Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/planemo-0.70.0.dist-info/METADATA @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
| author | shellac |
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| date | Sat, 02 May 2020 07:14:21 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.7/site-packages/planemo-0.70.0.dist-info/METADATA Sat May 02 07:14:21 2020 -0400 @@ -0,0 +1,2486 @@ +Metadata-Version: 2.1 +Name: planemo +Version: 0.70.0 +Summary: Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/). +Home-page: https://github.com/galaxyproject/planemo +Author: Galaxy Project and Community +Author-email: jmchilton@gmail.com +License: AFL +Keywords: planemo +Platform: UNKNOWN +Classifier: Development Status :: 5 - Production/Stable +Classifier: Intended Audience :: Developers +Classifier: Environment :: Console +Classifier: License :: OSI Approved :: Academic Free License (AFL) +Classifier: Operating System :: POSIX +Classifier: Topic :: Software Development +Classifier: Topic :: Software Development :: Code Generators +Classifier: Topic :: Software Development :: Testing +Classifier: Natural Language :: English +Classifier: Programming Language :: Python :: 2 +Classifier: Programming Language :: Python :: 2.7 +Classifier: Programming Language :: Python :: 3 +Classifier: Programming Language :: Python :: 3.5 +Classifier: Programming Language :: Python :: 3.6 +Classifier: Programming Language :: Python :: 3.7 +Classifier: Programming Language :: Python :: 3.8 +Description-Content-Type: text/x-rst +Requires-Dist: aenum +Requires-Dist: BeautifulSoup4 +Requires-Dist: bioblend (>=0.13.0) +Requires-Dist: Click +Requires-Dist: configparser +Requires-Dist: cwltool (==1.0.20191225192155) +Requires-Dist: docutils +Requires-Dist: ephemeris (>=0.10.3) +Requires-Dist: galaxy-containers +Requires-Dist: galaxy-tool-util (>=20.1.0.dev2) +Requires-Dist: galaxy-util (>=20.1.0.dev0) +Requires-Dist: glob2 +Requires-Dist: gxformat2 (>=0.8.0) +Requires-Dist: jinja2 +Requires-Dist: lxml +Requires-Dist: oyaml +Requires-Dist: pyaml +Requires-Dist: pyyaml +Requires-Dist: six (>=1.7.0) +Requires-Dist: virtualenv + +.. figure:: https://raw.githubusercontent.com/jmchilton/planemo/master/docs/planemo_logo.png + :alt: Planemo Logo + :align: center + :figwidth: 100% + :target: https://github.com/galaxyproject/planemo + +Command-line utilities to assist in developing Galaxy_ and `Common Workflow Language`_ tools. + +.. image:: https://readthedocs.org/projects/planemo/badge/?version=latest + :target: http://planemo.readthedocs.io/en/latest/?badge=latest + :alt: Documentation Status + +.. image:: https://badge.fury.io/py/planemo.svg + :target: https://pypi.python.org/pypi/planemo/ + :alt: Planemo on the Python Package Index (PyPI) + +.. image:: https://travis-ci.org/galaxyproject/planemo.png?branch=master + :target: https://travis-ci.org/galaxyproject/planemo + :alt: Build Status + +.. image:: https://travis-ci.org/jmchilton/planemo-extended-tests.svg?branch=master + :target: https://travis-ci.org/jmchilton/planemo-extended-tests + :alt: Build Status of Extended Tests + +.. image:: https://coveralls.io/repos/galaxyproject/planemo/badge.svg?branch=master + :target: https://coveralls.io/r/galaxyproject/planemo?branch=master + :alt: Coverage Status + +* Free software: Academic Free License version 3.0 +* Documentation: https://planemo.readthedocs.io. +* Code: https://github.com/galaxyproject/planemo + + +Quick Start +----------- + +----------------- +Obtaining +----------------- + +For a traditional Python installation of Planemo, first set up a virtualenv +for ``planemo`` (this example creates a new one in ``.venv``) and then +install with ``pip``. Planemo requires pip 7.0 or newer. + +:: + + $ virtualenv .venv; . .venv/bin/activate + $ pip install "pip>=7" # Upgrade pip if needed. + $ pip install planemo + +For information on updating Planemo, installing the latest development release, +or installing Planemo via `Bioconda <https://github.com/bioconda/bioconda-recipes>`__ +- checkout the `installation <http://planemo.readthedocs.io/en/latest/installation.html>`__ +documentation. + +Planemo is also available as a `virtual appliance +<https://planemo.readthedocs.io/en/latest/appliance.html>`_ bundled +with a preconfigured Galaxy server and set up for Galaxy_ and +`Common Workflow Language`_ tool development. +You can choose from open virtualization format (OVA_, .ova) or Docker_ +appliances. + +----------------- +Basics - Galaxy +----------------- + +This quick start will assume you have a directory with one or more Galaxy +tool XML files. If no such directory is available, one can be quickly created for +demonstrating ``planemo`` as follows ``project_init --template=demo mytools; cd mytools``. + +Planemo can check tool XML files for common problems and best +practices using the ``lint`` `command <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_ +(also aliased as ``l``). + +:: + + $ planemo lint + +Like many ``planemo`` commands - by default this will search the +current directory and use all tool files it finds. It can be explicitly +passed a path to tool files or a directory of tool files. + +:: + + $ planemo l randomlines.xml + +The ``lint`` command takes in additional options related to +reporting levels, exit code, etc. These options are described +in the `docs <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_ +or (like with all commands) can be accessed by passing ``--help`` to it. + +:: + + $ planemo l --help + Usage: planemo lint [OPTIONS] TOOL_PATH + +Once tools are syntactically correct - it is time to test. The ``test`` +`command <http://planemo.readthedocs.org/en/latest/commands.html#test-command>`__ +can be used to test a tool or a directory of tools. + +:: + + $ planemo test --galaxy_root=../galaxy randomlines.xml + +If no ``--galaxy_root`` is defined, Planemo will download and configure +a disposable Galaxy instance for testing. + +Planemo will create a HTML output report in the current directory named +``tool_test_output.html`` (override with ``--test_output``). See an +`example <http://galaxyproject.github.io/planemo/tool_test_viewer.html?test_data_url=https://gist.githubusercontent.com/jmchilton/9d4351c9545d34209904/raw/9ed285d3cf98e435fc4a743320363275949ad63c/index>`_ +of such a report for Tophat. + +Once tools have been linted and tested - the tools can be viewed in a +Galaxy interface using the ``serve`` (``s``) `command +<http://planemo.readthedocs.org/en/latest/commands.html#serve-command>`__. + +:: + + $ planemo serve + +Like ``test``, ``serve`` requires a Galaxy root and one can be +explicitly specified with ``--galaxy_root`` or installed dynamically +with ``--install_galaxy``. + +For more information on building Galaxy tools in general please check out +`Building Galaxy Tools Using Planemo`_. + +---------------------------------- +Basics - Common Workflow Language +---------------------------------- + +This quick start will assume you have a directory with one or more `Common Workflow +Language`_ YAML files. If no such directory is available, one can be quickly created for +demonstrating ``planemo`` as follows ``planemo project_init --template=seqtk_complete_cwl mytools; cd mytools``. + +Planemo can check tools YAML files for common problems and best +practices using the ``lint`` `command <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_ +(also aliased as ``l``). + +:: + + $ planemo lint + +Like many ``planemo`` commands - by default this will search the +current directory and use all tool files it finds. It can be explicitly +passed a path to tool files or a directory of tool files. + +:: + + $ planemo l seqtk_seq.cwl + +The ``lint`` command takes in additional options related to +reporting levels, exit code, etc. These options are described +in the `docs <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_ +or (like with all commands) can be accessed by passing ``--help`` to it. + +:: + + $ planemo l --help + Usage: planemo lint [OPTIONS] TOOL_PATH + +Once tools are syntactically correct - it is time to test. The ``test`` +`command <http://planemo.readthedocs.org/en/latest/commands.html#test-command>`__ +can be used to test a CWL tool, workflow, or a directories thereof. + +:: + + $ planemo test --engine cwltool seqtk_seq.cwl + +Planemo will create a HTML output report in the current directory named +``tool_test_output.html``. Check out the file ``seqtk_seq_tests.yml`` for +an example of Planemo test for a CWL tool. A test consists of any number of +jobs (with input descriptions) and corresponding output assertions. + +Checkout the `Commmon Workflow User Guide`_ for more information on developing +CWL tools in general and `Building Common Workflow Language Tools`_ for more +information on using Planemo to develop CWL tools. + +--------- +Tool Shed +--------- + +Planemo can help you publish tools to the Galaxy Tool Shed. +Check out `Publishing to the Tool Shed`_ for more information. + +------ +Conda +------ + +Planemo can help develop tools and Conda packages in unison. +Check out the `Galaxy <http://planemo.readthedocs.io/en/latest/writing_advanced.html#dependencies-and-conda>`__ or `CWL +<http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-conda-cwl>`__ version of the "Dependencies and Conda" tutorial +for more information. + +----------------------- +Docker and Containers +----------------------- + +Planemo can help develop tools that run in "Best Practice" containers for +scientific workflows. Check out the `Galaxy <http://planemo.readthedocs.io/en/latest/writing_advanced.html#dependencies-and-containers>`__ or `CWL +<http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-containers-cwl>`__ version of the "Dependencies and Containers" tutorial for more information. + +.. _Galaxy: http://galaxyproject.org/ +.. _GitHub: https://github.com/ +.. _Conda: http://conda.pydata.org/ +.. _Docker: https://www.docker.com/ +.. _Vagrant: https://www.vagrantup.com/ +.. _Travis CI: http://travis-ci.org/ +.. _`tools-devteam`: https://github.com/galaxyproject/tools-devteam +.. _`tools-iuc`: https://github.com/galaxyproject/tools-iuc +.. _Building Galaxy Tools Using Planemo: http://planemo.readthedocs.io/en/latest/writing_standalone.html +.. _Publishing to the Tool Shed: http://planemo.readthedocs.org/en/latest/publishing.html +.. _Common Workflow Language: https://www.commonwl.org/ +.. _Commmon Workflow User Guide: http://www.commonwl.org/user_guide/ +.. _Building Common Workflow Language Tools: http://planemo.readthedocs.io/en/latest/writing_cwl_standalone.html +.. _OVA: https://en.wikipedia.org/wiki/Open_Virtualization_Format + + + + + +History +------- + +.. to_doc + +--------------------- +0.70.0 (2020-01-29) +--------------------- + +* Temporarily add galaxy-util requirement `Pull Request 991`_ +* Make symlinks in tool tree work for planemo test `Pull Request 988`_ +* Reduce use of ``shell=True`` in subprocesses `Pull Request 989`_ +* Drop planemo database seed option `Pull Request 985`_ +* Don't execute ``untar_to()`` subprocesses through the shell `Pull Request 984`_ +* Allow setting database_connection for planemo test runs `Pull Request 986`_ +* Fix copy-paste mistakes `Pull Request 983`_ +* Add planemo list_repos command `Pull Request 982`_ +* Make container_register build files with headers and include base_image `Pull Request 980`_ +* Replace deprecated galaxy-lib requirement with galaxy-tool-util `Pull Request 978`_ +* Close all opened files (thanks to `@bernt-matthias`_). `Pull Request 979`_ +* Build single requirement container, log if requirement not in best-practice channels `Pull Request 977`_ +* Use tojson jinja2 filter instead of json.dumps `Pull Request 975`_ +* Add merge_test_reports command `Pull Request 974`_ +* Implement github workflow and fix profile commands if psql unavailable `Pull Request 976`_ +* Fix planemo lint --biocontainers if no build number in container `Pull Request 972`_ +* Update a training command (thanks to `@hexylena`_). `Pull Request 973`_ +* Allow passing through GALAXY_VIRTUAL_ENV variable to venv setup `Pull Request 971`_ +* Correct help text (thanks to `@hexylena`_). `Pull Request 970`_ +* Remove unneeded html5lib requirement `Pull Request 968`_ + +--------------------- +0.62.1 (2019-10-14) +--------------------- + +* Init & update submodules when installing and creating packages. Stop + distributing eggs (thanks to `@nsoranzo`_). 