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281 Commits
Author SHA1 Message Date
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
Michael R. Crusoe 03211a48ee names of package extras cannot contain underscores. https://packaging.python.org/en/latest/specifications/core-metadata/#provides-extra-multiple-use 2025-06-20 12:12:45 +01:00
Nate Coraor 6a887e0aff Fix galaxy-config script, move install to galaxy-dependencies in app package 2025-06-19 16:58:43 -04:00
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 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
John Chilton f91012244b New packages galaxy-tool-util-models, galaxy-tool-shed-schema. 
The galaxy-tool-shed-schema package is basically pydantic models for the whole tool shed API. It is used by both the backend code for the new tool shed and the testing code that runs on both the old and new tool shed.

The creation of galaxy-tool-util-models package is something I've wanted to do for a while - it should solve some TODOs I've left in the base. I think beyond enabling galaxy-tool-shed-schema package - the other nice thing is that galaxy-schema code can now rely on various tool stuff without requiring dependency on any of the parser or runtime code.

This should also fix things for the new record types in #19377. I've introduced a type that can be used tools and is included schema for collection creation. The galaxy-tool-util-models packages can now be dependended on by galaxy-schema and galaxy-tool-util and these two packages do not need to depend on each other - either direction of that dependency would make me uncomfortable. xref
https://github.com/galaxyproject/galaxy/actions/runs/13704893929/job/38327692654?pr=19377
 2025-04-16 12:47:37 +02:00
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
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
John Davis c1934993ef Merge branch 'release_24.2' 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/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
 2025-02-06 22:46:18 -05:00
John Davis e3b1795275 Start work on 24.2.1.dev0 2025-02-06 22:46:15 -05:00
John Davis 2bff8f5a9a Create version 24.2.0 2025-02-06 22:46:04 -05:00
Matthias Bernt 21f8bc80ad Merge branch 'release_24.2' into dev 2024-12-11 10:48:13 +01:00
Matthias Bernt b5c1637a45 Merge branch 'release_24.1' into release_24.2 
# 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
 2024-12-11 10:48:07 +01:00
Matthias Bernt 0f83529907 Start work on 24.1.5.dev0 2024-12-11 10:47:56 +01:00
Matthias Bernt db7395b423 Create version 24.1.4 2024-12-11 10:47:48 +01:00
Nicola Soranzo 4d211a3e8b Explicitly add cwl-utils to dependencies 
Imported e.g. in `lib/galaxy/tools/expressions/evaluation.py` .
No actual change to requirements files as it's already included as a
dependency of cwltool.
 2024-12-05 13:21:54 +00:00
Arash 0d21224657 Add python-slugify library to app/setup.cfg 2024-11-05 16:13:11 +01:00
Nicola Soranzo ac480e7df5 Drop use of deprecated imghdr standard library module 
which has been removed in the upcoming Python 3.13 .
 2024-10-31 12:09:21 +00:00
Nicola Soranzo f0420d70a3 Pin minimum package versions for Python 3.13 support 
Also:
- Cheetah3 package on PyPI has been renamed to CT3 since 3.3.0, see
  https://cheetahtemplate.org/news.html
 2024-10-31 12:09:20 +00:00
Björn Grüning 29cd291d5a Merge pull request #19050 from natefoo/installed-no-config 
Run installed Galaxy with no config and a simplified entry point
 2024-10-29 07:55:38 +01:00
Matthias Bernt 3d66d5f8ae Merge branch 'release_24.1' 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
 2024-10-25 12:51:19 +02:00
Matthias Bernt 17056521bd Start work on 24.1.4.dev0 2024-10-25 12:51:08 +02:00
Matthias Bernt 71f5048e52 Create version 24.1.3 2024-10-25 12:51:02 +02:00
Nate Coraor 3021508b97 Add mercurial as a dep to app package for tool installs 2024-10-24 09:31:30 -04:00
Nicola Soranzo 3f9cdb40be Disallow SQLAlchemy 2.0.36 
due to https://github.com/sqlalchemy/sqlalchemy/issues/12019 .
 2024-10-21 18:11:21 +01:00
Matthias Bernt c80ce1d431 Start work on 24.1.3.dev0 2024-09-25 15:02:09 +02:00
Matthias Bernt b34611f422 Create version 24.1.2 2024-09-25 15:01:59 +02:00
Matthias Bernt 7dd606a6b2 Merge branch 'release_24.1' 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
 2024-09-25 14:29:37 +02:00
Matthias Bernt a788fbdc6d Start work on 24.1.3.dev0 2024-09-25 14:29:29 +02:00
Matthias Bernt 04abcd5b34 Create version 24.1.2 2024-09-25 14:29:26 +02:00
John Davis 329aa9360d Update package dev versions 2024-07-02 17:07:31 -04:00
John Davis 4c3a425956 Merge branch 'release_24.1' 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/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
 2024-07-02 16:02:17 -04:00