Lorax

~~~~

- ``run_in_lorax_env`` script created to define the two required
environmental variables and activate the virtual environment
from either Anaconda or normal versions.

- ``configure_instance`` command defined to configure the supervisord
scripts.

- Supervisord is now used to start lorax and associated version.
supervisord>4.0 (currently only from git) is required due to python3
requirement.

- Setuptools >30 is now required, due to moving many things into setup.cfg.

- FastTree source now included in distribution; FastTree binary will be built
and put in virtual environment under name ``FastTree-lorax``.

- License is now 3-clause BSD (was 4-clause BSD).

- ``config_value`` command is now simply ``config``.

~~~~~~

- Redirected stderr on HMM check call.

- ``LORAX_INSTANCE_DIR`` environmental variable allows overriding the location of the instance
configuration file. Useful for installations where the default instance path is not
writable by the user.

- ``config_value`` with no arguments now indicates whether variables are set from instance
config files or environmental variables.

- ``config_value --verbose VAR`` gives verbose information about the type of the variable
and where it was set.

- The default type for ``config_value`` is now, in priority order:
* The type specified with the ``--vartype`` option, if it exists.
* The type of the extant variable.
* str if not previously defined and ``--vartype`` is not specified.

- ``config_value --type`` renamed to ``--vartype``, and now accepts any valid python type
for its argument. Types other than str and bool are parsed via JSON and have JSON
typing rules (including demanding use of double quotes in places). Note that for
complex types, you may have to enclose the argument in single quotes to keep the
shell from mangling it.


- `config_value VAR` now prints the value.

~~~~~~

- Code passes PEP8.

~~~~~

- `get_config` and `set_config` commands are now condensed to `config_value`
which does set if ``VALUE`` is defined, set get if now. If ``VAR`` is not
defined, ``config_value`` lists all variables along with whether they were
set from environmental variables or not.

-- Broke up ``PATH`` from a dictionary to be three simple key:value objects:
* DATA_PATH
* LOG_PATH
* DIR_MODE

~~~~~

- Package data moved to proper level of hierarchy.

- ``ALIGNMENT_QUEUE_TIMEOUT`` and ``TREE_QUEUE_TIMEOUT`` config parameters. Was defaulting to
180 seconds.

~~~~

- Logging format is now configurable.

- Added commands for easier setup:
* copy_test_files
* get_config
* set_config
* test_logging

- Added PhyD3 files to static and template folders.

- Added ``GET`` method for ``/alignment`` target to return MSA's.

- Created ``requirements.in`` and ``requirements.txt ``dependencies list via pip-sync.

- Removed ete3 in favor of biopython due to ete3 dependency problems with BSD.
Less control over Newick formatting, though...trees may not appear to be rooted
in some downstream programs.