1ab8530_ + +--------------------- +0.62.0 (2019-10-11) +--------------------- + +* Use ``unicodify()`` on exceptions and subprocess outputs (thanks to + `@nsoranzo`_) `Pull Request 944`_ +* Do not override ``None`` with empty string (thanks to `@ic4f`_). `Pull Request + 950`_ +* Update Docker template for training material generation (thanks to + `@bedroesb`_). `Pull Request 958`_ +* Add support for suite of repos with different owners (thanks to `@nsoranzo`_). + `Pull Request 959`_ +* Link for collection details updated in the docs (thanks to `@martin-raden`_). + `Pull Request 963`_ +* Move most tests to Python 3.7, drop Python 3.4 (thanks to `@nsoranzo`_). + `Pull Request 964`_ +* Remove confusing warning `Pull Request 966`_ + +--------------------- +0.61.0 (2019-07-08) +--------------------- + +* Training - fix empty repeat + some formatting (thanks to `@bebatut`_). `Pull + Request 926`_ +* Training - add bibliography to tutorial template (thanks to `@shiltemann`_). + `Pull Request 938`_ +* Training - support new class definition for input in workflow step (thanks to + `@bebatut`_). `Pull Request 943`_ +* Various tool tutorial fixes ahead of GCC 2019 (thanks to `@nsoranzo`_). + `Pull Request 940`_ +* Return validation error if doi is empty (thanks to `@nsoranzo`_). + `Pull Request 937`_ + +--------------------- +0.60.0 (2019-05-31) +--------------------- + +* Return validation error if doi is empty `Pull Request 937`_ +* Add junit as test reporter (thanks to `@selten`_). `Pull Request 935`_ +* Update galaxy.xsd for new python 3 compatibility attribute (thanks to `@martenson`_). `Pull Request + 931`_ +* Documentation: add a little warning for <param ... multiple="true"> (thanks to + `@bernt-matthias`_). `Pull Request 930`_ + +--------------------- +0.59.0 (2019-05-09) +--------------------- + +* Add ability to test data manager tools (thanks to `@mvdbeek`_). + `Pull Request 912`_ +* Update Training for new requirement definition (thanks to `@bebatut`_). + `Pull Request 913`_ +* Drop amqp workaround (thanks to `@mvdbeek`_). `Pull Request 917`_ +* Use ``yaml.safe_load()`` instead of deprecated ``load()`` (thanks to `@nsoranzo`_). + `Pull Request 921`_ +* Allow converting ``tool_test_report.json`` to xunit (thanks to `@mvdbeek`_). + `Pull Request 918`_ +* Fix error if testcase.data.job does not exist (thanks to `@mvdbeek`_). + `Pull Request 924`_ +* Fix deprecated ``getchildren()`` (thanks to `@nsoranzo`_). + `Pull Request 925`_ + +--------------------- +0.58.2 (2019-03-01) +--------------------- + +* Fix display of tool ids in planemo html report (thanks to `@mvdbeek`_). + `Pull Request 908`_ +* Single quotes for file names (thanks to `@bernt-matthias`_). `Pull Request + 909`_ +* Fix doc linting (thanks to `@mvdbeek`_). `Pull Request 910`_ +* Update TS categories (thanks to `@nsoranzo`_). 07dc6e0_ +* Close tag in doc help, to help with copy&paste (thanks to `@blankenberg`_). + `Pull Request 914`_ +* Update the tool XSD file (thanks to `@bgruening`_). `Pull Request 915`_ + +--------------------- +0.58.1 (2019-01-03) +--------------------- + +* Update galaxy-lib requirement to 18.9.2 to add Python 3.7 support (thanks to + `@nsoranzo`_). `Pull Request 906`_ +* Fix command run by `planemo test --skip_venv` (thanks to `@nsoranzo`_). + `Pull Request 907`_ + +--------------------- +0.58.0 (2019-01-01) +--------------------- + +* Remove deprecated ``sudo: false`` from .travis.yml (thanks to `@nsoranzo`_). + `Pull Request 902`_ +* Do not skip Galaxy client build for ``planemo serve``. Install Galaxy when the + directory specified with ``--galaxy_root`` does not exist or is empty. (thanks + to `@nsoranzo`_). `Pull Request 895`_, `Issue 845`_ + +--------------------- +0.57.1 (2018-11-23) +--------------------- + +* Fix username validation for shed linting (thanks to `@martenson`_). + `Pull Request 899`_, `Issue 898`_ + +--------------------- +0.57.0 (2018-11-19) +--------------------- + +* Allow ``workflow_convert`` to convert a native ``.ga`` workflows to format 2 (yaml). + `Pull Request 896`_ +* New command (``workflow_edit``) to open workflow in a synchronized graphical editor. + `Pull Request 894`_ +* Conda tutorial fixes (thanks to `@nsoranzo`_). `Pull Request 876`_ +* Enable ``--conda_use_local`` option for ``planemo test`` (thanks to + `@nsoranzo`_). `Pull Request 876`_ +* When testing, skip workflow outputs that do not have a `label` set (thanks to + `@bgruening`_). `Pull Request 893`_ +* Add ``__repr__`` for ``TestCase`` to improve debugging Planemo + (thanks to `@bgruening`_). `Pull Request 892`_ +* Increase IO polling interval over time (thanks to `@martenson`_). + `Pull Request 891`_ +* Sync galaxy xsd and fix tests (thanks to `@mvdbeek`_). + `Pull Request 889`_ +* Linting fix for ``W605`` (thanks to `@martenson`_). `Pull Request 888`_ +* Add icon for repeat parameters in training (thanks to `@bebatut`_). + `Pull Request 887`_ + +--------------------- +0.56.0 (2018-10-30) +--------------------- + +* Allow selection of Python version when starting managed Galaxy + (thanks to `@mvdbeek`_). `Pull Request 874`_ +* Change the channel priority of conda (again). (thanks to `@bgruening`_). + `Pull Request 867`_ +* Some small english corrections (thanks to `@hexylena`_). `Pull Request 868`_ +* Print the list of excluded paths when running ``ci_find_repos`` + (thanks to `@nsoranzo`_). `Pull Request 877`_ +* Improved XSD lint reporting. `Pull Request 871`_ +* Fix Planemo writing a file called ``gx_venv_None``. `Pull Request 870`_ +* Update cwltool and galaxy-lib dependencies for Python 3.7 (thanks to + `@nsoranzo`_). `Pull Request 864`_ +* Fix to make workflow testing more robust. + `Pull Request 882`_ + +--------------------- +0.55.0 (2018-09-12) +--------------------- + +* Add commands to create Galaxy training materials (thanks to `@bebatut`_). + `Pull Request 861`_ +* Fix `planemo test` when TEMP env variable contain spaces (thanks to + `@nsoranzo`_). + `Pull Request 851`_ +* Support testing a completely remote galaxy instance (thanks to `@hexylena`_). + `Pull Request 856`_ +* Allow naming history from command line (thanks to `@hexylena`_). + `Pull Request 860`_ +* Sync galaxy.xsd from galaxy repo (thanks to `@nsoranzo`_). + `Pull Request 866`_ +* Fix ServeTestCase.test_shed_serve test (thanks to `@nsoranzo`). bad810a_ + +--------------------- +0.54.0 (2018-06-06) +--------------------- + +* Better support for testings against different versions of Galaxy efficiently and robustly. + `Pull Request 849`_ +* New database version (thanks to `@bgruening`_). + `Pull Request 847`_ +* Hyperlink DOIs against preferred resolver (thanks to `@katrinleinweber`_). + `Pull Request 850`_ +* Tests for collection inputs to workflows. `Pull Request 843`_ +* Bring in Ephemeris sleep function - hopefully makes serve tests a bit more robust. + b12b117_ +* More tutorial testing, tutorial updates. + 016b923_, 324c776_, 2002b49_ +* More isolated ``test_shed_upload.py`` tests. 72d2ca7_ +* Add filetype support for workflow test inputs (thanks to `@bgruening`_). + `Pull Request 842`_ +* Add ``--no_shed_install`` option, to prevent shed installs as part of workflow testing. + `Pull Request 841`_ +* Small docs fix (thanks to `@hexylena`_). `Pull Request 848`_ + +--------------------- +0.53.0 (2018-05-22) +--------------------- + +* Make Planemo testing easier for CWL tools and workflows in various ways and update + tutorials to reflect these simplifications. `Pull Request 837`_ +* Test and fix running workflow tests against externally managed Galaxy servers. + `Pull Request 833`_, `Pull Request 836`_ +* Allow using URIs for inputs of workflow test. `Pull Request 840`_ +* Slide Galaxy testing window to include 18.05 and drop 17.09. `Pull Request 838`_ + +--------------------- +0.52.0 (2018-05-20) +--------------------- + +* Allow optional disabling of Galaxy single user mode. `Pull Request 835`_ +* Fix for path pasting options during workflow testing. `Pull Request 834`_ + +--------------------- +0.51.0 (2018-05-19) +--------------------- + +* Fix essentially all Conda_ and BioContainers_ related functionality to allow parity between + CWL_ and existing Galaxy functionality - fixes and enhances many commands including ``lint``, + ``conda_install``, ``conda_env``, ``test``, ``run``, and ``mull``. + `Pull Request 828`_ +* Add two new tutorials for `Conda + <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-conda>`__ + and `Container + <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-containers>`__ + development with CWL tools that mirrors the existing tutorials for Galaxy tools - including new + CWL exercises, answers, and example project templates. + 347c622_ +* Improve the CWL generated by the ``tool_init`` command to properly deal with + ``SoftwareRequirement`` s and generate more idiomatic CWL. + `Pull Request 820`_, a5c72e3_ +* Add new engine type (``--engine toil``) for testing and running CWL_ tools (requires + manually installing Toil_ with ``pip install toil`` in Planemo's environment). + `Pull Request 831`_ +* Add `documentation <http://planemo.readthedocs.io/en/latest/test_format.html>`__ + for the Galaxy Workflow and CWL_ test format files (includes information on configuring + various test engines). + `Pull Request 832`_ +* Better default logging config for CWL development. `Pull Request 830`_ +* Various fixes for the ``conda_search`` command. `Pull Request 826`_ +* Fix test coverage configuration. `Pull Request 822`_ +* Reorganize .travis.yml for clarity. `Pull Request 829`_ +* More isolated, robust unit tests that use git_. + `Pull Request 827`_, `Pull Request 818`_ +* Fix default list of best-practice Conda channels. `Pull Request 825`_ +* Refactor tests to speed up quick tests - fewer buggy URLs fetched in "quick" mode. + `Pull Request 823`_ +* Fix upload configuration of workflow testing to default (overrideable) external Galaxies + to not use path pasting. + `Pull Request 816`_ +* Fix test number parsing for workflow tests. `Pull Request 817`_ + +--------------------- +0.50.1 (2018-05-11) +--------------------- + +* Fix the process of waiting on Galaxy to boot up for the Docker Galaxy container ``--engine``. + +--------------------- +0.50.0 (2018-05-10) +--------------------- + +* Fixes and small CLI tweaks to get the Docker Galaxy container working as an ``--engine`` for the + run, serve, and test commands. + +--------------------- +0.49.2 (2018-05-09) +--------------------- + +* Various small fixes for new external Galaxy engine type. + +--------------------- +0.49.1 (2018-05-06) +--------------------- + +* Fix PyPI_ README rendering for 0.49.0 release changes. + +--------------------- +0.49.0 (2018-05-06) +--------------------- + +* Implement external Galaxy engine. `Pull Request 781`_ +* Restructure serve testing code for reuse. `Pull Request 795`_ +* Improve test report handling for JSON generated via galaxy-lib testing + script. `Pull Request 799`_ +* Improve how various branches of Galaxy are tested. `Pull Request 800`_ +* Added documentation for ``GALAXY_MEMORY_MB`` (thanks to `@bernt-matthias`_). + `Pull Request 801`_ +* Log tool config in verbose logging mode. `Pull Request 802`_ +* Replace ``r`` channel with ``conda-forge`` (thanks to `@bgruening`_). + `Pull Request 805`_ +* Sync ``galaxy.xsd`` with latest Galaxy updates (thanks to `@nsoranzo`_). + `Pull Request 806`_ +* Use ``requests.get()`` when validating http URLs (thanks to `@nsoranzo`_). + `Pull Request 809`_ +* Do not consider tools with "deprecated" in the path (thanks to + `@bgruening`_). `Pull Request 810`_ +* Automatically load tools shipped with Galaxy when testing, running, or serving + workflows that reference these tools. `Pull Request 790`_ +* Revise README and touch up documentation in general. `Pull Request 787`_ +* Various small changes to testing and test framework. `Pull Request 792`_ +* Various Python 3 fixes. 