Jobarchitect

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

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.

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

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

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

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

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

Changed
^^^^^^^

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

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

Changed
^^^^^^^

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

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

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