Merge branch 'release/0.13.0'

AUTHORS.md

@@ -24,5 +24,5 @@ Erik Schmidt, and Chris Barnes provided direction to the development effort.
 
 Radha Kandula, Mohan Das Katragadda, Ruchi Desai, Yang Li, Kumar Sadhu,
 Alex Loiacono, Erik Schmidt, Nicholas Rejack, Philip Chase, Roy Keyes,
-and Andrei Sura provided code to make this project awesome.
+Andrei Sura, and Taeber Rapczak provided code to make this project awesome.
 We are nothing without our developers.

CHANGELOG

@@ -1,3 +1,79 @@
+2014-11-20 v0.13.0
+
+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
+
+2014-10-07 v0.12.0
+
+* 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 `[email protected]` email for consistency with `setup.py` (Andrei Sura)
+ * Document installation from binaries: `pip install redi-py` (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-py/0.11.3 (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)
+
 2014-09-23 v0.11.3
 
  * Summary: Update config-example to work with new sample project

MANIFEST.in

@@ -3,7 +3,7 @@ include LICENSE.txt
 include AUTHORS.md
 include README.md
 include setup.py
-recursive-include bin *.py
+recursive-include redi *.py
 recursive-include test *.py
-recursive-include doc *
+recursive-include docs *
 

Makefile

@@ -23,17 +23,17 @@ help:
 
 test: tests
 tests: coverage
-	[ ! -d config/rules ] || PYTHONPATH=bin \
-		python -munittest discover config/rules
+	[ ! -d config/rules ] || python -munittest discover config/rules
+	rm -f .coverage
+	rm -rf cover/
+	rm -f coverage.xml nosetests.xml
 
 coverage:
-	ARCHFLAGS=$(ARCHFLAGS) PYTHONPATH=bin \
-		python setup.py nosetests
+	ARCHFLAGS=$(ARCHFLAGS) python setup.py nosetests
 
 lint:
 	which pylint || sudo easy_install pylint
-	ARCHFLAGS=$(ARCHFLAGS) PYTHONPATH=bin \
-		pylint -f parseable bin | tee pylint.out
+	ARCHFLAGS=$(ARCHFLAGS) pylint -f parseable redi | tee pylint.out
 
 clean:
 	find . -type f -name "*.pyc" -print | xargs rm -f
@@ -59,6 +59,7 @@ clean:
 	rm -f person_form_event_tree_with_data.xml
 	rm -rf vagrant/data/
 	rm -f vagrant/redi.db
+	rm -f config-example/report.xml
 
 pypi:
 	#https://pythonhosted.org/Distutils2/distutils/packageindex.html

README.md

@@ -1,7 +1,7 @@
 RED-I Project
 =============
 
-![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.10014.png ".")
+[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.10014.png ".")](http://dx.doi.org/10.5281/zenodo.10014)
 
 Introduction
 ------------