| 0108d65 | John Davis | 22 February 2024, 00:03:00 UTC | Create version 23.2.1 | 22 February 2024, 00:03:00 UTC |
| ea9e2fb | Marius van den Beek | 20 February 2024, 14:43:55 UTC | Merge pull request #17497 from mvdbeek/provide_working_url_for_to_every_request [23.2] Provide working routes.url_for every ASGI request | 20 February 2024, 14:43:55 UTC |
| e9c9107 | Marius van den Beek | 20 February 2024, 14:43:20 UTC | Cut out intermediate environ variable Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 20 February 2024, 14:43:20 UTC |
| 877b5f6 | John Davis | 20 February 2024, 13:41:29 UTC | Merge pull request #17499 from martenson/clean-magres [23.2] Add magres datatype | 20 February 2024, 13:41:29 UTC |
| bba92a8 | mvdbeek | 19 February 2024, 18:41:27 UTC | Add type annotation for fix_url_for I have no clue why this doesn't fail type checking since we don't have a hint for app.legacy_mapper, but ok. | 20 February 2024, 09:01:30 UTC |
| 322326e | Marius van den Beek | 19 February 2024, 18:33:00 UTC | Drop unnecessary string substitution Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 20 February 2024, 09:01:30 UTC |
| f4bc7f7 | mvdbeek | 19 February 2024, 17:38:50 UTC | Provide working routes.url_for every ASGI request | 20 February 2024, 09:01:30 UTC |
| 65dcd58 | Martin Cech | 19 February 2024, 19:47:31 UTC | re-add expanded related datatypes definitions | 19 February 2024, 19:47:31 UTC |
| d5587ce | Martin Cech | 19 February 2024, 19:42:24 UTC | remove duplicated datatype entry | 19 February 2024, 19:42:24 UTC |
| 319f9ef | Nalin Gupta | 08 February 2024, 16:59:56 UTC | Added urls for datatype descriptions | 19 February 2024, 19:41:14 UTC |
| 50e6656 | Nalin Gupta | 07 February 2024, 15:50:39 UTC | Added description tags to datatypes Added description (and sometimes description_url) tags for param, castep, den_fmt, call, cif and magres datatypes | 19 February 2024, 19:40:47 UTC |
| 75a6682 | Nalin Gupta | 09 January 2024, 10:19:08 UTC | Improved linting, Fixed PBC not showing for EXTXYZ Also removed set_peek() method from extxyz due to functionality being present in AtomicStructFile abstract class. | 19 February 2024, 19:40:16 UTC |
| 0e16e39 | Nalin Gupta | 08 January 2024, 09:53:39 UTC | Changed parent of AtomicStructFile Earlier parent class was Text but was changed to GenericMol file for XYZ and Extended XYZ files | 19 February 2024, 19:40:16 UTC |
| bf89543 | Nalin Gupta | 08 January 2024, 06:21:52 UTC | Moved ASE metadata parsing to abstract class Transfered the metadata parsing using the ASE IO library to an abstract class "AtomicStructFile" | 19 February 2024, 19:40:16 UTC |
| ded1e99 | Nalin Gupta | 02 January 2024, 08:50:55 UTC | Small fix made to magres metadata output | 19 February 2024, 19:40:16 UTC |
| b27bd51 | Nalin Gupta | 20 December 2023, 17:01:56 UTC | Added capability to show metadata for magres file | 19 February 2024, 19:40:15 UTC |
| f3f9e6c | Patrick Austin | 08 December 2023, 12:08:57 UTC | Fix CI linting, tests for Magres datatype #26 | 19 February 2024, 19:40:13 UTC |
| e765fe2 | Nalin Gupta | 06 December 2023, 22:22:50 UTC | Adding sniffer for magres datatype | 19 February 2024, 19:39:48 UTC |
| a7afcc9 | Marius van den Beek | 19 February 2024, 09:40:11 UTC | Merge pull request #17491 from jdavcs/23.2_fix_merge [23.2] Fix merge | 19 February 2024, 09:40:11 UTC |
| e0baa03 | John Davis | 18 February 2024, 20:39:32 UTC | Delete file added during forward merge of 23.1 | 18 February 2024, 20:39:32 UTC |
| b83b8bb | John Davis | 18 February 2024, 20:31:25 UTC | Merge branch 'release_23.1' into release_23.2 | 18 February 2024, 20:31:25 UTC |
| 3308279 | John Davis | 18 February 2024, 20:22:08 UTC | Merge branch 'release_23.0' into release_23.1 | 18 February 2024, 20:22:08 UTC |
