From 8253f9e3786fa8cc5a599f4a0e211fc2a1be3188 Mon Sep 17 00:00:00 2001 From: John Davis Date: Sat, 30 Nov 2024 01:37:16 -0500 Subject: [PATCH] 24.2 release notes --- doc/source/releases/24.2.rst | 775 +++++++++++++++++++++ doc/source/releases/24.2_announce.rst | 63 +- doc/source/releases/24.2_announce_user.rst | 149 ++++ doc/source/releases/24.2_prs.rst | 249 +++++++ doc/source/releases/25.0_announce.rst | 6 + 5 files changed, 1237 insertions(+), 5 deletions(-) create mode 100644 doc/source/releases/24.2.rst create mode 100644 doc/source/releases/24.2_announce_user.rst create mode 100644 doc/source/releases/24.2_prs.rst create mode 100644 doc/source/releases/25.0_announce.rst diff --git a/doc/source/releases/24.2.rst b/doc/source/releases/24.2.rst new file mode 100644 index 000000000000..bec7352440d6 --- /dev/null +++ b/doc/source/releases/24.2.rst @@ -0,0 +1,775 @@ + +.. to_doc + +24.2 +=============================== + +.. announce_start + +Enhancements +------------------------------- + +.. major_feature + + +.. feature + +* Add onedata templates + (thanks to `@bwalkowi `__). + `Pull Request 18457`_ +* Add linter to check validity of output filters + (thanks to `@bernt-matthias `__). + `Pull Request 19114`_ +* FITS file table graph visualization plugin + (thanks to `@francoismg `__). + `Pull Request 19003`_ +* Experimental galactic wizard + (thanks to `@dannon `__). + `Pull Request 15860`_ +* Allow OAuth 2.0 user defined file sources (w/Dropbox integration) + (thanks to `@jmchilton `__). + `Pull Request 18272`_ +* Add job metrics per invocation + (thanks to `@mvdbeek `__). + `Pull Request 19048`_ +* Feature - stdout live reporting + (thanks to `@gecage952 `__). + `Pull Request 16975`_ +.. enhancement_tag_viz + +* Fix MSA viz, new dependency specification options + (thanks to `@dannon `__). + `Pull Request 18760`_ +* Parse stored config details to script-based visualizations + (thanks to `@guerler `__). + `Pull Request 18651`_ +* Migrate NGL viewer to npm package + (thanks to `@guerler `__). + `Pull Request 18946`_ +* Support deferred datasets in visualizations + (thanks to `@davelopez `__). + `Pull Request 19097`_ +* Openlayer update to npm package + (thanks to `@hujambo-dunia `__). + `Pull Request 19134`_ +* Replace static Cytoscape plugin with npm package + (thanks to `@itisAliRH `__). + `Pull Request 19127`_ +* Update tiff viewer to use script entry_point + (thanks to `@guerler `__). + `Pull Request 19151`_ +* Migrate Venn Diagram to Script-Tag + (thanks to `@guerler `__). + `Pull Request 19153`_ +* Remove OpenLayers legacy files and add SVG logo + (thanks to `@guerler `__). + `Pull Request 19135`_ +.. enhancement_tag_datatypes + +* Add pod5 datatype + (thanks to `@TomHarrop `__). + `Pull Request 18419`_ +* Handle compressed content in dataset preview for all sequence classes + (thanks to `@PlushZ `__). + `Pull Request 18776`_ +* Improve usability of Directory datatype + (thanks to `@wm75 `__). + `Pull Request 17614`_ +* Add some Zarr-based datatypes + (thanks to `@davelopez `__). + `Pull Request 19040`_ +* Add XML based `vtk` datatype + (thanks to `@tStehling `__). + `Pull Request 19104`_ +.. enhancement_tag_tools + +* Update GPU JupyterLab tool + (thanks to `@anuprulez `__). + `Pull Request 18220`_ +* Add Tool-Centric APIs to the Tool Shed 2.0 + (thanks to `@jmchilton `__). + `Pull Request 18524`_ +* Add BlobToolkit to the list of interactive tools + (thanks to `@Delphine-L `__). + `Pull Request 18630`_ +* Remove some unused dynamic drill down options + (thanks to `@jmchilton `__). + `Pull Request 18892`_ +* Add filter null collection operation tool + (thanks to `@mvdbeek `__). + `Pull Request 18928`_ +* Jupyter Interactive Tool 1.0.1/24.07 + (thanks to `@natefoo `__). + `Pull Request 18861`_ +* Add Interactive Tool Ilastik + (thanks to `@lldelisle `__). + `Pull Request 16837`_ +.. enhancement_tag_workflows + +* Allow connecting text param into data column parameter + (thanks to `@mvdbeek `__). + `Pull Request 18674`_ +* Allow specifying multi-select workflow parameters + (thanks to `@mvdbeek `__). + `Pull Request 18715`_ +* Allow access