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comparison env/lib/python3.9/site-packages/gxformat2-0.15.0.dist-info/METADATA @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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1 Metadata-Version: 2.1
2 Name: gxformat2
3 Version: 0.15.0
4 Summary: Galaxy Workflow Format 2 Descriptions
5 Home-page: https://github.com/galaxyproject/gxformat2
6 Author: Galaxy Project and Community
7 Author-email: jmchilton@gmail.com
8 License: AFL
9 Keywords: galaxy
10 Platform: UNKNOWN
11 Classifier: Development Status :: 5 - Production/Stable
12 Classifier: Intended Audience :: Developers
13 Classifier: Environment :: Console
14 Classifier: License :: OSI Approved :: Academic Free License (AFL)
15 Classifier: Operating System :: POSIX
16 Classifier: Topic :: Software Development
17 Classifier: Topic :: Software Development :: Code Generators
18 Classifier: Topic :: Software Development :: Testing
19 Classifier: Natural Language :: English
20 Classifier: Programming Language :: Python :: 3
21 Classifier: Programming Language :: Python :: 3.5
22 Classifier: Programming Language :: Python :: 3.6
23 Classifier: Programming Language :: Python :: 3.7
24 Classifier: Programming Language :: Python :: 3.8
25 Requires-Dist: six (>=1.9.0)
26 Requires-Dist: bioblend
27 Requires-Dist: pyyaml
28
29
30 .. image:: https://readthedocs.org/projects/gxformat2/badge/?version=latest
31 :target: https://gxformat2.readthedocs.io/en/latest/
32
33 .. image:: https://badge.fury.io/py/gxformat2.svg
34 :target: https://pypi.python.org/pypi/gxformat2/
35
36 .. image:: https://github.com/galaxyproject/gxformat2/workflows/Python%20CI/badge.svg
37 :target: https://github.com/galaxyproject/gxformat2/actions?query=workflow%3A%22Python+CI%22
38
39 .. image:: https://github.com/galaxyproject/gxformat2/workflows/Java%20CI/badge.svg
40 :target: https://github.com/galaxyproject/gxformat2/actions?query=workflow%3A%22Java+CI%22
41
42 .. image:: https://img.shields.io/badge/latest%20schema-v19.09-blue
43 :target: http://galaxyproject.github.io/gxformat2/v19_09.html
44
45 Format 2
46 --------------
47
48 This package defines a high-level Galaxy_ workflow description termed "Format
49 2". The current schema version is v19_09 and the schema can be found
50 [here](http://galaxyproject.github.io/gxformat2/v19_09.html). This version of
51 workflow format can be consumed by Galaxy versions 19.09, 20.01, 20.05 and the
52 the forthcoming 20.09.
53
54 The Format 2 workflow description is still somewhat experimental and may
55 yet change in small potentially backward incompatible ways until the format is
56 exported by Galaxy by default.
57
58 The traditional Galaxy workflow description (files ending in .ga extension
59 sometimes called native workflows in this project) was not designed to be
60 concise and is neither readily human readable or human writable. Galaxy
61 workflow Format 2 is being designed to addresses all three of these limitations.
62 While also moving Galaxy's workflow description language toward standards such
63 as the Common Workflow Language.
64
65 gxformat2
66 --------------
67
68 This Python project can be installed from PyPI using ``pip``.
69
70 ::
71
72 $ pip install gxformat2
73
74 Checkout the project tests or how it used in projects such as Planemo and
75 Galaxy to see how to use the gxformat2 library. Reference documentation for
76 the `modules <https://gxformat2.readthedocs.io/en/latest/py-modindex.html>`__
77 can be found as part of the project's documentation.
78
79 This project also includes various scripts for working with Galaxy workflows.
80 Checkout their help for more information.
81
82 ::
83
84 $ gxwf-lint --help
85 $ gxwf-viz --help
86 $ gxwf-abstract-export --help
87
88 This library and associated scripts are licensed under the Academic Free License
89 version 3.0.
90
91 .. _Galaxy: http://galaxyproject.org/
92 .. _GitHub: https://github.com/
93 .. _Travis CI: http://travis-ci.org/
94
95
96
97
98 History
99 -------
100
101 .. to_doc
102
103 ---------------------
104 0.15.0 (2020-08-12)
105 ---------------------
106
107 * Lint types of default values.
108 * Fix bugs in schema related to differing type names between Galaxy and CWL.
109 * Generate cwl v1.2 instead of cwl v1.2.0-dev5 release now that it has been released.
110 * More testing of linting and CWL 1.2 export.
111
112 ---------------------
113 0.14.0 (2020-08-11)
114 ---------------------
115
116 * Bug fix where native export had explicit outputs declaration still in it (wouldn't break anything, but
117 was deceptive).
118 * Fixes for experimental CWL 1.2 abstract export.
119 * Improve script structures and documentation.
120 * Improve code structure - add more types, make more things immutable, mention mutability in docstrings.
121
122 ---------------------
123 0.13.1 (2020-08-03)
124 ---------------------
125
126 * Improve package structure - publish fixed sphinx docs, fix readme badges, add mypy typing support.
127
128 ---------------------
129 0.13.0 (2020-07-30)
130 ---------------------
131
132 * Add experimental export to CWL 1.2 using new abstract Operation classes.
