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view 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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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: https://github.com/galaxyproject/planemo/commit/411a8da21c92ba37c7ad95bfce9928d9b8fd998e .. _b8d90ab: https://github.com/galaxyproject/planemo/commit/b8d90abab8bf53ae2e7cca4317223c01af9ab68c .. _e8c1d45: https://github.com/galaxyproject/planemo/commit/e8c1d45f0c9a11bcf69ec2967836c3b8f432dd97 .. _78f8274: https://github.com/galaxyproject/planemo/commit/78f82747996e4a28f96c85ad72efe5e54c8c74bd .. _9e746b4: https://github.com/galaxyproject/planemo/commit/9e746b455e3b15219878cddcdeda722979639401 .. _ac4f828: https://github.com/galaxyproject/planemo/commit/ac4f82898f7006799142503a33c3978428660ce7 .. _834bfb2: https://github.com/galaxyproject/planemo/commit/834bfb2929d367892a3abe9c0b88d5a0277d7905 .. _dff4f33: https://github.com/galaxyproject/planemo/commit/dff4f33c750a8dbe651c38e149a26dd42e706a82 .. _a4110a8: https://github.com/galaxyproject/planemo/commit/a4110a85a770988e5cd3c31ccc9475717897d59c .. _21bb463: https://github.com/galaxyproject/planemo/commit/21bb463ad6c321bcb669603049a5e89a69766ad9 .. _af39061: 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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/