| 29f7a29 | Marius van den Beek | 16 February 2024, 14:25:25 UTC | Merge pull request #17481 from mvdbeek/succes_typo_fix [23.2] Fix succces typo | 16 February 2024, 14:25:25 UTC |
| c5632e5 | Marius van den Beek | 15 February 2024, 18:50:28 UTC | Merge pull request #17480 from bernt-matthias/topic/del-print [23.2] Remove two print statements | 15 February 2024, 18:50:28 UTC |
| 80c7cc2 | Matthias Bernt | 15 February 2024, 17:06:05 UTC | remove two print statements that I likely forgot the remove | 15 February 2024, 17:35:29 UTC |
| e781140 | mvdbeek | 15 February 2024, 17:09:47 UTC | Fix succces typo | 15 February 2024, 17:34:44 UTC |
| 44487a5 | Marius van den Beek | 15 February 2024, 15:39:13 UTC | Merge pull request #17474 from mvdbeek/fix_failed_metadata_state [23.2] Set metadata states on dataset association, not dataset | 15 February 2024, 15:39:13 UTC |
| 3cfe20c | Marius van den Beek | 15 February 2024, 11:34:43 UTC | Merge pull request #17477 from davelopez/23.2_backport_#17466 [23.2] Fix auto-select of file name in upload (Backport of #17466) | 15 February 2024, 11:34:43 UTC |
| 513ca74 | mvdbeek | 15 February 2024, 10:01:20 UTC | Drop overly complicated state setter logic I doubt anyone instinctively know when to use `._state`, `.state`, `.raw_set_dataset_state` or `.set_dataset_state` and I think that was part of what led to this bug. | 15 February 2024, 10:28:37 UTC |
| 4c9c809 | hujambo-dunia | 14 February 2024, 02:13:44 UTC | Fix for a regression change; Auto-select/highlight file name text in input field for usability; change was lost when not carried over to newer code platform from https://github.com/galaxyproject/galaxy/blob/release_23.1/client/src/mvc/upload/default/default-row.js#L139 | 15 February 2024, 09:18:00 UTC |
| 6d02125 | mvdbeek | 14 February 2024, 18:09:16 UTC | Set metadata states on dataset association, not dataset | 14 February 2024, 18:09:16 UTC |
| 51c5705 | Marius van den Beek | 14 February 2024, 15:48:31 UTC | Merge pull request #17471 from mvdbeek/merge_forward_conflict Merge release_23.1 into release_23.2 | 14 February 2024, 15:48:31 UTC |
| ccb3e90 | mvdbeek | 14 February 2024, 13:54:32 UTC | Merge branch 'release_23.1' into release_23.2 | 14 February 2024, 14:31:26 UTC |
| ed7c257 | Marius van den Beek | 13 February 2024, 17:14:29 UTC | Merge pull request #17406 from ahmedhamidawan/create_saveas_workflow_with_errors_bug [23.2] Fix creating new erronous workflow can produce multiple empty workflows | 13 February 2024, 17:14:29 UTC |
| f4229aa | Nicola Soranzo | 13 February 2024, 16:41:44 UTC | Merge pull request #17440 from mvdbeek/fix_it_templating [23.2] Build param dict before creating entrypoint | 13 February 2024, 16:41:44 UTC |
| 91d9d49 | Marius van den Beek | 13 February 2024, 16:19:03 UTC | Merge pull request #17459 from mvdbeek/backport_public_hdca_check [23.1] Only check access permissions in `/api/{history_dataset_collection_id}/contents/{dataset_collection_id}` | 13 February 2024, 16:19:03 UTC |
| d18003e | Ahmed Awan | 12 February 2024, 16:30:13 UTC | add api test for hdcas in public histories being accessible | 13 February 2024, 14:01:58 UTC |
| 4eab971 | Ahmed Awan | 09 February 2024, 15:57:59 UTC | remove `check_ownership` from `dataset_collections.contents` ... since this api only needs to `check_accessible` as it is not modifying a collection | 13 February 2024, 14:01:56 UTC |
| 8c3d967 | Ahmed Awan | 08 February 2024, 19:14:31 UTC | fix published history collections are empty on expand Only check ownership in `__get_history_collection_instance` if: `collection_instance.history.published` = False | 13 February 2024, 14:00:39 UTC |
| 9eebb60 | mvdbeek | 10 February 2024, 11:10:28 UTC | Sandwich IT entry point creating after param_dict building and env var creation | 13 February 2024, 13:57:12 UTC |
