Planemo

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* Implement ``Engine`` and ``Runnable`` abstractions - Planemo now has
beta support for testing Galaxy workflows and CWL_ tools with Galaxy and
any CWL_ artifact with cwltool_.
`Pull Request 454`_, 7be1bf5_
* Fix missing command_line in test output json. e38c436_
* More explicit Galaxy ``job_conf.xml`` handling, fixes bugs caused by
``galaxy_root`` having existing and incompatible ``job_conf.xml`` files
and makes it possible to specify defaults with fixed server name. c4dfd55_
* Introduce profile commands (``profile_create``, ``profile_delete``, and
``profile_list``) and profile improvements (automatic postgres database
creation support). `Pull Request 480`_, a87899b_
* Rework Galaxy test reporting to use structured data instead of XUnit
data. 4d29bf1_
* Refactor Galaxy configuration toward support for running Galaxy in
docker-galaxy-stable. `Pull Request 479`_

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* Tweak dependencies to try to fix cwltool_ related issues - such
as `Issue 475`_.

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* Implement Galaxy "profiles" - the ability to configure
perisistent, named environments for ``serve`` and ``test``.
5d08b67_
* Greatly improved ``serve`` command - make ``test-data``
available as an FTP folder, (on 16.07) automatically log
in an admin user, and many more options (such as those
required for "profiles" and a ``--daemon`` mode).
* Two fixes to ensure more consistent, dependable ``test`` output.
`Pull Request 472`_, f3c6917_
* Add code and documentation for linting (``lint``) and
building (``tool_init``) CWL_ tools. a4e6958_, b0b867e_,
4cd571c_
* If needed for Conda_ workaround, shorten ``config_directory``
path (thanks to `mvdbeek`_). efc5f30_
* Fix ``--no_cache_galaxy`` option (thanks to Gildas Le
Corguillé). d8f2038_
* Target draft 3 of CWL_ instead of draft 2. 775bf49_
* Fix ``cwltool`` dependency version - upstream changes broke
compatibility. `65b999d`_
* Add documentation section and slides about recent Galaxy
tool framework changes (with fix from `remimarenco`_). 069e7ba_
* Add IUC standards to Planemo docs. 2ae2b49_
* Improve collection-related contents in documentation
(thanks in part to `martenson`_).
fea51fc_, 13a5ae7_
* Add documentation on ``GALAXY_SLOTS`` and running planemo
on a cluster. 45135ff_, e0acf91_
* Revise command-line handling framework for consistency and
extension - allow extra options to be configured as
defaults ``~/.planemo.yml`` including ``--job_config_file``
and Conda_ configuration options. e769118_, 26e378e_
* Fix ``tool_init`` commans options typos (thanks to
Nitesh Turaga). 826d371_
* Refactor galaxy-related modules into submodules of a new
``planemo.galaxy`` package. 8e96864_
* Fix error message typo (thanks to `blankenberg`_). b1c8f1d_
* Update documentation for recent command additions. 3f4ab44_
* Rename option ``--galaxy_sqlite_database`` option to
``--galaxy_database_seed`` and fix it so it actually works.
f7554d1_
* Add ``--extra_tools`` option to ``serve`` command. 02a08a0_
* Update project testing to include linting documentation
(``docs/``), Python import order, and docstrings.
a13a120_, 6e1e726_, 95d5cba_


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* Revert "check ``.shed.yml`` owner against credentials during shed
creation", test was incorrect and preventing uploads.
`Pull Request 425`_, `Issue 246`_

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* Fix test summary report. `Pull Request 429`_
* Improve error reporting when running ``shed_test``. ce8e1be_
* Improved code comments and tests for shed related functionality.
89674cb_
* Rev `galaxy-lib`_ dependency to 16.4.1 to fix wget usage in
newer versions of wget. d76b489_

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* Drop support for Python 2.6. 93b7bda_
* A variety of fixes for ``shed_update``.
`Pull Request 428`_, `Issue 416`_
* Fix reporting of metadata updates for invalid shed updates.
`Pull Request 426`_, `Issue 420`_
* Check ``.shed.yml`` owner against credentials during shed creation.
`Pull Request 425`_, `Issue 246`_
* Fix logic error if there is a problem with ``shed_create``. 358a42c_
* Tool documentation improvements. 0298510_, a58a3b8_

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