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Commit Graph
935 Commits
Author SHA1 Message Date
Alireza Heidari 4625293a0f remove notification favorite field from backend and update schema, migration and tests 2023-06-14 14:16:11 +02:00
davelopez 0bc982d218 Add periodic task to cleanup expired notifications 2023-05-26 18:04:05 +02:00
davelopez ab20569413 Add config option to enable/disable notifications 2023-05-26 18:04:04 +02:00
mvdbeek 49c82389ff Merge branch 'release_23.0' into dev 2023-05-26 12:56:53 +02:00
Nicola Soranzo 7fea2db936 Merge branch 'release_22.05' into release_23.0 2023-05-25 13:53:52 +01:00
Nicola Soranzo 1fedac75ab Fix `mulled-update-singularity-containers` documentation 
The `mulled-singularity-testing` command was never added to the
`galaxy-tool-util` package.
 2023-05-25 08:32:20 +01:00
Minh Vu a59e0b4a27 refactored 2023-04-27 11:21:29 +02:00
Minh Vu aecbe0cff1 Option to display a different message on the export citations tool page 2023-04-27 11:19:33 +02:00
Dannon 47966341c9 Merge pull request #15628 from ElectronicBlueberry/training-recommendations 
Add suggested Training material to Tool Form
 2023-04-26 07:59:20 -04:00
mvdbeek 3d836f09a7 Merge branch 'release_23.0' into dev 2023-04-19 14:43:36 +02:00
Laila Los 568624ce70 match using tool id 
rename repository to owner
 2023-04-17 08:39:17 +02:00
Laila Los 0a26f58bc4 fix config description 2023-04-17 08:39:15 +02:00
Laila Los 8f6127a41f add configurable gtn integration 2023-04-17 08:39:09 +02:00
mvdbeek 0542ebf8aa Add `ca_certs option` for sentry client 2023-04-16 22:57:59 +02:00
Nicola Soranzo 116ca90fdd Merge pull request #15861 from dannon/drop-legacy-history-config 
Drop use_legacy_history from config
 2023-03-28 18:21:56 +01:00
Dannon Baker fd0690a8fb Drop use_legacy_history from config -- this is no longer possible. 2023-03-28 10:23:59 -04:00
Nicola Soranzo c2eebd0bbe Fix `'myst' cross-reference target not found` warnings 
Also:
- Use auto-generated table of contents in tool schema
 2023-03-27 15:07:21 +01:00
Nicola Soranzo 0f70c68fd9 Migrate to MyST-Parser for Markdown docs 
replacing deprecated recommonmark.

Fix https://github.com/galaxyproject/galaxy/issues/13005 .

Also:
- Drop not very useful ``doc/source/dev/file_upload.md`` .
- Small doc and link fixes.
 2023-03-27 15:01:27 +01:00
mvdbeek bd753160bb Merge branch 'release_23.0' into dev 2023-03-15 19:20:21 +01:00
John Davis dda56025cc Run make config-rebuild 2023-03-13 11:59:39 -04:00
John Chilton 7688ac27cc More object store documentation. 2023-03-06 16:54:49 -05:00
Martin Cech e236d6919a update the admin activation docs 2023-02-28 13:08:11 -08:00
Dannon Baker 3aac36d588 Drop myexperiment.org exports 2023-02-14 10:45:52 -05:00
mvdbeek a31eb0489c Use sentry-fastapi integration, expose sampling rate 2023-02-10 13:03:09 +01:00
Dannon d2a4339c88 Merge pull request #15131 from Paprikant/beacon-integration 
Beacon integration
 2023-01-19 22:00:28 -05:00
Benno Weiss b906e4296d Merge branch 'dev' of https://github.com/galaxyproject/galaxy into beacon-integration 2023-01-17 18:30:22 +01:00
Nicola Soranzo 39c0000c1b Bump minimum pip version to 20.3 . Ignore `--replace-pip and --no-replace-pip` startup options 
Pip 20.3 added support for PEP 600, i.e. manylinux wheels using platform
tags of the form "manylinux_${GLIBCMAJOR}_${GLIBCMINOR}_${ARCH}". Fix
installation of dependencies like pysam 0.20.0 wheels, which otherwise need
to be built from source and can fail as reported by @assuntad23 in
https://gist.github.com/assuntad23/3022db63a6878f044a209961dd40e592

