Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/planemo-0.70.0.dist-info/METADATA @ 5:9b1c78e6ba9c draft default tip
"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
| author | shellac |
|---|---|
| date | Mon, 01 Jun 2020 08:59:25 -0400 |
| parents | 79f47841a781 |
| children |
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--- a/env/lib/python3.7/site-packages/planemo-0.70.0.dist-info/METADATA Thu May 14 16:47:39 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2486 +0,0 @@ -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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_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: 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