| c94ec0d | Marius van den Beek | 13 February 2024, 10:32:21 UTC | Merge pull request #17456 from davelopez/23.1_fix_bulk_operation_menu_bis [23.1] Fix history bulk operations menu (part 2) | 13 February 2024, 10:32:21 UTC |
| b7b5c05 | davelopez | 12 February 2024, 16:20:36 UTC | Increase readability | 12 February 2024, 16:20:36 UTC |
| 811f8cf | davelopez | 12 February 2024, 16:06:58 UTC | Fix bulk menu conditions | 12 February 2024, 16:06:58 UTC |
| 79fee2a | davelopez | 12 February 2024, 16:06:20 UTC | Add more test conditions for bulk menu | 12 February 2024, 16:06:20 UTC |
| f130a3e | davelopez | 12 February 2024, 10:17:31 UTC | Refactor test to reduce selector duplication | 12 February 2024, 10:17:31 UTC |
| 3aa8442 | mvdbeek | 08 February 2024, 10:42:43 UTC | Build param dict before creating entrypoint Fixes https://github.com/galaxyproject/galaxy/issues/17438. | 10 February 2024, 11:15:12 UTC |
| 8809779 | mvdbeek | 10 February 2024, 11:14:59 UTC | Add templating to test IT | 10 February 2024, 11:15:12 UTC |
| d483675 | Marius van den Beek | 10 February 2024, 10:40:40 UTC | Merge pull request #17448 from ahmedhamidawan/23.0_datasetStore_saveDatasets_fix [23.0] Fix `datasetStore.saveDatasets` bug | 10 February 2024, 10:40:40 UTC |
| 9d0a200 | Marius van den Beek | 10 February 2024, 10:38:53 UTC | Merge pull request #17445 from nuwang/make_extra_props_more_defensive More defensive access of extra props in filesources | 10 February 2024, 10:38:53 UTC |
| 948c013 | Ahmed Awan | 09 February 2024, 20:59:56 UTC | [23.0] Fix `datasetStore.saveDatasets` bug When we update the datasets in the `datasetStore`, we can sometimes set multiple properties to undefined. This happens because a dataset in the store fetched from `/api/datasets/${id}` has a keys mismatch from a dataset coming from `/api/histories/${historyId}/contents` in `watchHistory`, where the latter has lesser keys. To address this, I replaced 'localItem' with 'item' in the loop that updates the keys, ensuring the correct properties are retained during the store update. | 09 February 2024, 20:59:56 UTC |
| 8884dfa | John Davis | 09 February 2024, 18:41:34 UTC | Merge branch 'release_23.1' into release_23.2 | 09 February 2024, 18:41:34 UTC |
| 7bffadb | John Davis | 09 February 2024, 18:37:33 UTC | Merge branch 'release_23.0' into release_23.1 | 09 February 2024, 18:37:33 UTC |
| c7a5e4f | Nuwan Goonasekera | 09 February 2024, 11:11:45 UTC | Code review suggestion Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com> | 09 February 2024, 14:07:52 UTC |
| bffb7a9 | nuwang | 09 February 2024, 10:27:29 UTC | Use dataclass to initialize default values | 09 February 2024, 11:29:33 UTC |
| ae982a2 | nuwang | 09 February 2024, 06:33:24 UTC | Add initializers to filesource options | 09 February 2024, 11:29:32 UTC |
| bed5c5e | Marius van den Beek | 09 February 2024, 08:29:50 UTC | Merge pull request #17446 from jdavcs/23.0_truebug [23.0] Fix bug: true >> True | 09 February 2024, 08:29:50 UTC |
| c1f0aad | John Davis | 09 February 2024, 06:09:00 UTC | Fix typo | 09 February 2024, 06:09:00 UTC |
| e70ff43 | Marius van den Beek | 08 February 2024, 14:41:04 UTC | Merge pull request #17439 from mvdbeek/backport_model_store_fixes [23.2] Backport model store fixes | 08 February 2024, 14:41:04 UTC |
| 2d702a7 | mvdbeek | 08 February 2024, 11:22:32 UTC | Merge branch 'release_23.1' into release_23.2 | 08 February 2024, 11:22:32 UTC |
| 0008b4d | mvdbeek | 08 February 2024, 11:21:53 UTC | Merge branch 'release_23.0' into release_23.1 | 08 February 2024, 11:21:53 UTC |
| 4c1c8e2 | Marius van den Beek | 08 February 2024, 11:20:32 UTC | Merge pull request #17384 from ahmedhamidawan/fix_genome_build_filter_postgres [23.0] Fix History contents `genome_build` filter postgresql bug | 08 February 2024, 11:20:32 UTC |
