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updated release notes for 0.9.9.7

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ssadedin committed Apr 23, 2019
1 parent d95c877 commit 893d55ecfdf43ce8ab4356dd52992e90f1bd21a2
Showing with 51 additions and 26 deletions.
  1. +51 −26 ReleaseNotes.txt
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=========== Changes for Bpipe Version 0.9.9.7 ============

- support aliasing to string values in addition to outputs
- Fix incorrect "abnormal termination" messages
printed to console when pipeline stopped with 'bpipe stop'

- Fix incorrect 'pre-existing' printed for outputs that were
created by pipeline

- Fix genome not accessible in pipeline the first time downloaded,
printing error

- Preliminary support for executing pipelines on Google Cloud Services
(Compute Engine) and mounting storage for pipelines from Google Cloud
Storage

- Preliminary support for executing pipelines on Amazon Web Services
using EC2 and mounting storage for pipelines from S3

- The 'groovy' command can now run embedded groovy (executed outside
Bpipe) using the groovy runtime bundled with Bpipe

- Support aliasing to string values in addition to outputs

- experimental support for beforeRun hook in command config
- Experimental support for beforeRun hook in command config: execute
arbitrary groovy code before a command executes

- re-execute checks if a commmand in the same stage has executed
- Re-execute checks if a commmand in the same stage has executed

- synchronize initialization of dir watcher to fix sporadic
ConcurrentModificationExceptions

- many performance improvements, esp. for large, highly
- Many performance improvements, esp. for large, highly
parallel pipelines

- support configuration for number of retries for status
- Support configuration for number of retries for status
polling of HPC jobs

- fix empty embedded parallel stage list causing resolution of incorrect
- Fix empty embedded parallel stage list causing resolution of incorrect
downstream input

- add support for 'optional' to make input optional, and 'flag' to add flags
- Add support for 'optional' to make input optional, and 'flag' to add flags
in commands eg: ${input.csv.optional.flag('--csv')}

- fix leak of 'var' variables across branches when 'using' applied to
- Fix leak of 'var' variables across branches when 'using' applied to
pipeline stage

- fix error if 4 or more arguments passed to "to" in transform
- Fix error if 4 or more arguments passed to "to" in transform

- fix bpipe complaining spurious outputs not created on retry,
- Fix bpipe complaining spurious outputs not created on retry,
but not original run

- fix some bugs where branch names were not being observed
- Fix some bugs where branch names were not being observed

- fix branch name sometimes inserted without separating period for transforms
- Fix branch name sometimes inserted without separating period for transforms

- avoid redundantly putting branch name into files
- Avoid redundantly putting branch name into files

- improved detail in error / log messages in a few places
- Improved detail in error / log messages in a few places

- add region.bedFlag(flag) method for convenience when passing
- Add region.bedFlag(flag) method for convenience when passing
regions to commands

- new operator: merge point operator (>>>) automatically configures a stage
- New operator: merge point operator (>>>) automatically configures a stage
to merge outputs from a previous parallel split

- fix missing branch and '..' in filenames
- Fix missing branch and '..' in filenames

- change: globally defined variables must now be held constant
- Change: globally defined variables must now be held constant
once pipeline starts

- fix split regions not stable between runs, set region id as branch
- Fix split regions not stable between runs, set region id as branch
name

- fix bed.split producing different splits if run
- Fix bed.split producing different splits if run
repeatedly on same bed

- fix errors output if SLF4J referenced in user loaded libraries
- Fix errors output if SLF4J referenced in user loaded libraries

- fix npe / improve error message when filter used with mismatching output ext
- Fix npe / improve error message when filter used with mismatching output ext

- fix error in stage body resulting in confusing 'no associated storage'
- Fix error in stage body resulting in confusing 'no associated storage'
assertion failure

- support for 'var' expressions in main pipeline script to define optional
- Support for 'var' expressions in main pipeline script to define optional
variables

- add 'allowForeign' option to 'from' to let it process non-outputs
- Add 'allowForeign' option to 'from' to let it process non-outputs

- lessen the retries and retry interval when file cannot be cleaned
- Lessen the retries and retry interval when file cannot be cleaned
up

- Support for sending to Gitlab using 'send' command

- JMS support now responds to 'ping' message with 'pong' reply
if JMS 'Reply-To' is set to allow for status monitoring


=========== Changes for Bpipe Version 0.9.9.5 ============

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