Toil

* Deprecate subprocessDockerCall(). 2653
* Move wallTime to a label so we can use exact timestamps. 2664
* Capture and log standard output/error from batch systems. 2662
* Add an option to set custom AWS IAM roles. 2656
* Add a ToilNodeType tag to distinguish leader vs. workers. 2658
* Slurm: include both exit code and terminating signal in job return status. 2646
* Update requests package. 2610
* HTCondorBatchSystem(): fixes and features. 2647
* Update cwltool from 1.0.20180820141117 -> 1.0.20190228155703 2609
* Add an option to set disableCaching to false. 2584
* Speed up S3 bucket deletion. 2597
* Tolerate missing jobs/workers in stats expando. 2533
* Add private IP support to node operations. 2569
* Encode logs for gzip. 2595

_Bug Fixes_
* Improve NoSuchFileException usage and robustness. 2593
* Make sure we always have current package lists. 2675
* Make sure to use --tmpdir-prefix to place workdir and jobstore. 2587
* Subprocess dockercall bytestring compatibility for py2/3. 2677
* Address python3 deprecation warnings. 2668
* Fix python3.7 break on __new__ static method. 2659
* Get value of taskId in Mesos' killTask method. 2661
* Stop NamedTemporaryFile tampering. 2638
* StatsAndLogging(): ensure json.load() receives only string input. 2641
* Reduce max size of files allowed to be inlined in SDB. 2440
* Increase hardcoded encapsulate follow-on resources. 2591
* Ensure TOIL_DOCKER_REGISTRY variable is in version_template. 2583
* Use current python executable. 2599

Thank you to our contributors: mr-c, arostamianfar, adamnovak, kwwette, liinus, saimeCS, cdunn2001, Fifan31, jeffrey856!

* Support for CWL s3 imports. 2522
* Support for running custom init commands in docker (allowing auth in private dockers). 2561
* Add --no-read-only option to the CWL runner. 2531
* Add support for assuming roles. 2527
* Added an adapter to allow Boto 2 to use credentials obtained via Boto 3. 2527
* Add a flag for running CWL internal jobs on workers. 2524
* Added CWL tests for http, https, and s3 file imports. 2234
* Begin testing python3 in gitlab. 2518
* Relegate pytest dependency to the dev reqs. 2508
* WDL changes to enable resource usage. 2495
* Sphinx and pathlib2 dependencies. 2490 2493
* Upgrade appliance to Ubuntu 16.04. 2480
* Update cwltool from 1.0.20180820141117 -> 1.0.20181118133959 2469
* Add CWL's --preserve-entire-environment option. 2481
* Bump minimum version of galaxy-lib (17.9.3 -> 17.9.9). 2476
* Added all tutorial scripts to unit testing. 2426
* More python3 support added. 2405
* Update the CoreOS AMI. 2430
* Simplify log creation in leader. 2423
* Support for hardlinks and greater testing for toil status. 2402
* Pymesos port. 2366 2338
* Use displayName for CWLJob to show stats in toil --stats. 2397

_Bug Fixes_
* Import errors. 2558
* Fix boto3 credentials for permanent credentials. 2549
* Fix bug in Toil stats. 2513
* Replace some str objects as real FileIDs. 2500
* Remove linear-time bottleneck from Mesos batch system. 2498
* Slurm and py3 fixes. 2494
* Safeguard unintentional boto imports. 2489
* Fix broken readthedocs build. 2485
* Specify region in prometheus. 2437
* Fixed bytestring-string tagging. 2472
* LSF log job id on error. 2450
* Fix massive slowdown when many jobs are running. 2439
* Make ServiceManager stop blocking while (most) services are established. 2441
* Default to bash on the leader node rather than sh. 2435
* resource.getusage returns KB already, so dividing by 1024 yields MB. 2425
* Recognize conda virtual envs. 2422

Thank you to our contributors: mr-c, arostamianfar, adamnovak, nikhil, lamby, gijzelaerr, joelarmstrong, markasbach, davidjsherman, psafont, jsmedmar, bencvdb, emlys, ionox0, ibebio, MarkFilus!

* 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