8cfe9e9_, 41f7df1_ +* Fixes for Galaxy 18.0X releases. + `Pull Request 803`_, dc443d6_ + +--------------------- +0.48.0 (2018-02-28) +--------------------- + +* Run all CI tests against Python 3 (thanks to `@nsoranzo`_). + `Pull Request 768`_ and `Pull Request 774`_ +* Python 3 fix - subprocess with ``universal_newlines=True`` + (thanks to `@peterjc`_). + `Pull Request 764`_ +* Record CWL_ conformance test results using JUnit xml + (thanks to `@mr-c`_). + `Pull Request 756`_ +* Restore run test case for simple Galaxy tools. + `Pull Request 769`_ +* Enhancements to Galaxy profiles and workflow testing. + `Pull Request 773`_ +* Fix resolving & installing shed repositories from workflows for ``test`` + and ``run`` commands. + `Pull Request 776`_ +* Implement planemo command to convert format 2 workflows into .ga workflows. + `Pull Request 771`_ +* Add a native Galaxy workflow (.ga) testing test. + `Pull Request 770`_ +* Drop Brew support but add more detailed install instructions. + `Pull Request 761`_ +* Clean up CWL_ conformance test execution. `Pull Request 753`_ +* Assorted small CWL_ and deamon serve fixes. `Pull Request 759`_ + + +--------------------- +0.47.0 (2017-11-18) +--------------------- + +* Update to the latest Galaxy tool XSD (thanks to `@nsoranzo`_). + `Pull Request 747`_ +* Re-fix problem when shed_update would fail if nothing to update + (thanks to `@nsoranzo`_). `Pull Request 747`_ +* Update instructions for installation via conda (thanks to `@nsoranzo`_) . + `Pull Request 743`_ +* Bug fix for MacOS `chmod` doesn't support `--recursive` flag. + (thanks to `@dfornika`_). `Pull Request 739`_ +* Bug fix to also `socket.error` when linting URLs + (thanks to `@nsoranzo`_). `Pull Request 738`_ +* Disable broken tests. `Pull Request 745`_ + +--------------------- +0.46.1 (2017-09-26) +--------------------- + +* Rev to latest versions of bioblend_ and `galaxy-lib`_ for various fixes + related to CWL_. + +--------------------- +0.46.0 (2017-09-15) +--------------------- + +* Change behavior of ``--docker`` flag, for a few releases it would require + Galaxy use a container for every non-upload tool. This breaks various + conversion tools for instance and so was reverted. + `Pull Request 733`_ +* Add 'Accept' header when linting doc URLs (thanks to `@nsoranzo`_). + `Pull Request 725`_ +* Fix `--conda_auto_install` help (thanks to `@nsoranzo`_). + `Pull Request 727`_ +* Incremental progress toward CWL support via Galaxy. + `Pull Request 729`_, `Pull Request 732`_ +* Update galaxy-lib to latest version to fix various issues. + `Pull Request 730`_ +* Fix lint detected problems with documentation. + `Pull Request 731`_ + +--------------------- +0.45.0 (2017-09-06) +--------------------- + +* Update to the latest `galaxy-lib`_ for Conda fixes. (thanks `@nsoranzo`_) + and updated CWL_ utilities. `Pull Request 716`_, `Pull Request 723`_ +* Update Conda_ channel order to sync with Bioconda_ + (thanks to `@nsoranzo`_). `Pull Request 715`_ +* Experimental support running CWL_ workflows through the CWL_ fork of Galaxy. +* Mention ``planemo command --help`` in main help + (thanks to `@peterjc`_). `Pull Request 709`_ +* Bugfix handle ``None`` requirement versions when registering containers + (thanks to `@bgruening`_). `Pull Request 704`_ +* Bugfix for dependencies by pinning ruamel.yaml version + (thanks to `@mvdbeek`_). `Pull Request 720`_ + +--------------------- +0.44.0 (2017-06-22) +--------------------- + +* Fix and improve Galaxy root option specification options. + `Pull Request 701`_, 8a608e0_ +* Update `planemo mull` to use a default action of `build-and-test` since + `build` no longer cleans up itself. ecc1bc2_ +* Add a command to pre-install Involucro_. + `Pull Request 702`_ + +--------------------- +0.43.0 (2017-06-22) +--------------------- + +* Remove stdio from generated tools - just use exit_code for everything. + 91b6fa0_ +* Implement some ad-hoc documentation tests. `Pull Request 699`_ +* A large number of small enhancements and fixes for the documentation and + example projects. + +--------------------- +0.42.1 (2017-06-16) +--------------------- + +* Fix Readme typos (thanks to `@manabuishii`_) 904d77a_ +* Fix `container_register` to create pull requests against the newly finalized home of the + multi-package-containers registry repository. + 9636682_ +* Fix `use_global_config` and `use_env_var` for options with unspecified defaults. + 475104c_ + + +--------------------- +0.42.0 (2017-06-15) +--------------------- + +* Conda/Container documentation and option naming improvements. `Pull Request + 684`_ +* Sync `galaxy.xsd` with latest upstream Galaxy updates (thanks to `@nsoranzo`_). + `Pull Request 687`_ +* Fix `ci_find_repos` command to not filter repos whose only modifications where + in subdirs (thanks to `@nsoranzo`_). + `Pull Request 688`_ +* Update `container_register` for mulled version 2 and repository name changes. + `Pull Request 689`_ +* Better pull request messages for the `container_register` command. + `Pull Request 690`_ + +--------------------- +0.41.0 (2017-06-05) +--------------------- + +* Fix ``shed_update`` not fail if there is nothing to update + (thanks to `@nsoranzo`_). `Issue 494`_, `Pull Request 680`_ +* Conda documentation and option naming improvements. + `Pull Request 683`_ +* Implement ``container_register`` for tool repositories. + `Pull Request 675`_ +* Fix ``hub`` binary installation for Mac OS X. + `Pull Request 682`_ + +--------------------- +0.40.1 (2017-05-03) +--------------------- + +* Fix data manager configuration to not conflict with original Galaxy at + ``galaxy_root`` (thanks to `@nsoranzo`_). `Pull Request 662`_ +* Fix ``filter_paths()`` to not partial match paths when filtering shed repositories + (thanks to `@nsoranzo`_). `Pull Request 665`_ +* Fix description when creating ``.shed.yml`` files (thanks to `@RJMW`_). + `Pull Request 664`_ + +--------------------- +0.40.0 (2017-03-16) +--------------------- + +* Implement instructions and project template for GA4GH Tool Execution + Challenge Phase 1. 84c4a73_ +* Eliminate Conda hack forcing ``/tmp`` as temp directory. b4ae44d_ +* Run dependency script tests in isolated directories. 32f41c9_ +* Fix OS X bug in ``planemo run`` by reworking it to wait using urllib instead of sockets. + 3129216_ + +--------------------- +0.39.0 (2017-03-15) +--------------------- + +* Implement documentation and examples for Conda-based dependency development (under + "Advanced" topics). + `Pull Request 642`_, `Pull Request 643`_ +* Implement documentation and examples for container-based dependency development (under + "Advanced" topics). + 0a1abfe_ +* Implement a ``planemo conda_search`` command for searching best practice channels + from the command line. + `Pull Request 642`_ +* Allow Planemo to work with locally built Conda packages using the ``--conda_use_local`` + command. + `Pull Request 643`_, `Issue 620`_ +* Implement an ``open`` (or just ``o``) command to quickly open the last test results + (or any file if supplied). `Pull Request 641`_ +* Linting improvements and fixes due to `galaxy-lib`_ update. + * WARN on test output names not found or not matching. + * INFO correct information about stdio if profile version is found. + * WARN if profile version is incorrect. + * INFO profile version + * Fix ``assert_command`` not detected as a valid test (fixes `Issue 260`_). +* Have ``lint --conda_requirements`` check that at least one actual requirement is found. + 6638caa_ +* Allow ``conda_install`` to work with packages as well as just tools. + 8faf661_ +* Add ``--global`` option to conda_install to install requirements into global Conda setup + instead of using an environment. + 8faf661_ +* Implement ``planemo lint --biocontainer`` that checks that a tool has an available BioContainer + registered. + 0a1abfe_ +* Add more options and more documentation to the ``planemo mull`` command. + 0a1abfe_ +* Hack around a bug in Conda 4.2 that makes it so ``planemo mull`` doesn't work out of the box on + Mac OS X. + 0a1abfe_ +* Allow URIs to be used instead of paths for a couple operations. ce0dc4e_ +* Implement non-strict CWL parsing option. 4c0f100_ +* Fixes for changes to cwltool_ and general CWL-relate functionality. + 3c95b7b_, 06bcf19_, 525de8f_, 9867e56_, 9ab4a0d_ +* Eliminate deprecated XML-based abstraction from ``planemo.tools``. 04238d3_ +* Fix ``MANIFEST.in`` entry that was migrated to galaxy-lib. ced5ce2_ +* Various fixes for the command ``conda_env``. `Pull Request 640`_ +* Improved command help - both formatting and content. `Pull Request 639`_ +* Implement a ``--no_dependency_resolution`` option disabling conda dependency + resolver. + `Pull Request 635`_, `Issue 633`_ +* Tests for new linting logic. `Pull Request 638`_ +* Fix bug where tool IDs needs to be lowercase for the shed (thanks to + `@bgruening`_). + `Pull Request 649`_ +* Update seqtk version targetted by intro docs. e343b67_ +* Various other Conda usability improvements. `Pull Request 634`_ + +--------------------- +0.38.1 (2017-02-06) +--------------------- + +* Fix bug with ``shed_lint --urls`` introduced in 0.38.0. + 84ebc1f_ + +--------------------- +0.38.0 (2017-02-06) +--------------------- + +* Trim down the default amount of logging during testing. + `Pull Request 629`_, `Issue 515`_ +* Improved log messages during shed operations. 08c067c_ +* Update tool XSD against latest Galaxy. + fca4183_, 03c9658_ +* Fix bug where ``shed_lint --tools`` for a suite lints the same tools multiple + times. + `Issue 564`_, `Pull Request 628`_ + +--------------------- +0.37.0 (2017-01-25) +--------------------- + +* Update to the latest `galaxy-lib`_ release. This means new installs start with + Miniconda 3 instead of Minicoda 2 and at a newer version. This fixes many + Conda_ related bugs. +* Change defaults so that Conda automatically initializes and performs tool installs + by default from within the spawned Galaxy server. The trio of flags + ``--conda_dependency_resolution``, ``--conda_auto_install``, and ``--conda_auto_init`` + are effectively enabled by default now. 4595953_ +* Use the Galaxy cached dependency manager by default (thanks to `@abretaud`_). + `Pull Request 612`_ +* Test Conda dependency resolution for more versions of Galaxy including the forthcoming + release of 17.01. +* Update to the latest Galaxy tool XSD for various tool linting fixes. 32acd68_ +* Fix pip ignores for ``bioconda_scripts`` (thanks to `@nturaga`_) + `Pull Request 614`_ + +--------------------- +0.36.1 (2016-12-12) +--------------------- + +* Fix move error when using ``project_init``. + `Issue 388`_, `Pull Request 610`_ +* Improved integration testing for ``test`` command. `Pull Request 609`_ +* Update CWL links to v1.0 (thanks to `@mr-c`_). + `Pull Request 608`_ + +--------------------- +0.36.0 (2016-12-11) +--------------------- + +* Bring in latest tool XSD file from Galaxy (thanks to `@peterjc`_). + `Pull Request 605`_ +* PEP8 fixes for various linting problems + (thanks to `@peterjc`_). + `Pull Request 606`_ +* Update tool syntax URL to new URL (thanks to `@mvdbeek`_). + `Pull Request 602`_ + +--------------------- +0.35.0 (2016-11-14) +--------------------- + +* Native support for building bioconductor tools and recipes + (thanks to `@nturaga`_). `Pull Request 570`_ +* Fixes for running Galaxy via docker-galaxy-stable (thanks to + `@bgruening`_). 50d3c4a_ +* Import order linting fixes (thanks to `@bgruening`_). + +--------------------- +0.34.1 (2016-10-12) +--------------------- + +* Mimic web browser to validate user help URLs fixing `Issue 578`_ + (thanks to `@peterjc`_). `Pull Request 591`_ +* Fix for Bioconda recipes depending on ``conda-forge`` (thanks to `@nsoranzo`_). + `Pull Request 590`_ + + +--------------------- +0.34.0 (2016-10-05) +--------------------- + +* Implement ``mull`` command to build containers for tools based on Conda_ + recipes matching requirement definitions. 08cef54_ +* Implement ``--mulled_containers`` flag on ``test``, ``serve``, and ``run`` + commands to run tools in "mulled" containers. Galaxy will first search + locally cache containers (such as ones built with ``mull``), then search + the mulled namespace of `quay.io`_, and finally build one on-demand if + needed using `galaxy-lib`_ and Involucro_ developed by `@thriqon`_. +* Implement ``--conda_requirements`` flag on ``lint`` command to ensure requirements + can be resolved in best practice channels. 9da8387_ +* Allow ``conda_install`` command over multiple tool paths. 