| 327dfa0 | mvdbeek | 08 February 2024, 10:08:15 UTC | Merge branch 'release_23.1' into release_23.2 | 08 February 2024, 10:08:15 UTC |
| 62ee88d | Marius van den Beek | 08 February 2024, 10:04:07 UTC | Merge pull request #17433 from davelopez/23.1_fix_bulk_operations_menu [23.1] Fix history bulk operations menu conditions | 08 February 2024, 10:04:07 UTC |
| 87321dc | John Chilton | 25 January 2024, 15:03:06 UTC | Fix overlapping names in extra files for model stores. | 08 February 2024, 10:01:22 UTC |
| b8cf19f | John Chilton | 25 January 2024, 14:49:44 UTC | Utilities for higher level composite tests in test_model_store. | 08 February 2024, 10:01:17 UTC |
| cf8e72f | John Chilton | 23 January 2024, 18:08:37 UTC | Minimal test case demonstrating model stores break on implicit conversions. | 08 February 2024, 10:01:13 UTC |
| 2259e1f | John Chilton | 23 January 2024, 18:04:04 UTC | More de-duplication in test_model_store.py. | 08 February 2024, 10:01:09 UTC |
| 570a055 | John Chilton | 23 January 2024, 17:57:45 UTC | Reduce duplication in test_model_store. | 08 February 2024, 10:01:02 UTC |
| 406dda2 | Marius van den Beek | 08 February 2024, 09:57:00 UTC | Merge pull request #17419 from martenson/multi-input-sorting [23.2] add a test for multi input element when hda and dces are mixed together | 08 February 2024, 09:57:00 UTC |
| cb97ef1 | Marius van den Beek | 08 February 2024, 09:55:36 UTC | Merge pull request #17426 from davelopez/23.1_encode_tool_link_consistently [23.1] Encode tool link consistently | 08 February 2024, 09:55:36 UTC |
| 5e14d03 | Nicola Soranzo | 07 February 2024, 22:50:08 UTC | Merge branch 'release_23.1' into release_23.2 | 07 February 2024, 22:50:08 UTC |
| 52933ed | Nicola Soranzo | 07 February 2024, 22:48:53 UTC | Merge branch 'release_23.0' into release_23.1 | 07 February 2024, 22:48:53 UTC |
| f5bb817 | Martin Cech | 07 February 2024, 17:27:49 UTC | Merge pull request #17427 from jmchilton/workflow_label_modal_fix [23.2] Fix workflow report markdown editor toolbox becoming non-responsive. | 07 February 2024, 17:27:49 UTC |
| c654c88 | Marius van den Beek | 07 February 2024, 14:42:28 UTC | Merge pull request #17429 from nsoranzo/release_23.0_python-multipart_0.0.7 [23.0] Update python-multipart to 0.0.7 | 07 February 2024, 14:42:28 UTC |
| 1e84387 | Marius van den Beek | 07 February 2024, 14:42:10 UTC | Merge pull request #17431 from davelopez/23.2_fix_upload_target_history [23.2] Fix target history when uploading files | 07 February 2024, 14:42:10 UTC |
| f60f0ae | davelopez | 07 February 2024, 13:58:52 UTC | Fix new edge case where all items might be already deleted This case was previously prevented at the UI level but should be considered here. | 07 February 2024, 13:58:52 UTC |
| bc0b3eb | davelopez | 07 February 2024, 13:52:53 UTC | Fix menu display conditions to adapt to "any" filter | 07 February 2024, 13:52:53 UTC |
| 5f14cd2 | davelopez | 07 February 2024, 13:50:28 UTC | Add test coverage for "any" state in menu options | 07 February 2024, 13:50:28 UTC |
| a42993e | davelopez | 07 February 2024, 11:18:14 UTC | Fix target history when uploading files | 07 February 2024, 11:18:14 UTC |
| de8d456 | Nicola Soranzo | 07 February 2024, 05:44:11 UTC | Add missing Werkzeug test requirement Used in `test/unit/util/test_get_url.py` since commit 69ebbb761aa610c1eab2f92a385c34b47259ac32 . Pin Werkzeug in `lib/galaxy/dependencies/dev-requirements.txt` to latest version compatible with pytest-httpserver 1.0.6 . Fix unit test collection error on Python 3.11: ``` File "/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.11/site-packages/pytest_httpserver/httpserver.py", line 26, in <module> from werkzeug.http import parse_authorization_header ImportError: cannot import name 'parse_authorization_header' from 'werkzeug.http' (/home/runner/work/galaxy/galaxy/galaxy root/.tox/unit-coverage/lib/python3.11/site-packages/werkzeug/http.py) ``` | 07 February 2024, 05:44:42 UTC |
