Redi

* Update badges in README (Taeber Rapczak)
* Merge pull request 230 from PFWhite/feature/rediRunDebugDocs (Christopher P. Barnes)
* Update redi-run-debug.md (Patrick White)
* added docs for debuging redi runs (Patrick White)
* Update README-example-files.md (Michael Buchholz)
* Improve configuration examples for use in vagrant installs (Roy Keyes)
* Merge pull request 212 from ctsit/develop (Nicholas Rejack)
* Merge pull request 211 from nrejack/fix_getemrdata_unittest (Nicholas Rejack)
* Fixing broken unittest TestGetEMRData. Skipping problematic test. See issue 210. (Nicholas Rejack)

* Updating .gitignore. (Nicholas Rejack)
* Adding new test to verify behavior when keep_all_events is set to True. (Nicholas Rejack)
* Adding new logic to properly update event tree when keep_all_events is True. (Nicholas Rejack)
* Updating new test to test when keep_all_events is True (Nicholas Rejack)
* Modifying redi.py to correctly increment events in the case where we are keeping all. (Nicholas Rejack)
* Improving error logging when preprocessors fail. (Nicholas Rejack)
* Adding setuptools_scm to install_requires in setup.py. (Nicholas Rejack)
* fixed merge messages left in TODO (Christopher Barnes)

* modify TestSortElementTree to test for new commandline switch for keeping all results that bypasses the compress events functions (Christopher Barnes)
* Updating GetTheDocs URL in README.md (Nicholas Rejack)
* Allow setuptools_scm to set the version when it's importing redi.py (Nicholas Rejack)
* docs/conf.py needs to get the version from one directory up. (Nicholas Rejack)
* Adding 2 necessary elements to validate formEvents with HCV RNA forms. Fixing whitespace. (Nicholas Rejack)
* Adding setuptools_scm to docs/conf.py. Now using dynamically-set version number (based on Git tag) (Nicholas Rejack)
* Adding setuptools_scm to redi.py. Now using dynamically-set version number (based on Git tag) (Nicholas Rejack)
* Adding setuptools_scm to setup.py. Now using dynamically-set version number (based on Git tag) (Nicholas Rejack)
* Fixing broken test by reordering XML statements so they validate. (Nicholas Rejack)
* Modifying redi/redi.py to add validation for XSD for formEvents.xml (Nicholas Rejack)
* Added redi/utils/formEvents.xsd to validate formEvents.xml (Nicholas Rejack)
* add info on tests needed before I can make a pull request, to TODO (Christopher Barnes)
* comment out test for --keep-all, add TODO to fix this later (Christopher Barnes)
* Add 2 TODOs that cover issues with the timestamp and how it affects conmeds. (Buck72)
* take the -keep-all logic out of get_key_date (Christopher Barnes)
* take the -keep-all logic out of get_key_date (Christopher Barnes)
* add keep-all-results logic to get_key_dates (Christopher Barnes)
* add keep-all-results logic to get_key_dates (Christopher Barnes)
* mod TestSortElementTree.py to have test keep-all results inputs (Christopher Barnes)
* mod TestSortElementTree.py to have correct number of args(3) to handle new input keep-all (Christopher Barnes)
* fixed incorrect ref to input_file to input_file_path on line 400 in _run (Christopher Barnes)
* set flase correctly in sort elements to turn OFF compression (Christopher Barnes)
* add keep all to create person xml func (Christopher Barnes)
* add keep all to create person xml func (Christopher Barnes)
* add keep all to create person xml func (Christopher Barnes)
* change all refs to --kepp all to use true and false (Christopher Barnes)
* fix inputs to sort_element_tree, pass in keep all results (Christopher Barnes)
* fix inputs to _run, change inputfilename to input_file_path (Christopher Barnes)
* fix inputs to _run, added -K and -f args and set defaults to none (Christopher Barnes)
* process raw file correctly as part of keep all results (Christopher Barnes)
* process raw file correctly as part of keep all results (Christopher Barnes)
* cleanup -K keep all switch (Christopher Barnes)
* cleanup -K keep all switch (Christopher Barnes)
* cleanup -K keep all switch (Christopher Barnes)
* add switch to keep all results (Christopher Barnes)

* Summary: Hotfix to fix logging behavior when input file is not present.

* Fixing check for input file in redi.py. Now log the file's location only if it's there. (Nicholas Rejack)
* Update README.md (Nicholas Rejack)

* Summary: RED-I now accepts a file as input from the command line, using -f FILENAME.

* add tests to validate the input file used with the commandline switch -f or --file (Christopher Barnes)
* move logger setup and config to start sooner since it is needed by other functions (Christopher Barnes)
* add testdata.csv to use as test input for commandline options test and development (Christopher Barnes)
* added .coverage, cover/, coverage.xml and nosettest.xml to .gitignore. The are local to my test runs (Christopher Barnes)
* add TODO items (Christopher Barnes)
* add todo item for adding a switch to allow another sorting behavior for data points and events (Christopher Barnes)
* Fixing broken test. (Nicholas Rejack)
* added raw text file to def _run and function signature (Kevin Steven Hanson)
* moved raw txt exception out of run function (Kevin Steven Hanson)
* adding option to bypass raw.txt with an if else block that makes more sense than my previous one (Kevin Steven Hanson)
* Fixing bad operator. (Nicholas Rejack)
* Adding code to catch if user tries to use -e and -f at same time (Nicholas Rejack)
* added ability to use input file and bypass hard coded raw.txt (Kevin Steven Hanson)
* i called logger in my agruement before it was defined, my bad (Kevin Steven Hanson)
* adding info statement to work with logger for -f argument (Kevin Steven Hanson)
* Added the missing usage for the file input. (Buck72)
* Add the flag for input file for REDI to use. (Buck72)
* created input file path to hanlde -f file handle with a basic print statement for now (Kevin Steven Hanson)
* add .eggs as correction for directory name to .gitignore (Christopher Barnes)
* add .egg and virtualenvironment folder venv from instructions to .gitignore (Christopher Barnes)
* Adding a new exception to watch for in redcapClient.py: ConnectionError (Nicholas Rejack)

* Summary: Improved handling of network issues while sending to REDCap.

* Adding exception handling for NewConnectionError in redi/utils/redcapClient.py (Nicholas Rejack)
* Adding parenthesis to REDCAP_RECORDS_PROGRAM in vagrant/Makefile (Nicholas Rejack)