D3r

-------------------
* Execute tasks in stage in parallel.
`Issue 202 <https://github.com/drugdata/D3R/issues/202>`_
* Use absolute path for custom celpp weeks.
`Issue 204 <https://github.com/drugdata/D3R/issues/204>`_
* Check that Schrodinger env variable is set before using.
`Issue 205 <https://github.com/drugdata/D3R/issues/205>`_
* Capture Schrodinger version in weekly outputs.
`Issue 206 <https://github.com/drugdata/D3R/issues/206>`_
* Save number of submitted targets for each participant to REST API.
`Issue 207 <https://github.com/drugdata/D3R/issues/207>`_
* Handle and prevent empty PDB files created by Schrodinger.
`Issue 208 <https://github.com/drugdata/D3R/issues/208>`_

--------------------
* Additional fix for ftp connection refused
`Issue 181 <https://github.com/drugdata/D3R/issues/181>`_

--------------------
* Fix for failed test in 1.11.1

--------------------

* Email participant when submission is empty.
`Issue 197 <https://github.com/drugdata/D3R/issues/197>`_

* Allow spaces in passwords in ftp config file.
`Issue 198 <https://github.com/drugdata/D3R/issues/198>`_

--------------------

* Fixed minor bug where unit tests for molfilevalidator.py failed when valid
openeye license was available.
`Issue 177 <https://github.com/drugdata/D3R/issues/177>`_

* Added retry to external submission download to prevent complete failure of
download in event of network hiccup
`Issue 181 <https://github.com/drugdata/D3R/issues/181>`_

* Fixed bug where median value incorrectly calculated in evaluate.py. Instead
of averaging middle two values for case of even number of elements, the old
code just chose the latter value.
`Issue 183 <https://github.com/drugdata/D3R/issues/183>`_

* Fixed bug where median value incorrectly calculated in post_evaluation.py.
Instead of averaging middle two values, the old code just chose the latter
value.
`Issue 184 <https://github.com/drugdata/D3R/issues/184>`_

* Updated BlastNFilterSummary class (used by celppreports.py) to calculate
number of targets found by counting target .txt files if value is not in
summary.txt file
`Issue 187 <https://github.com/drugdata/D3R/issues/187>`_

* Added call to website REST service in EvaluationTask and PostEvaluationTask
to persist evaluation results to website. This change added a new flag
--websiteserviceconfig that requires a configuration file.
`Issue 188 <https://github.com/drugdata/D3R/issues/188>`_

* Fixed bug in evaluate.py wait_and_check() function which caused it to
prematurely give up on an alignment.
`Issue 189 <https://github.com/drugdata/D3R/issues/189>`_

* Changed evaluate.py so it now writes final.log directly to output directory.
`Issue 190 <https://github.com/drugdata/D3R/issues/190>`_

* Moved code under if __main__ into main() function to facilitate testing.
`Issue 191 <https://github.com/drugdata/D3R/issues/191>`_

* Add RMSD.csv to files uploaded in EvaluationTask get_uploadable_files().
`Issue 192 <https://github.com/drugdata/D3R/issues/192>`_

* Changed logging in evaluate.py to use module logger instead of root logger
`Issue 194 <https://github.com/drugdata/D3R/issues/194>`_

--------------------

* **Breaking change** Added new flag to celpprunner.py --smtpconfig
that lets a user specify smtp configuration information.
At the same time removed --replyto --smtp, and --smtpport since
those options would be confusing to have also in place.
`Issue 166 <https://github.com/drugdata/D3R/issues/166>`_

* molfilevalidator.py has new command line option --excludedir to
let caller ignore directories when looking for mol files.
`Issue 167 <https://github.com/drugdata/D3R/issues/167>`_

* Fixed bug where a network hiccup raised an exception during
DataImportTask causing celpprunner.py to exit prematurely.
`Issue 168 <https://github.com/drugdata/D3R/issues/168>`_

* Improved error message output when a participant uploads a
malformed challenge data package.
`Issue 169 <https://github.com/drugdata/D3R/issues/169>`_

* Version of D3R is now output in post evaluation summary email.
`Issue 172 <https://github.com/drugdata/D3R/issues/172>`_

* Fixed bug where celpprunner.py was not sending an email to
people in --summaryemail list if a task fails.
`Issue 171 <https://github.com/drugdata/D3R/issues/171>`_

* Post evaluation summary email now outputs lines with NA
values for any submissions that failed
`Issue 130 <https://github.com/drugdata/D3R/issues/130>`_