Mercurial > repos > bcclaywell > argo_navis
diff venv/lib/python2.7/site-packages/planemo-0.16.0.dist-info/METADATA @ 0:d67268158946 draft
planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
| author | bcclaywell |
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| date | Mon, 12 Oct 2015 17:43:33 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/venv/lib/python2.7/site-packages/planemo-0.16.0.dist-info/METADATA Mon Oct 12 17:43:33 2015 -0400 @@ -0,0 +1,917 @@ +Metadata-Version: 2.0 +Name: planemo +Version: 0.16.0 +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 :: 2.6 +Classifier: Programming Language :: Python :: 2.7 +Requires-Dist: Click +Requires-Dist: six +Requires-Dist: pyyaml +Requires-Dist: jinja2 +Requires-Dist: docutils +Requires-Dist: PyGithub +Requires-Dist: bioblend +Requires-Dist: glob2 + +.. 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 + +.. image:: https://readthedocs.org/projects/pip/badge/?version=latest + :target: https://planemo.readthedocs.org + +.. image:: https://badge.fury.io/py/planemo.svg + :target: https://pypi.python.org/pypi/planemo/ + +.. image:: https://travis-ci.org/galaxyproject/planemo.png?branch=master + :target: https://travis-ci.org/galaxyproject/planemo + +.. image:: https://coveralls.io/repos/galaxyproject/planemo/badge.svg?branch=master + :target: https://coveralls.io/r/galaxyproject/planemo?branch=master + + +Command-line utilities to assist in building and publishing Galaxy_ tools. + +* Free software: Academic Free License version 3.0 +* Documentation: https://planemo.readthedocs.org. +* Code: https://github.com/galaxyproject/planemo + +Quick Start +----------- + +This quick start demonstrates using ``planemo`` commands to help +develop Galaxy tools. Planemo can quickly be installed via +Homebrew_ or as a more traditional Python project. + +To install using Homebrew_ or linuxbrew_: + +:: + + brew tap galaxyproject/tap + brew install planemo + +For a more traditional Python installation simply setup a virtualenv +for ``planemo`` (this example creates a new one in ``.venv``) and then +install with ``pip``. + +:: + + % virtualenv .venv; . .venv/bin/activate + % pip install planemo + +Planemo is also available a `virtual appliance +<https://planemo.readthedocs.org/en/latest/appliance.html>`_ for Docker_ or Vagrant_ (bundled +with a preconfigured Galaxy server optimized for tool development). + +This quick start will assume you will have a directory with one or more +tool XML files. If none is available, one can be quickly create for +demonstrating ``planemo`` as follows ``mkdir mytools; cd mytools; planemo +project_init --template=demo``. + +Planemo can check tools containing XML 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 other tool files or a directory of tool files. :: + + % planemo l randomlines.xml + +The ``lint`` command takes in a additional options related to +reporting levels, exit code, etc.... These options are descirbed here +or (like all available commands) be accessed by passing it ``--help``.:: + + % planemo l --help + Usage: planemo lint [OPTIONS] TOOL_PATH + ... + +Once tools are syntically 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 directory of tools.:: + + % planemo test --galaxy_root=../galaxy-central randomlines.xml + +If no ``--galaxy_root`` is defined, ``planemo`` will check for a default in +`~/.planemo.yml +<http://planemo.readthedocs.org/en/latest/configuration.html>`_) and finally +search the tool's parent directories for a Galaxy root directory (developing +tools under Galaxy ``tools`` directory is a common development workflow). +Planemo can also