Metadata-Version: 2.1
Name: gxformat2
Version: 0.11.1
Summary: Galaxy Workflow Format 2 Descriptions
Home-page: https://github.com/galaxyproject/gxformat2
Author: Galaxy Project and Community
Author-email: jmchilton@gmail.com
License: AFL
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
Requires-Dist: six (>=1.9.0)
Requires-Dist: bioblend
Requires-Dist: pyyaml


.. image:: https://readthedocs.org/projects/pip/badge/?version=latest
   :target: https://gxformat2.readthedocs.org

.. image:: https://badge.fury.io/py/gxformat2.svg
   :target: https://pypi.python.org/pypi/gxformat2/

.. image:: https://travis-ci.org/jmchilton/gxformat2.png?branch=master
   :target: https://travis-ci.org/jmchilton/gxformat2

.. image:: https://coveralls.io/repos/jmchilton/gxformat2/badge.svg?branch=master
   :target: https://coveralls.io/r/jmchilton/gxformat2?branch=master


This package defines a high-level Galaxy_ workflow description termed "Format
2". At this point, these workflows are defined entirely client side and
transcoded into traditional (or Format 1?) Galaxy workflows.

The traditional Galaxy workflow description is not meant to be concise and is
neither readily human readable or human writable. Format 2 addresses all three
of these limitations.

Format 2 workflow is a highly experimental format and will change rapidly in
potentially backward incompatible ways until the code is merged into the
Galaxy server and enabled by default.

* 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/
.. _Travis CI: http://travis-ci.org/




History
-------

.. to_doc

---------------------
0.11.1 (2020-02-25)
---------------------

* Bug fix for gxwf-lint invocation from setup.py installed script.

---------------------
0.11.0 (2020-02-25)
---------------------

* Validate Galaxy Markdown in workflow reports as part of linting.
* Improved null handling in native ga workflow linting.
* Enhancements to workflow linting from Python. Lint for lack of documentation,
  tools using the test toolshed, and implement special linting for training
  material workflows to ensure a tag matches the workflow topic.
* Add gxwf-viz script that produces a cytoscape visualization of a workflow.

---------------------
0.10.1 (2019-12-07)
---------------------

* Bug fix to handle outputs without labels in Format 2 - they
  don't validate per se but they are important for testing in the
  Galaxy framework.

---------------------
0.10.0 (2019-12-06)
---------------------

* Implement scheam, validation, linting (for Format 2 and .ga).
* Handle new reports field in Galaxy 19.09 workflows.
* Numerous fixes for conversiion to and from native workflows.
* Numerous new test cases.
* Implement Java project for valiating and linting both kinds of workflows.

---------------------
0.9.0 (2019-07-08)
---------------------

* Implement default values in gxformat2.

---------------------
0.8.4 (2019-06-24)
---------------------

* Fix output IDs of 0.    

---------------------
0.8.3 (2019-05-23)
---------------------

* Implement set_columns PJA.

---------------------
0.8.2 (2019-03-16)
---------------------

* Allow another API return option for experimental tool creation API.

---------------------
0.8.1 (2019-03-11)
---------------------

* Implement change datatype PJA.

---------------------
0.8.0 (2018-11-01)
---------------------

* Implement experimental CWL-style step defaults (see Galaxy PR #6850).

---------------------
0.7.1 (2018-10-09)
---------------------

* Various small fixes for changes in 0.7.1.

---------------------
0.7.0 (2018-10-08)
---------------------

* Add some basic test cases.
* Allow ID-map style listing of steps.
* Ordered load (in addition to existing dump functionality) or ordering of steps in ID-map style variant works.
* Allow CWL-style $graph defs that can define multiple workflows in a single file.
* Initial work on de-duplicating subworkflow definitions on import.
* Fix position handling while exporting workflow.

---------------------
0.6.1 (2018-10-01)
---------------------

* Fix export of non-data parameters and implicit workflow connections.

---------------------
0.6.0 (2018-10-01)
---------------------

* Various fixes, allow id map style workflow input definitions.

---------------------
0.5.0 (2018-10-01)
---------------------

* More fixes for PJA, add the ``doc`` keyword to format 2 workflows to match CWL workflows. Map to and from native Galaxy workflows as annotations.

---------------------
0.4.0 (2018-10-01)
---------------------

* Fixes for exporting PJA when exporting workflows from native .ga to format 2.

---------------------
0.3.2 (2018-10-01)
---------------------

* Fixes for exporting workflow outputs from native .ga to format 2, support for modern map style output definitions like CWL 1.0.

---------------------
0.3.1 (2018-10-01)
---------------------

* Fixes for exporting subworkflows from native .ga to format 2.

---------------------
0.3.0 (2018-09-30)
---------------------

* More cwl style inputs, initial work on conversion from native workflows, various small fixes and tweaks.

---------------------
0.2.0 (2018-02-21)
---------------------

* Bring in latest Galaxy updates - Python 3 fixes, safe YAML usage, and more PJA implemented.

---------------------
0.1.1 (2016-08-15)
---------------------

* Fix one Python 3 incompatibility.

---------------------
0.1.0 (2016-05-02)
---------------------

* Initial version - code from Galaxy's test framework with changes
  based on planemo testing.