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291 Commits
Author SHA1 Message Date
Marius van den Beek 7d6bce7983 Merge pull request #20851 from ksuderman/20750-ijson-parser 
Use a streaming based parser (ijson) when setting metadata for biom1 files.
 2025-09-25 21:19:45 +02:00
mvdbeek 28f562b8e1 Add package requirements 2025-09-25 18:08:58 +02:00
mvdbeek ac8ec8c08d Merge branch 'release_25.0' into dev 
# Conflicts:
#	client/package.json
#	lib/galaxy/version.py
#	package.json
#	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/meta/HISTORY.rst
#	packages/meta/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/schema/HISTORY.rst
#	packages/schema/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_shed/HISTORY.rst
#	packages/tool_shed/setup.cfg
#	packages/tool_shed_schema/HISTORY.rst
#	packages/tool_shed_schema/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tool_util_models/HISTORY.rst
#	packages/tool_util_models/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_client/HISTORY.rst
#	packages/web_client/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
 2025-09-23 19:10:06 +02:00
mvdbeek 3118cd2de2 Start work on 25.0.4.dev0 2025-09-23 19:09:48 +02:00
mvdbeek 1492e51b24 Create version 25.0.3 2025-09-23 19:09:42 +02:00
Matthias Bernt 70444d3177 Merge branch 'release_25.0' into dev 
# Conflicts:
#	client/package.json
#	lib/galaxy/version.py
#	package.json
#	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/meta/HISTORY.rst
#	packages/meta/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/schema/HISTORY.rst
#	packages/schema/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_shed/HISTORY.rst
#	packages/tool_shed/setup.cfg
#	packages/tool_shed_schema/HISTORY.rst
#	packages/tool_shed_schema/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tool_util_models/HISTORY.rst
#	packages/tool_util_models/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_client/HISTORY.rst
#	packages/web_client/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
 2025-08-13 14:34:10 +02:00
Matthias Bernt 2533594f58 Start work on 25.0.3.dev0 2025-08-13 14:34:04 +02:00
Matthias Bernt 34d077d19c Create version 25.0.2 2025-08-13 14:33:57 +02:00
Nate Coraor 3daf07de4b Merge branch 'release_25.0' into dev 
# Conflicts:
#	client/package.json
#	lib/galaxy/version.py
#	package.json
#	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/meta/HISTORY.rst
#	packages/meta/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/schema/HISTORY.rst
#	packages/schema/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_shed/HISTORY.rst
#	packages/tool_shed/setup.cfg
#	packages/tool_shed_schema/HISTORY.rst
#	packages/tool_shed_schema/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tool_util_models/HISTORY.rst
#	packages/tool_util_models/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_client/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
 2025-06-20 16:37:15 -04:00
Nate Coraor 751b52f1ec Start work on 25.0.2.dev0 2025-06-20 16:37:11 -04:00
Nate Coraor 5915a88342 Create version 25.0.1 2025-06-20 16:37:07 -04:00
Nate Coraor 96523d4570 Merge remote-tracking branch 'upstream/release_25.0' into dev 2025-06-20 16:18:47 -04:00
Nicola Soranzo 8b8d9794fa Fix one more package extra name containing underscores 2025-06-20 12:12:59 +01:00
John Chilton 85d634ae9f Implement fetch workbooks. 2025-06-19 22:54:56 -04:00
Nate Coraor 713a1b57a0 Pin isa-rwval minimum in data package 2025-06-19 14:40:50 -04:00
Ahmed Awan 0f9561ec32 Fix package versions 2025-06-18 12:23:14 -05:00
Ahmed Awan 3000e4343d Merge branch 'release_25.0' into dev 
# Conflicts:
#	lib/galaxy/version.py
#	packages/app/HISTORY.rst
#	packages/auth/HISTORY.rst
#	packages/config/HISTORY.rst
#	packages/data/HISTORY.rst
#	packages/files/HISTORY.rst
#	packages/job_execution/HISTORY.rst
#	packages/job_metrics/HISTORY.rst
#	packages/meta/HISTORY.rst
#	packages/navigation/HISTORY.rst
#	packages/objectstore/HISTORY.rst
#	packages/schema/HISTORY.rst
#	packages/selenium/HISTORY.rst
#	packages/test_api/HISTORY.rst
#	packages/test_base/HISTORY.rst
#	packages/test_driver/HISTORY.rst
#	packages/tool_shed/HISTORY.rst
#	packages/tool_util/HISTORY.rst
#	packages/tours/HISTORY.rst
#	packages/util/HISTORY.rst
#	packages/web_apps/HISTORY.rst
#	packages/web_framework/HISTORY.rst
#	packages/web_stack/HISTORY.rst
 2025-06-18 12:00:07 -05:00
Ahmed Awan 0d223a99b2 Start work on 25.0.1.dev0 2025-06-18 11:59:57 -05:00
Ahmed Awan b15565d03e Create version 25.0.0 2025-06-18 11:59:32 -05:00
Nate Coraor d8998d5227 Merge branch 'release_25.0' into dev 2025-06-17 12:17:34 -04:00
Nate Coraor cb08cd758f Merge branch 'release_24.2' into release_25.0 
# 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/meta/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/schema/HISTORY.rst
#	packages/schema/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_shed/HISTORY.rst
#	packages/tool_shed/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
 2025-06-17 12:17:33 -04:00
Nate Coraor dcd4cdca08 Start work on 24.2.5.dev0 2025-06-17 12:17:28 -04:00
Nate Coraor 7b1e4465bf Create version 24.2.4 2025-06-17 12:17:16 -04:00
Nicola Soranzo 8e9d05f5de Disallow SQLAlchemy 2.0.41 
due to //github.com/sqlalchemy/sqlalchemy/issues/12600 .