to invocation via shared or published history + (thanks to `@mvdbeek `__). + `Pull Request 18707`_ +* Modelling for Test Assertions + (thanks to `@jmchilton `__). + `Pull Request 18787`_ +* Implement Pydantic model for workflow test format. + (thanks to `@jmchilton `__). + `Pull Request 18884`_ +* Improvements to Planemo test format based on feedback/discussions + (thanks to `@jmchilton `__). + `Pull Request 18889`_ +* Allow CORS requests to /api/workflow_landings + (thanks to `@mvdbeek `__). + `Pull Request 18963`_ +* Workflow landing improvements + (thanks to `@mvdbeek `__). + `Pull Request 18979`_ +* Always validate hashes when provided + (thanks to `@nsoranzo `__). + `Pull Request 19110`_ +* Workflow Landing Requests + (thanks to `@jmchilton `__). + `Pull Request 18807`_ +* Implement Declarative Testing for Workflow Behaviors + (thanks to `@jmchilton `__). + `Pull Request 18542`_ +* Allow recovering a normalized version of workflow request state from API + (thanks to `@jmchilton `__). + `Pull Request 18985`_ +.. enhancement_tag_ui + +* Enable verbatimModuleSyntax, fix jest usage + (thanks to `@dannon `__). + `Pull Request 18595`_ +* Make vite tool shed client proxy configurable + (thanks to `@mvdbeek `__). + `Pull Request 18988`_ +* Upgrade `openapi-typescript` to 7.0.2 + swap to `openapi-fetch` + (thanks to `@davelopez `__). + `Pull Request 18532`_ +.. enhancement_tag_jobs + +* Record container id and type in core job metrics + (thanks to `@mvdbeek `__). + `Pull Request 18579`_ +* Add type annotations to ``JobRunnerMapper`` and related code + (thanks to `@nsoranzo `__). + `Pull Request 19115`_ +* Allow to overwrite `real_system_username` per destination + (thanks to `@bernt-matthias `__). + `Pull Request 18945`_ +.. enhancement_tag_admin + +* Remove `defaults` channel for conda usage + (thanks to `@bernt-matthias `__). + `Pull Request 18757`_ +* Allow setting a few global defaults for file source plugin types + (thanks to `@jmchilton `__). + `Pull Request 18909`_ +* Bring your own file sources: Add the WebDAV template and configuration + (thanks to `@sanjaysrikakulam `__). + `Pull Request 18598`_ +* Decouple user email from role name + (thanks to `@jdavcs `__). + `Pull Request 18966`_ +* Support high-availability setups for the interactive tools proxy + (thanks to `@kysrpex `__). + `Pull Request 18481`_ +* Minor config documentation enhancements + (thanks to `@bgruening `__). + `Pull Request 18499`_ +* Better cleanup of sharing roles on user purge + (thanks to `@jdavcs `__). + `Pull Request 19096`_ +.. enhancement + +* Updates the About Page + (thanks to `@guerler `__). + `Pull Request 18461`_ +* Moves Libraries from Masthead to Activity Bar + (thanks to `@guerler `__). + `Pull Request 18468`_ +* Adds an option to restore activity bar defaults + (thanks to `@guerler `__). + `Pull Request 18469`_ +* Add errors fast api + (thanks to `@arash77 `__). + `Pull Request 18093`_ +* Add task expiration to persistent task monitor + (thanks to `@davelopez `__). + `Pull Request 18551`_ +* Improve datasets permissions API schema typing + (thanks to `@davelopez `__). + `Pull Request 18563`_ +* Group tool templating exceptions in sentry + (thanks to `@mvdbeek `__). + `Pull Request 18570`_ +* Add a new version of the production s3fs file source template with the writable configuration variable added + (thanks to `@sanjaysrikakulam `__). + `Pull Request 18575`_ +* Move history multiview item actions to top + (thanks to `@ahmedhamidawan `__). + `Pull Request 18265`_ +* Improve update user API payload schema + (thanks to `@davelopez `__). + `Pull Request 18602`_ +* Improve update history payload schema + (thanks to `@davelopez `__). + `Pull Request 18618`_ +* Rev pinned gxformat2 + (thanks to `@jmchilton `__). + `Pull Request 18624`_ +* Improve typing for archived histories API schema + (thanks to `@davelopez `__). + `Pull Request 18586`_ +* Reduce unnecessary requests when browsing tool repositories in Admin Panel + (thanks to `@davelopez `__). + `Pull Request 18632`_ +* Improve types around User in schema and client + (thanks to `@davelopez `__). + `Pull