Changelogs » Jobarchitect

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Jobarchitect

0.7.0

--------------------
  
  Added
  ^^^^^
  
  - Option to sketchjob CLI to use overlay as a filter for which identifiers will be processed
  
  Changed
  ^^^^^^^
  
  - JobSketcher.sketch() now takes a list of identifiers to process, and checks that those identifiers
  are in the dataset.

0.6.0

--------------------
  
  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

--------------------
  
  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 :doc:`design` document for more details about the thought process
  that led to this redesign
  
  
  Removed
  ^^^^^^^
  
  - CWL support

0.4.0

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

0.3.0

--------------------
  
  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

--------------------
  
  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 <http://jobarchitect.readthedocs.io/>`_
  - API documentation to sphinx generated docs
  - Change log to sphinx generated docs
  - Better docstrings

0.1.0

--------------------
  
  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
  ^^^^^^^^