Redi

* Fixed major flaw in the Throttle class introduced in v0.13.0
* Added --bulk-send-blanks, which will send all blank form-events together
* Added support for redcap_plugins to our vagrant testing and sample project
* Added new Makefile targets for various helper tasks like profiling and clearing the IP ban list
* Installed mcrypt package for PHP to enable plugins in vagrant
* Added a REDCap plugin to generate URLs for enhanced error reporting
* Fixed 34: Data Import Report totals only reflect most recent run
* Added execution time to the report

The focus of this release has been clean up. Related functions were moved into
their own files for easier maintenance and comprehension. Reports were enhanced
and bugs related to them were fixed. Throttling and uploading were both
re-examined and new algorithms implemented which, during testing, run-times
decreased anywhere between 12 and 57%.

* Add new REDCap Rate Limit throttling algorithm
* Improve speed of marking events as sent
* Add script that generates enrollment records
* Rename "bin" to "redi"
* Write report.html to data directory instead of current directory
* Write report.xml to data directory instead of configuration directory
* Added helper class `bin/utils/rawxml.py` to store information about the
input file (can add more info if needed)
* Extract report creation and sending from _run()
* Add more useful aliases for vagrant box
* Updated documentation
* Enhanced report
* Add the `report.html` as attachment

* Summary: Converted documentation to .rst format, enable key-based access to SFTP servers to fetch data, enable installation via fetching from the PyPI repository.

* remove parse_args() function (Radha Kandula)
* Add docopt to redi (Radha Kandula)
* Small fix for the README links (Andrei Sura)
* Use the `cts-it-redctsi.ufl.edu` email for consistency with `setup.py` (Andrei Sura)
* Document installation from binaries: `pip install redi` (Andrei Sura)
* Restore the short README.md because it is referenced by `setup.py` (Andrei Sura)
* Remove unused `doc` folder All `*.rst` files are in now in the `docs` folder (Andrei Sura)
* Move `doc/flowcharts` to `docs/flowcharts` (Andrei Sura)
* Fix links in `README.rst` (Andrei Sura)
* Replace `README.md` by a shorter `README.rst` because we have the full content in `docs/about.rst` (Andrei Sura)
* Add `help` tasks in the the main `Makefile` (Andrei Sura)
* Fix some misspellings of REDCap (Taeber Rapczak)
* Fix configuration files to allow uploadig to the pypi.python.org repo see https://pypi.python.org/pypi/redi/ (Andrei Sura)
* Fix broken documentation links during conversion to `*.rst` (Andrei Sura)
* Remove files `setup.rst and test.rst` from `docs/api` to avoid unnecessary document creation (Andrei Sura)
* added default emr password of None (Nicholas Rejack)
* removed emr sftp server password from required parameters (Nicholas Rejack)
* removed author name (Radha Kandula)
* Make `GetEmrData.py` immune to `string` passed as port number (Andrei Sura)
* Add `requirements.txt` file for RTD (Andrei Sura)
* Use default theme in `docs/conf.py` (Andrei Sura)
* Edit one method doc to verify if sphinx can pick it (Andrei Sura)
* Save important files for docs `sphix-ification` (Andrei Sura)
* Save converted files from `doc/*.md` to `docs/*.rst` (Andrei Sura)
* Copy images from `doc/images` to `docs/images` for the ReST migration (Andrei Sura)
* implemented review comments for pull request 84 (Radha Kandula)
* Add contact info to `README.md` (Andrei Sura)
* Update AUTHORS.md (Andrei Sura)
* Expand documentation about `Installation Steps Using Source Code` + Add short section `How to Use RED-I` (Andrei Sura)
* One line documentation fix for deprecated `--keep=yes` (Andrei Sura)
* Reformat `describing_a_redcap_form_to_red-i.md` for shorter lines + Moved `screenshot-field-name-lookup.png` to the `images` folder (Andrei Sura)
* add fields() function to Event class to get all the fields of it (Radha Kandula)
* Rules for clearing values using keyword 'cancel' (Radha Kandula)
* Fix anchors for document sections in README.md (Andrei Sura)
* Link to Philip's RED-I presentation from the main README.md (Andrei Sura)
* Link to our code review guidelines `doc/code-review-checklist.md` from the main README.md (Andrei Sura)
* Add the removed pieces from README.md as seprate files in the `doc/` folder (Andrei Sura)
* Add more links to existing files in the `doc/` folder from README.md (Andrei Sura)
* Add support for --record parameter in redcap_records.py (Philip Chase)
* Fix issue with download file name when connecting to sftp (Andrei Sura)
* Remove developer specific details from main README.md (Andrei Sura)
* Add dependency on `sftpserver` to `.travis.yml` (Andrei Sura)
* Add unit test for connecting to sftp with a private key (Andrei Sura)
* Use new `sfpt_server_*` params when connecting to sftp with a private key (Andrei Sura)
* Use `EmrFileAccessDetails` object for passing new sftp params: * sftp_server_port * sftp_server_private_key * sftp_server_private_key_pass (Andrei Sura)
* Correct names for two tasks in `vagrant/Makefile` (Andrei Sura)
* Improve documentation in `config-example/settings.ini` Closes issue 63 (Andrei Sura)
* Remove unused script: `exportForms.sh` (Andrei Sura)
* Use boolean args `keep` and `emrdata` Closes issue 53 with dedicated unit test class `TestArgs` (Andrei Sura)

