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2123 Commits
Author SHA1 Message Date
Martin Cech 6fa4fbba88 Merge pull request #19202 from nsoranzo/drop_thumbs_up 
[PROCEDURES] Drop thumbs up reaction as pull request approval method
 2024-12-05 21:58:09 +01:00
mvdbeek 40388b4dab Merge branch 'release_24.2' into dev 2024-11-26 16:47:33 +01:00
Nicola Soranzo 916890f5ab Drop thumbs up reaction as pull request approval method 
Also clarify that a -1 is a veto for normal pull requests as well,
as mentionied in the "Vetoes" subsection below.
 2024-11-25 16:00:29 +00:00
John Davis 6bc9940445 Merge pull request #17600 from bernt-matthias/datatype-lint 
[24.2] Add linters for datatypes
 2024-11-22 10:36:44 -05:00
Nicola Soranzo 1b54c0bcd8 Calculate hash for new non-deferred datasets when finishing a job 
This is configurable with two new options:
- `calculate_dataset_hash`: in which cases Galaxy should calculate
  a hash for a new dataset. Possible values: 'always', 'upload'
  (the default), 'never'.
- `hash_function`. Possible values: 'md5', 'sha1', 'sha256', 'sha512'

Hashes are calculated via a Celery task, so currently only if
the 'enable_celery_tasks' option is set to true.
 2024-11-21 15:55:14 +00:00
Dannon Baker e858bf01a2 Make config-rebuild 2024-11-18 20:42:12 -05:00
Dannon Baker 944ac9c786 Make openai key configurable 2024-11-18 09:11:20 -05:00
M Bernt f2c105d84f Merge branch 'dev' into datatype-lint 2024-11-11 16:19:21 +01:00
Marius van den Beek 9b39ec7ef3 Merge pull request #18996 from martenson/schema-cond 2024-11-01 03:43:13 -04:00
Nicola Soranzo 93078d949a Replace poetry with uv 
for lightning-fast Python dependency updates.

To update all dependencies (as done by the GitHub action):

$ make update-dependencies

To update only one package:

./lib/galaxy/dependencies/update.sh -p <PKG>
 2024-10-31 10:22:52 +00:00
Nate Coraor d622d2d8f1 Remove conda_auto_init default from schema as suggested 2024-10-28 14:50:01 -04:00
Nate Coraor 90caa402a5 Disable conda_auto_init default = true when not running from source 2024-10-24 10:05:41 -04:00
Matthias Bernt be3c547161 document format of extension 2024-10-22 09:28:31 +02:00
Martin Cech c6ead00287 run make config-revuild 2024-10-15 12:03:25 +02:00
John Chilton edc5bc2a8f Allow oauth2 file sources with Dropbox initial implementation. 2024-10-14 15:16:41 +02:00
Marius van den Beek fcb3bdff2b Merge pull request #18598 from sanjaysrikakulam/webdav_as_user_file_source 
Bring your own file sources: Add the WebDAV template and configuration
 2024-10-14 12:16:28 +02:00
Nicola Soranzo 6a24eaa65c Drop `html_theme_path` option deprecated in sphinx-rtd-theme 3.0.0rc1 
See https://sphinx-rtd-theme.readthedocs.io/en/stable/changelog.html
 2024-10-13 21:21:30 +01:00
Sanjay Srikakulam 22863a1ccb Add new config parameter for file sources temp dir and update the webdav file source 2024-10-10 10:44:40 +00:00
Sanjay Srikakulam 3d28b2b9c9 remove use_temp_files configuration parameter 2024-10-10 10:40:58 +00:00
Sanjay Srikakulam 1c9c33ee8d lint fix 2024-10-10 10:40:58 +00:00
Sanjay Srikakulam 2ca28420fe Add images of the webdav conf and template and update file source templates image 2024-10-10 10:40:58 +00:00
Sanjay Kumar Srikakulam 83eabbe054 lint fix 2024-10-10 10:40:58 +00:00
Sanjay Kumar Srikakulam 22791a8d43 Add WebDAV as user file source 
Adds WebDAV example template, configuration and updates the docs, and the file source model along with the client API schema
 2024-10-10 10:40:58 +00:00
John Chilton ab70b5be6a Rebuild schema... 2024-10-05 17:23:26 -04:00
John Chilton ad73e9e838 Tool Request models. 2024-09-30 13:25:02 -04:00
John Davis d0d0838c51 Merge pull request #18481 from kysrpex/interactivetoolssqlalchemy 
Support high-availability setups for the interactive tools proxy
 2024-09-04 18:04:53 -04:00
José Manuel Domínguez 9ee6636f4a Rename interactivetools_map_sqlalchemy to interactivetoolsproxy_map 2024-09-03 14:17:12 +02:00
Nicola Soranzo c778a2ae3f Remove conda defaults channel from more places 2024-09-02 14:03:18 +01:00
Polina Polunina ed48f84aa7 add data source doc to the list in index 2024-08-27 12:28:00 +02:00
John Chilton da220efd23 First pass at workflow step models - linked and unlinked. 
Work scoped out in 18536.
 2024-08-23 09:46:44 -04:00
José Manuel DomínguezandJohn Davis 018e5417c2 Mention that interactivetools_map_sqlalchemy overrides interactivetools_map in the latter's description 
Co-authored-by: John Davis <jdavcs@gmail.com>
 2024-08-09 09:58:30 +02:00
José Manuel Domínguez ffa8ea4f4d Fix typos in descriptions of interactivetools_map and interactivetools_map_sqlalchemy 
Authored-by: John Davis <jdavcs@gmail.com>
 2024-08-09 09:42:30 +02:00
Nicola Soranzo c222fdd66f Add Alireza to committers group 2024-07-29 17:33:06 +01:00
José Manuel Domínguez c1fd2b569b Merge branch 'dev' into interactivetoolssqlalchemy 2024-07-23 12:19:58 +02:00
José Manuel Domínguez dddf5ba9f6 Add note in interactive tools docs page informing about interactivetools_map_sqlalchemy setting 
Refer to SQLite docs page describing situations where a client/server RDBMS works better and provide an example. Link to the `interactivetools_map_sqlalchemy` on the Galaxy configuration page.
 2024-07-22 17:22:25 +02:00
José Manuel Domínguez ce6d0f73c5 Configure SQLAlchemy interactive tool maps via new interactivetools_map_sqlalchemy setting 
Define a new configuration property `interactivetools_map_sqlalchemy` to store interactivetool proxy mappings on a RDBMS supported by SQLAlchemy.

