Fyrd

This version brings a major overhaul to the structure of the code, while leaving the API mostly intact. Importantly, it fixes the issue that resulted in the local mode not using 100% of CPU power.

Major Changes

• Completely rewrote the local mode to use Pyro4 and SQLAlchemy, it is now much, much faster and more stable
• Batch system definitions now fully modular and are contained in the fyrd.batch_systems package. options.py has also been moved into this package, which allows any programmer to add a new batch system definition to fyrd by just editing the contents of that small subpackaged
• Updated console script to allow running arbitrary shell scripts on the console with fyrd run or submitting any number of existing job files using fyrd sub. Added the new alias scripts frun and fsub for those new modes also. Both new modes will accept the --wait argument, meaning that they will block until the jobs complete.
• Documentation overhauled to update API and add instructions on creating a new batch system, these instructions are duplicated in the README within the batch_systems package folder.
• Full support for array job parsing for both torque and slurm. We now create on job entry for each array job child, instead of for each array job. To manage this, the fyrd.queue.Queue.QueueJob class was moved to fyrd.queue.QueueJob and split to add a child class, fyrd.queue.QueueChild. All array jobs not have one fyrd.queue.QueueJob job, plus one fyrd.queue.QueueChild job for each of their children, which are stored in the children dictionary in the fyrd.queue.QueueJob class.
• Added a get method to the fyrd.queue.Queue class to allow a user to get outputs from a list of jobs, loops continuously through the jobs so that jobs are not lost.
• Added tqdm as a requirement and enabled progressbars in multi-job wait and get

Minor Changes

• Updated the documentation to include a changelog, which will only contain change information for version 0.6.2a1 onwards.
• Added additional tests to cover the new changes as well as generally increase test suite coverage.
• Several small bug fixes