Metadata-Version: 1.1
Name: galaxy-lib
Version: 18.9.2
Summary: Subset of Galaxy (http://galaxyproject.org/) core code base designed to be used a library.
Home-page: https://github.com/galaxyproject/galaxy-lib
Author: Galaxy Project and Community
Author-email: jmchilton@gmail.com
License: AFL
Description: 
        .. image:: https://readthedocs.org/projects/galaxy-lib/badge/?version=latest
           :target: http://galaxy-lib.readthedocs.io/en/latest/?badge=latest
           :alt: Documentation Status
        
        .. image:: https://badge.fury.io/py/galaxy-lib.svg
           :target: https://pypi.python.org/pypi/galaxy-lib/
        
        .. image:: https://travis-ci.org/galaxyproject/galaxy-lib.png?branch=master
           :target: https://travis-ci.org/galaxyproject/galaxy-lib
        
        Overview
        --------
        
        A small subset of the Galaxy_ project for reuse outside the core. This subset has minimal dependencies and is Python 3 compatible.
        
        * Free software: Academic Free License version 3.0
        * Documentation: https://galaxy-lib.readthedocs.org.
        * Code: https://github.com/galaxyproject/galaxy-lib
        
        
        .. _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
        .. _Common Workfow Language: http://common-workflow-language.github.io
        
        
        
        
        History
        -------
        
        .. to_doc
        
        ---------------------
        18.9.2 (2019-01-02)
        ---------------------
        
        * Implement option for uploading local test data.
        * Bring in the latest Galaxy changes, which provide Python 3.7 support.
        
        ---------------------
        18.9.1 (2018-09-15)
        ---------------------
        
        * More work improving channel handling for mulled containers.
        
        ---------------------
        18.9.0 (2018-09-14)
        ---------------------
        
        * Update Conda channel order (thanks to @bgruening).
        * Bring in the latest Galaxy changes and add Galaxy XSD to the project.
        * Various cwltool fixes (thanks to @nsoranzo).
        
        ---------------------
        18.5.15 (2018-09-12)
        ---------------------
        
        * More tweaks to CWL tool loading to support newer versions of cwltool.
        
        ---------------------
        18.5.14 (2018-09-12)
        ---------------------
        
        * Improved tool linting and reporting thanks to @natefoo and @nsoranzo.
        * Add support for newer cwltool thanks to @nsoranzo.
        * Improved mulled building thanks to @pcm32.
        
        ---------------------
        18.5.13 (2018-05-23)
        ---------------------
        
        * Small updates to test parsing to support Galaxy workflow testing.
        
        ---------------------
        18.5.12 (2018-05-22)
        ---------------------
        
        * Update test data processing to allow URIs in Galaxy workflow tests.
        
        ---------------------
        18.5.11 (2018-05-16)
        ---------------------
        
        * Parse CWL SoftwareRequirements to Galaxy requirements (required to fix various Planemo functionality
          for CWL tools).
        
        ---------------------
        18.5.10 (2018-05-10)
        ---------------------
        
        * Docker logging API fix for Planemo.
        
        ---------------------
        18.5.9 (2018-05-07)
        ---------------------
        
        * Update CWL linting to target CWL 1.0.
        
        ---------------------
        18.5.8 (2018-05-06)
        ---------------------
        
        * Better error handling for Conda searching (thanks to @bgruening).
        * Update against the latest Galaxy codebase.
        * Add Galaxy tool linting to ensure versions are PEP 440 compliant (thanks to @davebx).
        
        ---------------------
        18.5.7 (2018-03-12)
        ---------------------
        
        * More tool testing client fixes, this time for ephemeris.
        
        ---------------------
        18.5.6 (2018-03-12)
        ---------------------
        
        * Bring in the latest Galaxy dev branch - includes code cleanup and many Python 3 fixes from
          @nsoranzo as well as client code for executing tool tests against external Galaxy instances.
        * Extend tool testing client from Galaxy's dev branch with even more data collection for compatiblity
          with Planemo.
        
