Download

  1. Title Binary Release 0.9.9
  2. Release 0.9.9
  3. Link bpipe-0.9.9.tar.gz


  4. Changes for Bpipe Version 0.9.9 
    ==============================
    
    **NOTE:** see 0.9.9_beta_1 changes for further changes since previous release
    
       - SGE: Merge branch 'sge_fixes', including:
    
         * Fix #156, #142, Bpipe may hang or ignore job cancel / delete
           using SGE executor 
    
         * add -terse to sge default command options
    
         * change to support separate options:
           'sge_pe' and 'procs' rather than combined.  
           (Old combined form still supported for back compat.) 
    
         * jobs are created using user modifiable command template,
           specified via jobTemplate configuration parameter
           which can be object with string value of path to template,
           or a closure which will be executed dynamically to obtain the
           path
    
         * fix incorrect reporting that stop command
           failed in sge 
    
         * use Bpipe resolved working directory instead of $PWD since
           it is not guaranteed to be defined
            
         * fix cases of failure due to string procs variable 
           getting overridden with integer (dynamic calculation
           of $threads variable)
    
         * fix incorrectly sending slots as well as pe for some
           configurations 
    
         * support individual parameters for SGE options instead of compiling 
           them into 'additional_options' 
            
       - Fix choosing "terminate" not working for some executors 
         (issue #162) 
         
       - PBS-pro: combine multiple resource limits into single 
         statement, add support for procs, memory requests
         
       - Experimental option for some executors to disable buffering of 
         standard output, applies to torque, slurm, pbs-pro. Set "stdbuf" as 
         option to have bpipe run commands using 'stdbuf' command to disable 
         output buffering, when output from commands is delayed in appearing
         in Bpipe log.
    
       - Performance optimisations for large / complex pipelines:
    
         * Cache output graph in serialised form to avoid reading property 
           files at startup 
         
         * Reduce massive logging of outputs when large number of
           inputs and outputs in single stage 
        
       - Add 'bpipe errors' and 'bpipe log -e' command to 
         show output for failed commands 
         
       - Add support to display per command output using the 
         bpipe log -c <cmd id> 
    
       - Fix 'bpipe test' printing exceptions and hanging on 'multi'
         statement 
        
       - Fix regression causing possible failure when stage has 
         outputs but no inputs 
         
       - update gradle wrapper script, include changes omitted from
         2.0 upgrade 
         
       - Fix files in subdirectory not resolved when whole file name 
         matches input extension 
         
       - Fix variable specified with 'using' not overriding global value 
         
       - Fix 'check' results possibly leaking between branches 
         
       - Fix reading output.dir causing potential modification of
         output directory