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d40fb56b98a05f96afee7ca23def37e75a305ffd
Commit Graph
691 Commits
Author SHA1 Message Date
Yakubov, Sergey d40fb56b98 Merge branch 'dev' into oidc_tokens 2023-03-27 10:41:56 -04:00
John ChiltonandNicola Soranzo 2f2dae29f7 Apply suggestions from code review 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2023-03-08 13:06:11 -05:00
John Chilton a0a2690670 Does this fix kombu? 2023-03-07 15:46:56 -05:00
mvdbeek 756d047e1c Merge branch 'release_23.0' into dev 2023-03-06 18:08:05 +01:00
mvdbeek 026b906616 Merge branch 'release_22.05' into release_23.0 2023-03-03 16:40:49 +01:00
Matthias Bernt 0451ad485b package name with dashes 2023-03-02 09:27:55 +01:00
Matthias Bernt 684ae67bd7 add conda_package_streaming to tool_util setup.cfg 2023-03-01 22:13:15 +01:00
Marius van den Beek 24d7809f4a Merge pull request #15446 from bernt-matthias/conda-package-fmt-change 
Fix for new style conda packages
 2023-03-01 15:42:18 +01:00
Nicola Soranzo 35d8f6a04a Unpin Beaker requirement 
This was initially pinned in https://github.com/galaxyproject/galaxy/pull/11192
but I cannot recall why exactly.
 2023-03-01 12:29:28 +00:00
Matthias Bernt 910ca41c22 add conda_package_streaming to tool_util setup.cfg 2023-02-26 10:44:38 +01:00
John Chilton c692ad8292 Merge pull request #15497 from usegalaxy-au/unified-filesources 
Unify url handling with filesources
 2023-02-22 10:07:19 -05:00
nuwang 4ccd124c41 Add more interface docs, regenerate client schema 2023-02-10 00:00:52 +05:30
nuwang 11ccfff186 Add s3fs to test requirements 2023-02-09 18:13:32 +05:30
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
Yakubov, Sergey 15051d41d0 add msal package dependency (for auth via azure ad) 2023-02-02 10:03:38 -05:00
Nicola Soranzo 4ca163b9ca Add support for Python 3.11 
- Update Python dependencies that didn't have a cp311 wheel: h5py and
  psycopg2-binary.
- For packages for which there is no recent version that works on all
  Python versions supported by Galaxy (numpy and scipy), replace old
  requirement with multiple Python-version-specific requirements.
 2023-02-02 01:18:25 +00:00
Nicola Soranzo a850a47419 Update pysam depedency to 0.20.0 
Fix `pysam.index()` calls which now use samtools 1.16 where
`samtools index input output` doesn't work any more if `output` is the path
of an already existing file, but `samtools index -o output input` works
fine.

Also:
- Pre-create the (empty) index file for mock test datasets as a unit test
  reproducer of the above issue.
- Fix `test_cram` unit test that wasn't checking the return value of
  `CRAM.set_index_file()`, which was in fact returning False because
  `test-data/2.cram` was not sorted (updated now).
 2023-01-01 03:37:53 +00:00
Nicola Soranzo 6d43c44c96 Extract list of packages ordered by dependency dag for reuse 
Also:
- Add missing ones: `navigation`, `selenium`, `tours`
- Fix `galaxy-selenium` requirements
 2022-12-13 16:57:37 +00:00
Nicola Soranzo ee7d51f2f5 Merge branch 'release_22.05' into dev 2022-12-09 11:36:00 +00:00
Nicola Soranzo 1eceea2a45 Add/remove/pin/unpin Python requirements 2022-12-09 02:01:26 +00:00
mvdbeek 8ff70c0bf5 Add script that builds all packages 2022-12-08 14:57:04 +01:00
mvdbeek 9c92c55a31 Reset all package HISTORY.rst file to 22.5.0.dev0 2022-12-08 13:24:06 +01:00
mvdbeek 3e4411b8f5 Merge branch 'release_22.05' into dev 2022-12-08 12:37:31 +01:00
mvdbeek fa21013dbe Merge branch 'release_22.01' into release_22.05 2022-12-08 12:35:37 +01:00
mvdbeek 4523cf9702 Bump to next dev version 2022-12-08 12:32:19 +01:00
mvdbeek 438012be66 Bump galaxy-util version to 22.1.2 2022-12-08 12:28:19 +01:00
mvdbeek c818c1e36a Update changelog 2022-12-08 12:27:36 +01:00
mvdbeek 173177e12e Add missing pyparsing dependency to galaxy-util 2022-12-08 12:01:55 +01:00
mvdbeek dc7c8e7ac6 Pin packaging to below 22 2022-12-08 12:01:55 +01:00
John Davis 0aa0feb610 Merge pull request #15004 from jdavcs/dev_mypy_workflow 
Run mypy on a fully loaded galaxy venv for stricter type checking
 2022-11-30 22:30:37 -05:00
Nicola Soranzo 3d5bcff5c1 Add pkce to dev/test requirements 
So `test_authenticate_set_pkce_verifier_cookie` unit test is not skipped.
 2022-11-30 16:34:32 +00:00
John DavisandNicola Soranzo 786a3e4375 Don't pip-install lint requirements for package tests 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-11-30 11:31:22 -05:00
John Davis 724ff9e17b Install mypy for package tests 2022-11-29 18:40:18 -05:00
John Davis 03732a7516 Re-add jinja2 to config package requirements 2022-11-21 18:12:04 -05:00
John Davis b934b27ea0 Move custom tempates unit test into app; rm jinja2 package dep from config 2022-11-21 18:12:04 -05:00
John Davis 86cc0f2b69 Move custom templates into the config package 2022-11-21 18:12:04 -05:00
Nicola Soranzo 2b362fbd1d Merge branch 'release_22.05' into dev 2022-11-17 22:50:45 +00:00
Nicola Soranzo 988f4e583c Merge branch 'release_22.01' into release_22.05 2022-11-17 22:48:35 +00:00
mvdbeek df7712927b Start work on galaxy-tool-util 22.1.6 2022-11-14 10:28:55 +01:00
mvdbeek 642c28a3e9 Release galaxy-tool-util-22.1.5 2022-11-14 10:22:28 +01:00
John Davis b11c18eb21 Merge pull request #14825 from neoformit/dev-html-email 
Looks great! Thanks, @neoformit 

For future ref/todo: we do need a more systematic/unified approach to handling path construction that handles tests that are arun both as standalone unit tests and as part of package tests (as per observation by @neoformit)
 2022-11-10 11:30:42 -05:00
Nicola Soranzo 1048abe3cf Update cwltool pin 2022-11-10 01:13:41 +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
Nicola Soranzo f5deb24dbb Use dnspython to check specifically for an "MX" DNS record 
when validating the domain name of the email address for a new user.

Fix https://github.com/galaxyproject/galaxy/issues/14829 .
 2022-11-03 12:08:35 +01:00
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
John Davis da83e159da Add jijna2 requirement to package install requirements 2022-11-01 10:31:28 -04:00
Cameron Hyde c03c94d0d9 Add jinja2 to test-requirements.txt 2022-11-01 13:58:31 +10:00
Nicola Soranzo 11597099a1 Merge branch 'release_22.05' into dev 2022-10-28 13:27:44 +01:00
Nicola Soranzo 06f518220f Merge branch 'release_22.01' into release_22.05 2022-10-28 13:25:16 +01:00
mvdbeek 238ab85379 Start work on galaxy-tool-util 22.1.5 2022-10-28 10:31:56 +02:00