        ---------------------
        18.5.5 (2018-03-06)
        ---------------------
        
        * Fix mulled to use shlex.quote to escape single quotes in test command
          (thanks to @mbargull).
        * Make markupsafe a dependency since it is import unconditionally in galaxy.tools.toolbox
          (thanks to @mbargull).
        * Python 3 fix for assertion testing.
        
        ---------------------
        18.5.4 (2018-03-01)
        ---------------------
        
        * Make conda image for mulled builds configurable via an environment variable
          (thanks to @mbargull).
        
        ---------------------
        18.5.3 (2018-02-28)
        ---------------------
        
        * Fix path module for import on Windows for Pulsar.
        
        ---------------------
        18.5.2 (2018-02-28)
        ---------------------
        
        * Various fixes for library usage mostly related to Conda (with help from @nsoranzo).
        
        ---------------------
        18.5.1 (2018-02-26)
        ---------------------
        
        * Redo last release - pushed to PyPI without actually including the desired fix.
        
        ---------------------
        18.5.0 (2018-02-26)
        ---------------------
        
        * Another Python 3 fix for Planemo.
        * Fix galaxy-lib version - this has actually been tracking the 18.05 release of Galaxy for the last two releases.
        
        ---------------------
        18.1.0 (2018-02-26)
        ---------------------
        
        * More Python 3 fixes for Planemo thanks to @nsoranzo.
        * Bring in the latest Galaxy development branch.
        
        ---------------------
        17.9.12 (2018-02-22)
        ---------------------
        
        * Python 3 fix for Planemo thanks to @nsoranzo.
        * Fix bad merge of miniconda update for mulled work.
        
        ---------------------
        17.9.11 (2018-02-22)
        ---------------------
        
        * Update to the latest Galaxy dev just prior to the branch of 18.01.
        * Python 3 fixes.
        
        ---------------------
        17.9.10 (2017-11-23)
        ---------------------
        
        * Added docs for using mulled-build with your own quay.io account
          (thanks to @jerowe).
        * Catch errors in Conda search if nothing is found (preventing planemo-monitor
          from functioning properly) (thanks to @bgruening).
        * Make multi-requirement container building via mulled more stable
          (thanks to @bgruening).
        
        ---------------------
        17.9.9 (2017-09-27)
        ---------------------
        
        * Bring in latest updates from the 17.09 branch of Galaxy - including updating the default target Conda version and fixes for module resolution.
        
        ---------------------
        17.9.8 (2017-09-26)
        ---------------------
        
        * Bring in updated CWL utilities from the upstream work on CWL integration.
        
        ---------------------
        17.9.7 (2017-09-19)
        ---------------------
        
        * Bring in updated CWL utilities from the upstream work on CWL integration.
        
        ---------------------
        17.9.6 (2017-09-15)
        ---------------------
        
        * Remove ``command`` lint check that is no longer valid.
        
        ---------------------
        17.9.5 (2017-09-06)
        ---------------------
        
        * Bring in updated CWL utilities from the upstream work on CWL integration.
        
        ---------------------
        17.9.4 (2017-09-06)
        ---------------------
        
        * Bring in various Galaxy updates including numerous Conda fixes and changes (thanks to @nsoranzo).
        * Improved error handling when parsing tool reStructuredText (thanks to @erasche).
        * Updated CWL utilities.
        
        ---------------------
        17.9.3 (2017-06-27)
        ---------------------
        
        * Bug fix in from_dict parsing of tool dependency specs.
        
        ---------------------
        17.9.2 (2017-06-22)
        ---------------------
        
        * Sync with mulled enhancements and fixes from Galaxy's development branch.
        
        ---------------------
        17.9.1 (2017-06-17)
        ---------------------
        
        * Various small Singularity fixes and enhancements.
        
        ---------------------
        17.9.0 (2017-06-11)
        ---------------------
        
        * Bring in latest Galaxy dev changes.
        * Implement support for building Singularity mulled containers.
        * Implement mulled version 2 package hashing.
        * Fix default namespace for mulled operations from mulled to biocontainers.
        
        ---------------------
        17.5.11 (2017-05-31)
        ---------------------
        
        * Fix HISTORY.rst formatting to properly render release on PyPI.
        * Fix bug in new offline Conda search function introduced in 17.5.10.
        
