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

..

special_topics

Update doc/source/admin/special_topics/mulled_containers.rst

2025-06-12 13:50:32 -04:00

_inc_proxy_prereq.md

Migrate to MyST-Parser for Markdown docs

2023-03-27 15:01:27 +01:00

_inc_proxy_serving_root.md

Migrate to MyST-Parser for Markdown docs

2023-03-27 15:01:27 +01:00

_inc_proxy_ssl.md

Migrate to MyST-Parser for Markdown docs

2023-03-27 15:01:27 +01:00

apache.md

Migrate to MyST-Parser for Markdown docs

2023-03-27 15:01:27 +01:00

authentication.md

Fix `'myst' cross-reference target not found` warnings

2023-03-27 15:07:21 +01:00

carbon_emissions.md

Move carbon intensity reference data to backend and add admin docs

2023-06-24 13:53:34 +02:00

cluster.md

Migrate to MyST-Parser for Markdown docs

2023-03-27 15:01:27 +01:00

conda_faq.rst

A few more updates to the tool deps documentation

2021-06-07 20:54:23 -04:00

config_logging.rst

Doc fixes

2022-08-19 18:33:20 +01:00

config-template-secrets-create.png

Implement file source templates

2024-05-20 12:18:47 -04:00

config-template-secrets-edit.png

Implement file source templates

2024-05-20 12:18:47 -04:00

config.rst

Display 'Config Options' as subheading of 'Galaxy Configuration'

2022-09-27 15:03:03 -04:00

container_resolvers.rst

Fix bug in admin/container docs section title markup

2024-05-13 21:03:39 -04:00

data_tables.md

change text in a minor way

2024-04-18 18:55:38 +02:00

data.md

Implement file source to integrate Galaxy with RSpace

2025-05-09 12:04:46 +02:00

db_migration.md

Add documentation on handling a deadlock error during db migration

2025-02-05 15:03:33 -05:00

dependency_resolvers.rst

Remove conda defaults channel from more places

2024-09-02 14:03:18 +01:00

dropbox_callback.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

dropbox_client_creds.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

dropbox_create_app_options_1.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

dropbox_create_button.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

dropbox_scopes.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

file_source_azure_configuration_template.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

file_source_azure_configuration.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

file_source_dropbox_configuration_template.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

file_source_dropbox_configuration.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

file_source_elabftw_configuration_template.png

Set writable: true in file source template for eLabFTW

2025-02-13 15:33:56 +01:00

file_source_elabftw_configuration.png

Set writable: true in file source template for eLabFTW

2025-02-13 15:33:56 +01:00

file_source_ftp_configuration_template.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

file_source_ftp_configuration.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

file_source_invenio_configuration_template.png

Add InvenioRDM file source configuration documentation and templates

2025-02-17 13:44:19 +01:00

file_source_invenio_configuration.png

Add InvenioRDM file source configuration documentation and templates

2025-02-17 13:44:19 +01:00

file_source_posix_configuration_template.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

file_source_posix_configuration.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

file_source_rspace_configuration_template.png

Implement file source to integrate Galaxy with RSpace

2025-05-09 12:04:46 +02:00

file_source_rspace_configuration.png

Implement file source to integrate Galaxy with RSpace

2025-05-09 12:04:46 +02:00

file_source_s3fs_configuration_template.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

file_source_s3fs_configuration.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

file_source_templates.png

Implement file source to integrate Galaxy with RSpace

2025-05-09 12:04:46 +02:00

file_source_webdav_configuration_template.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

file_source_webdav_configuration.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

