CHANGELOG

This project uses semantic versioning. This change log uses principles from keep a changelog.

[Unreleased]

Added

Changed

Deprecated

Removed

Fixed

Security

[0.6.0] - 2017-06-15

Added

  • Agent now creates the output directory that it will pass to the “smart” tool via the --output-directory

Changed

  • “Smart” tool interface parameter name changed from --output-path to --output-directory
  • Singularity template

Fixed

  • Naming of sketchjob input argument

[0.5.0] - 2017-06-15

Added

  • Ability to access file level metadata from dataset items when running a Python analysis script

Changed

  • Tools now need to comply with a specific command line interface to be able to run using scripts produced by sketchjob. The command line interface of such “smart” scripts should have no positional arguments and has three required named arguments: --dataset-path, --identifier, and --output-path. Furthermore, such “smart” analysis scripts should only work on one item in a dataset as it is the responsibility of sketchjob and the jobarchitect agent to split the dataset into individual jobs.
  • For jobs that do not adhere to the command line interface above one will have to write thin Python wrappers, for examples have a look at the scripts in tests/sample_smart_tools/
  • Requiring the use of “smart” tools removes the need to make use of CWL, so its support has been removed
  • See the Design document for more details about the thought process that led to this redesign

Removed

  • CWL support

[0.4.0] - 2017-06-08

Changed

  • Now using CWL (Common Workflow Language) to specify program to be run on dataset.

[0.3.0] - 2017-02-07

Changed

  • Move JobSpec from jobarchitect to jobarchitect.backends module
  • JobSpec class now stores absolute paths
  • Update Dockerfile to set entrypoint to sketchjob

[0.2.0] - 2017-02-06

Added

  • singularity job command backend
  • sketchjob CLI options for selecting wrapper script
  • Templates for both job command and wrapper script creation
  • jobarchitect.backends.render_script function
  • Hosting of docs on readthedocs
  • API documentation to sphinx generated docs
  • Change log to sphinx generated docs
  • Better docstrings

[0.1.0] - 2017-02-03

Added

  • sketchjob CLI
  • _analyse_by_ids CLI
  • Support script and files to build docker image
  • jobarchitect.JobSpec class
  • jobarchitect.agent.analyse_by_identifiers function
  • jobarchitect.agent.Agent class
  • jobarchitect.backends.generate_docker_job backend
  • jobarchitect.sketchjob.generate_jobspecs function
  • jobarchitect.sketchjob.sketch function
  • jobarchitect.sketchjob.JobSketcher class
  • jobarchitect.utils.mkdir_parents function
  • jobarchitect.utils.output_path_from_hash function
  • jobarchitect.utils.split_dataset function
  • jobarchitect.utils.path_from_hash function

Changed

Deprecated

Removed

Fixed

Security