133
134 ---------------------
135 0.12.0 (2020-07-27)
136 ---------------------
137
138 * Drop support for Python 2 - to support next bullet.
139 * Update schema parser for recent changes to schema salad.
140
141 ---------------------
142 0.11.4 (2020-07-27)
143 ---------------------
144
145 * Added abstraction for uniform access to workflow outputs across formats.
146
147 ---------------------
148 0.11.3 (2020-07-23)
149 ---------------------
150
151 * Bug fixes for exporting newer input concepts from native to Format 2.
152 * Added abstraction for uniform access to workflow inputs across formats.
153
154 ---------------------
155 0.11.2 (2020-07-22)
156 ---------------------
157
158 * Rework cytoscape and helpers for reuse from Planemo.
159 * Rev markdown validator for and from latest Galaxy changes.
160
161 ---------------------
162 0.11.1 (2020-02-25)
163 ---------------------
164
165 * Bug fix for gxwf-lint invocation from setup.py installed script.
166
167 ---------------------
168 0.11.0 (2020-02-25)
169 ---------------------
170
171 * Validate Galaxy Markdown in workflow reports as part of linting.
172 * Improved null handling in native ga workflow linting.
173 * Enhancements to workflow linting from Python. Lint for lack of documentation,
174 tools using the test toolshed, and implement special linting for training
175 material workflows to ensure a tag matches the workflow topic.
176 * Add gxwf-viz script that produces a cytoscape visualization of a workflow.
177
178 ---------------------
179 0.10.1 (2019-12-07)
180 ---------------------
181
182 * Bug fix to handle outputs without labels in Format 2 - they
183 don't validate per se but they are important for testing in the
184 Galaxy framework.
185
186 ---------------------
187 0.10.0 (2019-12-06)
188 ---------------------
189
190 * Implement scheam, validation, linting (for Format 2 and .ga).
191 * Handle new reports field in Galaxy 19.09 workflows.
192 * Numerous fixes for conversiion to and from native workflows.
193 * Numerous new test cases.
194 * Implement Java project for valiating and linting both kinds of workflows.
195
196 ---------------------
197 0.9.0 (2019-07-08)
198 ---------------------
199
200 * Implement default values in gxformat2.
201
202 ---------------------
203 0.8.4 (2019-06-24)
204 ---------------------
205
206 * Fix output IDs of 0.
207
208 ---------------------
209 0.8.3 (2019-05-23)
210 ---------------------
211
212 * Implement set_columns PJA.
213
214 ---------------------
215 0.8.2 (2019-03-16)
216 ---------------------
217
218 * Allow another API return option for experimental tool creation API.
219
220 ---------------------
221 0.8.1 (2019-03-11)
222 ---------------------
223
224 * Implement change datatype PJA.
225
226 ---------------------
227 0.8.0 (2018-11-01)
228 ---------------------
229
230 * Implement experimental CWL-style step defaults (see Galaxy PR #6850).
231
232 ---------------------
233 0.7.1 (2018-10-09)
234 ---------------------
235
236 * Various small fixes for changes in 0.7.1.
237
238 ---------------------
239 0.7.0 (2018-10-08)
240 ---------------------
241
242 * Add some basic test cases.
243 * Allow ID-map style listing of steps.
244 * Ordered load (in addition to existing dump functionality) or ordering of steps in ID-map style variant works.
245 * Allow CWL-style $graph defs that can define multiple workflows in a single file.
246 * Initial work on de-duplicating subworkflow definitions on import.
247 * Fix position handling while exporting workflow.
248
249 ---------------------
250 0.6.1 (2018-10-01)
251 ---------------------
252
253 * Fix export of non-data parameters and implicit workflow connections.
254
255 ---------------------
256 0.6.0 (2018-10-01)
257 ---------------------
258
259 * Various fixes, allow id map style workflow input definitions.
260
261 ---------------------
262 0.5.0 (2018-10-01)
263 ---------------------
264
265 * 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.
266
267 ---------------------
268 0.4.0 (2018-10-01)
269 ---------------------
270
271 * Fixes for exporting PJA when exporting workflows from native .ga to format 2.
272
273 ---------------------
274 0.3.2 (2018-10-01)
275 ---------------------
276
277 * Fixes for exporting workflow outputs from native .ga to format 2, support for modern map style output definitions like CWL 1.0.
278
279 ---------------------
280 0.3.1 (2018-10-01)
281 ---------------------
282
283 * Fixes for exporting subworkflows from native .ga to format 2.
284
285 ---------------------
286 0.3.0 (2018-09-30)
287 ---------------------
288
289 * More cwl style inputs, initial work on conversion from native workflows, various small fixes and tweaks.
290
291 ---------------------
292 0.2.0 (2018-02-21)
293 ---------------------
294
295 * Bring in latest Galaxy updates - Python 3 fixes, safe YAML usage, and more PJA implemented.
296
297 ---------------------
298 0.1.1 (2016-08-15)
299 ---------------------
300
301 * Fix one Python 3 incompatibility.
302
303 ---------------------
304 0.1.0 (2016-05-02)
305 ---------------------
306
307 * Initial version - code from Galaxy's test framework with changes
308 based on planemo testing.
309
310