        ---------------------
        17.5.10 (2017-05-30)
        ---------------------
        
        * Always clean up build directory in mulled commands (thanks to @johanneskoester).
        * Expose offline mode in Conda search utility (for repeated fast searches).
        * When publishing mulled containers - use quay.io API to publish them as public.
        * Add explicit option ``--check-published`` to ``mulled-build-*``.
        * Fix auto-installation of Involucro on first attempt.
        * Handle explicit tags in ``mulled-build-files`` and add an implicit tag of ``0`` if none found.
        * Fix tab parsing in ``mulled-build-files``.
        
        ---------------------
        17.5.9 (2017-05-16)
        ---------------------
        
        * Make mulled-search to search biocontainers instead of mulled repository by default
          (thanks to @tom-tan).
        * Allow setting a new base image with mulled-build.
        
        ---------------------
        17.5.8 (2017-04-23)
        ---------------------
        
        * Fix mulled image cleanup. #55.
        
        ---------------------
        17.5.7 (2017-03-15)
        ---------------------
        
        * Updates to CWL library functionality for several months worth of CWL tool updates.
        * Allow finding tools by a URI-like strings (e.g. ``file://``, ``http://``, ``dockstore://``).
        * Bring in latest Galaxy updates.
        
        ---------------------
        17.5.6 (2017-03-01)
        ---------------------
        
        * Expanded options for mulled CLI tools and library functionality.
          Fixes #49.
        
        ---------------------
        17.5.5 (2017-02-26)
        ---------------------
        
        * Fix bug in 17.5.4 where under certain conditions conda-build would attempt to be setup
          with the conda --use-local flag - which is not allowed.
        
        ---------------------
        17.5.4 (2017-02-26)
        ---------------------
        
        * Fix local builds Conda support to reflect conda-build is required.
        * Fix default target path for miniconda installs.
        
        ---------------------
        17.5.3 (2017-02-24)
        ---------------------
        
        * Update against the latest Galaxy dev branch changes.
        * Update Conda utilities to allow using locally built packages.
        
        ---------------------
        17.5.2 (2017-02-21)
        ---------------------
        
        * Conda utility enhancements to fix a Planemo bug.
        
        ---------------------
        17.5.1 (2017-02-21)
        ---------------------
        
        * Various improvements to Galaxy tool linting.
        
        ---------------------
        17.5.0 (2017-02-16)
        ---------------------
        
        * Bring in the last of the Galaxy dev changes.
        * Allow Conda installs to target global Conda config (for Planemo)
        
        ---------------------
        17.1.2 (2017-01-23)
        ---------------------
        
        * Bring in the last of the Galaxy dev changes before branch of release_17.01.
        * Improvements to mulled testing thanks to @mvdbeek.
        
        ---------------------
        17.1.1 (2016-12-14)
        ---------------------
        
        * Revert changes to shell command execution in Galaxy that had unintended consequences for Planemo.    
        
        ---------------------
        17.1.0 (2016-12-12)
        ---------------------
        
        * Improved mulled logging thanks to @bgruening.
        * Bring in the latest Galaxy dev changes.
        
        ---------------------
        16.10.10 (2016-10-24)
        ---------------------
        
        * Fix mulled package data fetching for Mac OS X (thanks to @dannon).
        
        ---------------------
        16.10.9 (2016-10-21)
        ---------------------
        
        * Small fixes including to reflect mulled name on quay.io changed to biocontainers.
        
        ---------------------
        16.10.8 (2016-10-10)
        ---------------------
        
        * More mulled enhancements and bug fixes thanks to @bgruening and @daler.
        
        ---------------------
        16.10.7 (2016-10-08)
        ---------------------
        
        * More mulled enhancements and bug fixes thanks to @bgruening.
        * Fix bioconda support by adding conda-forge to list of default channels.
        
        ---------------------
        16.10.6 (2016-10-07)
        ---------------------
        
        * More mulled enhancements thanks to @bgruening.
        
        ---------------------
        16.10.5 (2016-10-04)
        ---------------------
        
        * Some docstring cleanup and minor tweaks to Conda support for downstream planemo mulled work.
        
