ChangelogΒΆ

  • v0.7.0 (2017-12-12):

    • Standardize NGSTk function naming.
    • Introduce Stage as a model for a logically related set of pipeline processing steps.
    • Introduce Pipeline framework for automated processing phase execution and checkpointing.
    • Add ability to start and/or stop a pipeline at arbitrary checkpoints.
    • Introduce new state for a paused/halted pipeline.
    • Improve spawned process shutdown to avoid zombie processes.
  • v0.6 (2017-08-24):

    • Adds ‘dynamic recovery’ capability. For jobs that are terminated by an interrupt, such as a SIGINT or SIGTERM (as opposed to a failed command), pypiper will now set a dynamic recovery flags. These jobs, when restarted, will automatically pick up where they left off, without requiring any user intervention. Previously, the user would have to specify recover mode (-R). Now, recover mode forces a recover regardless of failure type, but interrupted pipelines will auto-recover.
    • Pypiper now appropriately adds cleanup files intermediate files for failed runs. It adds them to the cleanup script.
    • Improves error messages so only a single exception is raised with a more direct relevance to the user/
    • Pypiper will automatically remove existing flags when the run starts, eliminating the earlier issue of confusion due to multiple flags present on runs that were restarted.
    • Fixes a bug that caused a pipeline to continue if a SIGTERM is given during a process that was marked nofail.
    • Pypiper now can handle multiple SIGTERMs without one canceling the shutdown procedure begun by the other.
    • Major improvements to documentation and tutorials.
    • Adds report_figure function.
  • v0.5 (2017-07-21):

    • Adds preliminary support for handling docker containers
    • Updates docs, adds Hello World example
    • Adds ‘waiting’ flag
    • Eliminates extra spaces in reported results
    • Pypiper module is version aware
    • Updates Success time format to eliminate space
    • Improves efficiency in some ngstk merging functions
  • v0.4 (2017-01-23):

    • First major public release!
    • Revamps pypiper args
    • Adds parallel compression/decompression with pigz
    • Various small bug fixes and speed improvements