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  1. Title 0.9.9 Beta Release
  2. Release 0.9.9_beta_1
  3. Link bpipe-0.9.9_beta_1.tar.gz


  4. - Fix content type not set causing errors with some smtp
         connections 
        
       - Issue #155: Update to gradle 2.0 to avoid compile failure with JDK9 
        
       - Performance optimisations for large numbers of inputs /
         outputs 
        
       - Should report error if is referenced and
         finds no inputs 
        
       - Give a hint about which 'from' clause
         pattern did not find a match in error message 
        
       - Fix typo causing exception while logging error message 
        
       - Fix: setting branch name from within stage causes incorrect
         branches downstream 
        
       - Fix input resolved as output in rare circumstances 
        
       - Fix transform ...  to followed by double
         output variable extensions (.foo.bar) failing with confusing
         error message 
        
       - Fix procs not set in torque job when using variable 
        
       - Make bpipe return exit code reflecting whether pipeline 
         succeeded or failed 
    
       - Fix: bpipe may fail to cleanup files created in subdirectories 
            
       - Better / fairer scheduling for dynamically allocated $thread variables 
       
       - Support for ranges in procs parameter, eg: procs = 1..10, or
         uses(threads:1..10) { ...  } 
    
       - Fix: failure to parallelize stages inside a list added to 
         another list, eg: [foo, bar] + [fubar,fug] 
        
       - Issue #148: bpipe parsing commandline memory
         specification incorrectly 
    
       - Issue #150: Cannot pass blank parameter via command line 
        
       - Various documentation fixes
        
       - Fix: junit tests were not executed 
    
       - Additional SGE options, SGE options moved inside script 
    
       - fix: commands run using torque / pbs not using -e flag for bash,
         thus only treated as failed if last command fails
        
       - support for aliasing inputs to outputs via 'forward <x> to
         <y>' to allow an input to be virtually treated as a named
         output within the pipeline 
    
       - fix: bpipe terminating if ssh session terminates while showing bpipe log 
         in foreground directly after initial launch 
        
       - save output from LSF (to assist in debugging failed LSF commands)
        
       - fix stages not found when defined in bpipe lib folder and referenced in
         segment declaration if used after load 
        
       - Switch to use html format for emails by default 
    
       - allow user to configure email format with 'format' attribute in
         configuration 
    
       - allow multiple templates per notification type with different formats 
    
       - fix problems in using 'send'
         and 'file' to send explicit files based on templates 
        
       - Fix high thread concurrency used when large number of concurrent branches 
         created by one pipeline branch 
        
       - Explicitly destroy process after waiting
         until streams closed to ensure file handles not leaked 
        
       - fix some cases where Bpipe could report file as missing when
         created in slow syncing distributed file system
        
       - Allow more screen width when using 'bpipe checks', better formatting 
         of check display 
    
       - Add option to list checks rather than enter interactive mode 
        
       - fix some cases where commands might not
         be stopped, and outputs not cleaned up when using bpipe
         stop.  Update saved command info after cleanup.  
        
       - ensure stop time is always set for commands 
    
       - close possible file handle leak in (undocumented) capture command
    
       - fix: more robust checking for file existence on distributed file systems which 
         may exhibit delays before files become visible locally
        
       - Avoid misleading termination message when user deliberately stops 
         pipeline 
    
       - Incorrect input used as basis for output file name in transforms inside 
         'from', if competing input available from previous stage
       
       - fix: rare deadlocks - use dedicated thread pool per pipeline tier to 
         avoid possibility of deadlocks in heavily nested pipelines