2e4e5fc_ +* Update pip_ as part of setting virtual environment in ``Makefile`` target. + 19b2ee9_ +* Add script to auto-update Bioconda_ recipe for Planemo and open a pull request. + f0da66f_ + +--------------------- +0.33.2 (2016-09-28) +--------------------- + +* Fix HISTORY.rst link problem that prevented correct display of content on PyPI_. + +--------------------- +0.33.1 (2016-09-28) +--------------------- + +* Fix ``lint --urls`` false positives by being more restrictive with what is considered a URL + (fixed by `@hexylena`_ after detailed report from `@peterjc`_). + `Issue 573`_, `Pull Request 579`_ + +--------------------- +0.33.0 (2016-09-23) +--------------------- + +* Enable XSD validation of tools by default (restore old behavior with + ``planemo lint --no_xsd``). 1ef05d2_ +* Implement a ``conda_lint`` command to lint Conda_ recipes based + on `anaconda-verify`_. 6a6f164_ +* Implement ``clone`` and ``pull_request`` commands to ease PRs + (with documentation fixes from `@martenson`_). + e925ba1_, ea5324f_ +* Update `galaxy.xsd`_ to allow version_command's to have an interpreter + attribute. 7cca2e4_ +* Apply improvement from `@nsoranzo`_ for Planemo's use of + `git diff <https://git-scm.com/docs/git-diff>`__. + 6f91719_ +* Pull in downstream refactoring of ``tool_init`` code from `@nturaga`_'s + Bioconductor_ work. ccdd2d5_ +* Update to latest `Tool Factory`_ code from `tools-iuc`_. ca88b0c_ +* Small code cleanups. b6d8294_, d6da3a8_ +* Fixup docs in ``planemo.xml.validation``. +* Allow skipping newly required lxml_ dependency in `setup.py`_. 34538de_ + +--------------------- +0.32.0 (2016-09-16) +--------------------- + +* Enhance ``planemo lint --xsd`` to use a fairly complete and newly official XSD + definition. `Pull Request 566`_ +* Migrate and update documentation related to tool XML macros and handling + multiple outputs from the Galaxy wiki (with help from `@bgruening`_, `@mvdbeek`_, + and `@nsoranzo`_). `Pull Request 559`_ +* Documentation fixes (thanks to `@ramezrawas`_). `Pull Request 561`_ +* Do not fail URL linting in case of too many requests (thanks to `@nsoranzo`_). + `Pull Request 565`_ + +--------------------- +0.31.0 (2016-09-06) +--------------------- + +* Implement new commands to ``ci_find_repos`` and ``ci_find_tools`` to ease + CI scripting. + `Pull Request 555`_ + +--------------------- +0.30.2 (2016-09-01) +--------------------- + +* Fix another problem with Conda_ prefix handling when using + ``--conda_dependency_resolution``. f7b6c7e_ + +--------------------- +0.30.1 (2016-09-01) +--------------------- + +* Fix a problem with Conda_ prefix handling when using + ``--conda_dependency_resolution``. f7b6c7e_ +* Fix for quote problem in ``update_planemo_recipe.bash``. 6c03de8_ +* Fix to restore linting of ``tests/`` directory and fix import order throughout + module. ef4b9f4_ + +--------------------- +0.30.0 (2016-09-01) +--------------------- + +* Update to the latest `galaxy-lib`_ release and change Conda_ semantics to match + recent updates to Galaxy. For the most robust Conda_ usage - use planemo 0.30+ + with Galaxy 16.07 or master. + 07d94bd_ +* Implement the ``--conda_auto_init`` flag for ``conda_install``. ca19910_ +* Allow the environment variable ``PLANEMO_CONDA_PREFIX`` to set a default + for ``--conda_prefix``. + 24008ab_ +* Fixup documentation regarding installs and Conda_. ce44e87_ +* Fix and lint Python module import order throughout project. + `Pull Request 550`_ +* Use ``cp`` rather than symlink to ``$DOWNLOAD_CACHE`` in the + ``dependency_script`` command (thanks to `@peterjc`_). c2204b3_ +* Fixes for the Homebrew recipe updater. c262b6d_ + +--------------------- +0.29.1 (2016-08-19) +--------------------- + +* Improved handling of Python 2.7 specific dependencies. + +--------------------- +0.29.0 (2016-08-19) +--------------------- + +* Look for sha256sum checksums during shed_lint (thanks to `@peterjc`_). + `Pull Request 539`_ +* An assortment fixes and enhancements to the ``dependency_script`` command + (thanks to `@peterjc`_). `Pull Request 541`_, `Pull Request 545`_ +* Fix shed_build to respect exclude: in .shed.yml (thanks to `@nsoranzo`_). + `Pull Request 540`_ +* Fix linting of tool URLs (thanks to `@nsoranzo`_). `Pull Request 546`_ + +--------------------- +0.28.0 (2016-08-17) +--------------------- + +* Fixes for bioblend_ v0.8.0 (thanks to `@nsoranzo`_). 9fdf490_ +* Enable shed repo type update (thanks to `@nsoranzo`_). 3ceaa40_ +* Create suite repositories with repository_suite_definition type by default + (thanks to `@nsoranzo`_). + 057f4f0_ +* Include ``shed_lint`` in script run by ``travis_init`` (thanks to `@peterjc`_). + `Pull Request 528`_ +* Minor polish to the ``travis_init`` command (thanks to `@peterjc`_). + `Pull Request 512`_ +* Update pip_ and setuptools on TravisCI; fix travis_init (thanks to `@peterjc`_). + `Pull Request 521`_ +* Shorten command one line descriptions for main help (thanks to `@peterjc`_). + `Pull Request 510`_ +* Use ``planemo test --no_cache_galaxy`` under TravisCI (thanks to `@peterjc`_). + `Pull Request 513`_ +* Improve and fix docs ahead of GCC 2016 (thanks to `@martenson`_). + `Pull Request 498`_, 725b232_ +* Add description of ``expect_num_outputs`` to planemo FAQ. a066afb_ +* Revise planemo tools docs to be more explicit about collection identifiers. + a811e65_ +* Add more docs on existing dynamic tool output features. `Pull Request 526`_ +* Fix serve command doc (thanks to `@nsoranzo`_). 8c088c6_ +* Fix `make lint-readme` (RST link errors) (thanks to `@peterjc`_). + `Pull Request 525`_ +* Add union bedgraph example to project templates (for GCC demo example). + d53bcd6_ +* Add Flow Cytometry Analysis, Data Export, and Constructive Solid Geometry as + shed categories (thanks to `@bgruening`_, `@gregvonkuster`_, and `@nsoranzo`_). + e890ab5_, 08bb354_, e2398fb_ +* Remove duplicated attribute in docs/writing/bwa-mem_v5.xml (thanks to + Paul Stewart `@pstew`_). + `Pull Request 507`_ + +--------------------- +0.27.0 (2016-06-22) +--------------------- + +* Use ephemeris to handle syncing shed tools for workflow actions. + 1c6cfbb_ +* More planemo testing enhancements for testing artifacts that aren't + Galaxy tools. `Pull Request 491`_ +* Implement ``docker_galaxy`` engine type. eb039c0_, `Issue 15`_ +* Enhance profiles to be Dockerized Galaxy-aware. `Pull Request 488`_ +* Add linter for DOI type citation - thanks to `@mvdbeek`_. + `Pull Request 484`_ + +--------------------- +0.26.0 (2016-05-20) +--------------------- + +* 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`_ + +--------------------- +0.25.1 (2016-05-11) +--------------------- + +* Tweak dependencies to try to fix cwltool_ related issues - such + as `Issue 475`_. + +--------------------- +0.25.0 (2016-05-11) +--------------------- + +* 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_ + + +--------------------- +0.24.2 (2016-04-25) +--------------------- + +* Revert "check ``.shed.yml`` owner against credentials during shed + creation", test was incorrect and preventing uploads. + `Pull Request 425`_, `Issue 246`_ + +--------------------- +0.24.1 (2016-04-08) +--------------------- + +* 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_ + +--------------------- +0.24.0 (2016-03-29) +--------------------- + +* 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_ + +--------------------- +0.23.0 (2016-02-15) +--------------------- + +* Fix duplicated attributes with Conda_ resolver (thanks + to Björn Grüning). `Pull Request 403`_ +* Upgrade to latest version of `galaxy-lib`_ for more linting. +* Attempt to better handle conditional dependency on cwltool. + +--------------------- +0.22.2 (2016-01-14) +--------------------- + +* Fixed bug targetting forthcoming release of Galaxy 16.01. + +--------------------- +0.22.1 (2016-01-14) +--------------------- + +* Fixed problem with PyPI_ build artifacts due to submodule's not + being initialized during previous release. + +--------------------- +0.22.0 (2016-01-13) +--------------------- + +* Add ``--skip_venv`` to support running Galaxy 16.01 inside of + conda environments. 9f3957d_ +* Implement conda support. f99f6c1_, ad3b2f0_, 5e0b6d1_ +* Update LICENSE for Planemo to match Galaxy. 15d33c7_ +* Depend on new `galaxy-lib`_ on PyPI_ instead of previous hacks.... + `Pull Request 394`_ +* Fix egg caching against master/15.10. 6d0f502_ +* Fix bug causing shed publishing of ``.svn`` directories. + `Issue 391`_ +* Bug fixes for Conda_ support thanks to `@bgruening`_. 63e456c_ +* Fix document issues thanks to `@einon`_. + `Pull Request 390`_ +* Improve client for shed publishing to support newer shed backend + being developed by `@hexylena`_. `Pull Request 394`_ +* Tool Shed ``repo_id`` change, `@hexylena`_. `Pull Request 398`_ +* Various other small changes to testing, project structure, and + Python 3 support. + +--------------------- +0.21.1 (2015-11-29) +--------------------- + +* Fix serious regression to ``test`` command. 94097c7_ +* Small fixes to release process. 4e1377c_, 94645ed_ + +--------------------- +0.21.0 (2015-11-29) +--------------------- + +* If ``virtualenv`` not on ``PATH``, have Planemo create one for Galaxy. + 5b97f2e_ +* Add documentation section on testing tools installed in an existing + Galaxy instance. 1927168_ +* When creating a virtualenv for Galaxy, prefer Python 2.7. + e0577e7_ +* Documentation fixes and improvements thanks to `@martenson`_. + 0f8cb10_, 01584c5_, b757791_ +* Specify a minimum ``six`` version requirement. 1c7ee5b_ +* Add script to test a planemo as a wheel. 6514ff5_, `Issue 184`_ +* Fix empty macro loading. `Issue 362`_ +* Fix an issue when you run ``shed_diff --shed_target local`` thanks + to Gwendoline Andres and Gildas Le Corguillé at ABiMS Roscoff. + `Pull Request 375`_ +* Fix ``shed_diff`` printing to stdout if ``-o`` isn't specified. + f3394e7_ +* Small ``shed_diff`` improvements to XML diffing and XUnit reporting. + af7448c_, 83e227a_ +* More logging of ``shed_diff`` results if ``--verbose`` flagged. + 9427b47_ +* Add ``test_report`` command for rebuilding reports from structured JSON. + 99ee51a_ +* Fix option bug with Click 6.0 thanks to `@bgruening`_. 2a7c792_ +* Improved error messages for test commands. fdce74c_ +* Various fixes for Python 3. 2f66fc3_, 7572e99_, 8eda729_, 764ce01_ +* Use newer travis container infrastructure for testing. 6d81a94_ +* Test case fixes. 98fdc8c_, 0e4f70a_ + +--------------------- +0.20.0 (2015-11-11) +--------------------- + +* 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_ + +--------------------- +0.19.0 (2015-11-03) +--------------------- + +* 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_ + +--------------------- +0.18.1 (2015-10-22) +--------------------- + +* Fix issue with test reporting not being populated. 