5.7.1
Changelog
Highlighted Features Added
AWS Batch Batch System (#3956)
AGC Integration (#4039) + More AGC integration (#4067) + AGC megabranch (#4113)
Scale TES to be able to run reasonably-sized workflows on Funnel on Kubernetes with the AWS job store (#3927)
CWL
Run CWL conformance tests via WES (#4052)
Implement and test CWL loadContents from URLs to fix #4125 (#4126)
Add CWL tests under ARM (#4038)
Cache results of cwltool version lookup (#4141)
Misc
SGE batch system change to support serial jobs. (#4022)
Performance testing for Graviton instances (#4123)
Stop waiting on hostpath volumes to exist (#4146)
Catch and warn about jobs going away too slowly on FileJobStore (#4149)
Add documentation for the type-checking hooks (#4117)
Pod murder bot (#4060)
Contrib hook scripts (#4105)
Allow newer google-cloud-storage (#4114)
Use environment variable to set parallel partition name (#4096)
Register pytest markers (#4103)
Mention --export=ALL for SLURM environments (#4100) (#4102)
Allow persisting workflow state in WES server across container recreation (#4082)
Change toil kill to use the job store shared file API to find pig.log (#4075)
Bring back kill loop in the single_machine batch system but with a timeout (#4070)
Reorganize Locking (#4059)
Add and test preemptability constraints (#4044)
Enhanced types (#3975)
Use an init process that reaps zombies on toil clusters (#3974)
Add launch cluster support for ARM (#3971)
Feat: square bracket to period separator (#4008)
Add AGC health check endpoint (#3997)
Tolerate and require typed Werkzeug (#4011)
Add more static URLs for Singularity debs (#4007)
Bug Fixes
Update WES set up docs (#4027)
Add real time logs (#4031)
Fail fast if Docker builder is missing (#4001)
Make Toil version be reported as a string in WES (#4013)
Fix assorted typos within assorted comments (#4023)
Make file store case insensitive (#4153)
Pre-lex commands for qsub (#4150)
Update Cactus and exclude broken networkx (#4107)
Make toil kill work when the leader is on another machine (#4084)
Wrong filename in output (#4139)
Tolerate a missing VersionID key to fix #4129 (#4130)
Only import from typing_extensions on old Python where we install it (#4090)
Allow missing username and fix Docker build (#4077)
Leave more time for concurrency measurement to fix #4012 (#4068)
Stop people asking for ARM Mesos clusters to fix #4057 (#4058)
Thank you to our contributors: @mr-c, @adamnovak, @w-gao, @jonathanxu18, @Hexotical, @gmloose, @kannon92, @douglowe, @gcapes, and @pmiddend!
