Toil

* 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

* 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.