Lorax

~~~~

- Changed the tree output to be rooted, entailing a change in the exact Newick format used.
Root node names are family names. Trees are now ladderized. ete3 is now a dependency.

- Added the ``/rq`` dashboard target. rq_dashboard is now a dependency.

- Added commands.

- Changed startup methods considerably. See the startup scripts for details.

~~~~

- Names of executables are now configuration parameters. This allows for overriding of executable
names on platforms where the name may vary.

- Added DELETE target for superfamiles.

- Calculation methods now return JSON dictionaries of job listings that include the following:
* ``id``: id string
* ``description``: description string, e.g., "FastTree tree of superfamily aspartic_peptidases.myseqs"
* ``status``: job.status, e.g., "deferred"
* ``tasktype``: "align" or "tree"
* ``taskname``: name of aligner or builder
* ``family``: name of family
* ``superfamily``: name of superfamily
* ``is_queued``: True if queued. This will not be true until after alignment in some cases.
* ``is_started``: True if job is running.
* ``is_finished``: True if job is finished (since queue was reset).
* ``is_failed``: True if job failed due to an error.
* ``created_at``: ISO format job creation time or "None".
* ``enqueued_at``: ISO format time of queueing or "None".
* ``ended_at``: ISO format ending time or "None".
* ``started_at``: ISO format start time or "None".
* ``estimated_job_time``: Estimated run time (wallclock) in seconds.
* ``queue_name``: Name of queue (for future queries)
* ``queue_position``: position in queue, if queued, or length of queue if not.
* ``estimated_queue_time``: Estimated wallclock time of preceding jobs, in seconds.
For now all estimated times are bogus and simply placeholders until timing models are established.

- Config parameters are settable via environmental variables starting with ``"LORAX_"``.

- Configuration parameters are now settable by instance as a pyfile.

- Improved logfile content.

- Removed ``/config`` target as insecure.

- Changed configuration from ``config.json`` to a Flask-standard pyfile. See ``default_settings.py``.

~~~~

- Added ``/trees/<family>/hmmalign_FastTree`` target to chain calculations.

- Added a polling method in ``test_all.sh`` to poll a URL until >= 0, useful for status polls.

- Queueing for FastTree calculation via rq added. Expects a queue named ``"FastTree"``.

~~~~

- Added superfamily targets.

- Added test_all.sh script to do full testing.

- Changed "tree" target to ``tree.nwk``.

- Compute stats on HMM files and return as part of HMM addition. If hmmstats fails,
abort with 417 and delete the HMM file.

- Added /trees/families.json target.

- More run-time arguments.

- Renamed /config target as /config.json

- Returned JSON objects are now reponses of type 'application/json'.

- Added /log.txt target that returns the current log file.

- Added click as a dependency, removed ``flaskrun.py``.

- Moved config.py code to __init__.py.

- Removed AutoIndex of / directory.

- Changed HMM from ``POST`` to ``PUT`` for consistency with HTML specs. Added ``put_HMM.sh`` script.

- Removed test for <family> naming, anything that passes Path addition will work.

~~~~~