gxformat2 0.16.0.dev0

0.16.0.dev0

0.15.0 (2020-08-12)

• Lint types of default values.

• Fix bugs in schema related to differing type names between Galaxy and CWL.

• Generate cwl v1.2 instead of cwl v1.2.0-dev5 release now that it has been released.

• More testing of linting and CWL 1.2 export.

0.14.0 (2020-08-11)

• Bug fix where native export had explicit outputs declaration still in it (wouldn’t break anything, but was deceptive).

• Fixes for experimental CWL 1.2 abstract export.

• Improve script structures and documentation.

• Improve code structure - add more types, make more things immutable, mention mutability in docstrings.

0.13.1 (2020-08-03)

• Improve package structure - publish fixed sphinx docs, fix readme badges, add mypy typing support.

0.13.0 (2020-07-30)

• Add experimental export to CWL 1.2 using new abstract Operation classes.

0.12.0 (2020-07-27)

• Drop support for Python 2 - to support next bullet.

• Update schema parser for recent changes to schema salad.

0.11.4 (2020-07-27)

• Added abstraction for uniform access to workflow outputs across formats.

0.11.3 (2020-07-23)

• Bug fixes for exporting newer input concepts from native to Format 2.

• Added abstraction for uniform access to workflow inputs across formats.

0.11.2 (2020-07-22)

• Rework cytoscape and helpers for reuse from Planemo.

• Rev markdown validator for and from latest Galaxy changes.

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.