Adding logging

[brendanreardon]

In this pull request, we are add logging to the method using the module logging from the Python standard library.

Additions:

• A new output is produced by the method with the .log file extension. The file will be named based on the --patient_id parameter, for {patient_id}.log. This will provide a timestamped log of what the method is doing.
• The config.ini file now has generate_figures as an additional toggle within the function_toggle section. This will enable or disable figures being generated by moalmanac.

Revisions:

• The interpreter version in config.ini was increased from 0.7.0 to 0.7.1.
• The description of inputs document was updated to include --config and --dbs as required arguments, and --preclinical-dbs as an optional argument. Missed in pull request #21.

Pre-pull request check list,

• Relevant documentation has been updated
• All unit tests pass
• All outputs pre- and post- changes match by md5 hash
• All files changed have been reviewed

[brendanreardon]

All unit tests pass

Outputs match by hash when comparing pre- and post- pull request. Attaching outputs from run_example.py.
pre-and-post-logging-outputs.zip

[brendanreardon]

All files modified have been reviewed.

[brendanreardon]

Uploading an example log here.
example.log

[brendanreardon]

Merging pull request.