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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`.