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175 Commits
Author SHA1 Message Date
mvdbeek 0f2ef4dc0c Merge branch 'release_23.1' into dev 2023-09-14 13:43:50 +02:00
mvdbeek 63442d1d72 Fix regex validation for global inline flags 
Fixes https://github.com/galaxyproject/galaxy/issues/16676
 2023-09-13 12:00:57 +02:00
mvdbeek 1ee35c46bb Add dparse to app requirements 2023-09-01 15:07:06 +02:00
mvdbeek 521405136a Merge branch 'release_23.1' into dev 2023-07-29 12:28:41 +02:00
mvdbeek c314336705 Merge branch 'release_23.0' into release_23.1 
# Conflicts:
#	lib/galaxy/version.py
#	packages/app/HISTORY.rst
#	packages/app/setup.cfg
#	packages/auth/HISTORY.rst
#	packages/auth/setup.cfg
#	packages/config/HISTORY.rst
#	packages/config/setup.cfg
#	packages/data/HISTORY.rst
#	packages/data/setup.cfg
#	packages/files/HISTORY.rst
#	packages/files/setup.cfg
#	packages/job_execution/HISTORY.rst
#	packages/job_execution/setup.cfg
#	packages/job_metrics/HISTORY.rst
#	packages/job_metrics/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/selenium/HISTORY.rst
#	packages/selenium/setup.cfg
#	packages/test_api/HISTORY.rst
#	packages/test_api/setup.cfg
#	packages/test_base/HISTORY.rst
#	packages/test_base/setup.cfg
#	packages/test_driver/HISTORY.rst
#	packages/test_driver/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tours/HISTORY.rst
#	packages/tours/setup.cfg
#	packages/util/HISTORY.rst
#	packages/util/setup.cfg
#	packages/web_apps/HISTORY.rst
#	packages/web_apps/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
 2023-07-29 12:28:39 +02:00
mvdbeek 2fbbfd8417 Start work on 23.0.6.dev0 2023-07-29 12:28:35 +02:00
mvdbeek af730bc6b5 Create version 23.0.5 2023-07-29 12:28:32 +02:00
Nicola Soranzo 45e020e760 Merge branch 'release_23.1' into dev 2023-07-24 17:04:54 +01:00
Nicola Soranzo 0a73e1c512 Merge branch 'release_23.0' into release_23.1 2023-07-24 15:16:11 +01:00
Nicola Soranzo 741ecf6f44 Pin pysam to >=0.21.0 
This reverts commit 353c08cbb9 .

