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88 Commits
Author SHA1 Message Date
mvdbeek 5e9dd557d5 Add basic unit test for lint_inputs 
This could of course be extended much more.
 2019-08-04 11:58:39 +02:00
Nicola Soranzo bbf17354c5 Fix broken link in `galaxy-app` package 
Broken in commit 42cf61fd36 .
 2019-07-19 02:36:36 +01:00
Martin Cech 00600e4006 Merge pull request #8298 from jmchilton/selenium_package 
Create galaxy-selenium package.
 2019-07-18 15:17:42 -04:00
John Chilton be7e881961 Merge pull request #8345 from ic4f/dev_toolutil_tests_restruct 
Restructure unit tests for tool_util package
 2019-07-17 16:47:59 -04:00
John Chilton da28369526 Merge pull request #8342 from nsoranzo/galaxy-tool-test 
Add ``galaxy-tool-test`` entry-point to ``galaxy-tool-util`` package
 2019-07-17 16:46:08 -04:00
Sergey Golitsynskiy 6fb6727d6d Merge remote-tracking branch 'upstream/dev' into dev_toolutil_tests_restruct 2019-07-16 23:16:59 -04:00
Sergey Golitsynskiy 0e4e1d9249 Restructure unit tests for tool_util package 
This replaces a previous (now closed) PR:
https://github.com/galaxyproject/galaxy/pull/8279

A few changes:
- tests for code in galaxy/tool_util moved under test/unit/tool_util
- common parts (used in both tools and tool_util) factored out into
  unittest_utils/sample_data.py
- symlink to sample_data.py in test/unit/tool_util/ is needed to make
  the tool_util package tests run. This is not an ideal solution, but it
  avoids duplication of the sample data used by tests in tools/ and
  tool_util/.
 2019-07-16 20:15:45 -04:00
Nicola Soranzo 8e8c64308a Fix use of `PIP_PROGRESS_BAR` env variable 
`PIP_PROGRESS_BAR` environment variable is used by `pip` to set the value
for the `--progress-bar` option. It seems that specifying it also only the
command line does not override it in some configurations, e.g. on TravisCI
Linux builds of BioBlend, see e.g.

https://travis-ci.org/galaxyproject/bioblend/jobs/558857557
 2019-07-16 17:17:32 +01:00
Nicola Soranzo 751806d371 Add `galaxy-tool-test entry-point to galaxy-tool-util` package 
As it was in galaxy-lib.
 2019-07-16 11:19:31 +01:00
Sergey Golitsynskiy ac5d7dfd46 Merge remote-tracking branch 'upstream/dev' into dev_unittest_bugfix 2019-07-15 19:17:44 -04:00
Martin Cech e45d7959a7 Merge pull request #8308 from jmchilton/push_scripts_into_subpackages 
Push galaxy-meta scripts into appropiate subpackages.
 2019-07-15 18:45:13 -04:00
Sergey Golitsynskiy 3df3ff0bec Fix package test 
The cause of this is related to pulling tool_util out of tools:
https://github.com/galaxyproject/galaxy/pull/8279

The solution here is a temporary hack (add helper module, util.py, to
tests/, then make tests a package).

