Planemo

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

* More complete I/O capturing for XUnit. 6409449_
* Check for select parameter without options when linting tools.
`Issue 373`_
* Add ``--cwl_engine`` argument to ``cwl_run`` command. dd94ddc_
* Fixes for select parameter linting. 8b31850_
* Fix to demultiplexing repositories after tool uploads. `Issue 361`_
* Fix to update planemo for Galaxy wheels. 25ef0d5_
* Various fixes for Python 2.6 and Python 3.
c1713d2_, 916f610_, c444855_

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

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

* Initial implementation of ``cwl_run`` command that runs a
CWL tool and job file through Galaxy. 49c5c1e_
* Add ``--cwl`` flag to ``serve`` to experimentally serve CWL tools
in Galaxy.
`Pull Request 339`_
* Implement highly experimental ``cwl_script`` command to convert
a CWL job to a bash script. 508dce7_
* Add name to all XUnit reports (thanks to `hexylena`_).
`Pull Request 343`_
* Capture stdout and stderr for ``shed_diff`` and ``shed_update``
XUnit reports. `Pull Request 344`_
* More tool linting (conditionals) thanks to `hexylena`_.
`Pull Request 350`_
* UTF-8 fixes when handling XUnit reports. `Pull Request 345`_
* Add `Epigenetics` as Tool Shed category. `Pull Request 351`_
* Merge changes to common modules shared between Galaxy, Planemo, and Pulsar (thanks to `natefoo`_).
`Pull Request 356`_
* Add ``--cite_url`` to ``tool_init``. fdb1b51_
* ``tool_init`` bug fix. f854138_
* Fix `setup.py`_ for cwltool and bioblend_ changes. 1a157d4_
* Add option to specify template sqlite database locally. c23569f_
* Add example IPython notebooks to docs. c8640b6_

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

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

* Fix issue with test reporting not being populated. 19900a6_

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

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

* Improvements to ``docker_shell`` usability (thanks to `kellrott`_).
`Pull Request 334`_
* Add docker pull attempt when missing Dockerfile (thanks to `kellrott`_).
`Pull Request 333`_
* Fix bug inferring which files are tool files (thanks to `hexylena`_).
`Pull Request 335`_, `Issue 313`_
* Initial work toward automating brew recipe update. 4d6f7d9_, `Issue 329`_

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

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

* Implement basic XUnit report option for ``shed_update`` (thanks to `martenson`_).
`Pull Request 322`_
* Fix issues with producing test outputs. 572e754_
* Xunit reporting improvements - refactoring, times, diff output (thanks to `hexylena`_).
`Pull Request 330`_
* Implement project governance policy and update developer code of conduct to
match that of the Galaxy project. `Pull Request 316`_
* Update filters for account for new ``.txt`` and ``.md`` test outputs
(thanks to `hexylena`_). `Pull Request 327`_
* Add verbose logging to galaxy test output handling problems. 5d7db92_
* Flake8 fixes (thanks to `martenson`_). 949a36d_
* Remove uses of deprecated ``mktemp`` Python standard library function
(thanks to `hexylena`_). `Pull Request 330`_

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

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

* Adding new command ``dependency_script`` to convert Tool Shed dependencies
into shell scripts - thanks to `peterjc`_.
`Pull Request 310`_, f798c7e_, `Issue 303`_
* Implement profiles in sheds section of the ``~/.planemo.yml``.
`Pull Request 314`_

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