If set, it takes precedence over `interactivetools_map`. When unset, a SQLite mapping file located at `interactivetools_map` is used (as usual).
 2024-07-22 17:22:24 +02:00
John Chilton aca192eeaf SVG generation for tool state docs... 2024-07-15 09:46:13 -04:00
John Chilton 5359f8ba74 Input parameter schema. 2024-07-15 09:46:13 -04:00
Marius van den Beek a7fb571143 Merge pull request #18499 from bgruening/obs_cache_size 
small docs enhancement
 2024-07-11 11:33:32 +02:00
Nicola Soranzo ddc1cc1087 Merge pull request #18452 from martenson/com-proc 
[PROCEDURES] remove davebx from committers list
 2024-07-09 14:01:35 +01:00
Martin Cech 7264a82589 regenerate config sample and docs 2024-07-05 09:19:40 -07:00
Björn Grüning 3724309809 small docs enhancement 2024-07-05 10:46:44 +02:00
José Manuel Domínguez 967b59140e Merge branch 'refs/heads/dev' into interactivetoolssqlalchemy 2024-07-04 13:52:59 +02:00
José Manuel Domínguez b54bf35518 Support using a table in any database supported by SQLAlchemy as mapping for interactive tools 
Replace the class `InteractiveToolSqlite` in lib/galaxy/managers/interactivetool.py with a new class `InteractiveToolPropagatorSQLAlchemy`. The new class implements a SQLAlchemy "propagator" for `InteractiveToolManager` (on the same file). This propagator writes the mappings to the table named after the value of `DATABASE_TABLE_NAME`, in the database specified by the SQLAlchemy database url passed to its constructor. Change the constructor of `InteractiveToolManager` so that it uses `InteractiveToolPropagatorSQLAlchemy`.

Change the method `_process_config` of `galaxy.config.GalaxyAppConfiguration` so that it converts the value of `interactivetools_map` to a SQLAlchemy database url if it is a path.

Update documentation to reflect these changes.
 2024-07-02 11:24:34 +02:00
John Davis 7721bf377f Update doc/source/dev/create_release.rst 2024-06-28 11:42:01 +02:00
M BerntandMartin Cech df044c4fff Update doc/source/dev/create_release.rst 
Co-authored-by: Martin Cech <marten@bx.psu.edu>
 2024-06-28 11:33:49 +02:00
Martin Cech 631d348018 adjust committers membership 2024-06-28 10:45:24 +02:00
M Bernt d006411178 Minor additions to release process 2024-06-28 10:28:19 +02:00
Dannon Baker 6ec7521e1a Merge remote-tracking branch 'upstream/release_24.0' into release_24.1 2024-06-28 09:48:27 +02:00
John Davis c774caf7ab Add admin note on fastapi 2024-06-21 13:20:55 -04:00