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comparison env/lib/python3.7/site-packages/ephemeris-0.10.5.dist-info/METADATA @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 Metadata-Version: 2.1
2 Name: ephemeris
3 Version: 0.10.5
4 Summary: Ephemeris is an opinionated library and set of scripts for managing the bootstrapping of Galaxy project plugins - tools, index data, and workflows.
5 Home-page: https://github.com/galaxyproject/ephemeris
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 :: 2
21 Classifier: Programming Language :: Python :: 2.7
22 Requires-Dist: six (>=1.9.0)
23 Requires-Dist: PyYAML
24 Requires-Dist: bioblend (>=0.10.0)
25 Requires-Dist: Jinja2
26 Requires-Dist: galaxy-tool-util (>=19.9.0.dev5)
27 Requires-Dist: futures ; python_version < "3"
28
29
30 .. image:: https://readthedocs.org/projects/pip/badge/?version=latest
31 :target: https://ephemeris.readthedocs.org
32
33 .. image:: https://badge.fury.io/py/ephemeris.svg
34 :target: https://pypi.python.org/pypi/ephemeris/
35
36 .. image:: https://travis-ci.org/galaxyproject/ephemeris.png?branch=master
37 :target: https://travis-ci.org/galaxyproject/ephemeris
38
39 .. image:: https://api.codacy.com/project/badge/Coverage/e12102174b4e452c871cd2bafedaec60
40 :target: https://www.codacy.com/app/galaxyproject/ephemeris?utm_source=github.com&utm_medium=referral&utm_content=galaxyproject/ephemeris&utm_campaign=Badge_Coverage
41
42 .. image:: https://api.codacy.com/project/badge/Grade/e12102174b4e452c871cd2bafedaec60
43 :target: https://www.codacy.com/app/galaxyproject/ephemeris?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=galaxyproject/ephemeris&amp;utm_campaign=Badge_Grade
44
45 Ephemeris is a small Python library and set of scripts for managing the
46 bootstrapping of Galaxy_ plugins - tools, index data, and workflows.
47
48 * Free software: Academic Free License version 3.0
49 * Documentation: https://ephemeris.readthedocs.org.
50 * Code: https://github.com/galaxyproject/ephemeris
51
52
53 .. _Galaxy: http://galaxyproject.org/
54 .. _GitHub: https://github.com/
55 .. _Docker: https://www.docker.com/
56 .. _Homebrew: http://brew.sh/
57 .. _linuxbrew: https://github.com/Homebrew/linuxbrew
58 .. _Vagrant: https://www.vagrantup.com/
59 .. _Travis CI: http://travis-ci.org/
60
61
62
63
64 History
65 -------
66
67 .. to_doc
68
69 ---------------------
70 0.10.5 (2020-02-29)
71 ---------------------
72
73 * Fix `shed-tools test -t workflow_tools.yml` (thanks to `@nsoranzo`_). `Pull
74 Request 155`_
75 * Fix installing tool dependencies from yaml list (thanks to `@mvdbeek`_).
76 `Pull Request 154`_
77 * Cast exceptions to string using unicodify (thanks to `@mvdbeek`_). `Pull
78 Request 150`_
79 * Add description when creating folders with setup_data_libraries (thanks to
80 `@abretaud`_). `Pull Request 149`_
81
82 ---------------------
83 0.10.4 (2019-10-05)
84 ---------------------
85
86 * When polling for repo install status, ensure the correct revision is being
87 checked (thanks to `@natefoo`_). `Pull Request 146`_
88 * Add install_tool_deps command (thanks to `@innovate-invent`_). `Pull Request
89 145`_
90
91 ---------------------
92 0.10.3 (2019-07-18)
93 ---------------------
94
95 * Add install-tool-deps command that will install tool dependencies
96 (thanks to `@innovate-invent`_). `Pull Request 130`_
97 * Require galaxy-tool-util instead of galaxy-lib (thanks to `@nsoranzo`_).