19900a6_ + +--------------------- +0.18.0 (2015-10-20) +--------------------- + +* 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`_ + +--------------------- +0.17.0 (2015-10-19) +--------------------- + +* 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`_ + +--------------------- +0.16.0 (2015-10-07) +--------------------- + +* 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`_ + +--------------------- +0.15.0 (2015-10-01) +--------------------- + +* Template framework for reporting including new markdown and plain + text reporting options for testing - thanks to `@hexylena`_. + `Pull Request 304`_ +* XUnit style reporting for ``shed_diff`` command - thanks to + `@hexylena`_. `Pull Request 305`_ +* Add new ``shed_build`` command for building repository tarballs - + thanks to `@kellrott`_. `Pull Request 297`_ +* Fix exit code handling for ``lint`` commands - thanks to `@mvdbeek`_. + `Pull Request 292`_ +* Improved documentation for ``serve`` command - thanks to `@lparsons`_. + `Pull Request 312`_ +* Tiny backward compatible Python 3 tweaks for `Tool Factory`_ - thanks + to `@peterjc`_. dad2d9d_ +* Fixed detection of virtual environment in ``Makefile`` - thanks to + `@lparsons`_. `Pull Request 311`_ +* Updates to Galaxy XSD - thanks to `@mr-c`_. `Pull Request 309`_ +* Allow reading shed key option from an environment variable. + `Pull Request 307`_ +* Allow specifying host to serve Galaxy using ``-host`` - thanks in + part to `@chambm`_. `Pull Request 301`_ +* Allow specifying defaults for ``-host`` and ``--port`` in + ``~/.planemo.yml``. `Pull Request 301`_ +* Improve ``~/.planemo.yml`` sample comments - thanks to `@martenson`_. + `Pull Request 287`_ +* Update tool shed categories - thanks to `@bgruening`_. `Pull Request 285`_ +* Improved output readibility for ``diff`` command - thanks to `@martenson`_. `Pull Request 284`_ + +--------------------- +0.14.0 (2015-08-06) +--------------------- + +* Allow ``-t`` as shorthand for ``--shed_target`` (thanks to Peter Cock). + `Pull Request 278`_ +* Fix ``tool_init`` command to use ``from_work_dir`` only if file in command + (thanks to bug report and initial fix outline by Gildas Le Corguillé). + `Pull Request 277`_ +* Various documentation fixes (thanks in part to Peter Cock and Daniel + Blankenberg). `Pull Request 256`_, `Pull Request 253`_, `Pull Request 254`_, + `Pull Request 255`_, `Pull Request 251`_, `Issue 272`_ + +--------------------- +0.13.2 (2015-07-06) +--------------------- + +* Fix project_init for missing files. cb5b906_ +* Various documentation improvements. + +--------------------- +0.13.1 (2015-07-01) +--------------------- + +* Fix for ``shed_init`` producing non-standard type hints. `Issue 243`_, + f0610d7_ +* Fix tool linting for parameters that define an ``argument`` but not a + ``name``. `Issue 245`_, aad1eed_ +* Many doc updates including a tutorial for developing tools in a test-driven + fashion and instructions for using the planemo appliance through Kitematic + (with Kitematic screenshots from E. Rasche). + +--------------------- +0.13.0 (2015-06-28) +--------------------- + +* If planemo cannot find a Galaxy root, it will now automatically fetch + one (specifing ``--galaxy_install`` will still force a fetch). + `Pull Request 235`_ +* `Docuementation <http://planemo.readthedocs.org/en/latest/appliance.html>`__ + has been updated to reflect new and vastly improved Docker and Vagrant + virtual appliances are now available, as well as a new VirtualBox OVA + variant. +* Update linting for new tool XML features (including ``detect_errors`` + and output collections). `Issue 233`_, 334f2d4_ +* Fix ``shed_test`` help text. `Issue 223`_ +* Fix code typo (thanks to Nicola Soranzo). `Pull Request 230`_ +* Improvements to algorithm used to guess if an XML file is a tool XML file. + `Issue 231`_ +* Fix configuration file handling bug. `Issue 240`_ + +--------------------- +0.12.2 (2015-05-23) +--------------------- + +* Fix ``shed_test`` and ``shed_serve`` for test and local tool sheds. + f3cafaa_ + +--------------------- +0.12.1 (2015-05-21) +--------------------- + +* Fix to ensure the tab completion script is in the Python source tarball + (required for setting up tab-completion for Homebrew). 6b4e7a6_ + +--------------------- +0.12.0 (2015-05-21) +--------------------- + +* Implement a ``--failed`` flag for the ``test`` command to rerun + previously faied tests. `Pull Request 210`_ +* Implement ``shed_update`` to upload contents and update repository + metadata. `Pull Request 216`_ +* Implement ``shed_test`` and ``shed_serve`` commands to test and view + published artifacts in the Tool Shed. `Pull Request 213`_, `Issue 176`_ +* Add shell tab-completion script. 37dcc07_ +* Many more commands allow specifing multiple tool and/or repository targets. + `Issue 150`_ +* Add -m as alias for --message in planemo shed_upload (thanks to + Peter Cock). `Pull Request 200`_ +* Add ``--ensure_metadata`` option to ``shed_lint`` to ensure ``.shed.yml`` + files contain many repository. `Pull Request 215`_ +* More developer documentation, additional ``make`` targets including ones + for setting up git pre-commit hooks. cc8abb6_, `Issue 209`_ +* Small README improvement (thanks to Martin Čech) b53006d_ +* Fixes for shed operation error handling (thanks to Martin Čech). + `Pull Request 203`_, `Pull Request 206`_ +* Fix for "smart" ``shed_diff`` not in the repository root directory + (thanks to Peter Cock). `Pull Request 207`_, `Issue 205`_ +* Recursive ``shed_diff`` with directories not yet in Tool Shed. + `Pull Request 208`_ +* Improve error handling and reporting for problematic ``--shed_target`` + values. `Issue 217`_ +* Fix typos in lint messages. `Issue 211`_ + + +--------------------- +0.11.1 (2015-05-12) +--------------------- + +* Fix default behavior for ``planemo lint`` to use current directory if + explicit paths are not supplied. 1e3668a_ + +--------------------- +0.11.0 (2015-05-12) +--------------------- + +* More compact syntax for defining multiple custom inclusions in ``.shed.yml`` + files - thanks to Peter Cock. `Issue 180`_, `Pull Request 185`_, + `Pull Request 196`_ +* Prevent ambigous destinations when defining custom inclusions in + ``.shed.yml``- thanks to Peter Cock. `Pull Request 186`_ +* ``lint`` now warns if tool ids contain whitespace. `Pull Request 190`_ +* Handle empty tar-balls gracefully on older Python versions - thanks + to Peter Cock. `Pull Request 187`_ +* Tweak quoting in ``cp`` command - thanks to Peter Cock. 6bcf699_ +* Fix regression causing testing to no longer produce "pretty" test + results under certain circumstances. `Issue 188`_ +* Fix for recursive ``shed_diff`` folder naming. `Issue 192`_ +* Fix output definitions to ``tool_init`` command. `Issue 189`_ + +--------------------- +0.10.0 (2015-05-06) +--------------------- + +* Extend ``shed_lint`` to check for valid actions in tool_dependencies.xml + files. 8117e03_ +* Extend ``shed_lint`` to check for required files based on repository type. + `Issue 156`_ +* Ignore common editor backup files during ``shed_upload``. `Issue 179`_ +* Fix missing file when installing from source via PyPI_. `Issue 181`_ +* Fix ``lint`` to verify ``data`` inputs specify a ``format`` attribute. + 8117e03_ +* Docstring fix thanks to `@peterjc`_. fe7ad46_ + + +--------------------- +0.9.0 (2015-05-03) +--------------------- + +* Add new logo to the README thanks to `@petrkadlec`_ from `puradesign.cz + <http://puradesign.cz/en>`__ and `@carlfeberhard`_ from the Galaxy Project. + `Issue 108`_ +* Implement smarter ``shed_diff`` command - it now produces a meaningful + exit codes and doesn't report differences if these correspond to attributes + that will be automatically populated by the Tool Shed. `Issue 167`_ +* Use new smarter ``shed_diff`` code to implement a new ``--check_diff`` + option for ``shed_upload`` - to check for meaningful differences before + updating repositories. `Issue 168`_ +* Record git commit hash during ``shed_upload`` if the ``.shed.yml`` is + located in a git repository. `Issue 170`_ +* Allow ``shed_`` operations to operate on git URLs directly. `Issue 169`_ +* Fail if missing file inclusion statements encountered during ``.shed.yml`` + repository resolution - bug reported by `@peterjc`_. `Issue 158`_ +* Improved exception handling for tool shed operations including new + ``--fail_fast`` command-line option. * `Issue 114`_, `Pull Request 173`_ +* Implement more validation when using the ``shed_init`` command. 1cd0e2d_ +* Add ``-r/--recursive`` option to ``shed_download`` and ``shed_diff`` + commands and allow these commands to work with ``.shed.yml`` files defining + multipe repositories. 40a1f57_ +* Add ``--port`` option to the ``serve`` and ``tool_factory`` commands. + 15804be_ +* Fix problem introduced with `setup.py`_ during the 0.9.0 development cycle + - thanks to `@peterjc`_. `Pull Request 171`_ +* Fix clone bug introduced during 0.9.0 development cycle - thanks to + `@bgruening`_. `Pull Request 175`_ + +--------------------- +0.8.4 (2015-04-30) +--------------------- + +* Fix for Travis CI testing picking up invalid tests (reported by `@takadonet`_). `Issue 161`_ +* Fix tar ordering for consistency (always sort by name) - thanks to `@peterjc`_. `Pull Request 164`_, `Issue 159`_ +* Fix exception handling related to tool shed operations - thanks to `@peterjc`_. `Pull Request 155`_, b86fe1f_ + +--------------------- +0.8.3 (2015-04-29) +--------------------- + +* Fix bug where ``shed_lint`` was not respecting the ``-r/--recursive`` flag. + 9ff0d2d_ +* Fix bug where planemo was producing tar files incompatible with the Tool + Shed for package and suite repositories. a2ee135_ + +--------------------- +0.8.2 (2015-04-29) +--------------------- + +* Fix bug with ``config_init`` command thanks to `@bgruening`_. `Pull Request 151`_ +* Fix unnessecary ``lint`` warning about ``parallelism`` tag reported by + `@peterjc`_. 9bf1eab_ + +--------------------- +0.8.1 (2015-04-28) +--------------------- + +* Fixes for the source distribution to allow installation of 0.8.0 via Homebrew. + +--------------------- +0.8.0 (2015-04-27) +--------------------- + +* Implement the new ``shed_lint`` command that verifies various aspects of tool + shed repositories - including XSD_ validation of ``repository_dependencies.xml`` + and ``tool_dependencies.xml`` files, best practices for README files, and the + contents of ``.shed.yml`` files. This requires the lxml_ library to be available + to Planemo or the application xmllint_ to be on its ``PATH``. `Pull Request 130`_ + `Issue 89`_ `Issue 91`_ 912df02_ d26929e_ 36ac6d8_ +* Option to enable experimental XSD_ based validation of tools when ``lint`` + is executed with the new ``--xsd`` flag. This validation occurs against the + unofficial `Galaxy Tool XSD project <https://github.com/JeanFred/Galaxy-XSD>`__ + maintained by `@JeanFred`_. This requires the lxml_ library to be + available to Planemo or the application xmllint_ to be on its ``PATH``. + `Pull Request 130`_ 912df02_ +* Allow skipping specific linters when using the ``lint`` command using the new + ``--skip`` option. 26e3cdb_ +* Implement sophisticated options in ``.shed.yml`` to map a directory to many, + custom Tool Shed repositories during shed operaitons such ``shed_upload`` + including automatically mapping tools to their own directories and automatically + building suites repositories. `Pull Request 143`_ +* Make ``shed_upload`` more intelligent when building tar files so that package + and suite repositories may have README files in source control and they will + just be filtered out during upload. 53edd99_ +* Implement a new ``shed_init`` command that will help bootstrap ``.shed.yml`` + files in the specified directory. cc1a447_ +* Extend ``shed_init`` to automatically build a ``repository_rependencies.xml`` + file corresponding to a Galaxy workflow (``.ga`` file). `Issue 118`_ 988de1d_ +* In addition to a single file or directory, allow ``lint`` to be passed multiple + files. 343902d_ `Issue 139`_ +* Add ``-r/--recursive`` option to ``shed_create`` and ``lint`` commands. 63cd431_ + 01f2af9_ +* Improved output formatting and option to write diffs to a file for the + ``shed_diff`` command. 965511d_ +* Fix lint problem when using new Galaxy testing features such as expecting + job failures and verifing job output. `Issue 138`_ +* Fix typo in ``test`` help thanks to first time contributor `@pvanheus`_. + `Pull Request 129`_ 1982076_ +* Fix NPE on empty ``help`` element when linting tools. `Issue 124`_ +* Fix ``lint`` warnings when ``configfiles`` are defined in a tool. 1a85493_ +* Fix for empty ``.shed.yml`` files. b7d9e96_ +* Fix the ``test`` command for newer versions of nose_. 33294d2_ +* Update help content and documentation to be clear ``normalize`` should not + be used to update the contents of tool files at this time. 08de8de_ +* Warn on unknown ``command`` attributes when linting tools (anything but + ``interpreter``). 4f61025_ +* Various design, documentation (including new documentation on Tool Shed + `publishing <http://planemo.readthedocs.org/en/latest/publishing.html>`__), + and testing related improvements (test coverage has risen from 65% to over + 80% during this release cycle). + +--------------------- +0.7.0 (2015-04-13) +--------------------- + +* Implement `shed_create` command to create Tool Shed repositories from + ``.shed.yml`` files (thanks to E. Rasche). `Pull Request 101`_ +* Allow automatic creation of missing repositories during ``shed_upload`` + with the new ``--force_repository_creation`` flag (thanks to E. Rasche). + `Pull Request 102`_ +* Allow specifying files to exclude in ``.shed.yml`` when creating tar files + for ``shed_upload`` (thanks to Björn Grüning). `Pull Request 99`_ +* Resolve symbolic links when building Tool Shed tar files with + ``shed_upload`` (thanks to Dave Bouvier). `Pull Request 104`_ +* Add a `Contributor Code of Conduct + <https://planemo.readthedocs.org/en/latest/conduct.html>`__. + `Pull Request 113`_ +* Omit ``tool_test_output.json`` from Tool Shed tar file created with + ``shed_upload`` (thanks to Dave Bouvier). `Pull Request 111`_ +* Update required version of bioblend_ to ``0.5.3``. Fixed `Issue 88`_. +* Initial work on implementing tests cases for Tool Shed functionality. + 182fe57_ +* Fix incorrect link in HTML test report (thanks to Martin Čech). 