Toil

* Attempt to make batch system more robust and debuggable. 2959
* Kubernetes Shared Caching. 3012
* Test python3.8 and build a python3.8 appliance. 3028
* Use the original pymesos. 3036
* Detect more kinds of virtual environment and normalize prefixes. 3035
* Do More Hashing. Can't have enough. 3025
* Replace reissued jobs message with better progress indicators. 3044
* Detect insufficient resources and deadlocks more usefully. 3043

_Bug Fixes_
* Don't list specific CWL features, try them all (and fix some CWL running bugs). 3015
* Always honor TOIL_GRIDENGINE_PE and never assume a site-dependent default. 3041

Thank you to our contributors: mr-c, arostamianfar, adamnovak, diekhans!

This release moves to python3 only, dropping all python2.7 compatibility, and also deprecates the command "cwltoil" in favor of "toil-cwl-runner".

* Update cwltool version (==1.0.20190906054215 -> <=2.0.20200126090152). 2969
* Drop the long-deprecated cwltoil. 2843
* Dropped python2.7. 2973
* Port provisioner tests and only test py3.6. 2842
* CWL: Refactor of link merge + conditionals + pickValue. 2845
* Add import subprocess to executor.py. 2976
* Encode mtail stdin to utf-8 and flush. 2978
* Encode framework message as utf-8 as well. 2981
* Make the output files for grid engine batch systems not try and be in per-host directories. 2956
* Use file locks instead of PID polling to see if other processes sharing the cache are alive. 2982
* Size downloads during download. 2989
* Add timeouts to all SQLite connect statements. 2993
* Eliminate sleep time on --restart. 2990
* Add support for --awsEc2ExtraSecurityGroupId. 2997
* Add moveExports option. 2983
* Set worker threads as dameon to prevent hanging process on error. 2998
* Cut the Threads. 2999
* [Part 1] CWL v1.1 Support 2985
* [Part 2] CWL v1.1 Support 3000
* Update Sphinx and let its version float. 3011
* Add --enableUnlimitedPreemptableRetries option. 2896
* Add less and vim to docker. 3017
* Improve and Unify Log Dumping. 3008
* Make dependency on Python3.6+ machine-readable in setup.py. 3021
* Improve slurm update frequency. 3026
* Make Sphinx a make prepare component and not a dependency. 3023
* Use forked pymesos and http-parser dependencies. 3024

_Bug Fixes_
* Fix python3 string/bytes error when using --printLogs. 3005
* Fix connection between Kubernetes and Leader. 3004

Thank you to our contributors: mr-c, arostamianfar, adamnovak, jeffrey856, kaushik-work, glmxndr, johnbradley, cmarkello, diekhans!

This is the last version of Toil that supports python2.7 and allows the command word "cwltoil" (now "toil-cwl-runner").

* Update ssh and docker setup files. 2958
* Update EC2 instance types. 2962
* Source toil environment as a configuration file. 2960
* Scan for the latest caching database instead of using a hard link. 2948
* Specify py3.6 or py3.x instead of just py3 in appliance. 2966

_Bug Fixes_
* Fix database being locked when trying to write in the CachingFileStore. 2955
* Fix py3 spot market scaling. 2971

Thank you to our contributors: mr-c, arostamianfar, adamnovak, jeffrey856!

Functionally the same as Toil Version 3.22.0.

* Make an appliance for Python 3. 2937
* Use status to properly get the HTTP status code from boto. 2934
* Use atomic file copy when writing to posix file system. 2912
* Improve Kubernetes job timing. 2922
* Increase SQLite DB timeout to 60s. 2913
* Consider pods that are very close to their memory limits to be stuck. 2895
* Constantly reload Kubernetes config. 2869
* Up the disk to the default as well as the memory. 2880
* Tolerate unnecessary bucket cleanup. 2894
* Add checksum verification for AWS job store. 2889
* Change python3.6 ppa to deadsnakes. 2888
* Change Kubernetes job sizing logic. 2877
* Added env var TOIL_KUBERNETES_OWNER. 2872
* Raise job limits to be more than their requests. 2868
* Remove all Azure support from toil. 2860

_Bug Fixes_
* Exclude .nfs files from deferred function search. 2930
* Fix cpu_count() to actually read quotas. 2933
* Compile http-parser so that it doesn't break pip dependencies. 2940
* Use an http-parser for pymesos that builds on 3.7+. 2931
* Fix botocredAdapter. 2904
* Make sure to commit when giving away files. 2914
* Actually call the implemented size polling method. 2916
* Set Docker vars back to ?=. 2908
* LSF: Don't check for Status <EXIT>, as that breaks the error code finding. 2863

Thank you to our contributors: mr-c, arostamianfar, adamnovak, jeffrey856, diekhans!

* Add kubernetes watch. 2848
* Add service account configuration for Kubernetes. 2851
* Head object 404 with encryption. 2853
* Tests for Kubernetes. 2838
* Turn usernames into non-spooky Kubernetes name components. 2836
* Make examples a symlink to make examples discoverable. 2834
* Kubernetes BatchSystem Support. 2786
* Specify GCE coreos image by family name instead of specific version. 2829
* Add toil-cwl-runner --provenance. 2785
* Revise caching more. 2770
* Bump psutil >= 3.0.1, <6. 2790
* Add "failed_" prefix to failed logs. 2792
* Add --writeLogsFromAllJobs option. 2781
* Expose --default-container to toil-cwl-runner. 2784
* Update cwltool from 1.0.20190228155703 -> 1.0.20190815141648. 2764
* Pass jobID to Torque Wrapper. 2762
* Limit Length of Log Names. 2755
* Add CWL options --strict-memory-limit, --relax-path-checks, and --leave-container. 2718
* Update EC2 nodes and script. 2709
* Redesign File Job Store layout. 2669

_Bug Fixes_
* Fix for passing default values between Workflows. 2831
* Ignore checking versioning consistency when cleaning s3 jobstore. 2826
* Ensure terminated ignored nodes are cleared from batch system. 2789
* Fix Slurm sbatch command. 2777
* Typo in gridengine.py. 2778
* CWL fixes. 2783
* Clarify `/data` mountpoint for `dockerCall`. 2747
* Fix CWL tmpdir to be unique per job. 2745
* Protect against potential AWS truncated downloads. 2731
* Fix runningOnEC2 to work with all instances. 2734
* Prevent Toil from zipping entire dirs. 2728
* Changes to lsf.py to make it compatible on lsf9 and lsf10. 2726
* Remove X86_64 type requirement from lsf support. 2723
* Clean up temporary directories cwltoil uses to hold output streams. 2690

Thank you to our contributors: mr-c, arostamianfar, adamnovak, jeffrey856, tthyer, kaushik-work, dleehr, ionox0, psafont, mb1069, tobiaszjarosiewicz, gconcepcion, byee4, smoe, TMiguelT, jvivian-atreca!