98 `Pull Request 143`_
99 * Release to PyPI on tag (thanks to `@mvdbeek`_). `Pull Request 142`_
100 * Make Data library creation more robust
101 (thanks to `@erasche`_). `Pull Request 138`_
102 * Make tool testing more robust (thanks to
103 `@mvdbeek`_). `Pull Request 137`_, `Pull Request 136`_
104
105 ---------------------
106 0.10.2 (2019-06-04)
107 ---------------------
108
109 * Fix default message check (thanks to `@mvdbeek`_). `Pull Request 135`_
110
111 ---------------------
112 0.10.1 (2019-06-04)
113 ---------------------
114
115 * Fix timeout handling when installing repositories
116 (thanks to `@mvdbeek`_). `Pull Request 134`_
117
118 ---------------------
119 0.10.0 (2019-05-29)
120 ---------------------
121
122 * fix doc building and regenerate (thanks to `@martenson`_). `Pull Request
123 129`_
124 * fix default for 'parallel_tests' typo (thanks to `@martenson`_). `Pull
125 Request 127`_
126 * Include some additional stats for xunit reporting (thanks to `@mvdbeek`_).
127 `Pull Request 126`_
128 * Handle timeout gracefully for UWSGI connection (thanks to `@pcm32`_). `Pull
129 Request 123`_
130 * Update Docs for User Name (Should be Email) (thanks to `@rdvelazquez`_).
131 `Pull Request 122`_
132 * remove the python invocation from usage examples (thanks to `@martenson`_).
133 `Pull Request 121`_
134 * Fix crash when too_with_panel is empty (thanks to `@jvanbraekel`_). `Pull
135 Request 120`_
136 * Test tools in parallel, with regular user permissions, without a shared
137 filesystem (thanks to `@mvdbeek`_). `Pull Request 118`_
138 * use latest documentation dependencies to fix documentation build issue
139 (thanks to `@rhpvorderman`_). `Pull Request 114`_
140 * Refactor shed tool functionality. Removed deprecated options from
141 shed-tools CLI.
142 shed-tools update now also accepts tool list, so tools in galaxy can
143 be selectively updated. Improved algorithm leads to much faster
144 skipping of already installed tools, which makes the installation
145 of tools much faster on an already populated galaxy.
146 (thanks to `@rhpvorderman`_).
147 `Pull Request 104`_
148 * Add ``pytest``, enable coverage testing (thanks to `@rhpvorderman`_).
149 `Pull Request 105`_
150 * Make ``setup_data_libraries.py`` check for existence before recreation of
151 libraries.
152 (thanks to `@Slugger70`_).
153 `Pull Request 103`_
154 * Catch failures on requests to the installed repo list when doing post-
155 timeout spinning on installation in ``shed-tools`` (thanks to `@natefoo`_).
156 `Pull Request 97`_
157 * Fix coverage reporting on codacy (thanks to `@rhpvorderman`_).
158 `Pull Request 106`_
159 * Run-data-managers now outputs stderr of failed jobs (thanks to `@rhpvorderman`_).
160 `Pull Request 110`_
161
162 ---------------------
163 0.9.0 (2018-05-23)
164 ---------------------
165
166 * Update data managers when updating tools (thanks to `@rhpvorderman`_).
167 `Pull Request 78`_, `Issue 69`_
168 * Run data managers aggressive parallelization and refactoring (thanks to
169 `@rhpvorderman`_).
170 `Pull Request 79`_
171 * Makes publishing of imported workflows available (thanks to `@pcm32`_).
172 `Pull Request 74`_
173 * Add option to test tools on update/install for Galaxy 18.05 (thanks to `@jmchilton`_).
174 `Pull Request 81`_
175 * Upload 2.0 support for data library creation (thanks to `@jmchilton`_).
176 `Pull Request 89`_
177 * Fixes to revision parsing in tools.yaml (thanks to `@bgruening`_).
178 `Pull Request 70`_
179 * Add Codacy monitoring and badge (thanks to `@jmchilton`_).
180 `Pull Request 73`_
181 * Fix typo in project organization document (thanks to `@blankenberg`_).
182 `Pull Request 86`_
183 * Fix hardcoded log paths (thanks to `@rhpvorderman`_).
184 `Pull Request 85`_
185 * Fix ``shed-tools`` update argparse handling (thanks to `@rhpvorderman`_).
186 `Pull Request 88`_
187 * Fix a few lint issues (thanks to `@jmchilton`_).