4c71299_ +* Download Galaxy from the new, official Github repository. 7c69bf6_ +* Update travis_test to install stable planemo from PyPI_. 39fedd2_ +* Enable caching on ``--install_galaxy`` by default (disable with + ``--no_cache_galaxy``). d755fe7_ + +--------------------- +0.6.0 (2015-03-16) +--------------------- + +* Many enhancements to the tool building documentation - descriptions of macros, collections, simple and conditional parameters, etc... +* Fix ``tool_init`` to quote file names (thanks to Peter Cock). `Pull Request 98`_. +* Allow ignoring file patterns in ``.shed.yml`` (thanks to Björn Grüning). `Pull Request 99`_ +* Add ``--macros`` flag to ``tool_init`` command to generate a macro file as part of tool generation. ec6e30f_ +* Add linting of tag order for tool XML files. 4823c5e_ +* Add linting of ``stdio`` tags in tool XML files. 8207026_ +* More tests, much higher test coverage. 0bd4ff0_ + +--------------------- +0.5.0 (2015-02-22) +--------------------- + +* Implement ``--version`` option. `Issue 78`_ +* Implement ``--no_cleanup`` option for ``test`` and ``serve`` commands to + persist temp files. 2e41e0a_ +* Fix bug that left temp files undeleted. `Issue 80`_ +* More improvements to release process. fba3874_ + +--------------------- +0.4.2 (2015-02-21) +--------------------- + +* 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`_ + +--------------------- +0.4.1 (2015-02-16) +--------------------- + +* Fix README.rst so it renders properly on PyPI_. + +--------------------- +0.4.0 (2015-02-16) +--------------------- + +* 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. + +--------------------- +0.3.1 (2015-02-15) +--------------------- + +* Fixes to get PyPI_ workflow working properly. + +--------------------- +0.3.0 (2015-02-13) +--------------------- + +* 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_ + +--------------------- +0.2.0 (2015-01-13) +--------------------- + +* 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`_ + +--------------------- +0.1.0 (2014-12-16) +--------------------- + +* Moved repository URL to https://github.com/galaxyproject/planemo. +* Support for publishing to the Tool Shed. `Pull Request 6`_ +* Support for producing diffs (``shed_diff``) between local repositories and + the Tool Shed (based on scripts by Peter Cock). `Pull Request 33`_ +* Use tool's local test data when available - add option for configuring + ``test-data`` target. `Pull Request 1`_ +* Support for testing tool features dependent on cached data. 44de95c_ +* Support for generating XUnit tool test reports. 82e8b1f_ +* Prettier HTML reports for tool tests. 05cc9f4_ +* Implement ``share_test`` command for embedding test result links in pull + requests. `Pull Request 40`_ +* Fix for properly resolving links during Tool Shed publishing (thanks to Dave + Bouvier). `Pull Request 29`_ +* Fix for citation linter (thanks to Michael Crusoe for the bug report). af39061_ +* Fix tool scanning for tool files with fewer than 10 lines (thanks to Dan + Blankenberg). a2c13e4_ +* Automate more of Travis CI testing so the scripts added to tool repository + can be smaller. 20a8680_ +* Documentation fixes for Travis CI (thanks to Peter Cock). `Pull Request 22`_, + `Pull Request 23`_ +* Various documentation fixes (thanks to Martin Čech). 36f7cb1_, b9232e5_ +* Various smaller fixes for Docker support, tool linting, and documentation. + +--------------------- +0.0.1 (2014-10-04) +--------------------- + +* Initial work on the project - commands for testing, linting, serving Galaxy + tools - and more experimental features involving Docker and Homebrew. 7d07782_ + +.. github_links +.. _Pull Request 991: https://github.com/galaxyproject/planemo/pull/991 +.. _Pull Request 988: https://github.com/galaxyproject/planemo/pull/988 +.. _Pull Request 989: https://github.com/galaxyproject/planemo/pull/989 +.. _Pull Request 985: https://github.com/galaxyproject/planemo/pull/985 +.. _Pull Request 984: https://github.com/galaxyproject/planemo/pull/984 +.. _Pull Request 986: https://github.com/galaxyproject/planemo/pull/986 +.. _Pull Request 983: https://github.com/galaxyproject/planemo/pull/983 +.. _Pull Request 982: https://github.com/galaxyproject/planemo/pull/982 +.. _Pull Request 980: https://github.com/galaxyproject/planemo/pull/980 +.. _Pull Request 978: https://github.com/galaxyproject/planemo/pull/978 +.. _Pull Request 979: https://github.com/galaxyproject/planemo/pull/979 +.. _Pull Request 977: https://github.com/galaxyproject/planemo/pull/977 +.. _Pull Request 975: https://github.com/galaxyproject/planemo/pull/975 +.. _Pull Request 974: https://github.com/galaxyproject/planemo/pull/974 +.. _Pull Request 976: https://github.com/galaxyproject/planemo/pull/976 +.. _Pull Request 972: https://github.com/galaxyproject/planemo/pull/972 +.. _Pull Request 973: https://github.com/galaxyproject/planemo/pull/973 +.. _Pull Request 971: https://github.com/galaxyproject/planemo/pull/971 +.. _Pull Request 970: https://github.com/galaxyproject/planemo/pull/970 +.. _Pull Request 968: https://github.com/galaxyproject/planemo/pull/968 +.. _1ab8530: https://github.com/galaxyproject/planemo/commit/1ab8530 +.. _Pull Request 966: https://github.com/galaxyproject/planemo/pull/966 +.. _Pull Request 964: https://github.com/galaxyproject/planemo/pull/964 +.. _Pull Request 963: https://github.com/galaxyproject/planemo/pull/963 +.. _Pull Request 959: https://github.com/galaxyproject/planemo/pull/959 +.. _Pull Request 958: https://github.com/galaxyproject/planemo/pull/958 +.. _Pull Request 950: https://github.com/galaxyproject/planemo/pull/950 +.. _Pull Request 944: https://github.com/galaxyproject/planemo/pull/944 +.. _Pull Request 926: https://github.com/galaxyproject/planemo/pull/926 +.. _Pull Request 937: https://github.com/galaxyproject/planemo/pull/937 +.. _Pull Request 938: https://github.com/galaxyproject/planemo/pull/938 +.. _Pull Request 943: https://github.com/galaxyproject/planemo/pull/943 +.. _Pull Request 940: https://github.com/galaxyproject/planemo/pull/940 +.. _Pull Request 937: https://github.com/galaxyproject/planemo/pull/937 +.. _Pull Request 935: https://github.com/galaxyproject/planemo/pull/935 +.. _Pull Request 931: https://github.com/galaxyproject/planemo/pull/931 +.. _Pull Request 930: https://github.com/galaxyproject/planemo/pull/930 +.. _Pull Request 913: https://github.com/galaxyproject/planemo/pull/913 +.. _Pull Request 917: https://github.com/galaxyproject/planemo/pull/917 +.. _Pull Request 921: https://github.com/galaxyproject/planemo/pull/921 +.. _Pull Request 918: https://github.com/galaxyproject/planemo/pull/918 +.. _Pull Request 924: https://github.com/galaxyproject/planemo/pull/924 +.. _Pull Request 925: https://github.com/galaxyproject/planemo/pull/925 +.. _Pull Request 912: https://github.com/galaxyproject/planemo/pull/912 +.. _Pull Request 915: https://github.com/galaxyproject/planemo/pull/915 +.. _Pull Request 914: https://github.com/galaxyproject/planemo/pull/914 +.. _07dc6e0: https://github.com/galaxyproject/planemo/commit/07dc6e0 +.. _Pull Request 910: https://github.com/galaxyproject/planemo/pull/910 +.. _Pull Request 909: https://github.com/galaxyproject/planemo/pull/909 +.. _Pull Request 908: https://github.com/galaxyproject/planemo/pull/908 +.. _Pull Request 907: https://github.com/galaxyproject/planemo/pull/907 +.. _Pull Request 906: https://github.com/galaxyproject/planemo/pull/906 +.. _Pull Request 902: https://github.com/galaxyproject/planemo/pull/902 +.. _Pull Request 895: https://github.com/galaxyproject/planemo/pull/895 +.. _Issue 845: https://github.com/galaxyproject/planemo/issues/845 +.. _Issue 898: https://github.com/galaxyproject/planemo/issues/898 +.. _Pull Request 899: https://github.com/galaxyproject/planemo/pull/899 +.. _Pull Request 896: https://github.com/galaxyproject/planemo/pull/896 +.. _Pull Request 894: https://github.com/galaxyproject/planemo/pull/894 +.. _Pull Request 876: https://github.com/galaxyproject/planemo/pull/876 +.. _Pull Request 893: https://github.com/galaxyproject/planemo/pull/893 +.. _Pull Request 892: https://github.com/galaxyproject/planemo/pull/892 +.. _Pull Request 891: https://github.com/galaxyproject/planemo/pull/891 +.. _Pull Request 889: https://github.com/galaxyproject/planemo/pull/889 +.. _Pull Request 888: https://github.com/galaxyproject/planemo/pull/888 +.. _Pull Request 887: https://github.com/galaxyproject/planemo/pull/887 +.. _Pull Request 882: https://github.com/galaxyproject/planemo/pull/882 +.. _Pull Request 877: https://github.com/galaxyproject/planemo/pull/877 +.. _Pull Request 874: https://github.com/galaxyproject/planemo/pull/874 +.. _Pull Request 871: https://github.com/galaxyproject/planemo/pull/871 +.. _Pull Request 870: https://github.com/galaxyproject/planemo/pull/870 +.. _Pull Request 864: https://github.com/galaxyproject/planemo/pull/864 +.. _Pull Request 867: https://github.com/galaxyproject/planemo/pull/867 +.. _Pull Request 868: https://github.com/galaxyproject/planemo/pull/868 +.. _bad810a: https://github.com/galaxyproject/planemo/commit/bad810a +.. _Pull Request 851: https://github.com/galaxyproject/planemo/pull/851 +.. _Pull Request 856: https://github.com/galaxyproject/planemo/pull/856 +.. _Pull Request 860: https://github.com/galaxyproject/planemo/pull/860 +.. _Pull Request 866: https://github.com/galaxyproject/planemo/pull/866 +.. _Pull Request 861: https://github.com/galaxyproject/planemo/pull/861 +.. _324c776: https://github.com/galaxyproject/planemo/commit/324c776 +.. _72d2ca7: https://github.com/galaxyproject/planemo/commit/72d2ca7 +.. _b12b117: https://github.com/galaxyproject/planemo/commit/b12b117 +.. _016b923: https://github.com/galaxyproject/planemo/commit/016b923 +.. _2002b49: https://github.com/galaxyproject/planemo/commit/2002b49 +.. _Pull Request 843: https://github.com/galaxyproject/planemo/pull/843 +.. _Pull Request 842: https://github.com/galaxyproject/planemo/pull/842 +.. _Pull Request 841: https://github.com/galaxyproject/planemo/pull/841 +.. _Pull Request 847: https://github.com/galaxyproject/planemo/pull/847 +.. _Pull Request 848: https://github.com/galaxyproject/planemo/pull/848 +.. _Pull Request 849: https://github.com/galaxyproject/planemo/pull/849 +.. _Pull Request 850: https://github.com/galaxyproject/planemo/pull/850 +.. _Pull Request 836: https://github.com/galaxyproject/planemo/pull/836 +.. _Pull Request 833: https://github.com/galaxyproject/planemo/pull/833 +.. _Pull Request 837: https://github.com/galaxyproject/planemo/pull/837 +.. _Pull Request 840: https://github.com/galaxyproject/planemo/pull/840 +.. _Pull Request 838: https://github.com/galaxyproject/planemo/pull/838 +.. _Pull Request 834: https://github.com/galaxyproject/planemo/pull/834 +.. _Pull Request 835: https://github.com/galaxyproject/planemo/pull/835 +.. _347c622: https://github.com/galaxyproject/planemo/commit/347c622 +.. _Pull Request 832: https://github.com/galaxyproject/planemo/pull/832 +.. _Pull Request 831: https://github.com/galaxyproject/planemo/pull/831 +.. _Pull Request 830: https://github.com/galaxyproject/planemo/pull/830 +.. _Pull Request 829: https://github.com/galaxyproject/planemo/pull/829 +.. _Pull Request 828: https://github.com/galaxyproject/planemo/pull/828 +.. _Pull Request 826: https://github.com/galaxyproject/planemo/pull/826 +.. _Pull Request 827: https://github.com/galaxyproject/planemo/pull/827 +.. _Pull Request 825: https://github.com/galaxyproject/planemo/pull/825 +.. _Pull Request 820: https://github.com/galaxyproject/planemo/pull/820 +.. _Pull Request 823: https://github.com/galaxyproject/planemo/pull/823 +.. _Pull Request 822: https://github.com/galaxyproject/planemo/pull/822 +.. _a5c72e3: