Toil

* Allow batch creation of jobs.
* CWL: run internal jobs locally, not on cluster.
* TOIL_TEST_QUICK environment variable for running a subset of tests.
* Allow clusters with multiple node types.
* Put jobName into the _toil_worker arguments.
* GridEngine: cache instead of block for statePollingWait

_Bug Fixes_
* CWL: avoid early removal of the temporary outdir
* Fixed AWS readFileStream deadlock on partial reads.
* Use a socket to get the public-facing IP

Thank you to our external contributors: chapmanb, ryanking, mr-c

Adds missed commits that should have been in 3.10.0.

* Full CWL 1.0.1 support.
* Improved documentation with better examples.
* Added option to link files when importing into fileJobStore.
* Allowed some interactive support
* Improved local testing targets.
* Sleep support for all state-querying functions in batch.
* Opened up UDP traffic within AWS clusters.
* Set mesosMasterAddress default to private IP.
* CWL: symlink jobStore files instead of copying.

_Bug Fixes_
* Fixed getEmptyFileStoreID.
* Automatically use the correct LSF units.
* Fixed failure in resolve_indirect_inner in cwltoil.py.
* Fixed docker tests failing on Mac.
* Stopped log level option defaults from clobbering each other.
* Various other minor bug fixes.

Thank you to our external contributors:
mr-c, tetron, liuxf09, ryanking, OliverEvans96, alaindomissy, brainstrom, chapmanb, nazamy, jmchilton, stefanoberri

* Added a plugin batch systems that abstracts option settings for batch systems.
* Fixed mysterious fail with rsync `--protect-args` on OS-X.
* Added environment variable TOIL_AWS_KEYNAME for setting AWS credentials during tests.
* Tests now timeout with pytest rather than Jenkins.
* Added support for PBSPro (Torque's proprietary version).
* Fixed resolution of symlinks for hard links bug.
* Added an option to set root volume on leader and worker nodes.
* Fixed autoscaler crash.
* Added environment variable TOIL_TORQUE_ARGS for setting Torque arguments.
* Fixed hot-deployment with python-3-supporting libraries.
* Fixed race in ClusterScaler test.
* Several logging improvements and fixes.
* Pip show now displays license info.

- Don't error if job hasn't been submitted yet (resolves 1666)
- Match doc to reality for --preserve-environment
- CWL: symlink jobStore files instead of copying
- When killing tasks, make sure to reap child processes in the process groups
- Better error checking in piped docker commands
- Fix case where a job has been put in currentjobs, but not yet dispatc…
- Use hard links instead of copied files on import to file job store
- CWL: Add support for InitalWorkDirRequirement
- Set proper value for service job preemptable requirement
- Use chunked transfer in AWS job store importing
- Lower timeout for domain binding in Toil Clean
- Add `import os`.

* Updated documentation at http://toil.readthedocs.io/en/latest/
* Improved Azure support
* Remove upper limit on size of jobs in AWS job store
* CWL workflows can now take advantage of Toil Autoscaling
* CWLToil bug fixes and enhancements
* Toil Appliance updated to Mesos version 1.0.1
* Improve scalability of Mesos batch system
* Better error message for unfulfilled promises
* Fix handling of checkpointed jobs
* Fix service job deadlock detection
* Allow disabling of hot deployment mechanism