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  1. Title Bpipe Binary Release 0.9.9.8
  2. Release 0.9.9.8
  3. Link bpipe-0.9.9.8.tar.gz


  4. =========== Changes for Bpipe Version 0.9.9.8 ============
    
    
       - Feature: options statement for easy parsing of script specific
         command line arguments 
    
       - Add workaround to fix possible failure on old pipelines checking 
         file existence 
         
       - BUG: Fix spurious error printed if broken symbolic link present 
    
       - BUG: prevent agent launched commands hanging due to if bpipe prompts 
         for information
         
       - Feature: add fileSystemSyncTimeMs which allows for customizable delay in 
         file system sync before failing pipeline on missing output 
         
       - BUG: fix regression - transform using regex does not substitute groups
         
         eg: transform('(.*)_R1.fastq') to("\$1.txt") { ...  } 
    
       - Many fixes / optimisations to GCloud usage: 
         - make workingDirectory specified for stage automatically
           placed within mounted storage 
        
         - inherit region from main config inside
           filesystems, so it does not need to be double specified
             
         - support preemptible flag passed to google cloud
           instances 
             
         - add sha1 hash of pipeline path / host to
           instanceid to make it unique b/w pipelines 
    
         - fix region configured
           for cloud executor overriding region specified with -L 
    
         - search for root input files in all filesystems, not only
             those configured as storages for stages 
             
         - fix zone flag missing from gcloud commands, don't
           die mounting storage if instance not created 
    
         - support using split / partitioned regions in cloud provider storage 
             
       - BUG: Don't start executor pools when user is only testing the pipeline 
         
       - BUG: ensure that executors clean up even if they error in stop
         command 
         
       - Fix table output format so it shows correctly in GitHub markdown 
         
       - Better behavior for bpipe test with send, and send for missing outputs 
         
       - BUG: input patterns with dir in the pattern causing error / exception 
         
       - Feature: support for reply -to in JMS bpipe agent 
         
         If the reply-to or JMSReplyTo header is set, the bpipe agent will now 
         send a message containing the original command and pipeline success / fail 
         to specified reply-to address (allows eg: camel inOut routing)
         
       - BUG: Fix inverted logic causing incorrect detection of file existence 
         when file is out of sync, causing file systems with high latency 
         to fail sporadically
         
       - Better tolerance of file system sync issues for files referenced 
         using file(...) 
         
       - BUG: `from` sometimes failing to ensure specified input is resolved in
         preference to other available inputs preceding it in the
         pipeline 
         
       - BUG: from sometimes selecting incorrect input in complex scenarios 
         
       - BUG: fix file system watchers still created even if poller watcher specified,
         hence still resulting in file watcher exhaustion errors
         
       - BUG: -d option not respected in some situations, incorrect output dir may
         be used if default output already referenced 
         
       - Feature: Support for Groovy 2.5.6 via optional gradle.properties setting
         
       - Feature: support for template dirs created by bpipe agent with incrementing 
         values. Directories containing {inc} will be named with auto-incrementing
         counter.
         
       - Feature: 'terminateOnError' flag in send attributes causes 
         notification failure as to be treated as error 
         
       - BUG: improve unfriendly / incorrect behavior when duplicate mappings exist in transform 
         
       - BUG: checks sometimes re-executing when not necessary 
         
       - Feature: `bpipe touch` command updates files from current run 
         of pipeline to new timestamps so they do not re-run on `bpipe run`.