https://github.com/galaxyproject/planemo/commit/a5c72e3 +.. _Pull Request 818: https://github.com/galaxyproject/planemo/pull/818 +.. _Pull Request 816: https://github.com/galaxyproject/planemo/pull/816 +.. _Pull Request 817: https://github.com/galaxyproject/planemo/pull/817 +.. _Pull Request 795: https://github.com/galaxyproject/planemo/pull/795 +.. _Pull Request 799: https://github.com/galaxyproject/planemo/pull/799 +.. _Pull Request 800: https://github.com/galaxyproject/planemo/pull/800 +.. _Pull Request 781: https://github.com/galaxyproject/planemo/pull/781 +.. _Pull Request 801: https://github.com/galaxyproject/planemo/pull/801 +.. _Pull Request 802: https://github.com/galaxyproject/planemo/pull/802 +.. _Pull Request 803: https://github.com/galaxyproject/planemo/pull/803 +.. _Pull Request 805: https://github.com/galaxyproject/planemo/pull/805 +.. _Pull Request 806: https://github.com/galaxyproject/planemo/pull/806 +.. _Pull Request 809: https://github.com/galaxyproject/planemo/pull/809 +.. _Pull Request 810: https://github.com/galaxyproject/planemo/pull/810 +.. _Pull Request 787: https://github.com/galaxyproject/planemo/pull/787 +.. _Pull Request 792: https://github.com/galaxyproject/planemo/pull/792 +.. _dc443d6: https://github.com/galaxyproject/planemo/commit/dc443d6 +.. _8cfe9e9: https://github.com/galaxyproject/planemo/commit/8cfe9e9 +.. _41f7df1: https://github.com/galaxyproject/planemo/commit/41f7df1 +.. _Pull Request 790: https://github.com/galaxyproject/planemo/pull/790 +.. _Pull Request 776: https://github.com/galaxyproject/planemo/pull/776 +.. _Pull Request 774: https://github.com/galaxyproject/planemo/pull/774 +.. _Pull Request 773: https://github.com/galaxyproject/planemo/pull/773 +.. _Pull Request 771: https://github.com/galaxyproject/planemo/pull/771 +.. _Pull Request 770: https://github.com/galaxyproject/planemo/pull/770 +.. _Pull Request 769: https://github.com/galaxyproject/planemo/pull/769 +.. _Pull Request 768: https://github.com/galaxyproject/planemo/pull/768 +.. _Pull Request 764: https://github.com/galaxyproject/planemo/pull/764 +.. _Pull Request 761: https://github.com/galaxyproject/planemo/pull/761 +.. _Pull Request 759: https://github.com/galaxyproject/planemo/pull/759 +.. _Pull Request 756: https://github.com/galaxyproject/planemo/pull/756 +.. _Pull Request 753: https://github.com/galaxyproject/planemo/pull/753 +.. _Pull Request 747: https://github.com/galaxyproject/planemo/pull/747 +.. _Pull Request 745: https://github.com/galaxyproject/planemo/pull/745 +.. _Pull Request 743: https://github.com/galaxyproject/planemo/pull/743 +.. _Pull Request 739: https://github.com/galaxyproject/planemo/pull/739 +.. _Pull Request 738: https://github.com/galaxyproject/planemo/pull/738 +.. _Pull Request 725: https://github.com/galaxyproject/planemo/pull/725 +.. _Pull Request 727: https://github.com/galaxyproject/planemo/pull/727 +.. _Pull Request 729: https://github.com/galaxyproject/planemo/pull/729 +.. _Pull Request 730: https://github.com/galaxyproject/planemo/pull/730 +.. _Pull Request 731: https://github.com/galaxyproject/planemo/pull/731 +.. _Pull Request 733: https://github.com/galaxyproject/planemo/pull/733 +.. _Pull Request 732: https://github.com/galaxyproject/planemo/pull/732 +.. _Pull Request 704: https://github.com/galaxyproject/planemo/pull/704 +.. _Pull Request 709: https://github.com/galaxyproject/planemo/pull/709 +.. _Pull Request 715: https://github.com/galaxyproject/planemo/pull/715 +.. _Pull Request 716: https://github.com/galaxyproject/planemo/pull/716 +.. _Pull Request 720: https://github.com/galaxyproject/planemo/pull/720 +.. _Pull Request 723: https://github.com/galaxyproject/planemo/pull/723 +.. _8a608e0: https://github.com/galaxyproject/planemo/commit/8a608e0 +.. _ecc1bc2: https://github.com/galaxyproject/planemo/commit/ecc1bc2 +.. _Pull Request 702: https://github.com/galaxyproject/planemo/pull/702 +.. _Pull Request 701: https://github.com/galaxyproject/planemo/pull/701 +.. _Pull Request 699: https://github.com/galaxyproject/planemo/pull/699 +.. _91b6fa0: https://github.com/galaxyproject/planemo/commit/91b6fa0 +.. _904d77a: https://github.com/galaxyproject/planemo/commit/904d77a +.. _9636682: https://github.com/galaxyproject/planemo/commit/9636682 +.. _475104c: https://github.com/galaxyproject/planemo/commit/475104c +.. _Pull Request 684: https://github.com/galaxyproject/planemo/pull/684 +.. _Pull Request 687: https://github.com/galaxyproject/planemo/pull/687 +.. _Pull Request 688: https://github.com/galaxyproject/planemo/pull/688 +.. _Pull Request 689: https://github.com/galaxyproject/planemo/pull/689 +.. _Pull Request 690: https://github.com/galaxyproject/planemo/pull/690 +.. _Issue 494: https://github.com/galaxyproject/planemo/issues/494 +.. _Pull Request 665: https://github.com/galaxyproject/planemo/pull/665 +.. _Pull Request 675: https://github.com/galaxyproject/planemo/pull/675 +.. _Pull Request 680: https://github.com/galaxyproject/planemo/pull/680 +.. _Pull Request 682: https://github.com/galaxyproject/planemo/pull/682 +.. _Pull Request 683: https://github.com/galaxyproject/planemo/pull/683 +.. _Pull Request 662: https://github.com/galaxyproject/planemo/pull/662 +.. _Pull Request 665: https://github.com/galaxyproject/planemo/pull/665 +.. _Pull Request 664: https://github.com/galaxyproject/planemo/pull/664 +.. _84c4a73: https://github.com/galaxyproject/planemo/commit/84c4a73 +.. _32f41c9: https://github.com/galaxyproject/planemo/commit/32f41c9 +.. _3129216: https://github.com/galaxyproject/planemo/commit/3129216 +.. _b4ae44d: https://github.com/galaxyproject/planemo/commit/b4ae44d +.. _3c95b7b: https://github.com/galaxyproject/planemo/commit/3c95b7b +.. _06bcf19: https://github.com/galaxyproject/planemo/commit/06bcf19 +.. _525de8f: https://github.com/galaxyproject/planemo/commit/525de8f +.. _9867e56: https://github.com/galaxyproject/planemo/commit/9867e56 +.. _ce0dc4e: https://github.com/galaxyproject/planemo/commit/ce0dc4e +.. _4c0f100: https://github.com/galaxyproject/planemo/commit/4c0f100 +.. _04238d3: https://github.com/galaxyproject/planemo/commit/04238d3 +.. _ced5ce2: https://github.com/galaxyproject/planemo/commit/ced5ce2 +.. _9ab4a0d: https://github.com/galaxyproject/planemo/commit/9ab4a0d +.. _Pull Request 640: https://github.com/galaxyproject/planemo/pull/640 +.. _0a1abfe: https://github.com/galaxyproject/planemo/commit/0a1abfe +.. _Pull Request 649: https://github.com/galaxyproject/planemo/pull/649 +.. _Issue 620: https://github.com/galaxyproject/planemo/issues/620 +.. _Pull Request 643: https://github.com/galaxyproject/planemo/pull/643 +.. _Pull Request 642: https://github.com/galaxyproject/planemo/pull/642 +.. _Pull Request 641: https://github.com/galaxyproject/planemo/pull/641 +.. _Pull Request 639: https://github.com/galaxyproject/planemo/pull/639 +.. _Pull Request 635: https://github.com/galaxyproject/planemo/pull/635 +.. _Issue 633: https://github.com/galaxyproject/planemo/issues/633 +.. _Issue 260: https://github.com/galaxyproject/planemo/issues/260 +.. _Pull Request 638: https://github.com/galaxyproject/planemo/pull/638 +.. _6638caa: https://github.com/galaxyproject/planemo/commit/6638caa +.. _8faf661: https://github.com/galaxyproject/planemo/commit/8faf661 +.. _e343b67: https://github.com/galaxyproject/planemo/commit/e343b67 +.. _Pull Request 634: https://github.com/galaxyproject/planemo/pull/634 +.. _84ebc1f: https://github.com/galaxyproject/planemo/commit/84ebc1f +.. _03c9658: https://github.com/galaxyproject/planemo/commit/03c9658 +.. _08c067c: https://github.com/galaxyproject/planemo/commit/08c067c +.. _fca4183: https://github.com/galaxyproject/planemo/commit/fca4183 +.. _Issue 564: https://github.com/galaxyproject/planemo/issues/564 +.. _Pull Request 628: https://github.com/galaxyproject/planemo/pull/628 +.. _Issue 515: https://github.com/galaxyproject/planemo/issues/515 +.. _Pull Request 629: https://github.com/galaxyproject/planemo/pull/629 +.. _Pull Request 614: https://github.com/galaxyproject/planemo/pull/614 +.. _32acd68: https://github.com/galaxyproject/planemo/commit/32acd68 +.. _4595953: https://github.com/galaxyproject/planemo/commit/4595953 +.. _Pull Request 612: https://github.com/galaxyproject/planemo/pull/612 +.. _Issue 388: https://github.com/galaxyproject/planemo/issues/388 +.. _Pull Request 610: https://github.com/galaxyproject/planemo/pull/610 +.. _Pull Request 609: https://github.com/galaxyproject/planemo/pull/609 +.. _Pull Request 608: https://github.com/galaxyproject/planemo/pull/608 +.. _Pull Request 605: https://github.com/galaxyproject/planemo/pull/605 +.. _Pull Request 606: https://github.com/galaxyproject/planemo/pull/606 +.. _Pull Request 602: https://github.com/galaxyproject/planemo/pull/602 +.. _Pull Request 570: https://github.com/galaxyproject/planemo/pull/570 +.. _9228416: https://github.com/galaxyproject/planemo/commit/9228416 +.. _50d3c4a: https://github.com/galaxyproject/planemo/commit/50d3c4a +.. _Issue 578: https://github.com/galaxyproject/planemo/issues/578 +.. _Pull Request 591: https://github.com/galaxyproject/planemo/pull/591 +.. _Pull Request 590: https://github.com/galaxyproject/planemo/pull/590 +.. _f0da66f: https://github.com/galaxyproject/planemo/commit/f0da66f +.. _19b2ee9: https://github.com/galaxyproject/planemo/commit/19b2ee9 +.. _9da8387: https://github.com/galaxyproject/planemo/commit/9da8387 +.. _08cef54: https://github.com/galaxyproject/planemo/commit/08cef54 +.. _2e4e5fc: https://github.com/galaxyproject/planemo/commit/2e4e5fc +.. _2e4e5fc: https://github.com/galaxyproject/planemo/commit/2e4e5fc +.. _Issue 573: https://github.com/galaxyproject/planemo/issues/573 +.. _Pull Request 579: https://github.com/galaxyproject/planemo/pull/579 +.. _ccdd2d5: https://github.com/galaxyproject/planemo/commit/ccdd2d5 +.. _e925ba1: https://github.com/galaxyproject/planemo/commit/e925ba1 +.. _ea5324f: https://github.com/galaxyproject/planemo/commit/ea5324f +.. _ca88b0c: https://github.com/galaxyproject/planemo/commit/ca88b0c +.. _b6d8294: https://github.com/galaxyproject/planemo/commit/b6d8294 +.. _6a6f164: https://github.com/galaxyproject/planemo/commit/6a6f164 +.. _d6da3a8: https://github.com/galaxyproject/planemo/commit/d6da3a8 +.. _1ef05d2: https://github.com/galaxyproject/planemo/commit/1ef05d2 +.. _7cca2e4: https://github.com/galaxyproject/planemo/commit/7cca2e4 +.. _34538de: https://github.com/galaxyproject/planemo/commit/34538de +.. _6f91719: https://github.com/galaxyproject/planemo/commit/6f91719 +.. _Pull Request 566: https://github.com/galaxyproject/planemo/pull/566 +.. _Pull Request 559: https://github.com/galaxyproject/planemo/pull/559 +.. _Pull Request 561: https://github.com/galaxyproject/planemo/pull/561 +.. _Pull Request 565: https://github.com/galaxyproject/planemo/pull/565 +.. _Pull Request 555: https://github.com/galaxyproject/planemo/pull/555 +.. _a8e797b: https://github.com/galaxyproject/planemo/commit/a8e797b +.. _6c03de8: https://github.com/galaxyproject/planemo/commit/6c03de8 +.. _ef4b9f4: https://github.com/galaxyproject/planemo/commit/ef4b9f4 +.. _f7b6c7e: https://github.com/galaxyproject/planemo/commit/f7b6c7e +.. _07d94bd: https://github.com/galaxyproject/planemo/commit/07d94bd +.. _ca19910: https://github.com/galaxyproject/planemo/commit/ca19910 +.. _24008ab: https://github.com/galaxyproject/planemo/commit/24008ab +.. _ce44e87: https://github.com/galaxyproject/planemo/commit/ce44e87 +.. _Pull Request 550: https://github.com/galaxyproject/planemo/pull/550 +.. _c2204b3: https://github.com/galaxyproject/planemo/commit/c2204b3 +.. _c262b6d: https://github.com/galaxyproject/planemo/commit/c262b6d +.. _Pull Request 539: https://github.com/galaxyproject/planemo/pull/539 +.. _Pull Request 541: https://github.com/galaxyproject/planemo/pull/541 +.. _Pull Request 540: https://github.com/galaxyproject/planemo/pull/540 +.. _Pull Request 545: https://github.com/galaxyproject/planemo/pull/545 +.. _Pull Request 546: https://github.com/galaxyproject/planemo/pull/546 +.. _3ceaa40: https://github.com/galaxyproject/planemo/commit/3ceaa40 +.. _057f4f0: https://github.com/galaxyproject/planemo/commit/057f4f0 +.. _9fdf490: https://github.com/galaxyproject/planemo/commit/9fdf490 +.. _8c088c6: https://github.com/galaxyproject/planemo/commit/8c088c6 +.. _e2398fb: