ChangelogΒΆ

  • v0.6 (2017-07-21):
    • New
      • Add support for implied_column section of the project config file
      • Add support for Python 3
      • Merges pipeline interface and protocol mappings. This means we now allow direct pointers to pipeline_interface.yaml files, increasing flexibility, so this relaxes the specified folder structure that was previously used for pipelines_dir (with config subfolder).
      • Allow URLs as paths to sample sheets.
      • Allow tsv format for sample sheets.
      • Checks that the path to a pipeline actually exists before writing the submission script.
    • Changed
      • Changed LOOPERENV environment variable to PEPENV, generalizing it to generic models
      • Changed name of pipelines_dir to pipeline_interfaces (but maintained backwards compatibility for now).
      • Changed name of run column to toggle, since run can also refer to a sequencing run.
      • Relaxes many constraints (like resources sections, pipelines_dir columns), making project configuration files useful outside looper. This moves us closer to dividing models from looper, and improves flexibility.
      • Various small bug fixes and dev improvements.
      • Require setuptools for installation, and pandas 0.20.2. If numexpr is installed, version 2.6.2 is required.
      • Allows tilde in pipeline_interfaces
  • v0.5 (2017-03-01):
    • New
      • Add new looper version tracking, with –version and -V options and printing version at runtime
      • Add support for asterisks in file paths
      • Add support for multiple pipeline directories in priority order
      • Revamp of messages make more intuitive output
      • Colorize output
      • Complete rehaul of logging and test infrastructure, using logging and pytest packages
    • Changed
      • Removes pipelines_dir requirement for models, making it useful outside looper
      • Small bug fixes related to all_input_files and required_input_files attributes
      • More robust installation and more explicit requirement of Python 2.7
  • v0.4 (2017-01-12):
    • New
      • New command-line interface (CLI) based on sub-commands
      • New subcommand (looper summarize) replacing the summarizePipelineStats.R script
      • New subcommand (looper check) replacing the flagCheck.sh script
      • New command (looper destroy) to remove all output of a project
      • New command (looper clean) to remove intermediate files of a project flagged for deletion
      • Support for portable and pipeline-independent allocation of computing resources with Looperenv.
    • Changed
      • Removed requirement to have pipelines repository installed in order to extend base Sample objects
      • Maintenance of sample attributes as provided by user by means of reading them in as strings (to be improved further)
      • Improved serialization of Sample objects