ReleaseNotes.txt

=========== Changes for Bpipe Version 0.9.12 ============

   - FEATURE: add display of cores into stats table 
    
   - FEATURE: support for Groovoy 3.0 and JDK11+

   - FEATURE: experimental 'dev' mode - use `bpipe dev`
     to enter test mode that highlights
     input and outputs in commands, hot updates with changes
     and shows branch/command context
     
   - FEAUTRE: support for optional outputs via .optional pseudo
     extension 

   - FEATURE: named branches - use multiply syntax with 
     groovy Map literal as alternative to list, to create named 
     parallel branches

   - FEATURE: dynamic splits. Use `forwardSplit(...)` to create
     pipeline branches that are dynamically determined by result
     of a previous stage. (see [docs](https://docs.bpipe.org/Guides/ParallelTasks/#splitting-dynamically-on-arbitrary-metadata))

   - FEATURE: Command configuration can now be done based on stage name rather
     than command name. This significantly relieves the need to add dedicated
     config names to commands in order to adjust their configuration.
     
   - FIX: Slurm executor polling not operating correctly
     
   - FIX: Don't create stray empty .bpipe folders
     
   - FIX: Autoarchive leaving behind empty dirs on some file systems 

   - DEPRECATED: the Multi command is no deprecated as there are no scenarios where
     this is preferred over paralleising using branching structures
     
   - FIX: wrong input may be used in from(multiple) transform() to() construct 

   - FEATURE: duplicate output files are now explicitly detected and warned about

   - FEATURE: enhanced warnings and messages when transform / produce / filter
     do not create expected files

=========== Changes for Bpipe Version 0.9.11 ============

   - FEATURE: support for required attribute on notification 
     channels to ensure pipeline failure if channel config fails 

   - FEATURE: experimental support for virtual file extensions / file type 
     mappings , defined using: filetype  <virtual ext> : [ 'ext.one', 'ext.two',...]
 
   - FEATURE: agent will wait for commands to finish if it is asked to run
     multiple in the same directory at the same time

   - FEATURE: support for "queue" command : schedules pipeline to run after
     another one finishes in a directory 

   - FIX: only match process owned by user when checking for running bpipe process 

   - FEATURE(experimental): from clause can now be added in pipeline definition to
     cause inputs to prioritise from a given stage, with branch matching

   - FEATURE: update aws sdk to support latest instance types 

   - FEATURE: EC2 commands now show name of stage via name tag, eg. in aws console 

   - FEAUTURE: accept aws creds from environment if not defined in bpipe.config
     using standard AWS env variables for token / secret

   - FEATURE: support direct transfer of files via scp for AWSEC2 executor.
     If storage config setting is not defined and 'transfer' setting is true
     then Bpipe will utilise scp to transfer input/output files to EC2 instances

   - FEATURE: allow queue to be overridden within pipeline when sending 
     to JMS channel via explicit 'queue' property

   - FEATURE: support replyTo as property for replying to JMS messages
     (rather than JMSReplyTo)

   - FEATURE: improved support for archiving: autoarchive and ability to run 
     archive command from outside bpipe dir 

   - FEATURE: implement support for 'required' and 'unique' as options on
     gitlab messages : ensures pipeline reports error status if 
     gitlab calls fail

   - FEATURE: support for experimental "when" feature to make stages conditional 

   - FEATURE: mask 'token' config property as sensitive info from log files 

   - FEATURE: support for setting R_LIBS_USER with R { r_libs="..." } 
     setting in bpipe.config

   - FEATURE: add checks to result message returned in reply-to on 
     JMS messages 

   - FEATURE: allow specification of gitlab projects by id when
     sending to gitlab

   - FEATURE: show custom title in bpipe startup when configured 
     using title : '...'  or title '...'

   - FEATURE: support to set env variables for commands via bpipe.config,
     by added env = <key> : <value>, ... to command config
 
   - FIX: http send not retried on bpipe retry if initial attempt failed 

   - FIX: errors printed by trying to send JSON via SMTP 

   - FIX: adjust bpipe agent jvm options to reduce footprint on large servers 

   - FIX: fix transform of wildcard (eg: *.txt) to multiple outputs 
     resulting in regex error 

   - FIX: undefined pipeline variable somtimes shows bpipe internal stack trace 

   - FIX: possible concurrentmodification errors when user-specificed config 
     referenced concurrently in stages / reports

   - FIX: fix multilevel branch names not reflected in file names 

   - FIX: error thrown when creating diagram using 'bpipe diagram ...'

   - Support for reservation of gpus with torque (set gpus=N in command config)

   - FIX: body of message relayed in JMS message header (causing parse fail in 
     some clients / protocols) 

   - FIX: fix regex in transform matching multi inputs only resolving single 

   - FIX: fix error when literal regex used as transform input specifier 

   - FIX: previous dirty state carrying over causing unexpected
     cleanup of good files 

   - FIX: put retry around output dir watcher to handle race conditions 
     / file system hiccups better 

   - FIX: Explicitly set pwd for singularity as this seems not always
     to occur by default 

   - FIX:: fix downstream reference to output created by check failing 
     on retry 

   - FIX: inability to create gitlab issue with empty content 

   - FIX: json output double encoded in .bpipe/sent files 

   - FIX: some commands not running with set -e by default 

   - FIX:: fix warning printed for dirty files even though 
     they don't exist, already notified

   - FIX: remove duplicates from printing of test outputs 

   - FIX: remove printout of shebang stripped statement