A better solution will be to separate test/unit/tools into tools/ and
tool_util/ - I intend to take care of it soon.
 2019-07-13 20:18:57 -04:00
Sergey Golitsynskiy 2bb7149aac Move modules to tool_util package 2019-07-12 18:14:51 +01:00
Marius van den Beek 2691a4470d Merge pull request #8310 from dglaetzer/dev 
Add and run tests for auth package
 2019-07-09 13:07:40 +02:00
Marius van den Beek 64c71ca7e1 Merge pull request #8290 from natefoo/remove-ci-pip-progress-bar 
Don't show the pip progress bar when installing under CI
 2019-07-09 12:17:49 +02:00
Nate Coraor adc496eae3 Disable progress bar when testing package builds in CI 2019-07-09 11:59:44 +02:00
dglaetzer ec454313ea dummy tests for auth package 2019-07-08 17:28:32 +02:00
John Chilton 9b287ef06c Push scripts into subpackages. 2019-07-08 16:38:10 +02:00
John Chilton 753a151c76 Add dump tour script to galaxy-selenium package. 2019-07-08 15:48:19 +02:00
John Chilton c9ef1b6fad Merge pull request #8302 from dglaetzer/dev 
dummy tests for containers package
 2019-07-08 15:41:48 +02:00
dglaetzer 2a42853bfa add tests 2019-07-08 12:55:43 +02:00
dglaetzer 84fd69faba dummy tests for containers 2019-07-08 12:54:55 +02:00
Nate Coraor 058fabc121 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into installable 2019-07-08 12:27:21 +02:00
John Chilton 377e48918d Create galaxy-selenium package. 
This is *not* the tests, it is the components for interacting with Galaxy via Selenium that can be used in any Galaxy UI automation context - not just tests. This includes a tiny CLI framework for building apps that drive Galaxy this way.
 2019-07-08 12:21:47 +02:00
John Chilton 23241a29d7 Merge pull request #8280 from dglaetzer/dev 
get tests on data package running
 2019-07-08 11:41:36 +02:00
Nate Coraor 751503958f Fixes from PR review 2019-07-08 11:28:04 +02:00
John Chilton 1815a6547a Bring top-level galaxy Python files into galaxy-app. 2019-07-07 19:45:48 +02:00
Nate Coraor 2034980b77 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into installable 2019-07-07 13:50:41 +02:00
Nate Coraor d72f87abde Move the galaxy metapackage to packages/ (incomplete) 2019-07-07 13:36:38 +02:00
dglaetzer 560565b4e6 link maf_utilities back to it's original directory, fix requirements 2019-07-07 10:56:17 +02:00
Nicola Soranzo 1b6be605b8 Fix imports 2019-07-06 17:40:13 +02:00
dglaetzer b9de9edfac Merge branch 'dev' into dev 2019-07-06 16:55:07 +02:00
dglaetzer 0ca1550903 Merge remote-tracking branch 'upstream/dev' into dev 2019-07-06 16:50:11 +02:00
John Chilton 6abd85417c Merge pull request #8241 from jmchilton/more_packages_3 
Implement galaxy-web-apps package outline.
 2019-07-06 16:41:31 +02:00
Nicola Soranzo fea38ae367 Move linters from tools into tool_util (#8276) 
Move linters from tools into tool_util
 2019-07-06 15:40:51 +02:00
John Chilton bda718b711 [packages] Fix pypi links in README badges. 2019-07-06 14:15:14 +02:00
John Chilton 49ef4d91c6 Pin numpy since 1.17 doesn't work on Python 2. 2019-07-06 14:15:13 +02:00
John Chilton 59bc1aff2b Implement outline of galaxy-web-apps packages. 
Bring in more tool shed stuff into app package also.
 2019-07-06 14:15:13 +02:00
John Chilton 9b47a2dfe0 Add galaxy-web-stack and galaxy-web-framework packages. 2019-07-06 14:15:13 +02:00
John Chilton dee02db3e0 Move more modules into galaxy-app. 2019-07-06 14:15:13 +02:00
damian 64b94a2b86 symlinked tool shed utils back to their original directory 2019-07-06 14:12:21 +02:00
damian 54d2ca01f8 moved common_util.py, encoding_util.py and xml_util.py from tool_shed/util to galaxy/util/tool_shed (for data package) 2019-07-06 13:58:52 +02:00
Sergey Golitsynskiy 79660bb58d Move linters from tools into tool_util 
Also, update setup.py for tool_util package.

Ref: https://github.com/galaxyproject/galaxy/issues/8240

Note: `make updaterst` has not been run; waiting on
https://github.com/galaxyproject/galaxy/pull/8270
 2019-07-06 11:44:03 +02:00
Gianmauro Cuccuru 4b2718ba40 Remove test_metadata.py symlink from packages/job_execution 
waiting for a better code decomposition.

xref. https://github.com/galaxyproject/galaxy/issues/8240
 2019-07-06 09:54:26 +02:00
Nicola Soranzo 2e1c3ee1c7 Run tests for galaxy-tool-util package 2019-07-06 00:54:08 +02:00
Nicola Soranzo 1c292702ca Update PROJECT_EMAIL and PyPI URL for old packages 2019-07-05 16:41:11 +02:00
Nicola Soranzo 64516cb92f Remove unnecessary symlinks 2019-07-05 16:34:59 +02:00
John ChiltonandNicola Soranzo 94201a9e81 Update packages/ per review 
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2019-07-05 16:34:39 +02:00
dglaetzer 9cf0924578 Update test.sh 2019-07-05 14:08:09 +02:00
dglaetzer be10a32aa9 run tests for tool_util 2019-07-05 11:10:07 +02:00