download and configure a disposable Galaxy instance just for +testing by passing it ``-install_galaxy`` instead of a Galaxy root.:: + + % planemo t --install_galaxy + +**Warning**: The features of Planemo that require a ``--galaxy_root`` will +only work with Galaxy releases from 2015. + +Planemo will create a HTML an output report in the current directory named +``tool_test_output.html`` (override with ``--test_output``). `Here <http://galaxyproject.github.io/planemo/tool_test_viewer.html?test_data_url=https://gist.githubusercontent.com/jmchilton/9d4351c9545d34209904/raw/9ed285d3cf98e435fc4a743320363275949ad63c/index>`_ is an +example 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``. + + +Experimental Features +--------------------- + +Planemo can also be used to explore some more experimental features related to +Galaxy tooling - including support for `Travis CI`_, Docker_, Homebrew_. + +----------- +Tool Shed +----------- + +For information on using Planemo to publish artifacts to the Galaxy Tool Shed, +check out the `Publishing to the Tool Shed`_ documentation on reathedocs.org. + +----------- +TravisCI +----------- + +When tools are ready to be published to GitHub_, it may be valuable to setup +contineous integration to test changes committed and new pull requests. +`Travis CI`_ is a service providing free testing and deep integration with +GitHub_. + +The ``travis_init`` `command +<http://planemo.readthedocs.org/en/latest/commands.html#travis_init- +command>`__ will bootstrap a project with files to ease contineous integration +testing of tools using a Planemo driven approach inspired by this great `blog +post <http://bit.ly/gxtravisci>`_ by `Peter Cock +<https://github.com/peterjc>`_. + +:: + + % planemo travis_init . + % # setup Ubuntu 12.04 w/tool dependencies + % vim .travis/setup_custom_dependencies.bash + % git add .travis.yml .travis + % git commit -m "Add Travis CI testing infrastructure for tools." + % git push # and register repository @ http://travis-ci.org/ + +In this example the file ``.travis/setup_custom_dependencies.bash`` should +install the dependencies required to test your files on to the Travis user's +``PATH``. + +This testing approach may only make sense for smaller repositories with a +handful of tools. For larger repositories, such as `tools-devteam`_ or +`tools-iuc`_ simply linting tool and tool shed artifacts may be more feasible. +Check out the ``.travis.yml`` file used by the IUC as `example +<https://github.com/galaxyproject/tools-iuc/blob/master/.travis.yml>`__. + +----------- +Docker +----------- + +Galaxy has `experimental support +<https://wiki.galaxyproject.org/Admin/Tools/Docker>`_ for running jobs in +Docker_ containers. Planemo contains tools to assist in development of Docker +images for Galaxy tools. + +A shell can be launched to explore the Docker enviornment referenced by tools +that are annotated with publically registered Docker images.:: + + % $(planemo docker_shell bowtie2.xml) + +For Docker containers still in development - a Dockerfile can be associated +with a tool by sticking it in the tool's directory. Planemo can then build +and tag a Docker image for this tool and launch a shell into it using the +following commands.:: + + % planemo docker_build bowtie2.xml # asssumes Dockerfile in same dir + % $(planemo docker_shell --from_tag bowtie2.xml) + +For more details see the documentation for the `docker_build +<http://planemo.readthedocs.org/en/latest/commands.html#docker_build-command>`__ +and `docker_shell +<http://planemo.readthedocs.org/en/latest/commands.html#docker_shell-command>`__ +commands. + +----------- +Brew +----------- + +The Galaxy development team is exploring different options for integrating +Homebrew_ and linuxbrew_ with Galaxy. One angle is resolving the tool requirements +using ``brew``. An experimental approach for versioning of brew recipes will be +used. See full discussion on the homebrew-science issues page here - +https://github.com/Homebrew/homebrew-science/issues/1191. Information on the +implementation can be found https://github.com/jmchilton/platform-brew until a +more permanent project home is setup. + +:: + + % planemo brew_init # install linuxbrew (only need if not already installed) + % planemo brew # install dependencies for all tools in directory. + % planemo brew bowtie2.xml # install dependencies for one tool + % which bowtie2 + bowtie2 not found + % . <(planemo brew_env --shell bowtie2.xml) # shell w/brew deps resolved + (bowtie2) % which bowtie2 + /home/john/.linuxbrew/Cellar/bowtie2/2.1.0/bin/bowtie2 + (bowtie2) % exit + % . <(planemo brew_env bowtie2.xml) # or just source deps in cur env + % which bowtie2 + /home/john/.linuxbrew/Cellar/bowtie2/2.1.0/bin/bowtie2 + +For more information see the documentation for the `brew +<http://planemo.readthedocs.org/en/latest/commands.html#brew-command>`__ +and `brew_env +<http://planemo.readthedocs.org/en/latest/commands.html#brew_env-command>`__ commands. + +.. _Galaxy: http://galaxyproject.org/ +.. _GitHub: https://github.com/ +.. _Docker: https://www.docker.com/ +.. _Homebrew: http://brew.sh/ +.. _linuxbrew: https://github.com/Homebrew/linuxbrew +.. _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 +.. _Publishing to the Tool Shed: http://planemo.readthedocs.org/en/latest/publishing.html + + + + +History +------- + +.. to_doc + +--------------------- +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 @erasche. + `Pull Request 304`_ +* XUnit style reporting for ``shed_diff`` command - thanks to + @erasche. `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 Eric 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 Eric Rasche). `Pull Request 101`_ +* Allow automatic creation of missing repositories during ``shed_upload`` + with the new ``--force_repository_creation`` flag (thanks to Eric 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 + <http://bioinformatics.oxfordjournals.org/content/early/2012/09/27/bioinformatics.bts573.full.pdf>`_. 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 Eric Rasche). `Pull Request 68`_ +* Fix diff formatting in test reports (thanks to Eric Rasche). + `Pull Request 63`_ +* Grab updated test database to speed up testing (thanks to approach from + Eric 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). 36f7cb11_, b9232e55_ +* 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 +.. _f798c7e: https://github.com/galaxyproject/planemo/commit/f798c7e +.. _Issue 303: https://github.com/galaxyproject/planemo/issues/303 +.. _Pull Request 310: https://github.com/galaxyproject/planemo/pull/310 +.. _Pull Request 314: https://github.com/galaxyproject/planemo/pull/314 +.. _dad2d9d: https://github.com/galaxyproject/planemo/commit/dad2d9d +.. _Pull Request 312: https://github.com/galaxyproject/planemo/pull/312 +.. _Pull Request 311: https://github.com/galaxyproject/planemo/pull/311 +.. _Pull Request 309: https://github.com/galaxyproject/planemo/pull/309 +.. _Pull Request 307: https://github.com/galaxyproject/planemo/pull/307 +.. _Pull Request 304: https://github.com/galaxyproject/planemo/pull/304 +.. _Pull Request 305: https://github.com/galaxyproject/planemo/pull/305 +.. _Pull Request 301: https://github.com/galaxyproject/planemo/pull/301 +.. _Pull