| 10ace7b | Nicola Soranzo | 06 February 2024, 17:33:18 UTC | Update python-multipart to 0.0.7 xref: https://github.com/tiangolo/fastapi/security/advisories/GHSA-qf9m-vfgh-m389 | 06 February 2024, 17:33:21 UTC |
| ee27cce | John Chilton | 06 February 2024, 16:32:58 UTC | Fix markdown editor toolbox becoming non-responsive. | 06 February 2024, 16:40:04 UTC |
| 7ff64b7 | Marius van den Beek | 06 February 2024, 14:27:57 UTC | Merge pull request #17414 from jdavcs/23.2_packages_build_1 [23.2] Cleanup versions, formatting in setup.cfg, HISTORY.rst in all packages | 06 February 2024, 14:27:57 UTC |
| d787727 | davelopez | 06 February 2024, 13:53:17 UTC | Add test case for tool IDs with `+` | 06 February 2024, 13:53:17 UTC |
| 22d5071 | davelopez | 06 February 2024, 13:30:49 UTC | Fix tool link encoding Makes it easier to share when pasting it in oder contexts outside the web browser. | 06 February 2024, 13:30:49 UTC |
| 71237cf | davelopez | 06 February 2024, 13:29:37 UTC | Add unit test for Tools copyLink utility | 06 February 2024, 13:29:37 UTC |
| c5742fc | Martin Cech | 02 February 2024, 20:41:06 UTC | add a test for multi input element when hda and dces are mixed together | 02 February 2024, 20:41:06 UTC |
| 019c495 | John Davis | 02 February 2024, 15:12:34 UTC | Fix formatting around new version in HISTORY.rst | 02 February 2024, 15:12:34 UTC |
| f7e6d16 | David López | 02 February 2024, 09:26:18 UTC | Merge pull request #17388 from davelopez/update_webdav_conf_sample [23.1] Set webdav file source to use temp files by default | 02 February 2024, 09:26:18 UTC |
| ac15c87 | John Davis | 02 February 2024, 02:54:54 UTC | Update package versions to 23.2.dev0 Update setup.cfg, HISTORY.rst. Make all dev package versions consistent. | 02 February 2024, 03:50:21 UTC |
| b83073f | John Davis | 01 February 2024, 21:57:55 UTC | Change version for schema and TS packages To make them consistent with other package versions: 23.1.0.dev0 >> 23.1.dev0. The extra "0" was likely added automatically by running the build_packages.sh script. | 01 February 2024, 23:34:11 UTC |
| 121e38d | John Davis | 01 February 2024, 21:44:49 UTC | Drop empty bullet points from package HISTORY.rst files | 01 February 2024, 21:44:49 UTC |
| 93e0725 | Ahmed Awan | 01 February 2024, 16:57:51 UTC | use POST api/workflows instead of `save_workflow_as` controller | 01 February 2024, 16:57:51 UTC |
| 5f60902 | Ahmed Awan | 01 February 2024, 16:16:58 UTC | fix workflow editor creater bugs Prevent the "expected Object got Array" error message. Ensure `CreatorEditor` is loaded with existing creator(s). | 01 February 2024, 16:25:46 UTC |
| 194f6bd | Ahmed Awan | 01 February 2024, 16:15:42 UTC | use `api/workflows` endpoint instead of `save_workflow_as` controller | 01 February 2024, 16:25:46 UTC |
| 9e4e81c | Ahmed Awan | 01 February 2024, 16:24:23 UTC | fix request handling on client for WorkflowEditor create/save as | 01 February 2024, 16:25:20 UTC |
| 0e499dc | Nicola Soranzo | 01 February 2024, 12:01:34 UTC | Merge branch 'release_23.1' into release_23.2 | 01 February 2024, 12:01:34 UTC |
| 11fdad0 | Nicola Soranzo | 01 February 2024, 12:00:50 UTC | Merge branch 'release_23.0' into release_23.1 | 01 February 2024, 12:00:50 UTC |
| 504053c | Marius van den Beek | 31 January 2024, 17:58:39 UTC | Merge pull request #17404 from nsoranzo/release_23.0_fix_docs_upload [23.0] Fix uploading of docs for release_NN.N branches | 31 January 2024, 17:58:39 UTC |
| e82b950 | Nicola Soranzo | 31 January 2024, 17:18:10 UTC | Fix uploading of docs for release_NN.N branches | 31 January 2024, 17:18:10 UTC |
