory in the map directory to avoid this.

implemented first part of export to create the omop database refactoring setup and publish functions, need to test the database and export all tables

Removed mistaken license section in readme.md which referred to MIT rather than apache 2.0. Closes #2

refactord build directory. Moved trud and omop to a vocab directory. Moved phen and copies to a workspace directory.

moved trud api key to an environment variable; stored trud versions in file trud_version.json to keep track of the source mappings when we commit to a repo

changed trud map directory to trud to align with the naming convention used for other dependancies such as omop. Added code source root directory as it assumed all codes where in the code directory from where the tool was run, which isn't the case. Added full usage documentation to readme

added acmc command line wrapper for entire toolkit moving parameter passing from trud, omop and main into acmc so that they are not just functions. Still work to do on parse.py which includes command line arguments and does nto need to as this should all be in the arg parser configuration. Refactored trud and omop so that the paths are all constants, and also check that the directories required exist as it was failing on requiring the code directory.