file_source_zenodo_configuration_template.png

Add Zenodo file source template documentation

2025-02-19 10:36:33 +01:00

file_source_zenodo_configuration.png

Add Zenodo file source template documentation

2025-02-19 10:36:33 +01:00

framework_dependencies.rst

Replace poetry with uv

2024-10-31 10:22:52 +00:00

galaxy_options.rst

Merge pull request #20510 from nsoranzo/remove_ToolDocumentCache

2025-07-29 17:03:42 +02:00

gen_diagrams.py

Fix isort linting

2025-05-09 12:14:20 +02:00

index.rst

Add basic documentation for admins

2025-05-12 10:54:56 +02:00

job_metrics.rst

Support setting and displaying timezone with the core metrics plugin

2025-05-06 11:45:51 -04:00

jobs.md

Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc

2024-06-21 16:58:21 +02:00

migrating_to_gunicorn.md

Migrate to MyST-Parser for Markdown docs

2023-03-27 15:01:27 +01:00

mq.md

Update Celery and Kombu links

2022-05-06 13:29:14 +01:00

nginx.md

fix docs for nginx

2025-08-11 11:10:50 +02:00

object_store_aws_s3_configuration_template.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

object_store_aws_s3_configuration.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

object_store_azure_configuration_template.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

object_store_azure_configuration.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

object_store_boto3_configuration_template.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

object_store_boto3_configuration.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

object_store_disk_configuration_template.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

object_store_disk_configuration.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

object_store_generic_s3_configuration_template.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

object_store_generic_s3_configuration.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

object_store_templates.png

Allow oauth2 file sources with Dropbox initial implementation.

2024-10-14 15:16:41 +02:00

options.rst

…

production.md

Update production docs to mention Celery

2024-04-05 17:08:28 +02:00

proxy_package_layout.rst

Drop remaining references to uWSGI

2022-03-21 13:44:37 +01:00

python.md

Python 3.8 as new minimum version

2023-11-26 18:34:09 +00:00

reports_options.rst

Remove old WSGI middleware that is no longer useful.

2022-11-10 05:28:24 -05:00

reports.rst

Drop uWSGI from Galaxy Reports documentation

2022-02-18 01:44:33 -05:00

s3_configuration_template.png

Implement file source templates

2024-05-20 12:18:47 -04:00

s3_configuration.png

Implement file source templates

2024-05-20 12:18:47 -04:00

scaling.md

Clarify how to separate job and workflow scheduling

2025-07-09 10:22:08 +02:00

search_for_new_screenshots.py

Implement file source to integrate Galaxy with RSpace

2025-05-09 12:04:46 +02:00

security.md

Migrate to MyST-Parser for Markdown docs

2023-03-27 15:01:27 +01:00

tool_panel.rst

Apply suggestions from code review

2023-11-27 13:40:33 +01:00

useful_scripts.rst

Add warning, gxadmin script ref to script, docs

2025-05-09 12:19:16 +02:00

user_defined_tools.md

Add basic documentation for admins

2025-05-12 10:54:56 +02:00

user_file_source_form_full_aws_public.png

Implement file source templates

2024-05-20 12:18:47 -04:00

user_file_source_form_full_azure.png

Implement file source templates

2024-05-20 12:18:47 -04:00

user_file_source_form_full_elabftw.png

Update eLabFTW file source template docs

2025-02-17 13:10:32 +01:00

user_file_source_form_full_ftp.png

Implement file source templates

2024-05-20 12:18:47 -04:00

user_file_source_form_full_invenio.png

Add InvenioRDM file source configuration documentation and templates

2025-02-17 13:44:19 +01:00

user_file_source_form_full_rspace.png

Implement file source to integrate Galaxy with RSpace

2025-05-09 12:04:46 +02:00

user_file_source_form_full_webdav.png

Add images of the webdav conf and template and update file source templates image

2024-10-10 10:40:58 +00:00

user_file_source_form_full_zenodo.png

Add Zenodo file source template documentation

2025-02-19 10:36:33 +01:00

user_object_store_form_full_aws_s3.png

Implement file source templates

2024-05-20 12:18:47 -04:00

user_object_store_form_full_azure.png

Implement file source templates

2024-05-20 12:18:47 -04:00

user_object_store_form_full_gcp_s3_interop.png

Implement file source templates

2024-05-20 12:18:47 -04:00