Merlin

Added
- A faq entry for --mpibind when using slurm on LC.
- Version of the openfoam workflow that works without docker.
- In 'merlin examples', a version of the openfoam workflow that works without docker.

Fixed
- The batch system will now check LSB_MCPU_HOSTS to determine the number
of nodes on blueos systems in case LSB_HOSTS is not present.
- A few typos, partially finished material, and developer comments in the tutorials.
- PEP-8 violations like unused imports, bad formatting, broken code.
- A bug where the batch shell was not overriding the default.

Changed
- Removed mysql dependencies and added sqlalchemy to the celery module.
- Removed mysql install from travis.
- Improved the celery worker error messages.
- The slurm launch for celery workers no longer uses the --pty option,
this can be added by setting launch_args in the batch section.
- Adjusted wording in openfoam_wf_no_docker example.

Added
- merlin example `null_spec`, which may be used to generate overhead data for merlin.

Fixed
- The task creation bottleneck.
- Bug that caused the `cmd` stdout and stderr files of a step to be overwritten by that same step's `restart`
section.

Changed
- Updated tutorial docs.
- Relocated code that ran upon import from file body to functions. Added the respective
function calls.

Added
- `HelpParser`, which automatically prints help messages when command line commands return an error.
- Optional ssl files for the broker and results backend config.
- A url keyword in the app.yaml file to override the entire broker or results backend configuration.
- The `all` option to `batch.nodes`.
- Auto zero-padding of sample directories, e.g. 00/00, 00/01 .. 10/10
- `$(MERLIN_STOP_WORKERS)` exit code that shuts down all workers
- The `merlin monitor` command, which blocks while celery workers are running.
This can be used at the end of a batch submission script to keep the
allocation alive while workers are present.
- The ~/.merlin dir will be searched for the results password.
- A warning whenever an unrecognized key is found in a Merlin spec; this may
help users find small mistakes due to spelling or indentation more quickly.

Fixed
- Bug that prevented an empty username for results backend and broker when using redis.
- Bug that prevented `OUTPUT_PATH` from being an integer.
- Slow sample speed in `hello_samples.yaml` from the hello example.
- Bug that always had sample directory tree start with "0"
- "Error" message whenever a non-zero return code is given
- The explicit results password (when not a file) will be read if certs path is None and it will be stripped of any whitespace.
- Misleading log message for `merlin run-workers --echo`.
- A few seconds of lag that occurred in all merlin cli commands; merlin was always searching
thru workflow examples, even when user's command had nothing to do with workflow examples.

Changed
- Updated docs from `pip3 install merlinwf` to `pip3 install merlin`.
- Script launching uses Merlin submission instead of subclassing maestro submit
- `$(MERLIN_HARD_FAIL)` now shuts down only workers connected to the bad step's queue
- Updated all tutorial modules

Changed
- Updated various aspects of tutorial documentation.

Added
- The walltime keyword is now enabled for the slurm and flux batch types.
- LAUNCHER keywords, (slurm,flux,lsf) for specifying arguments specific
to that parallel launcher in the run section.
- Exception messages to `merlin info`.
- Preliminary tutorial modules for early testers.

Removed
- The problematic step `stop_workers` in `feature_demo.yaml`.

Fixed
- Syntax errors in web doc file `merlin_variables.rst`.

Removed
- The exclusive and signal keywords and bind for slurm in a step. The bind
keyword is now lsf only.

Added
- cli test flag `--local`, which can be used in place of listing out the id of each
local cli test.
- A Merlin Dockerfile and some accompanying web documentation.
- Makefile target `release`.
- The merlin config now takes an optional --broker argument, the
value can be None, default rabbitmq broker, or redis for a redis
local broker.
- Missing doc options for run and run-workers.
- Check server access when `merlin info` is run.
- A port option to rabbitmq config options.
- Author and author_email to setup.py.

Removed
- Makefile targets `pull` and `update`.
- Unneeded variables from `simple_chain.yaml`.
- All `INFO`-level logger references to Celery.

Changed
- Updated the Merlin Sphinx web docs, including info about command line commands.
- Example workflows use python3 instead of python.
- Updated `merlin info` to lookup python3 and and pip3.
- Altered user in Dockerfile and removed build tools.
- MANIFEST.in now uses recursive-include.
- Updated docker docs.
- `make clean` is more comprehensive, now cleans docs, build files, and release files.
- The celery keyword is no longer required in `app.yaml`.