        ---------------------
        16.10.4 (2016-10-03)
        ---------------------
        
        * More mulled fixes and enhancements.
        
        ---------------------
        16.10.3 (2016-10-02)
        ---------------------
        
        * Small mulled and Conda related fix and enhancements.
        
        ---------------------
        16.10.2 (2016-09-30)
        ---------------------
        
        * Fix setup.py for features in 16.10.1.
        
        ---------------------
        16.10.1 (2016-09-29)
        ---------------------
        
        * Updates for recents changes to Galaxy and initial mulled scripts and container resolver.
        
        ---------------------
        16.10.0 (2016-08-31)
        ---------------------
        
        * Updates for recent changes to Galaxy.
        
        ---------------------
        16.7.10 (2016-08-04)
        ---------------------
        
        * Updates for recent change to Galaxy.    
        
        ---------------------
        16.7.9 (2016-06-13)
        ---------------------
        
        * Updates for recent changes to Galaxy and cwltool.
        
        ---------------------
        16.7.8 (2016-06-05)
        ---------------------
        
        * Updates to include Galaxy library for verifying test outputs
          and the latest dev changes to Galaxy.
        
        ---------------------
        16.7.7 (2016-05-23)
        ---------------------
        
        * Fixes to CWL and Docker libraries for Planemo.
        
        ---------------------
        16.7.6 (2016-05-11)
        ---------------------
        
        * Fixes to cwl processing for Planemo.
            
        ---------------------
        16.7.5 (2016-05-11)
        ---------------------
        
        * Updates to cwl processing for Planemo.
        
        ---------------------
        16.7.4 (2016-05-10)
        ---------------------
        
        * Updates to cwl processing for Planemo.
        
        ---------------------
        16.7.3 (2016-05-07)
        ---------------------
        
        * Updates to cwltool_deps for Planemo.
        
        ---------------------
        16.7.2 (2016-05-06)
        ---------------------
        
        * Updates to tool parsing and linting for Planemo.
        
        ---------------------
        16.7.1 (2016-05-02)
        ---------------------
        
        * Update against the latest development branch of Galaxy.
        
        ---------------------
        16.7.0 (2016-04-21)
        ---------------------
        
        * Update against the latest development branch of Galaxy.
        
        ---------------------
        16.4.1 (2016-04-08)
        ---------------------
        
        * Update against the latest development branch of Galaxy.
        
        ---------------------
        16.4.0 (2016-02-15)
        ---------------------
        
        * Update against the latest development branch of Galaxy.
        
        ---------------------
        16.1.9 (2016-01-14)
        ---------------------
        
        * Fix a bug in the source distribution of galaxy-lib.
        
        ---------------------
        16.1.8 (2016-01-12)
        ---------------------
        
        * Update against Galaxy's release_16.01 branch.
        
        ---------------------
        16.1.7 (2016-01-03)
        ---------------------
        
        * Update against Galaxy's dev branch - including conda updates,
          dependency resolution changes, and toolbox updates.
        
        ---------------------
        16.1.6 (2015-12-28)
        ---------------------
        
        * Additional fixes to setup.py and updates for recent changes to
          Galaxy's dev branch.
        
        ---------------------
        16.1.5 (2015-12-22)
        ---------------------
        
        * Fix another bug that was preventing dependency resolution from
          working in Pulsar.
        
        ---------------------
        16.1.4 (2015-12-22)
        ---------------------
        
        * Another setup.py fix for job metrics module.
        
        ---------------------
        16.1.3 (2015-12-22)
        ---------------------
        
        * Python 3 fixes and updates for recent Galaxy dev commits.
        
        ---------------------
        16.1.2 (2015-12-21)
        ---------------------
        
        * Fix for missing galaxy.tools.parser package in setup.py.
        * Fix LICENSE in repository.
        
        ---------------------
        16.1.1 (2015-12-20)
        ---------------------
        
        * Fix small issues with dependencies, naming, and versioning with first release.
        
        ---------------------
        16.1.0 (2015-12-20)
        ---------------------
        
        * Setup project.
        
        .. _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/
        
Keywords: galaxy
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 :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