 2025-05-19 19:23:05 +01:00
John Davis 9b63eaf76c Add script to delete old job metrics records 2025-05-09 12:19:14 +02:00
Eli Chadwick 138b993946 add roc-validator to package test requirements 2025-05-07 10:45:12 +01:00
John Davis f236237d81 Add script to delete old galaxy session records 2025-04-28 12:49:10 -04:00
mvdbeek 3c6b6c5971 Merge branch 'release_24.2' into dev 2025-03-26 09:51:08 +01:00
mvdbeek 648239a31f Merge branch 'release_24.1' into release_24.2 2025-03-26 09:48:18 +01:00
mvdbeek 953a972349 Merge branch 'release_24.0' into release_24.1 2025-03-26 09:44:07 +01:00
Nicola Soranzo fb6139449c Drop unused alembic-utils from galaxy-data package requirements 
Last use removed in https://github.com/galaxyproject/galaxy/pull/15876 .
 2025-03-25 13:59:13 +00:00
Leonid Kostrykin 8a7191982e Fix package tests 2025-03-25 14:36:47 +01:00
mvdbeek c6b2a34916 Merge branch 'release_24.2' into dev 
# 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/schema/HISTORY.rst
#	packages/schema/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_shed/HISTORY.rst
#	packages/tool_shed/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
 2025-03-16 11:38:19 +01:00
mvdbeek 6a610a1b4b Start work on 24.2.4.dev0 2025-03-16 11:38:12 +01:00
mvdbeek f82f1fc5e8 Create version 24.2.3 2025-03-16 11:37:42 +01:00
mvdbeek c996ec452f Merge branch 'release_24.2' into dev 
# 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/schema/HISTORY.rst
#	packages/schema/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_shed/HISTORY.rst
#	packages/tool_shed/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
 2025-03-08 11:44:14 +01:00
mvdbeek 7ad18a9d78 Start work on 24.2.3.dev0 2025-03-08 11:44:06 +01:00
mvdbeek c80d7d92a1 Create version 24.2.2 2025-03-08 11:44:03 +01:00
Matthias Bernt 9d876d1a52 Merge branch 'release_24.2' into dev 
# 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/schema/HISTORY.rst
#	packages/schema/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_shed/HISTORY.rst
#	packages/tool_shed/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
 2025-02-28 12:39:11 +01:00
Matthias Bernt 5547ad5db9 Start work on 24.2.2.dev0 2025-02-28 12:39:06 +01:00
Matthias Bernt 8ff7c9b1b8 Create version 24.2.1 2025-02-28 12:39:03 +01:00
Nicola Soranzo edd8bccf4f Drop support for Python 3.8 2025-02-25 19:20:46 +00:00
John Davis 4f8244bc10 Merge branch 'release_24.2' into dev 2025-02-11 21:03:18 -05:00
John Davis b56638b9d6 Start work on 24.2.1.dev0 2025-02-11 20:41:00 -05:00
John Davis 490257d237 Create version 24.2.0 
This is the final version 24.2.0.
It contains the content generated by the release script, minus the
duplicate content (which resulted from the existing 24.2.0 changelogs
that had been pushed upstream on 2/6/25).
 2025-02-11 20:36:31 -05:00
John Davis 898fcfc981 Merge branch 'release_24.2' into dev 2025-02-11 09:48:43 -05:00
John Davis a6f3d74f9b Remove isa-rwval dependency from data package 2025-02-10 16:53:01 -05:00
Nicola Soranzo 829c7459f9 Merge branch 'release_24.2' into dev 2025-02-08 21:14:23 +00:00
Nicola Soranzo 1bc76f0c40 Add Python 3.13 classifier to packages 
Follow-up on https://github.com/galaxyproject/galaxy/pull/18449 .
 2025-02-08 18:58:58 +00:00
John Davis 54f918d09c Fix package versions 2025-02-07 00:53:54 -05:00