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190 Commits
Author SHA1 Message Date
John Chilton f9e00f597a axe testing 2023-05-24 12:54:25 -04:00
John Davis 7084957ef0 Add TS alembic dir to ignore list in test scripts 
Otherwise alembic/env.py gets executed out of context at test collection
stage (via tox -e unit >> run_tests.sh), which raises an AttributeError
(alembic.context is not set in this case).
Same solution as in 3be1f6fef3

Also minor reformat.
 2023-02-08 00:33:48 -05:00
Nicola Soranzo 6c3741d388 Require selecting a test mode in `run_tests.sh` 
We have recently removed from this script the possibility to test
installed tools, which was the default when no test mode was
selected.

xref. https://github.com/galaxyproject/galaxy/pull/15326
 2023-01-18 17:53:26 +00:00
Dannon 2c65d8e755 Merge pull request #14035 from dannon/samples-rename 
Rename samples_tool_conf to sample_tool_conf
 2023-01-17 13:03:07 -05:00
Nicola Soranzo 39c0000c1b Bump minimum pip version to 20.3 . Ignore `--replace-pip and --no-replace-pip` startup options 
Pip 20.3 added support for PEP 600, i.e. manylinux wheels using platform
tags of the form "manylinux_${GLIBCMAJOR}_${GLIBCMINOR}_${ARCH}". Fix
installation of dependencies like pysam 0.20.0 wheels, which otherwise need
to be built from source and can fail as reported by @assuntad23 in
https://gist.github.com/assuntad23/3022db63a6878f044a209961dd40e592

Also:
- Install `wheel` to fix warning like `Using legacy setup.py install for
  beaker, since package 'wheel' is not installed.`
- Drop unnecessary `defaults` channel from conda commands.
- Fix "SC2223: This default assignment may cause DoS due to globbing. Quote
  it." errors reported by `shellcheck -x` .
 2023-01-17 15:01:38 +00:00
Dannon Baker d04fb67396 Rename samples_tool_conf to sample_tool_conf to match datatypes/data_manager naming convention 2023-01-10 10:03:23 -05:00
Nicola Soranzo 2cd3eb60ab Fix typos and wording 2023-01-04 09:40:24 +00:00
mvdbeek 3d17f022ee Drop unused run_tests.sh options 
Use planemo to test individual tools as needed.

Fixes https://github.com/galaxyproject/galaxy/issues/15231
 2022-12-19 11:02:54 +01:00
John Chilton 018d066e36 Useful test decorators and runtime support for annotating how tests will be used. 2022-11-26 11:28:36 -05:00
John Chilton aeac8c6060 Restore test framework features... 2022-11-26 11:28:36 -05:00
Nicola Soranzo 581d001828 Remove unused `require_new and GALAXY_TEST_HISTORY_ID` 2022-11-07 15:44:02 +00:00
Nicola Soranzo afa7b713bc Replace `GALAXY_TEST_INCLUDE_SLOW env variable with external_dependency_management` pytest marker 
Fix mulled tests missing tests in `test/unit/tool_util/test_conda_resolution.py` .

Also:
- Add `coverage` tox factor to generate coverage report.
 2022-11-03 21:43:37 +00:00
mvdbeek eec177839f Drop scripts/function_tests.py 2022-11-01 18:45:08 +00:00
Nicola Soranzo 5ca0aea54a Drop nose 
It's deprecated and unmaintained, and is broken under Python 3.10 .
 2022-11-01 18:45:07 +00:00
Nicola Soranzo 0391cd4b62 Rename FooBarTestCase test classes as TestFooBar in API, framework, performance, Selenium and ToolShed tests 
These are collected by pytest only because they are `unittest.TestCase` derived,
but normally pytest collects only test classes whose name starts with `Test`, see
https://docs.pytest.org/en/7.1.x/reference/reference.html#confval-python_classes