Request 297: https://github.com/galaxyproject/planemo/pull/297 +.. _Pull Request 287: https://github.com/galaxyproject/planemo/pull/287 +.. _Pull Request 285: https://github.com/galaxyproject/planemo/pull/285 +.. _Pull Request 284: https://github.com/galaxyproject/planemo/pull/284 +.. _Pull Request 292: https://github.com/galaxyproject/planemo/pull/292 +.. _cb5b906: https://github.com/galaxyproject/planemo/commit/cb5b906 +.. _Pull Request 251: https://github.com/galaxyproject/planemo/pull/251 +.. _Pull Request 255: https://github.com/galaxyproject/planemo/pull/255 +.. _Pull Request 254: https://github.com/galaxyproject/planemo/pull/254 +.. _Pull Request 253: https://github.com/galaxyproject/planemo/pull/253 +.. _Pull Request 256: https://github.com/galaxyproject/planemo/pull/256 +.. _Issue 272: https://github.com/galaxyproject/planemo/issues/272 +.. _Pull Request 277: https://github.com/galaxyproject/planemo/pull/277 +.. _Pull Request 278: https://github.com/galaxyproject/planemo/pull/278 +.. _Issue 243: https://github.com/galaxyproject/planemo/issues/243 +.. _Issue 245: https://github.com/galaxyproject/planemo/issues/245 +.. _aad1eed: https://github.com/galaxyproject/planemo/commit/aad1eed +.. _f0610d7: https://github.com/galaxyproject/planemo/commit/f0610d7 +.. _334f2d4: https://github.com/galaxyproject/planemo/commit/334f2d4 +.. _Pull Request 230: https://github.com/galaxyproject/planemo/pull/230 +.. _Pull Request 235: https://github.com/galaxyproject/planemo/pull/235 +.. _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 +.. _f3cafaa: https://github.com/galaxyproject/planemo/commit/f3cafaa +.. _6b4e7a6: https://github.com/galaxyproject/planemo/commit/6b4e7a6 +.. _Issue 176: https://github.com/galaxyproject/planemo/issues/176 +.. _Pull Request 216: https://github.com/galaxyproject/planemo/pull/216 +.. _Pull Request 213: https://github.com/galaxyproject/planemo/pull/213 +.. _Issue 150: https://github.com/galaxyproject/planemo/issues/150 +.. _37dcc07: https://github.com/galaxyproject/planemo/commit/37dcc07 +.. _30a9c3f: https://github.com/galaxyproject/planemo/commit/30a9c3f +.. _b53006d: https://github.com/galaxyproject/planemo/commit/b53006d +.. _Pull Request 203: https://github.com/galaxyproject/planemo/pull/203 +.. _Pull Request 200: https://github.com/galaxyproject/planemo/pull/200 +.. _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 215: https://github.com/galaxyproject/planemo/pull/215 +.. _Pull Request 216: https://github.com/galaxyproject/planemo/pull/216 +.. _Issue 217: https://github.com/galaxyproject/planemo/issues/217 +.. _Issue 211: https://github.com/galaxyproject/planemo/issues/211 +.. _cc8abb6: https://github.com/galaxyproject/planemo/commit/cc8abb6 +.. _Issue 209: https://github.com/galaxyproject/planemo/issues/209 +.. _Issue 206: https://github.com/galaxyproject/planemo/issues/206 +.. _Issue 205: https://github.com/galaxyproject/planemo/issues/205 +.. _Pull Request 207: https://github.com/galaxyproject/planemo/pull/207 +.. _1e3668a: https://github.com/galaxyproject/planemo/commit/1e3668a +.. _Issue 180: https://github.com/galaxyproject/planemo/issues/180 +.. _Pull Request 186: https://github.com/galaxyproject/planemo/pull/186 +.. _Pull Request 185: https://github.com/galaxyproject/planemo/pull/185 +.. _6bcf699: https://github.com/galaxyproject/planemo/commit/6bcf699 +.. _Issue 186: https://github.com/galaxyproject/planemo/issues/186 +.. _Issue 188: https://github.com/galaxyproject/planemo/issues/188 +.. _Pull Request 187: https://github.com/galaxyproject/planemo/pull/187 +.. _Issue 192: https://github.com/galaxyproject/planemo/issues/192 +.. _Issue 189: https://github.com/galaxyproject/planemo/issues/189 +.. _Pull Request 190: https://github.com/galaxyproject/planemo/pull/190 +.. _Pull Request 196: https://github.com/galaxyproject/planemo/pull/196 +.. _fe7ad46: https://github.com/galaxyproject/planemo/commit/fe7ad46 +.. _8117e03: https://github.com/galaxyproject/planemo/commit/8117e03 +.. _8117e03: https://github.com/galaxyproject/planemo/commit/8117e03 +.. _Issue 156: https://github.com/galaxyproject/planemo/issues/156 +.. _Issue 179: https://github.com/galaxyproject/planemo/issues/179 +.. _Issue 181: https://github.com/galaxyproject/planemo/issues/181 +.. _Issue 114: https://github.com/galaxyproject/planemo/issues/114 +.. _Pull Request 173: https://github.com/galaxyproject/planemo/pull/173 +.. _Issue 108: https://github.com/galaxyproject/planemo/issues/108 +.. _15804be: https://github.com/galaxyproject/planemo/commit/15804be +.. _Issue 158: https://github.com/galaxyproject/planemo/issues/158 +.. _Pull Request 171: https://github.com/galaxyproject/planemo/pull/171 +.. _1cd0e2d: https://github.com/galaxyproject/planemo/commit/1cd0e2d +.. _40a1f57: https://github.com/galaxyproject/planemo/commit/40a1f57 +.. _Pull Request 175: https://github.com/galaxyproject/planemo/pull/175 +.. _Issue 167: https://github.com/galaxyproject/planemo/issues/167 +.. _Issue 170: https://github.com/galaxyproject/planemo/issues/170 +.. _Issue 169: https://github.com/galaxyproject/planemo/issues/169 +.. _Issue 168: https://github.com/galaxyproject/planemo/issues/168 +.. _b86fe1f: https://github.com/galaxyproject/planemo/commit/b86fe1f +.. _Pull Request 155: https://github.com/galaxyproject/planemo/pull/155 +.. _Pull Request 164: https://github.com/galaxyproject/planemo/pull/164 +.. _Issue 159: https://github.com/galaxyproject/planemo/issues/159 +.. _Issue 161: https://github.com/galaxyproject/planemo/issues/161 +.. _a2ee135: https://github.com/galaxyproject/planemo/commit/a2ee135 +.. _9ff0d2d: https://github.com/galaxyproject/planemo/commit/9ff0d2d +.. _Pull Request 151: https://github.com/galaxyproject/planemo/pull/151 +.. _9bf1eab: https://github.com/galaxyproject/planemo/commit/9bf1eab +.. _Pull Request 143: https://github.com/galaxyproject/planemo/pull/143 +.. _Issue 139: https://github.com/galaxyproject/planemo/issues/139 +.. _Issue 89: https://github.com/galaxyproject/planemo/issues/#89 +.. _Issue 91: https://github.com/galaxyproject/planemo/issues/#91 +.. _d26929e: https://github.com/galaxyproject/planemo/commit/d26929e +.. _36ac6d8: https://github.com/galaxyproject/planemo/commit/36ac6d8 +.. _08de8de: https://github.com/galaxyproject/planemo/commit/08de8de +.. _4f61025: https://github.com/galaxyproject/planemo/commit/4f61025 +.. _1982076: https://github.com/galaxyproject/planemo/commit/1982076 +.. _Pull Request 129: https://github.com/galaxyproject/planemo/pull/129 +.. _912df02: https://github.com/galaxyproject/planemo/commit/912df02 +.. _Pull Request 130: https://github.com/galaxyproject/planemo/pull/130 +.. _1a85493: https://github.com/galaxyproject/planemo/commit/1a85493 +.. _53edd99: https://github.com/galaxyproject/planemo/commit/53edd99 +.. _988de1d: https://github.com/galaxyproject/planemo/commit/988de1d +.. _Issue 118: https://github.com/galaxyproject/planemo/issues/118 +.. _cc1a447: https://github.com/galaxyproject/planemo/commit/cc1a447 +.. _b7d9e96: https://github.com/galaxyproject/planemo/commit/b7d9e96 +.. _Issue 138: https://github.com/galaxyproject/planemo/issues/#138 +.. _Issue 124: https://github.com/galaxyproject/planemo/issues/#124 +.. _26e3cdb: https://github.com/galaxyproject/planemo/commit/26e3cdb +.. _63cd431: https://github.com/galaxyproject/planemo/commit/63cd431 +.. _965511d: https://github.com/galaxyproject/planemo/commit/965511d +.. _01f2af9: https://github.com/galaxyproject/planemo/commit/01f2af9 +.. _343902d: https://github.com/galaxyproject/planemo/commit/343902d +.. _33294d2: https://github.com/galaxyproject/planemo/commit/33294d2 +.. _4c71299: https://github.com/galaxyproject/planemo/commit/4c71299 +.. _Pull Request 111: https://github.com/galaxyproject/planemo/pull/111 +.. _Pull Request 99: https://github.com/galaxyproject/planemo/pull/99 +.. _Pull Request 101: https://github.com/galaxyproject/planemo/pull/101 +.. _Pull Request 102: https://github.com/galaxyproject/planemo/pull/102 +.. _Issue 88: https://github.com/galaxyproject/planemo/issues/88 +.. _182fe57: https://github.com/galaxyproject/planemo/commit/182fe57 +.. _Pull Request 104: https://github.com/galaxyproject/planemo/pull/104 +.. _7c69bf6: https://github.com/galaxyproject/planemo/commit/7c69bf6 +.. _39fedd2: https://github.com/galaxyproject/planemo/commit/39fedd2 +.. _d755fe7: https://github.com/galaxyproject/planemo/commit/d755fe7 +.. _Pull Request 113: https://github.com/galaxyproject/planemo/pull/113 +.. _Pull Request 98: https://github.com/galaxyproject/planemo/pull/98 +.. _0bd4ff0: https://github.com/galaxyproject/planemo/commit/0bd4ff0 +.. _Pull Request 99: https://github.com/galaxyproject/planemo/pull/99 +.. _ec6e30f: https://github.com/galaxyproject/planemo/commit/ec6e30f +.. _8207026: https://github.com/galaxyproject/planemo/commit/8207026 +.. _4823c5e: https://github.com/galaxyproject/planemo/commit/4823c5e +.. _2e41e0a: https://github.com/galaxyproject/planemo/commit/2e41e0a +.. _fba3874: https://github.com/galaxyproject/planemo/commit/fba3874 +.. _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 70: https://github.com/galaxyproject/planemo/issues/70 +.. _Pull Request 68: https://github.com/galaxyproject/planemo/pull/68 +.. _Issue 61: https://github.com/galaxyproject/planemo/issues/61 +.. _Pull Request 63: https://github.com/galaxyproject/planemo/pull/63 +.. _Pull Request 56: https://github.com/galaxyproject/planemo/pull/56 +.. _Pull Request 51: https://github.com/galaxyproject/planemo/pull/51 +.. _Pull Request 40: https://github.com/galaxyproject/planemo/pull/40 +.. _Pull Request 29: https://github.com/galaxyproject/planemo/pull/29 +.. _Pull Request 22: https://github.com/galaxyproject/planemo/pull/22 +.. _Pull Request 23: https://github.com/galaxyproject/planemo/pull/23 +.. _Pull Request 33: https://github.com/galaxyproject/planemo/pull/33 +.. _Pull Request 6: https://github.com/galaxyproject/planemo/pull/6 +.. _Pull Request 1: https://github.com/galaxyproject/planemo/pull/1 + +.. _3499ca0: https://github.com/galaxyproject/planemo/commit/3499ca0a15affcaf8ac9efc55880da40b0626679 +.. _85b9614: https://github.com/galaxyproject/planemo/commit/85b961465f46351507f80ddc3758349535060502 +.. _53a6766: https://github.com/galaxyproject/planemo/commit/53a6766cdebdddc976189f6dc6a264bb4105c4bf +.. _badc25f: https://github.com/galaxyproject/planemo/commit/badc25fca495b61457ffb2e027f3fe9cf17c798f +.. _411a8da: 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https://github.com/galaxyproject/planemo/commit/36f7cb114f77731f90860d513a930e10ce5c1ba5 +.. _b9232e55: https://github.com/galaxyproject/planemo/commit/b9232e55e713abbd1d9ce8b0b34cbec6c701dc17 + +.. _bioblend: https://github.com/galaxyproject/bioblend/ +.. _XSD: http://www.w3schools.com/schema/ +.. _lxml: http://lxml.de/ +.. _xmllint: http://xmlsoft.org/xmllint.html +.. _nose: https://nose.readthedocs.org/en/latest/ + +