188 `Pull Request 90`_
189
190 ---------------------
191 0.8.0 (2017-12-29)
192 ---------------------
193
194 * Many new documentation enhancements (thanks to @rhpvorderman, and others)
195 * rename of shed-install to shed-tools and add a new --latest and --revision argument (thanks to @rhpvorderman)
196 * many fixes and new tests by (thanks to @mvdbeek)
197 * Parallelization of run-data-managers (thanks to @rhpvorderman)
198 * run-data-managers now uses more advanced templating for less repetitive input yamls (thanks to @rhpvorderman)
199 * run-data-managers now checks if a genome index is already present before running the data manager (thanks to @rhpvorderman)
200 * ephemeris will now use https by default instead of http (thanks to @bgruening)
201
202 ---------------------
203 0.7.0 (2017-06-27)
204 ---------------------
205
206 * Many new documentation enhancements (thanks to @rhpvorderman, @erasche, and others) -
207 docs are now published to https://readthedocs.org/projects/ephemeris/.
208 * Fix problem with empty list options related to running data managers (thanks to @rhpvorderman).
209 * Enable data managers to run with API keys (thanks to @rhpvorderman).
210 * Add sleep command to wait for a Galaxy API to become available (thanks to @erasche).
211 * Preserve readable order of keys while processing tool lists (thanks to @drosofff).
212
213 ---------------------
214 0.6.1 (2017-04-17)
215 ---------------------
216
217 * Add Python 2 and 3 testing for all scripts against galaxy-docker-stable along with various
218 refactoring to reduce code duplication and Python 3 fixes. `#36
219 <https://github.com/galaxyproject/ephemeris/pull/36>`__
220
221 ---------------------
222 0.6.0 (2017-04-10)
223 ---------------------
224
225 * Add new connection options for setting up data libraries.
226
227 ---------------------
228 0.5.1 (2017-04-07)
229 ---------------------
230
231 * Fix new ``run-data-managers`` CLI entrypoint.
232
233 ---------------------
234 0.5.0 (2017-04-06)
235 ---------------------
236
237 * Add ``run-data-managers`` tool to trigger DM with multiple values and in order. `#30 <https://github.com/galaxyproject/ephemeris/pull/30>`_
238 * The workflow install tool now supports a directory of workflows. `#27 <https://github.com/galaxyproject/ephemeris/pull/27>`_
239 * enable global options in a tool yaml files, like `install_resolver_dependencies: true` `#26 <https://github.com/galaxyproject/ephemeris/pull/26>`_
240 * Mention mimum required galaxy versions. `#23 <https://github.com/galaxyproject/ephemeris/pull/23>`_ (thanks to @mvdbeek)
241
242
243 ---------------------
244 0.4.0 (2016-09-07)
245 ---------------------
246
247 * Be more generic in determining a server time-out (thanks to @afgane).
248 * Get tool list entrypoint and improvements (thanks to @mvdbeek).
249 * Rename ``tool_panel_section_name`` to ``tool_panel_section_label`` like
250 ansible-galaxy-tools (thanks to @nturaga).
251 * Add missing file ``tool_list.yaml.sample`` (thanks to @nturaga).
252
253 ---------------------
254 0.3.0 (2016-08-26)
255 ---------------------
256
257 * More robust shed-install script, install dependencies by default, improve logging
258 (thanks to @mvdbeek).
259
260 ---------------------
261 0.2.0 (2016-08-15)
262 ---------------------
263
264 * Add tool generate a tool list from a Galaxy workflow file
265 (thanks to @drosofff).
266 * Fix various code quality issues including adding beta support
267 for Python 3 (thanks in part to @mvdbeek).
268
269 ---------------------
270 0.1.0 (2016-06-15)
271 ---------------------
272
273 * Setup project, pull in scripts from `ansible-galaxy-tools
274 <https://github.com/galaxyproject/ansible-galaxy-tools>`__
275 and adapt them for usage as a library.
