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  1. Title 0.9.8.7 Binary Release
  2. Release 0.9.8.7
  3. Link bpipe-0.9.8.7.tar.gz


  4. =========== Changes for Bpipe Version 0.9.8.7 ============
    
       - check /proc on linux rather than relying on kill 
         0 to see if pipeline is running (enables cross
         user support for "bpipe log") 
        
       - Addition of documentation to Bpipe distro
        
       - fix failure to cleanup files with no parent directory 
         (regression) 
        
       - Add __future__ import for Python 2 and 3 compatibility 
         (fix failure on Mac when Python3 is default)
        
       - switch to HTML format for default email.  to switch back
         to text, use notifications { smtp { format="text" } } in
         bpipe.config.  
        
       - Fix presence of subdirectory in bpipe output meta data folder 
         causing bpipe to spew errors 
        
       - Fix files sometimes not cleaned up on distributd file system 
         where lag exists in synchronizing b/w nodes
    
       - Issue #128: use qsub -N to name job according to stage/filename 
        
       - support for overriding a stage with an alternative implementation 
         within a particular branch 
        
       - fix: authentication failures on passwordless SMTP
         server 
        
       - fix failure in cleanup if output properties file
         did not get optional canonicalPath property added 
        
       - comment out verbose log message creating large bpipe
         logfiles for long runs 
        
       - avoid encoding whole directory path into internal property file 
         names (fix 'file path too long errors' on file systems allowing only
         256 chars in file names)
        
       - fix parent branches not visible in children via branch property 
        
       - fix method missing error when multiplying by map by list 
        
       - Reformatting and summarizing of errors at end of pipeline to make 
         it easier to see where & why pipelines failed 
    
       - Aggregating identical errors from
         multiple branches together in output so that failures from
         many branches are less verbose 
    
       - Support for 'load' within a pipeline stage.  Loads into the 
         context of current branch rather than global. Pipeline stages 
         not supported, only variables.
        
       - prevent error if files used by Bpipe are not writable but
         are deletable 
        
       - prevent premature wildcard expansion of
         quoted arguments passed to Bpipe    
    
       - support for cleanup as command in pipeline stage 
        
       - prevent error if files used by Bpipe are not writable but 
         are deletable 
        
       - attempt to ensure log messages written
         even if exit due to outofmemory error 
        
       - log message if file is not cleaned up because it doesn't
         exist: help to diagnose problems with files not cleaned up 
       
       - better log info about where config files are 
        
       - allow memory to be integer for torque/slurm/etc, fix error
         querying status in torque/slurm/etc, include queuing system
         command id in bpipe status output 
        
       - show pending and waiting jobs with bpipe status, don't throw ugly error 
         if no commands ever run 
        
       - Fix: downstream references to inputs
         by index throwing "expected more inputs" error incorrectly 
       
       - avoid confusing stack overflow when user defines branch
         variable with same name as pipeline stage 
        
       - accept 'MB' or 'GB' in command line option for memory,
         cache runtime directory instead of creating new File objects
         all the time to figure it out 
        
       - prevent null pointer exception when list containing null 
         provided to 'from' 
       
       - fix multiple inputs not
         forwarding correctly when referenced using "$inputs" 
        
       - Bug fixes for lsf, added walltime option for Lsf 
        
       - caching of DAG lookups by
         canonical path to speed up large, complex pipelines 
        
       - caching of canonical path with check of basePath to ensure
         consistency 
        
       - fix dependency issues after
         cleanup when non-default output directory used 
        
       - Performance optimisations for systems where canonicalPath is
         very slow, better logging to resolve dependency issues