https://github.com/galaxyproject/planemo/commit/e2398fb +.. _Pull Request 526: https://github.com/galaxyproject/planemo/pull/526 +.. _Pull Request 528: https://github.com/galaxyproject/planemo/pull/528 +.. _Pull Request 525: https://github.com/galaxyproject/planemo/pull/525 +.. _a811e65: https://github.com/galaxyproject/planemo/commit/a811e65 +.. _Pull Request 521: https://github.com/galaxyproject/planemo/pull/521 +.. _a066afb: https://github.com/galaxyproject/planemo/commit/a066afb +.. _Pull Request 512: https://github.com/galaxyproject/planemo/pull/512 +.. _08bb354: https://github.com/galaxyproject/planemo/commit/08bb354 +.. _Pull Request 513: https://github.com/galaxyproject/planemo/pull/513 +.. _Pull Request 510: https://github.com/galaxyproject/planemo/pull/510 +.. _e890ab5: https://github.com/galaxyproject/planemo/commit/e890ab5 +.. _Pull Request 507: https://github.com/galaxyproject/planemo/pull/507 +.. _d53bcd6: https://github.com/galaxyproject/planemo/commit/d53bcd6 +.. _725b232: https://github.com/galaxyproject/planemo/commit/725b232 +.. _Pull Request 498: https://github.com/galaxyproject/planemo/pull/498 +.. _01584c5: https://github.com/galaxyproject/planemo/commit/01584c5 +.. _01f2af9: https://github.com/galaxyproject/planemo/commit/01f2af9 +.. _0298510: https://github.com/galaxyproject/planemo/commit/0298510 +.. _02a08a0: https://github.com/galaxyproject/planemo/commit/02a08a0 +.. _05cc9f4: 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+.. _1a85493: https://github.com/galaxyproject/planemo/commit/1a85493 +.. _1c6cfbb: https://github.com/galaxyproject/planemo/commit/1c6cfbb +.. _1c7ee5b: https://github.com/galaxyproject/planemo/commit/1c7ee5b +.. _1cd0e2d: https://github.com/galaxyproject/planemo/commit/1cd0e2d +.. _1e3668a: https://github.com/galaxyproject/planemo/commit/1e3668a +.. _2052db0: https://github.com/galaxyproject/planemo/commit/2052db0 +.. _20a8680: https://github.com/galaxyproject/planemo/commit/20a86807cb7ea87db2dbc0197ae08a40df3ab2bc +.. _21bb463: https://github.com/galaxyproject/planemo/commit/21bb463ad6c321bcb669603049a5e89a69766ad9 +.. _25ef0d5: https://github.com/galaxyproject/planemo/commit/25ef0d5 +.. _26e378e: https://github.com/galaxyproject/planemo/commit/26e378e +.. _26e3cdb: https://github.com/galaxyproject/planemo/commit/26e3cdb +.. _2a7c792: https://github.com/galaxyproject/planemo/commit/2a7c792 +.. _2ae2b49: https://github.com/galaxyproject/planemo/commit/2ae2b49 +.. _2e41e0a: 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_Issue 167: https://github.com/galaxyproject/planemo/issues/167 +.. _Issue 168: https://github.com/galaxyproject/planemo/issues/168 +.. _Issue 169: https://github.com/galaxyproject/planemo/issues/169 +.. _Issue 170: https://github.com/galaxyproject/planemo/issues/170 +.. _Issue 176: https://github.com/galaxyproject/planemo/issues/176 +.. _Issue 179: https://github.com/galaxyproject/planemo/issues/179 +.. _Issue 180: https://github.com/galaxyproject/planemo/issues/180 +.. _Issue 181: https://github.com/galaxyproject/planemo/issues/181 +.. _Issue 184: https://github.com/galaxyproject/planemo/issues/184 +.. _Issue 186: https://github.com/galaxyproject/planemo/issues/186 +.. _Issue 188: https://github.com/galaxyproject/planemo/issues/188 +.. _Issue 189: https://github.com/galaxyproject/planemo/issues/189 +.. _Issue 192: https://github.com/galaxyproject/planemo/issues/192 +.. _Issue 205: https://github.com/galaxyproject/planemo/issues/205 +.. _Issue 206: https://github.com/galaxyproject/planemo/issues/206 +.. _Issue 209: https://github.com/galaxyproject/planemo/issues/209 +.. _Issue 211: https://github.com/galaxyproject/planemo/issues/211 +.. _Issue 217: https://github.com/galaxyproject/planemo/issues/217 +.. _Issue 223: https://github.com/galaxyproject/planemo/issues/223 +.. _Issue 231: https://github.com/galaxyproject/planemo/issues/231 +.. _Issue 233: https://github.com/galaxyproject/planemo/issues/233 +.. _Issue 240: https://github.com/galaxyproject/planemo/issues/240 +.. _Issue 243: https://github.com/galaxyproject/planemo/issues/243 +.. _Issue 245: https://github.com/galaxyproject/planemo/issues/245 +.. _Issue 246: https://github.com/galaxyproject/planemo/issues/246 +.. _Issue 272: https://github.com/galaxyproject/planemo/issues/272 +.. _Issue 303: https://github.com/galaxyproject/planemo/issues/303 +.. _Issue 313: https://github.com/galaxyproject/planemo/issues/313 +.. _Issue 329: https://github.com/galaxyproject/planemo/issues/329 +.. _Issue 333: https://github.com/galaxyproject/planemo/issues/333 +.. _Issue 361: https://github.com/galaxyproject/planemo/issues/361 +.. _Issue 362: https://github.com/galaxyproject/planemo/issues/362 +.. _Issue 373: https://github.com/galaxyproject/planemo/issues/373 +.. _Issue 391: https://github.com/galaxyproject/planemo/issues/391 +.. _Issue 416: https://github.com/galaxyproject/planemo/issues/416 +.. _Issue 420: https://github.com/galaxyproject/planemo/issues/420 +.. _Issue 475: https://github.com/galaxyproject/planemo/issues/475 +.. _Issue 61: https://github.com/galaxyproject/planemo/issues/61 +.. _Issue 70: https://github.com/galaxyproject/planemo/issues/70 +.. _Issue 78: https://github.com/galaxyproject/planemo/issues/78 +.. _Issue 80: https://github.com/galaxyproject/planemo/issues/80 +.. _Issue 83: https://github.com/galaxyproject/planemo/issues/83 +.. _Issue 88: https://github.com/galaxyproject/planemo/issues/88 +.. _Issue 89: https://github.com/galaxyproject/planemo/issues/#89 +.. _Issue 91: https://github.com/galaxyproject/planemo/issues/#91 +.. _Pull Request 101: https://github.com/galaxyproject/planemo/pull/101 +.. _Pull Request 102: https://github.com/galaxyproject/planemo/pull/102 +.. _Pull Request 104: https://github.com/galaxyproject/planemo/pull/104 +.. _Pull Request 111: https://github.com/galaxyproject/planemo/pull/111 +.. _Pull Request 113: https://github.com/galaxyproject/planemo/pull/113 +.. _Pull Request 129: https://github.com/galaxyproject/planemo/pull/129 +.. _Pull Request 130: https://github.com/galaxyproject/planemo/pull/130 +.. _Pull Request 143: https://github.com/galaxyproject/planemo/pull/143 +.. _Pull Request 151: https://github.com/galaxyproject/planemo/pull/151 +.. _Pull Request 155: https://github.com/galaxyproject/planemo/pull/155 +.. _Pull Request 164: https://github.com/galaxyproject/planemo/pull/164 +.. _Pull Request 171: https://github.com/galaxyproject/planemo/pull/171 +.. _Pull Request 173: https://github.com/galaxyproject/planemo/pull/173 +.. _Pull Request 175: https://github.com/galaxyproject/planemo/pull/175 +.. _Pull Request 185: https://github.com/galaxyproject/planemo/pull/185 +.. _Pull Request 186: https://github.com/galaxyproject/planemo/pull/186 +.. _Pull Request 187: https://github.com/galaxyproject/planemo/pull/187 +.. _Pull Request 190: https://github.com/galaxyproject/planemo/pull/190 +.. _Pull Request 196: https://github.com/galaxyproject/planemo/pull/196 +.. _Pull Request 1: https://github.com/galaxyproject/planemo/pull/1 +.. _Pull Request 200: https://github.com/galaxyproject/planemo/pull/200 +.. _Pull Request 203: https://github.com/galaxyproject/planemo/pull/203 +.. _Pull Request 206: https://github.com/galaxyproject/planemo/pull/206 +.. _Pull Request 207: https://github.com/galaxyproject/planemo/pull/207 +.. _Pull Request 208: https://github.com/galaxyproject/planemo/pull/208 +.. _Pull Request 210: https://github.com/galaxyproject/planemo/pull/210 +.. _Pull Request 213: https://github.com/galaxyproject/planemo/pull/213 +.. _Pull Request 215: https://github.com/galaxyproject/planemo/pull/215 +.. _Pull Request 216: https://github.com/galaxyproject/planemo/pull/216 +.. _Pull Request 22: https://github.com/galaxyproject/planemo/pull/22 +.. _Pull Request 230: https://github.com/galaxyproject/planemo/pull/230 +.. _Pull Request 235: https://github.com/galaxyproject/planemo/pull/235 +.. _Pull Request 23: https://github.com/galaxyproject/planemo/pull/23 +.. _Pull Request 251: https://github.com/galaxyproject/planemo/pull/251 +.. _Pull Request 253: https://github.com/galaxyproject/planemo/pull/253 +.. _Pull Request 254: https://github.com/galaxyproject/planemo/pull/254 +.. _Pull Request 255: https://github.com/galaxyproject/planemo/pull/255 +.. _Pull Request 256: https://github.com/galaxyproject/planemo/pull/256 +.. _Pull Request 277: https://github.com/galaxyproject/planemo/pull/277 +.. _Pull Request 278: https://github.com/galaxyproject/planemo/pull/278 +.. _Pull Request 284: https://github.com/galaxyproject/planemo/pull/284 +.. _Pull Request 285: https://github.com/galaxyproject/planemo/pull/285 +.. _Pull Request 287: https://github.com/galaxyproject/planemo/pull/287 +.. _Pull Request 292: https://github.com/galaxyproject/planemo/pull/292 +.. _Pull Request 297: https://github.com/galaxyproject/planemo/pull/297 +.. _Pull Request 29: https://github.com/galaxyproject/planemo/pull/29 +.. _Pull Request 301: https://github.com/galaxyproject/planemo/pull/301 +.. _Pull Request 304: https://github.com/galaxyproject/planemo/pull/304 +.. _Pull Request 305: https://github.com/galaxyproject/planemo/pull/305 +.. _Pull Request 307: https://github.com/galaxyproject/planemo/pull/307 +.. _Pull Request 309: https://github.com/galaxyproject/planemo/pull/309 +.. _Pull Request 310: https://github.com/galaxyproject/planemo/pull/310 +.. _Pull Request 311: https://github.com/galaxyproject/planemo/pull/311 +.. _Pull Request 312: https://github.com/galaxyproject/planemo/pull/312 +.. _Pull Request 314: https://github.com/galaxyproject/planemo/pull/314 +.. _Pull Request 316: https://github.com/galaxyproject/planemo/pull/316 +.. _Pull Request 322: https://github.com/galaxyproject/planemo/pull/322 +.. _Pull Request 327: https://github.com/galaxyproject/planemo/pull/327 +.. _Pull Request 330: https://github.com/galaxyproject/planemo/pull/330 +.. _Pull Request 333: https://github.com/galaxyproject/planemo/pull/333 +.. _Pull Request 334: https://github.com/galaxyproject/planemo/pull/334 +.. _Pull Request 335: https://github.com/galaxyproject/planemo/pull/335 +.. _Pull Request 339: https://github.com/galaxyproject/planemo/pull/339 +.. _Pull Request 33: https://github.com/galaxyproject/planemo/pull/33 +.. _Pull Request 343: https://github.com/galaxyproject/planemo/pull/343 +.. _Pull Request 344: https://github.com/galaxyproject/planemo/pull/344 +.. _Pull Request 345: https://github.com/galaxyproject/planemo/pull/345 +.. _Pull Request 350: https://github.com/galaxyproject/planemo/pull/350 +.. _Pull Request 351: https://github.com/galaxyproject/planemo/pull/351 +.. _Pull Request 356: https://github.com/galaxyproject/planemo/pull/356 +.. _Pull Request 375: https://github.com/galaxyproject/planemo/pull/375 +.. _Pull Request 390: https://github.com/galaxyproject/planemo/pull/390 +.. _Pull Request 394: https://github.com/galaxyproject/planemo/pull/394 +.. _Pull Request 398: https://github.com/galaxyproject/planemo/pull/398 +.. _Pull Request 403: https://github.com/galaxyproject/planemo/pull/403 +.. _Pull Request 40: https://github.com/galaxyproject/planemo/pull/40 +.. _Pull Request 425: https://github.com/galaxyproject/planemo/pull/425 +.. _Pull Request 426: https://github.com/galaxyproject/planemo/pull/426 +.. _Pull Request 428: https://github.com/galaxyproject/planemo/pull/428 +.. _Pull Request 429: https://github.com/galaxyproject/planemo/pull/429 +.. _Pull Request 454: https://github.com/galaxyproject/planemo/pull/454 +.. _Pull Request 472: https://github.com/galaxyproject/planemo/pull/472 +.. _Pull Request 479: https://github.com/galaxyproject/planemo/pull/479 +.. _Pull Request 480: https://github.com/galaxyproject/planemo/pull/480 +.. _Pull Request 484: https://github.com/galaxyproject/planemo/pull/484 +.. _Pull Request 488: https://github.com/galaxyproject/planemo/pull/488 +.. _Pull Request 491: https://github.com/galaxyproject/planemo/pull/491 +.. _Pull Request 51: https://github.com/galaxyproject/planemo/pull/51 +.. _Pull Request 56: https://github.com/galaxyproject/planemo/pull/56 +.. _Pull Request 63: https://github.com/galaxyproject/planemo/pull/63 +.. _Pull Request 68: https://github.com/galaxyproject/planemo/pull/68 +.. _Pull Request 6: https://github.com/galaxyproject/planemo/pull/6 +.. _Pull Request 98: 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