Release Bpipe Version 0.9.9.9 · ssadedin/bpipe

Summary

This release includes a number of smaller features and improvements and
some important fixes.

NOTE: this version of Bpipe requires Java 1.8 or higher

Ability to filter gitlab issues identified
by title search for updating
Feature: support for 'debug' command that launches
groovy shell. Add debug() to pipeline stage to launch
interactive shell.
Revamp monitoring of command status for PBS/Torque
based pipelines, by pooling calls to qstat between
commands.
Feature: archive command to clean up .bpipe directory into
restorable zip file
Support referencing params set on command line in
bpipe.config
Bpipe pipelines can now accept the first line as a "shebang"
so that bpipe pipelines become executable scripts. ie: make
the first line of your pipeline: #!/path/to/bpipe

Fix not completely robust reading of exit code for
local commands (sometimes command succeeds when shouldn't)
Fix local commands not always terminating on explicit stop
Add setsid by default to local jobs on linux -
prevents some cases where jobs abort when precessing
ctrl-c after starting bpipe
Fix new gitlab issues with large content failing to send
Fix possible runaway killing of processes when
local preallocated jobs are explicitly stopped with
bpipe stop
Fix file notifications not always incrementing and
therefore overwriting previous notification
Fix notification manager not respecting timeout to allow for
setup of channels
Fix possible error due to race condition
reading read PID with local command executor
Fix file handle leak on some file systems with large scale
highly parallelised, long running pipelines
Fix the default file notification channel overwriting files from
other send channels
Fix possible error if input is referenced in details of send