Planemo

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* Fix `setup.py`_ for installing non-Python data from PyPI_ (required newer
for ``tool_factory`` command and reStructuredText linting). Thanks to
Damion Dooley for the bug report. `Issue 83`_

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* Fix README.rst so it renders properly on PyPI_.

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* Implement ``tool_init`` command for bootstrapping creation of new
tools (with `tutorial <http://planemo.readthedocs.org/en/latest/writing.html>`_.) 78f8274_
* Implement ``normalize`` command for reorganizing tool XML and macro
debugging. e8c1d45_
* Implement ``tool_factory`` command to spin up Galaxy pre-configured the
`Tool Factory`_. 9e746b4_
* Added basic linting of ``command`` blocks. b8d90ab_
* Improved linting of ``help`` blocks, including verifying valid
`reStructuredText`. 411a8da_
* Fix bug related to ``serve`` command not killing Galaxy properly when complete. 53a6766_
* Have ``serve`` command display tools at the top level instead of in shallow sections. badc25f_
* Add additional dependencies to ``setup.py`` more functionality works out
of the box. 85b9614_
* Fix terrible error message related to bioblend_ being unavailable.
`Issue 70`_
* Various smaller documentation and project structure improvements.

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* Fixes to get PyPI_ workflow working properly.

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* Add option (``-r``) to the ``shed_upload`` command to recursively upload
subdirectories (thanks to E. Rasche). `Pull Request 68`_
* Fix diff formatting in test reports (thanks to E. Rasche).
`Pull Request 63`_
* Grab updated test database to speed up testing (thanks to approach from
E. Rasche and Dannon Baker). `Issue 61`_, dff4f33_
* Fix test data command-line argument name (was ``test-data`` now it is
``test_data``). 834bfb2_
* Use ``tool_data_table_conf.xml.sample`` file if
``tool_data_table_conf.xml.test`` is unavailable. Should allow some
new tools to be tested without modifying Galaxy's global
``tool_data_table_conf.xml`` file. ac4f828_

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* Improvements to way Planemo loads its own copy of Galaxy modules to prevent
various conflicts when launching Galaxy from Planemo. `Pull Request 56`_
* Allow setting various test output options in ``~/.planemo.yml`` and disabling
JSON output. 21bb463_
* More experimental Brew and Tool Shed options that should not be considered
part of Planemo's stable API. See bit.ly/gxbrew1 for more details.
* Fix ``project_init`` for BSD tar (thanks to Nitesh Turaga for the bug
report.) a4110a8_
* Documentation fixes for tool linting command (thanks to Nicola Soranzo).
`Pull Request 51`_

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