* Summary: Update config-example to work with new sample project

* Fixed 73: Change use of redcap_server and redcap_uri settings
* Fixed 72: Remove circular dependency redi <--> redi_lib
* Fixed 68: Sample REDCap project is tied to a specific REDCap version number
* Fixed 64: Create a RED-I config to match the example REDCap project.
* Fixed 63: Add documentation within config-example/settings.ini to explain the use of each parameter
* Fixed 62: Regroup settings within settings.ini
* Fixed 60: Make a test data set of CBC and Chemistry data
* Fixed 59: Revise report sending code to note the locations of reports/email bodies in the console output
* Fixed 58: Remove project specific details from vagrant/Makefile
* Fixed 49: "Exceeded event list... Event count of 11 exceeds maximum of 11"
* Fixed 47: Do not hardcode smtp host/port
* Fixed 27: Update /vagrant/README.md to match new features
* Fixed 4: Create a working example REDCap Project suitable for RED-I Demonstration
* Fixed 3: No config-example folder

* Rename README_Travis_CI_Setup.md to `setup_travis_ci.md` Also move the related images to `images/setup_travis_ci`
* Cut the section about adding a new REDCap project from vagrant/README.md This resulted in creation of a new document: doc/add_new_redcap_project.md and associated files in dedicated folder: `images/add_new_redcap_project/`
* Remove deprecated document: `doc/README_test_against_redcap.md`
* Delete empty file: `vagrant/README-projects.md`

* Added scripts/compare_settings.sh to help find differences Example usage: ./compare_settings.sh ../config/settings.ini ../config-vcu/settings.ini
* Add clinical-commit-to-loinc.xml helper scripts
* Add synthetic_data tool, makefakedata.R
* Improve `bin/utils/redcap_records.py` - now works with json/xml

* Log information about rules loading

* Summary: performance improvements to speed up run time.

* Closes 42 - "redcap_records.py lost the events and fields arguments" (Andrei Sura)
* Remove implied assert of a formImportedFieldName (Taeber Rapczak)
* Add test showing formImportedFieldName is required (Taeber Rapczak)
* Refactor TestCopyDataToPersonFormEventTree.py (Taeber Rapczak)
* additional fix for 39 (Ruchi Vivek Desai)
* fixes 39 (Ruchi Vivek Desai)
* Update README with --skip-blanks and --verbose (Taeber Rapczak)
* Increase pylint score (Taeber Rapczak)
* Add suport for skipping blanks to generate_output (Taeber Rapczak)
* Add --skip-blanks flag (Taeber Rapczak)
* Add unit test to check for --skip-blanks (Taeber Rapczak)

* Replace clinicalComponentId with loinc_code in config-example
* BUG: Interpret `send_email` as bool - fixes 35
* Add verify_ssl switch to tell PyCap when to verify the ssl certificate of the REDCap server
* Add missing help text and fix typographical errors in vagrant/Makefile
* Add additional exported forms to rc_get target of vagrant/Makefile
* Remove demographic test data from vagrant folder and add Makefile target to copy this project-specific data from the config folder