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Author SHA1 Message Date
Nicola Soranzo f4b246f98e Merge pull request #20920 from galaxyproject/dependabot/github_actions/codecov/codecov-action-5 
Bump codecov/codecov-action from 3 to 5
 2025-09-18 23:35:43 +01:00
Nicola Soranzo b7bce25a9d Merge pull request #20922 from galaxyproject/dependabot/github_actions/docker/setup-buildx-action-3 
Bump docker/setup-buildx-action from 2 to 3
 2025-09-18 23:28:10 +01:00
Nicola Soranzo 505b9e0e76 Merge pull request #20919 from galaxyproject/dependabot/github_actions/docker/build-push-action-6 
Bump docker/build-push-action from 4 to 6
 2025-09-18 23:25:46 +01:00
Nicola Soranzo 3aa23da366 Merge pull request #20918 from galaxyproject/dependabot/github_actions/docker/login-action-3 
Bump docker/login-action from 2 to 3
 2025-09-18 23:24:00 +01:00
dependabot[bot] 9679cba8b5 Bump docker/setup-buildx-action from 2 to 3 
Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2 to 3.
- [Release notes](https://github.com/docker/setup-buildx-action/releases)
- [Commits](https://github.com/docker/setup-buildx-action/compare/v2...v3)

---
updated-dependencies:
- dependency-name: docker/setup-buildx-action
  dependency-version: '3'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2025-09-18 18:46:54 +00:00
dependabot[bot] 1b52e4acb0 Bump codecov/codecov-action from 3 to 5 
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 5.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v3...v5)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2025-09-18 18:46:35 +00:00
dependabot[bot] 4511289bd8 Bump docker/build-push-action from 4 to 6 
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4 to 6.
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](https://github.com/docker/build-push-action/compare/v4...v6)

---
updated-dependencies:
- dependency-name: docker/build-push-action
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2025-09-18 18:46:26 +00:00
dependabot[bot] 077f6b6c66 Bump docker/login-action from 2 to 3 
Bumps [docker/login-action](https://github.com/docker/login-action) from 2 to 3.
- [Release notes](https://github.com/docker/login-action/releases)
- [Commits](https://github.com/docker/login-action/compare/v2...v3)

---
updated-dependencies:
- dependency-name: docker/login-action
  dependency-version: '3'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2025-09-18 18:46:23 +00:00
Nicola Soranzo d6a5626ab5 Merge pull request #20915 from nsoranzo/enable_dependabot_gh_actions 
Enable dependabot version updates for GitHub actions
 2025-09-18 19:45:19 +01:00
Nicola Soranzo ea0e7abfd5 Enable dependabot version updates for GitHub actions 2025-09-17 21:42:17 +01:00
Aysam Guerler f05c8a83bc Merge pull request #20914 from guerler/allow_creating_visualizations 
Allow creation of visualizations without dataset
 2025-09-17 14:58:23 +03:00
David López e44d3f096d Merge pull request #20332 from davelopez/explore_short_term_storage_expiration_indicator 
Add short term storage expiration indicator to history items
 2025-09-17 13:13:57 +02:00
guerler f83d772ff9 Only populate dataset if available 2025-09-17 12:50:10 +03:00
guerler 9fc7a01c80 Ship template with jupyterlite 2025-09-17 12:41:43 +03:00
guerler 1c12fde91f Change label 2025-09-17 12:24:20 +03:00
guerler 158df791e9 Update jupyterlite, display example notebook 2025-09-17 12:18:04 +03:00
guerler de5e40e706 Streamline selection option generation 2025-09-17 11:31:18 +03:00
guerler 3111eb2c6f Add tests, update placeholder selection text 2025-09-17 11:06:31 +03:00
guerler f520c8df41 Skip dataset id in query if not available 2025-09-17 09:03:30 +03:00
guerler d7066bec23 Update jupyterlite to not require a dataset 2025-09-17 09:00:11 +03:00
Nicola Soranzo f26ba3e6a0 Merge pull request #20844 from nsoranzo/integration_tests_updates 
Integration tests updates
 2025-09-16 18:31:02 +01:00
guerler afb7ab580c Fix naming for consistency 2025-09-16 18:57:46 +03:00
guerler e70546bb3e Allow creation of visualizations without dataset 2025-09-16 18:56:08 +03:00
Nicola Soranzo 14988f5a08 Drop conntrack from the list of packages to install 
It will be installed as part of the medyagh/setup-minikube action.
 2025-09-16 15:40:18 +01:00
Nicola Soranzo 2a73ef7332 Drop unneeded postgres and rabbitmq services 
We are always running them via minikube since commit 992edaa8b4 .

