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231ea7db6e69a307db994801399377618f4a93b7
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1004 Commits
Author SHA1 Message Date
mvdbeek 231ea7db6e Merge branch 'release_25.0' into release_25.1 
# 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
 2025-11-18 16:02:27 +01:00
mvdbeek f764acd337 Start work on 25.0.5.dev0 2025-11-18 16:02:22 +01:00
mvdbeek cca180264e Create version 25.0.4 2025-11-18 16:02:15 +01:00
Nicola Soranzo 86e45d3c01 Add missing more-itertools dependency 
First use added in commit 8f7271d67d .
 2025-10-31 12:15:59 +00:00
mvdbeek 38a7d23fbc Drop setup-node action where possible 
Where we still use the action we don't install python dependencies.
 2025-09-28 10:05:41 +02:00
mvdbeek b488cf2694 Use nodejs-wheel to install node 2025-09-27 09:17:12 +02:00
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
Nicola Soranzo 7a65393d4b Merge branch 'release_25.0' into dev 2025-08-21 16:25:52 +01:00
Marius van den Beek fed092fe46 Merge pull request #20698 from davelopez/add_fsspec_support 
Add `fsspec` base implementation for File Source plugins
 2025-08-20 10:58:47 +02:00
Marius van den Beek 41a72b2ab9 Merge pull request #20592 from jmchilton/tool_landing 
Implement Data Landing Requests
 2025-08-19 14:55:55 +02:00
davelopez f45eb4ca1f Add fsspec to dependencies 2025-08-19 10:19:34 +02:00
Nicola Soranzo c16cd2da5e Remove `packages/meta/requirements.txt` 
Replacing it with some placeholder text in
https://github.com/galaxyproject/galaxy/commit/7a8399ca858c85e04f6ae6d280595d56e12ae2d9
wasn't particularly useful, as `git add` would ignore `.gitignore`
and keep tracking changes to it.
 2025-08-18 16:56:13 +01:00
John Chilton ad8dc1390d Component for displaying data fetch requests. 2025-08-18 11:08:05 -04:00
davelopez fcc87f110c Add entry point for galaxy file sources configuration validation 2025-08-18 16:57:00 +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
Nicola Soranzo 1d9d93ea50 Merge branch 'release_25.0' into dev 2025-08-07 15:54:38 +01:00
Marius van den Beek b48e97552f Merge pull request #19305 from jmchilton/sample_sheets 
Implement Sample Sheets
 2025-07-30 11:14:38 +02:00
Marius van den Beek 393e005ce9 Merge pull request #20510 from nsoranzo/remove_ToolDocumentCache 
Remove deprecated tool document cache
 2025-07-29 17:03:42 +02:00
John Chilton d26605517e Implement sample sheets. 2025-07-25 11:46:59 -04:00
Nicola Soranzo 7a8399ca85 Remove content from packages/meta/requirements.txt 2025-07-15 14:54:38 +01:00
Nicola Soranzo 6ec1249584 Merge branch 'release_25.0' into dev 2025-07-10 12:16:38 +01:00
Nicola Soranzo b2215984a9 Drop support for Python 3.7 in 5 packages 2025-07-08 16:48:36 +01:00
Nicola Soranzo 7ebd10829b Merge branch 'release_25.0' into dev 2025-06-25 22:52:37 +01:00
Nicola Soranzo 9007d8692d Remove deprecated `ToolDocumentCache` 
Close https://github.com/galaxyproject/galaxy/issues/20432 .
 2025-06-24 23:10:53 +01:00
Nicola Soranzo e8bdedef47 Fix description and metadata of some packages 2025-06-23 13:12:49 +01:00
Nicola Soranzo 1504579672 Merge branch 'release_25.0' into dev 2025-06-21 18:09:07 +01:00
Nate Coraor 2d8d235726 Use venv instead of virtualenv in package make setup-venv 2025-06-20 17:41:32 -04:00
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
Nate Coraor 423177986e Also update gravity pints in pyproject and config package tests 2025-06-20 12:15:36 -04:00
Nicola Soranzo 8b8d9794fa Fix one more package extra name containing underscores 2025-06-20 12:12:59 +01:00
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
Marius van den Beek 94ed4a6a9b Merge pull request #20531 from natefoo/config-script-fixes 
[25.0] Fix `galaxy-config` script, move install to `galaxy-dependencies` in app package
 2025-06-20 09:46:11 +02:00
Marius van den Beek a594358d91 Merge pull request #20527 from natefoo/isa-rwval-0.10.11 
[25.0] Pin isa-rwval 0.10.11, drop conditional import handling
 2025-06-20 09:43:07 +02:00
John Chilton 85d634ae9f Implement fetch workbooks. 2025-06-19 22:54:56 -04:00
Nate Coraor 6a887e0aff Fix galaxy-config script, move install to galaxy-dependencies in app package 2025-06-19 16:58:43 -04:00
Nate Coraor 713a1b57a0 Pin isa-rwval minimum in data package 2025-06-19 14:40:50 -04:00
Nate CoraorandNicola Soranzo ba5f68fbc4 Update packages/test.sh 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2025-06-19 14:24:39 -04:00
Nate Coraor eda7b605c9 Merge and update package build and install scripts 2025-06-19 13:31:42 -04:00
Nate Coraor 1599019e42 Update metapackage pins to dev version 2025-06-19 13:29:45 -04:00
Marius van den Beek 7f257f58f6 Undo packages_by_dep_dag.txt changes 2025-06-19 09:42:36 +02:00
Nate Coraor fde1201c75 Fixes for static handling and the web_client package 2025-06-18 21:48:19 -04:00