PubSpeed Initital Commit of Changes

Modified models.Article to include submit and accept dates and scrapers.pubmed to obtain those dates from Pubmed XML. Created a
modified version of the excel report to dump out results and sh and yaml files in examples/pubspeed for testing purposes.
PubSpeed initial working version

Running the loading and report generation from a python script for convenience. Some modifications still needed to the processing
step and somewhat unclear how the Pubmed searching is currently working.
Don't hard-code dir in docker script.
Updates for the pubspeed project with modifications to pubmed.py
Cleaninup pubspeed branch to test things for Kevin
Added try-except clause to catch invalid dates and set them to Unknown
Modified to enable script driven shell execution, a series of small bug fixes to prevent problems
Fix for date range bug at Pubmed eutils API
Updates to Dockerfile.
Give article scraper it's own run method.
Remove duplicate transaction wrapping for article scrapers.
Add 'journals' parameter to ncbi article scraper.

Also remove ArticleList which is keeping elements in memory.
Add example of using journals parameter.
Sorting out conflicts between my version and Ana's update
Updating the pubmed.py version with and other fixes from Ana's branch
Added new example in pubspeed directory under update
Finalised a running version of pubspeed project in examples, removed earlier versions
Removed the awful hack for date ranges including 1 Jan