Also:
- Install `wheel` to fix warning like `Using legacy setup.py install for
  beaker, since package 'wheel' is not installed.`
- Drop unnecessary `defaults` channel from conda commands.
- Fix "SC2223: This default assignment may cause DoS due to globbing. Quote
  it." errors reported by `shellcheck -x` .
 2023-01-17 15:01:38 +00:00
Nicola Soranzo 5826b429d4 Merge pull request #14849 from mahendrapaipuri/auth_ldap3 
Add LDAP authenticator variant using `ldap3` package
 2023-01-09 15:41:54 +00:00
Mahendra Paipuri c9487b851f Improve wording based on PR comments 2023-01-09 15:16:40 +01:00
Dannon Baker 9de4e72563 Rebuild config including gravity stuff 2022-12-22 21:25:41 -05:00
Laila Los 7d7ac4111b rebuild config 2022-12-22 16:59:27 +01:00
Laila Los 34cbbc5ad6 add persistant theme swapping 2022-12-21 14:01:34 +01:00
Dannon 241b245cbc Merge pull request #14791 from anuprulez/update_tool_recommendation 
Update tool recommendation API using transformers (neural network)
 2022-12-20 20:01:46 -05:00
Martin Cech 063405a1cd replace the png favicon with svg version 
goes down from 16kb to 9kb and preserves all details

add padding to masthead logo

it now has no padding in the image itself

Add margin to svg

drop padding

since we decided to include it in logos

Slightly increase margin further
 2022-12-20 15:44:07 -08:00
Dannon Baker c0fca38cf0 Config rebuild 2022-12-19 15:32:36 -05:00
Dannon 40cf2fcb70 Update doc/source/admin/special_topics/interactivetools.rst 2022-12-19 12:52:42 -05:00
Sveinung Gundersen 9d588b8ea7 Updated nginx config for upstream proxy of path-based ITs 2022-12-17 16:56:44 +01:00
Mahendra Paipuri 51bc263ad4 Merge branch 'galaxyproject:dev' into auth_ldap3 2022-12-12 11:29:22 +01:00
mahendrapaipuri 064734b477 Merge branch 'dev' into auth_ldap3 2022-12-11 17:33:53 +01:00
mahendrapaipuri 3cf26d3b4d Address PR comments 2022-12-11 17:31:38 +01:00
John Chilton 4bd80ce6ef Flush out documentation and service-info for DRS API a bit. 2022-12-08 10:08:01 -05:00
John Chilton 8ff9fe2610 Implement initial GA4GH DRS Support. 
- Implement APIs for serving Galaxy's public datasets as DRS objects.
- Implement support in galaxy.files.uris for DRS URIs so that upload, etc... can use DRS URIs from other data repositories.

The ways this can be improved are endless:

- New object ID patterns can be implemented to allow access to composite data, metadata files from a bundle view of datasets.
- New object ID patterns can be implemented to allow access to collections as bundles of datasets.
- More auth types and AccessMethods could be implemented for loading datasets from clients.
- Some sort of scheme for providing authenticated URLs to non-public data could be implemented to provide access to more of Galaxy's data if user's can implement.

Despite all these limitations - I think having the guts in like this provide useful points for interested parties to go and add functionality to enable their desired usecases.
 2022-12-08 10:07:11 -05:00
PaprikantandWolfgang Maier 095ade1a81 Update doc/source/admin/galaxy_options.rst 
Co-authored-by: Wolfgang Maier <maierw@posteo.de>
 2022-12-07 10:55:45 +01:00
Benno Weiss 5bd9212560 added admin config for beacon sharing 2022-12-07 10:53:24 +01:00
guerler 72fd52f087 Deprecate brand title text option, logo now contains text 2022-11-30 17:19:07 -05:00
Linelle 9c5f5bc3a2 changed references from sample XML to sample YML 
added a sentence about where to find the XMLs as well in case people are still using those (it's me, i'm people)
 2022-11-30 14:50:19 -05:00
Linelle ec504562e3 change resubmission example link from xml to yml 
Test case for resubmission location used to be https://github.com/galaxyproject/galaxy/blob/dev/test/integration/resubmission_job_conf.xml which leads to 404, have changed it to https://github.com/galaxyproject/galaxy/blob/dev/test/integration/resubmission_job_conf.yml and made it linked text instead of plain URL
 2022-11-30 14:29:52 -05:00
Nate Coraor 1cdb7b5bcd Replace XML job conf sample with YAML. 
Prefer loading job_conf.yml, fall back to job_conf.xml with a warning if
it exists.
 2022-11-17 19:58:24 -05:00
John Chilton 1a2a534695 Merge pull request #14965 from jmchilton/remove_no_longer_useful_wsgi_middleware 
Remove old WSGI middleware that is no longer useful.
 2022-11-10 23:13:45 +01:00
John Davis b11c18eb21 Merge pull request #14825 from neoformit/dev-html-email 
Looks great! Thanks, @neoformit 

For future ref/todo: we do need a more systematic/unified approach to handling path construction that handles tests that are arun both as standalone unit tests and as part of package tests (as per observation by @neoformit)
 2022-11-10 11:30:42 -05:00