Also:
- Update PostgreSQL image version to 17 in minikube test setup to
  sync it with the other CI workflows.
 2025-09-16 15:40:17 +01:00
Aysam Guerler 979ae54b0b Merge pull request #20907 from guerler/add_alignmentviewer 
Add Multiple Sequence Alignment Viewer 2.0
 2025-09-16 11:09:08 +03:00
guerler e5d489078a Bump to version 0.0.3, support stockholm format 2025-09-16 09:45:40 +03:00
Ahmed Hamid Awan 2d513e834c Merge pull request #20911 from ahmedhamidawan/merge_25.0_into_dev_sept 
Merge 25.0 into dev
 2025-09-15 21:06:30 -05:00
John Davis 9c0ef303ab Merge pull request #20845 from AustralianBioCommons/oidc-pipeline-config 
OIDC authentication pipeline - allow adding extra steps to the default pipeline
 2025-09-15 21:31:15 -04:00
Ahmed Hamid Awan 1265e5091d Merge pull request #20908 from guerler/avoid_overscroll_behavior 
Avoid overscroll behavior
 2025-09-15 19:39:44 -05:00
marius-mather 1f4cd32967 Rebuild config and skip pre-commit changes 2025-09-16 08:58:52 +10:00
Ahmed Awan ea22c0e765 drop eager param from get_invocation in error report method 2025-09-15 17:16:55 -05:00
Ahmed Awan f823afcc2a Merge remote-tracking branch 'upstream/release_25.0' into merge_25.0_into_dev_sept 2025-09-15 14:46:12 -05:00
John Chilton 66852487fa Merge pull request #20862 from jmchilton/pulsar_15_10 
Various Container Execution Enhancements (including GCP Batch support)
 2025-09-15 15:03:34 -04:00
John Davis 286fd6e6be Merge pull request #20905 from galaxybot/dev_auto_update_dependencies 
Update Python dependencies
 2025-09-15 09:43:35 -04:00
marius-mather fff7a92d1c Update unit tests to use attribute access 2025-09-15 13:30:38 +10:00
marius-mather c11e7529c8 Merge remote-tracking branch 'upstream/dev' into oidc-pipeline-config 2025-09-15 11:05:44 +10:00
marius-mather 2700989c56 Use attribute access to get app_config value 2025-09-15 11:02:18 +10:00
marius-mather 6d7deabdb7 Rebuild config docs 2025-09-15 10:49:45 +10:00
marius-mather 0a2399cb3e Improve config descriptions 2025-09-15 10:48:11 +10:00
Nicola Soranzo 7f569cdb43 Type annotation fixes for mypy 1.18.1 2025-09-14 22:14:39 +01:00
guerler 2c55e74d8a Fix datatype description 2025-09-14 13:15:26 +03:00
guerler 9997c0aeaf Avoid overscroll behavior 2025-09-14 13:01:01 +03:00
guerler c6ae06d5d0 Add a2m file format as fasta subclass 2025-09-14 12:50:11 +03:00
guerler 102fd5bbea Update package version, add new test file 2025-09-14 12:41:13 +03:00
guerler 346392a3c8 Add alignment viewer 2.0 2025-09-14 08:46:39 +03:00
galaxybot 060f48e1d9 Update Python dependencies 
by running `make update-dependencies`.
 2025-09-13 03:09:59 +00:00
John Davis 89b9a50da9 Merge pull request #20827 from arash77/add-pptx-datatype 
[25.0] Fix DOCX detection and add PPTX support
 2025-09-11 23:36:49 -04:00
John Davis c47bb0c4f6 Merge pull request #20895 from mvdbeek/add_ldda_purged 
[25.0] Add LDDA purged property
 2025-09-11 12:27:40 -04:00
John Davis fb46c0a866 Merge pull request #20893 from cat-bro/custos_authnz_compare_email_case_insensitive 
[25.0] Make check for existing user in custos_authnz.py case insensitive
 2025-09-11 12:01:54 -04:00