276
277 .. github_links
278 .. _Pull Request 155: https://github.com/galaxyproject/ephemeris/pull/155
279 .. _Pull Request 154: https://github.com/galaxyproject/ephemeris/pull/154
280 .. _Pull Request 150: https://github.com/galaxyproject/ephemeris/pull/150
281 .. _Pull Request 149: https://github.com/galaxyproject/ephemeris/pull/149
282 .. _Pull Request 146: https://github.com/galaxyproject/ephemeris/pull/146
283 .. _Pull Request 145: https://github.com/galaxyproject/ephemeris/pull/145
284 .. _Pull Request 130: https://github.com/galaxyproject/ephemeris/pull/130
285 .. _Pull Request 143: https://github.com/galaxyproject/ephemeris/pull/143
286 .. _Pull Request 142: https://github.com/galaxyproject/ephemeris/pull/142
287 .. _Pull Request 138: https://github.com/galaxyproject/ephemeris/pull/138
288 .. _Pull Request 137: https://github.com/galaxyproject/ephemeris/pull/137
289 .. _Pull Request 136: https://github.com/galaxyproject/ephemeris/pull/136
290 .. _Pull Request 135: https://github.com/galaxyproject/ephemeris/pull/135
291 .. _Pull Request 134: https://github.com/galaxyproject/ephemeris/pull/134
292 .. _Pull Request 129: https://github.com/galaxyproject/ephemeris/pull/129
293 .. _Pull Request 127: https://github.com/galaxyproject/ephemeris/pull/127
294 .. _Pull Request 126: https://github.com/galaxyproject/ephemeris/pull/126
295 .. _Pull Request 123: https://github.com/galaxyproject/ephemeris/pull/123
296 .. _Pull Request 122: https://github.com/galaxyproject/ephemeris/pull/122
297 .. _Pull Request 121: https://github.com/galaxyproject/ephemeris/pull/121
298 .. _Pull Request 120: https://github.com/galaxyproject/ephemeris/pull/120
299 .. _Pull Request 118: https://github.com/galaxyproject/ephemeris/pull/118
300 .. _Pull Request 114: https://github.com/galaxyproject/ephemeris/pull/114
301 .. _Pull Request 97: https://github.com/galaxyproject/ephemeris/pull/97
302 .. _Pull Request 103: https://github.com/galaxyproject/ephemeris/pull/103
303 .. _Pull Request 104: https://github.com/galaxyproject/ephemeris/pull/104
304 .. _Pull Request 105: https://github.com/galaxyproject/ephemeris/pull/105
305 .. _Pull Request 106: https://github.com/galaxyproject/ephemeris/pull/106
306 .. _Pull Request 110: https://github.com/galaxyproject/ephemeris/pull/110
307 .. _Pull Request 74: https://github.com/galaxyproject/ephemeris/pull/74
308 .. _Issue 69: https://github.com/galaxyproject/ephemeris/issues/69
309 .. _Pull Request 73: https://github.com/galaxyproject/ephemeris/pull/73
310 .. _Pull Request 78: https://github.com/galaxyproject/ephemeris/pull/78
311 .. _Pull Request 70: https://github.com/galaxyproject/ephemeris/pull/70
312 .. _Pull Request 86: https://github.com/galaxyproject/ephemeris/pull/86
313 .. _Pull Request 79: https://github.com/galaxyproject/ephemeris/pull/79
314 .. _Pull Request 85: https://github.com/galaxyproject/ephemeris/pull/85
315 .. _Pull Request 81: https://github.com/galaxyproject/ephemeris/pull/81
316 .. _Pull Request 90: https://github.com/galaxyproject/ephemeris/pull/90
317 .. _Pull Request 89: https://github.com/galaxyproject/ephemeris/pull/89
318 .. _Pull Request 88: https://github.com/galaxyproject/ephemeris/pull/88
319 .. _@abretaud: https://github.com/abretaud
320 .. _@bgruening: https://github.com/bgruening
321 .. _@blankenberg: https://github.com/blankenberg
322 .. _@rhpvorderman: https://github.com/rhpvorderman
323 .. _@pcm32: https://github.com/pcm32
324 .. _@jmchilton: https://github.com/jmchilton
325 .. _@Slugger70: https://github.com/Slugger70
326 .. _@natefoo: https://github.com/natefoo
327 .. _@martenson: https://github.com/martenson
328 .. _@mvdbeek: https://github.com/mvdbeek
329 .. _@rdvelazquez: https://github.com/rdvelazquez
330 .. _@jvanbraekel: https://github.com/jvanbraekel
331 .. _@innovate-invent: https://github.com/innovate-invent
332 .. _@erasche: https://github.com/erasche
333 .. _@nsoranzo: https://github.com/nsoranzo
334
335 .. _bioblend: https://github.com/galaxyproject/bioblend/
336 .. _nose: https://nose.readthedocs.org/en/latest/
337
338