Download

  1. Title Binary Release 0.9.8.6 Beta 2
  2. Release 0.9.8.6_beta_2
  3. Link bpipe-0.9.8.6_beta_2.tar.gz


  4. ========== Changes for Bpipe Version 0.9.8.6_beta_2 ============
    
       - avoid warnings due to project properties (thanks Davide) 
    
       - refactored email functionality to use user configurable
         templates 
    
       - fix notifications for pipeline finished saying
         pipeline failed when it didn't 
    
       - support for displaying information about checks at end of pipeline 
    
       - more information in SMTP notifications, including checks 
         
       - Added option to override all checks for cases where there are 
         very many that have failed 
         
       - changed unknown communication provider to be a warning instead 
         of a pipeline terminating exception.
    
       - fix relative symbolic link to Bpipe not resolving properly 
         under Mac/OSX 
    
       - fix possibility of commands sometimes
         not being cleaned up (add pause before terminating Bpipe,
         after terminating child processes) 
    
       - Fix Slurm not returning failure exit code when
         job cancelled via bpipe stop (causing outputs not to be
         cleaned up)
    
       - Added "checks" command and "override" command to display and 
         override checks respectively
    
       - Fix transforms sometimes applying in such a way
         as to add branch name with no period separating them from
         the rest of the file name (regression)
         
       - fix transforms producing null outputs when no period in 
         input file name  (regression)
         
       - support for rendering pipeline diagrams as SVG 
    
       - support for specifying pipeline stages to ignore 
         in diagrams via noDiagram="..." in bpipe.config (annotations to 
         come in the future) 
    
       - fix diagrams generated incorrectly if 'segment'
         command used 
    
       - fix documentation failing to generate unless script has a
         relative or absolute path prefixing it 
    
       - some tweaks to avoid rare cases double
         dots appearing in file names with transform 
    
       - 'succeed' should terminate parent branch when all child
         branches terminated via succeed 
    
       - support for running a pipeline "until" a specified stage
         ( -u)  
    
       - support for send to use HTML templates instead of
         inline HTML 
         
       - support for 'succeed' and 'fail' to share
         'send' syntax to generate an email or IM along with the
         termination of the branch 
    
       - fix slurm executor sometimes
         treating slurm stdout and stderr temp files 
         as real outputs of pipeline 
    
       - Fix space inserted when withFlag used with flags 
         ending with "=" 
         
       - fix variables and functions loaded via 'load' not available until 
         pipeline launched (inside run { } ) 
         
       - allow global resource limits (as supported by -l flag 
         to bpipe) to be specified in bpipe.config as well 
       - 
       - support for sending emails and
         instant message notifications explicitly 
         from script, using syntax: send text 'hello' to gtalk, 
         and more advanced forms (documentation to come) 
    
       - support for using
         explicit regex pattern to split files to parallel 
         paths (as opposed to simplified pattern syntax) 
         just add ~ to pattern 
         
       - fix (very rare) possibility for duplicate file
         names when referencing 'inputs' 
         variable 
         
       - added support for matching numbers
         in input splitting patterns ('#') 
    
       - added support for gradle wrapper 
         
       - added gradle wrapper for easier building
         (now just use gradlew instead - of gradle, and it
         self downloads) 
         
       - fix custom resources not enforced when
         provided as map 
    
       - fix default build to autodetect Gridgain
         jars and compile without if not 
         found 
    
       - get mail.jar from Maven so default checkout compiles 
         
       - changes to allow "single" queue to handle
         multiple tasks (vlsci) 
    
       - fix 'bpipe status' displaying incorrect command for SLURM, PBS
         possibly others