Also:
- Some type annotations
 2022-10-15 17:54:31 +01:00
Nicola Soranzo b204e8a8fd Add unit tests for CWL parsing 2022-06-22 03:25:55 +01:00
Sergey Golitsynskiy e8c12ae5fd Add alembic dir to ignore list in run_tests 
Otherwise alembic/env.py gets executed out of context at test collection
stage (via tox -e unit >> run_tests.sh), which raises an AttributeError
(alembic.context is not set in this case)
 2022-03-09 18:40:07 -05:00
Nicola Soranzo 4a31207701 Merge branch 'release_22.01' into dev 2022-02-28 20:21:56 +00:00
mvdbeek f4183ac5a0 Drop scripts/nosetests.py 2022-02-28 15:24:07 +01:00
mvdbeek c90e012fda Upload coverage results to codecov.io 2022-02-11 17:11:08 +01:00
Nicola Soranzo 98ecc39b1b Remove PhantomJS support, dropped in Selenium 4.0 2021-12-08 08:14:10 +00:00
John Chilton 9a586a58b9 Add CWL conformance API tests 
1) Download conformance tests to `test/functional/tools/cwl_tools` where
  they can be used also by framework and unit tests in the future.
2) Add populators to enable executing CWL conformance tests
3) Generate CWL conformance API tests only when needed for tests
 2021-11-23 14:10:21 +00:00
Nuwan Goonasekera 944e28a507 Remove tool_conf.xml.main which is no longer used 2021-08-25 21:41:06 +05:30
M BerntandMarius van den Beek f886978c40 Apply suggestions from code review 
- fix and simplify reading of env variable
- shorten doc

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2021-05-03 16:13:04 +02:00
Matthias Bernt 4697281406 doc 2021-05-03 12:55:23 +02:00
John Chilton e3dedd86bc Performance metrics for tests. 2021-02-12 20:44:05 -05:00
mvdbeek fa370998d8 Drop docker testing image 
We don't use this anymore and it's currently not building.
 2021-02-09 17:16:43 +01:00
Dave Bouvier 8d5d2e91a9 Grammar. 2021-01-11 21:59:32 -05:00
Dave Bouvier 3fe811ed7f Update coverage documentation. 2021-01-11 21:44:48 -05:00
John Chilton 0c69d41d6a Reword run_tests.sh to reflect cannot run qunit tests anymore and link to client docs. 2021-01-10 18:52:26 -05:00
John Chilton 083abd71eb Update run_tests.sh docs for defaults most python to pytest. 2021-01-10 18:52:26 -05:00
Nicola Soranzo 51f8f00afb Support complex markers in run_tests.sh 
Needed for the WIP CWL conformance tests.

Also, create self-contained HTML reports.
 2021-01-04 01:09:24 +00:00
mvdbeek 4f5f3dcfb2 Run selenium tests w/ pytest, github workflow 2020-11-22 18:44:33 +01:00
Dannon Baker 97ef4867aa Update build, etc., for swap 2020-08-11 10:26:06 -04:00
John Chilton bd02339d90 Implement integration Selenium tests. 2020-04-23 21:51:09 -04:00
mvdbeek 74a27f3de0 Move docker image build to ubuntu 18.04, drop unused stuff 2020-04-12 22:39:23 +01:00
Nicola Soranzo 437f51c2a6 Create Python3 virtualenv by default 
- Allow specifying Python to use to create virtualenv using GALAXY_PYTHON
  environment variable.
- Integrate Python support docs from https://galaxyproject.org/admin/python/
- Update virtualenv installation to use v16.7.9
 2020-02-09 02:54:24 +00:00
mvdbeek 33638c6796 Don't set GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION if GALAXY_TEST_DB_URI is set 
The actual database to target is generated dynamically, but since
GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION takes precedence the
wrong database is used.
 2020-01-09 14:40:48 +01:00
John Chilton 2266ffd87d Exclude galaxy_test when running unit tests. 2019-11-12 09:05:08 -05:00
John Chilton 72bae33923 Migrate selenium tests into lib/galaxy_test for packaging. 2019-11-12 09:05:08 -05:00
John Chilton d04c020747 Migrate api tests into lib/galaxy_test for packaging. 2019-11-12 09:05:08 -05:00
John Chilton 180d96c540 Refactor tool shed tests into tool shed namespace. 2019-11-12 09:05:07 -05:00
John Chilton 559b664b07 Refactor tool_shed webapp out of Galaxy. 2019-11-11 12:32:19 -05:00
Nicola Soranzo ac2af6a219 Set up a cache dir for pip when running tests with Docker 2019-11-04 13:51:31 +00:00
Nicola Soranzo 6b20da6533 Merge branch 'release_19.05' into release_19.09 2019-09-24 18:23:13 +01:00
John Chilton d89ea13449 Bugfix - Kill testing container when test script is killed. 2019-09-19 12:10:15 -04:00
Nate Coraor 058fabc121 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into installable 2019-07-08 12:27:21 +02:00
Nate Coraor 2964d830cd Excluded bundled tools from unit tests 2019-07-07 14:32:01 +02:00
Sergey Golitsynskiy b51c20ddfe Fix typo in run_tests.sh help text 2019-07-07 13:50:39 +02:00
Nate Coraor 37522f5e8e Merge branch 'dev' of https://github.com/galaxyproject/galaxy into installable 2019-07-05 16:05:17 +02:00