Toil

* Refactor stream writes in the fileJobStore to minimize holding open file handles
* Large python 2/3 compatibility changes (+ python 3 compatible mesos library: pymesos)
* Get status/PID API added
* CWL:fix support for user space overrides
* Update cwltool from 1.0.20180518123035 to 1.0.20180820141117
* support lsf 10 per core reservation
* WDL bucket outputs with orig names
* Grid engine job creation fix
* Add Mesos port forwarding and the ability to use a SOCKS proxy with toil ssh-cluster
* Require a jobstore to be specified when a provisioner is.
* Retry HTTP connections on BadStatusLine errors
* Quote() all Docker arguments
* log LSF job id to error on failure
* Improve test file cleanup
* retries for batch commands
* Update CoreOS AMI
* CWL workDir defaults to tmpdir_prefix now if not set by the user
* Set the default duration for batch systems with getWaitDuration()
* Coverage Evaluation

_Bug Fixes_
* AMI Fetch Timeout
* Stop logging every message twice in certain cases
* Fix htcondor in wheel breaking on Apple
* Fix toil kill
* Fix invalid qsub in torque.py

Thank you to our contributors: mr-c (big thanks for all of the CWL support!), MarkFilus, xzhub, ionox0, jsmedmar, bencvdb, tom-dyar, joelarmstrong, mwiens91, jessebrennan, and adamnovak!

* Add CWL destBucket runtime option to deposit CWL outputs into cloud buckets
* Update boto3 and boto
* Better Error messages when docker images are unavailable
* Broader checking for docker image existence prior to launching blindly
* Incremental Python2/3 compatibility improvements
* Enable support for specifying zone in all environment variables
* Expose `--force-docker-pull` and `--no-match-user` options from cwltool
* Add mem free option to UGE
* Convert most log messages to debug level
* Update cwltool from 1.0.20180518123035 to 1.0.20180521150620
* Incremental WDL Support Improvements (docker permissions, parsing, and improved logging)
* Documentation Housekeeping and Code Cleanup

_Bug Fixes_
* Stop FileJobStore DEBUG messages from sneaking out once for every job
* WDL Parsing Error
* Fix docker daemon detection depending on terminal size
* Checking virtualenv
* Properly filtering AWS security groups
* Fix a crash if job is larger than all available node types
* Avoid overwriting NVMe root volumes on current-gen AWS instances
* Don't call addNodes if the delta was met by unignoring nodes
* Fix AWSJobStore updates not working if values are shrunk
* Prevent worker from checking for nonexistant file


Thank you to our contributors: mr-c (big thanks for all of the CWL support!), jsmedmar, bencvdb, tom-dyar, joelarmstrong, mwiens91, jessebrennan, and adamnovak!

* More Robust WDL Support
* Reworked the Cluster Scaler Algorithm
* Updated subprocess32 to version 3.5.1
* Eliminated bd2k-lib dependencies
* apiDockerCall allows blocking now for both detached/attached images
* Util to fetch the latest AWS instance types
* Check if docker images specified by the Toil appliance are valid before running
* Reduce toil clean memory usage for AWS jobStores

_Bug Fixes_
* CWL fixes for handling promises / followOn jobs
* Fix occasional cPickle deadlocks
* Increased Google and Azure stability
* Google jobstore fixes
* fileJobStore deletion made more robust for NFS-like systems

Thank you to our external contributors: mr-c (big thanks for all of the CWL support!), chapmanb, ryanking, jmchilton, jorvis, evan-wehi, brainstorm, jsmedmar

* Azure Support (Beta)
* Google Support (Beta)

_Bug Fixes_
* CWL fixes.
* LSF cpu count fix.

Thank you to our external contributors: mr-c (big thanks for all of the CWL support!), chapmanb, ryanking, jmchilton, jorvis, evan-wehi, brainstorm, jsmedmar

* Added support for the HTCondor Batch System
* Updated documentation.
* Added the protobuf dependency for mesos.
* Updates for CWL (scheduling, update CWL ref runner, update conformance tests, expose cwltool's tempdir-prefix, expose user-space-docker-cmd, and always import links for CWL)
* Added an "all" option to install all extras.
* Check for venv in python 2 and 3.

_Bug Fixes_
* Added buffering for local file transfers to fix MemoryError bugs
* Fix race conditions for SLURM, GridEngine, Mesos, and Torque batch systems.
* Updated file size determination on Apple products.
* Fixed a bug when making the docs through Sphinx.
* Amended memory limit and reservation in LSF.
* Removed cwl-runner command, as it was interfering with the native CWL command.

Thank you to our external contributors: mr-c (big thanks for all of the CWL support!), chapmanb, ryanking, jmchilton, jorvis, evan-wehi, brainstorm, jsmedmar

releases/3.13.0-dirty
* WDL Alpha support
* Job store symlinking
* Updated cwltool support (version; fixes; testing)
* Better logging
* Option to get stderr from subprocessDockerCall
* Integration testing with ENCODE
* Cactus with autoscaling


_Bug Fixes_
* Fixed static provisioning
* Fixed launch-cluster bug when terminal size was too small
* Removed AWS specific code from the abstract provisioner

Thank you to our external contributors: mr-c, chapmanb, ryanking, jmchilton, jorvis, evan-wehi, brainstorm, jsmedmar

* Forkless mode for debugging
* Enabled Travis builds with a subset of tests (less than 15 minutes).
* DockerCall function changed to use docker API.
* Updated to Azure version 2.0.
* Added tempDir convenience function to job and made job.log an alias for fileStore.LogToMaster.
* Enhanced toil-cwl-runner to support SoftwareRequirements & BioContainers.
* Increased default retry count to 1.
* Deprecated cgcloud.
* Updated EC2 instance types.
* Upgraded pip to 9.0.1 and setup tools to 36.5.0 in appliance build.

*Bug fixes*
* Parasol parses jobStore path correctly.
* Parasol doesn't attempt to remove jobs that it didn't launch.
* Fixed problem with dynamic batch systems not always being created.
* Fix workflow effort being wasted if a single export fails.
* Added a default value for maxNodes.
* Fixed py.test collection errors when running locally.

Thank you to our external contributors: jmchilton, jorvis, evan-wehi, mr-c, brainstorm