pysam 0.20.0 doesn't build for Python 3.11 on macOS, so we need to
temporarily add the unnecessary Cython runtime dependency that
pysam 0.21 brings in.
 2023-07-21 00:58:33 +01:00
Rendani Gangazhe 753d199542 Merge dev and resolve conflicts 2023-07-03 10:54:25 +02:00
Nate Coraor 8fee25f084 Merge branch 'release_23.1' into dev 2023-06-30 17:14:03 -04:00
Nate Coraor ea07ddba98 Merge branch 'release_23.0' into release_23.1 
# Conflicts:
#	lib/galaxy/version.py
#	packages/app/HISTORY.rst
#	packages/app/setup.cfg
#	packages/auth/HISTORY.rst
#	packages/auth/setup.cfg
#	packages/config/HISTORY.rst
#	packages/config/setup.cfg
#	packages/data/HISTORY.rst
#	packages/data/setup.cfg
#	packages/files/HISTORY.rst
#	packages/files/setup.cfg
#	packages/job_execution/HISTORY.rst
#	packages/job_execution/setup.cfg
#	packages/job_metrics/HISTORY.rst
#	packages/job_metrics/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/selenium/HISTORY.rst
#	packages/selenium/setup.cfg
#	packages/test_api/HISTORY.rst
#	packages/test_api/setup.cfg
#	packages/test_base/HISTORY.rst
#	packages/test_base/setup.cfg
#	packages/test_driver/HISTORY.rst
#	packages/test_driver/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tours/HISTORY.rst
#	packages/tours/setup.cfg
#	packages/util/HISTORY.rst
#	packages/util/setup.cfg
#	packages/web_apps/HISTORY.rst
#	packages/web_apps/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
 2023-06-30 17:14:03 -04:00
Nate Coraor 25b52a97f7 Start work on 23.0.5.dev0 2023-06-30 17:14:00 -04:00
Nate Coraor 03d9eb63b8 Create version 23.0.4 2023-06-30 17:13:57 -04:00
Nate Coraor c18ed28896 Merge remote-tracking branch 'upstream/release_23.1' into dev 2023-06-30 15:57:32 -04:00
Nate Coraor 2ca678482f Merge remote-tracking branch 'upstream/release_23.0' into release_23.1 2023-06-30 15:56:50 -04:00
Nate Coraor ab1e0485d7 Pin pydantic in packages to <2 2023-06-30 14:51:18 -04:00
Rendani Gangazhe 33dcace1f0 Add lib/galaxy/carbon_emissions module symlink to packages/app/galaxy/ directory 2023-06-30 16:11:26 +02:00
Martin Cech 469ff484b6 Merge branch 'release_23.1' into dev 2023-06-27 15:17:21 -07:00
Nicola Soranzo 4c0e27c9ab Remove pin on `packaging` in packages 
Follow-up on https://github.com/galaxyproject/galaxy/pull/16058
where the pin was removed from ``pyproject.toml`` .
 2023-06-27 12:55:24 +01:00
mvdbeek bb65b07584 Merge branch 'release_23.1' into dev 2023-06-26 09:32:44 +02:00
mvdbeek 0b1a41bd86 Merge branch 'release_23.0' into release_23.1 
# Conflicts:
#	lib/galaxy/version.py
#	packages/app/HISTORY.rst
#	packages/app/setup.cfg
#	packages/auth/HISTORY.rst
#	packages/auth/setup.cfg
#	packages/config/HISTORY.rst
#	packages/config/setup.cfg
#	packages/data/HISTORY.rst
#	packages/data/setup.cfg
#	packages/files/HISTORY.rst
#	packages/files/setup.cfg
#	packages/job_execution/HISTORY.rst
#	packages/job_execution/setup.cfg
#	packages/job_metrics/HISTORY.rst
#	packages/job_metrics/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/selenium/HISTORY.rst
#	packages/selenium/setup.cfg
#	packages/test_api/HISTORY.rst
#	packages/test_api/setup.cfg
#	packages/test_base/HISTORY.rst
#	packages/test_base/setup.cfg
#	packages/test_driver/HISTORY.rst
#	packages/test_driver/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tours/HISTORY.rst
#	packages/tours/setup.cfg
#	packages/util/HISTORY.rst
#	packages/util/setup.cfg
#	packages/web_apps/HISTORY.rst
#	packages/web_apps/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
 2023-06-26 09:32:42 +02:00
mvdbeek 1ef440e92c Start work on 23.0.4.dev0 2023-06-26 09:32:37 +02:00
mvdbeek b4adbb4ec5 Create version 23.0.3 2023-06-26 09:32:32 +02:00
mvdbeek 5413333aac Merge branch 'release_23.0' into dev 
# Conflicts:
#	lib/galaxy/version.py
 2023-06-13 17:58:26 +02:00
mvdbeek 414abff510 Start work on 23.0.3.dev0 2023-06-13 17:58:19 +02:00
mvdbeek a7f0a365be Create version 23.0.2 2023-06-13 17:58:13 +02:00
Matthias Bernt aa9cc5b9e8 Start work on 23.1.dev0 2023-06-08 15:54:32 +02:00
Matthias Bernt f722e122f7 Create version 23.0.1 2023-06-08 15:54:28 +02:00
John ChiltonandNicola Soranzo a8f3f00374 Apply suggestions from code review 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2023-03-10 10:05:40 -05:00
John Chilton 44e8429201 Does this fix kombu? 2023-03-10 10:05:38 -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 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 9c92c55a31 Reset all package HISTORY.rst file to 22.5.0.dev0 2022-12-08 13:24:06 +01:00
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 Chilton 5a3069d283 Pulsar infrastructure improvements for TES execution and MQ-less Kubernetes. 
Updating the Pulsar job runner/client for https://github.com/galaxyproject/pulsar/pull/302 and as described in the new docs at https://pulsar.readthedocs.io/en/latest/containers.html.
 2022-10-16 09:56:58 +02:00
Nicola Soranzo dda6feb391 Remove redundant license info from package READMEs 
The license is already specified in `setup.cfg` , which is the
canonical place.
This will simplify the transition to the MIT license.
 2022-09-09 17:20:24 +01:00
John Chilton 12b34ff47c API tests for the tool shed. 2022-08-29 09:51:20 -04:00
Michael R. Crusoe 59ac92c1c8 mark galaxy packages as containing typing information 2022-07-26 23:27:36 +01:00
John Chilton db68ac271d Decouple galaxy-app and galaxy-selenium. 
That was a lazy shortcut on my part and should have never happened.

This resolves that and also another task on my todo list of making an easily pip installable, lightweight way of getting access to the tours validation script at the same time by restructuring packages and cleaning up the dependency structure.

The navigation piece of galaxy-selenium has been split out of into its own package and tours now depend on that directly. In order to have that lightweight access to the tour validation code - tours have also been split out of app. This will also encourage that package to continue to be decoupled nicely from the larger galaxy-app package.
 2022-06-27 12:56:22 -04:00
John Chilton 7aa9ac539a Allow static components in tours. 2022-06-20 12:20:00 -04:00
Nicola Soranzo c5f3d2d04c Modernise build of galaxy-app package 
Also:
- Add missing files to `MANIFEST.in`
- Add missing requirements
 2022-06-10 00:51:05 +01:00
Nicola Soranzo 73bf57e9a0 Remove unused and unnecessary code 
- `PROJECT_OWNER`, `PROJECT_USERAME`, `RAW_CONTENT_URL` and `_version_re` are unused.
- `:changelog:` hyperlink target is unnecessary.
- `test_suite` and `tests_require` are deprecated since setuptools v41.5.0
 2022-06-09 22:55:07 +01:00
Nicola Soranzo e9b2262dd3 Move mypy configuration to `mypy.ini` 
So packages can use `setup.cfg` to replace `setup.py` .
 2022-06-08 10:35:18 +01:00
John Chilton b63b3735c0 Merge pull request #14022 from nsoranzo/package_fixes 
Use setuptools custom package discovery instead of explicit listing
 2022-06-07 12:24:33 -04:00
Dannon 4644922783 Merge pull request #13655 from mvdbeek/metadata_embed 
Create data_fetch and set_metadata celery tasks
 2022-06-07 10:27:06 -04:00
Nicola Soranzo aeef3318a2 Use setuptools custom package discovery instead of explicit listing 2022-06-06 23:48:37 +01:00