Request 18645`_ +* Rip repository_registry out of tool shed 2.0 + (thanks to `@jmchilton `__). + `Pull Request 18647`_ +* Improve accept header API schema + (thanks to `@davelopez `__). + `Pull Request 18668`_ +* Another round of parameter model improvements + (thanks to `@jmchilton `__). + `Pull Request 18673`_ +* Another round of parameter model enhancements and tool tests + (thanks to `@jmchilton `__). + `Pull Request 18678`_ +* Dynamic Models for Tool Test Validation + (thanks to `@jmchilton `__). + `Pull Request 18679`_ +* Implement tool upgrade assistant + (thanks to `@jmchilton `__). + `Pull Request 18728`_ +* Cache pip directory as part of `setup-python` action + (thanks to `@nsoranzo `__). + `Pull Request 18789`_ +* Refactor FolderTopBar to TypeScript + (thanks to `@itisAliRH `__). + `Pull Request 18488`_ +* Update Visualization FastAPI + (thanks to `@arash77 `__). + `Pull Request 18792`_ +* Add Alireza to committers group + (thanks to `@nsoranzo `__). + `Pull Request 18613`_ +* Improvements to help terms & tool help + (thanks to `@jmchilton `__). + `Pull Request 18722`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 18578`_ +* Add wizard-like export view for workflow invocations + (thanks to `@davelopez `__). + `Pull Request 18796`_ +* Improvements to parameter models for test case inputs + (thanks to `@jmchilton `__). + `Pull Request 18743`_ +* Add docs on indexing for filter column + (thanks to `@bernt-matthias `__). + `Pull Request 18844`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 18864`_ +* Add unique constraints to the email and username fields in the galaxy_user table + (thanks to `@jdavcs `__). + `Pull Request 18493`_ +* Replace History Dataset Picker in Library Folder + (thanks to `@itisAliRH `__). + `Pull Request 18518`_ +* Allow using tracks and groups in visualization xml + (thanks to `@guerler `__). + `Pull Request 18779`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 18904`_ +* Add support for arbitrarily ordered image axes in image content assertions + (thanks to `@kostrykin `__). + `Pull Request 18891`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 18943`_ +* Add BioBlend tests + (thanks to `@arash77 `__). + `Pull Request 18975`_ +* Optimize to_history_dataset_association in create_datasets_from_library_folder + (thanks to `@arash77 `__). + `Pull Request 18970`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 18982`_ +* Add workflow to update PR title based on target branch version + (thanks to `@arash77 `__). + `Pull Request 18835`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 19031`_ +* Enable extra user preferences for remotely authorized users + (thanks to `@maartenschermer `__). + `Pull Request 18887`_ +* UI Improvements for Tool Shed 2.0 + (thanks to `@jmchilton `__). + `Pull Request 19041`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 19062`_ +* Annotate ``DatasetAssociationManager`` as generic type + (thanks to `@nsoranzo `__). + `Pull Request 19063`_ +* Better logging around tool loading + (thanks to `@jmchilton `__). + `Pull Request 19029`_ +* Add `galaxy-upload` link to `UploadModal` + (thanks to `@ahmedhamidawan `__). + `Pull Request 19055`_ +* Do not skip CI tests on missing tools + (thanks to `@jmchilton `__). + `Pull Request 19002`_ +* Add a filter for `labels` (tags) in Tool Search + (thanks to `@ahmedhamidawan `__). + `Pull Request 19076`_ +* Replace poetry with uv + (thanks to `@nsoranzo `__). + `Pull Request 19075`_ +* Add Python 3.13 support + (thanks to `@nsoranzo `__). + `Pull Request 18449`_ +* Allow deferred datasets to behave as URIs + (thanks to `@davelopez `__). + `Pull Request 19077`_ +* uv: Do not recalculate dependencies when exporting + (thanks to `@nsoranzo `__). + `Pull Request 19099`_ +* Test hash validation also for upload by path + (thanks to `@nsoranzo `__). + `Pull Request 19109`_ +* Integrate Tool Parameter Modeling into Linting (for Planemo) + (thanks to `@jmchilton `__). + `Pull Request 19073`_ +* Better search stuff in Tool Shed 2.0 + (thanks to `@jmchilton `__). + `Pull Request 19047`_ +* Enable specifying dataset hash in test jobs + (thanks to `@mvdbeek `__). + `Pull Request 19113`_ +* Access public history in job cache / job search + (thanks to `@mvdbeek `__). + `Pull Request 19108`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 19123`_ +* Also use miniforge docker for container building + (thanks to `@bernt-matthias `__). + `Pull Request 19128`_ +* Silence the quota manager for updates + (thanks to `@bernt-matthias `__). + `Pull Request 19046`_ +* Enhance relabel_from_file to work with any column pair in mapping file + (thanks to `@wm75 `__). + `Pull Request 19022`_ +* Irods ssl connection + (thanks to `@pauldg `__). + `Pull Request 19014`_ +* Update Japanese locale.js + (thanks to `@manabuishii `__). + `Pull Request 19101`_ +* Update vizarr version to 0.1.5 + (thanks to `@guerler `__). + `Pull Request 19142`_ +* Fix word wrapping in invocation panel list items + (thanks to `@ahmedhamidawan `__). + `Pull Request 19141`_ +* Add Workflow Title and Annotation sections + (thanks to `@hujambo-dunia `__). + `Pull Request 18762`_ +* Assert that `data_column` parameters have a valid `data_ref` + (thanks to `@bernt-matthias `__). + `Pull Request 18949`_ +* Switch update annotate image to new script entry_point + (thanks to `@guerler `__). + `Pull Request 19150`_ +* Workflow license and creator edit keyboard access + (thanks to `@itisAliRH `__). + `Pull Request 18936`_ +* More data access tests, some refactoring and cleanup + (thanks to `@jdavcs `__). + `Pull Request 18312`_ +* Add hint to the tool schema about runtime conditional changes + (thanks to `@martenson `__). + `Pull Request 18996`_ +* Undo stack UI + (thanks to `@ElectronicBlueberry `__). + `Pull Request 18548`_ +* Run installed Galaxy with no config and a simplified entry point + (thanks to `@natefoo `__). + `Pull Request 19050`_ +* A variety of improvements around tool parameter modeling (second try) + (thanks to `@jmchilton `__). + `Pull Request 19027`_ +* Parameter Model Improvements + (thanks to `@jmchilton `__). + `Pull Request 18641`_ +* Masthead Revision + (thanks to `@guerler `__). + `Pull Request 17927`_ +* Workflow Invocation view improvements + (thanks to `@ahmedhamidawan `__). + `Pull Request 18615`_ +* Add linters for datatypes + (thanks to `@bernt-matthias `__). + `Pull Request 17600`_ +.. small_enhancement + +* Update versions of GitHub actions + (thanks to `@nsoranzo `__). + `Pull Request 18197`_ +* Update openapi-typescript dependency to version 6.7.6 + (thanks to `@davelopez `__). + `Pull Request 18519`_ +* Mixed enhancements from CWL branch + (thanks to `@nsoranzo `__). + `Pull Request 18539`_ +* Fix some Toolshed 2.0 development paper-cuts + (thanks to `@davelopez `__). + `Pull Request 18538`_ +* Improvements to Tool Test Parsing + (thanks to `@jmchilton `__). + `Pull Request 18560`_ +* Drop unused datasets controller methods + (thanks to `@mvdbeek `__). + `Pull Request 18568`_ +* Consistent type imports, fixes and linting + (thanks to `@dannon `__). + `Pull Request 18589`_ +* Tighten user notification API response types + (thanks to `@davelopez `__). + `Pull Request 18599`_ +* More tool test typing + (thanks to `@jmchilton `__). + `Pull Request 18590`_ +* Remove unused functions in dataset managers + (thanks to `@jmchilton `__). + `Pull Request 18631`_ +* Better Typing for Tool Execution Plumbing + (thanks to `@jmchilton `__). + `Pull Request 18626`_ +* De-couple XML from tool interface for test collections + (thanks to `@jmchilton `__). + `Pull Request 18676`_ +* Update ExportToRemoteModal.vue to use TypeScript + (thanks to `@davelopez `__). + `Pull Request 18706`_ +* More typing, docs, and decomposition around tool execution + (thanks to `@jmchilton `__). + `Pull Request 18758`_ +* Migrate Visualizations API to FastAPI + (thanks to `@arash77 `__). + `Pull Request 18721`_ +* Refactor ``LibraryDatasetsManager`` and fix type annotation issue + (thanks to `@nsoranzo `__). + `Pull Request 18773`_ +* Update Mypy to 1.11.2 and fix new signature override errors + (thanks to `@nsoranzo `__). + `Pull Request 18811`_ +* Remove Build Dataset Pair option from history actions + (thanks to `@guerler `__). + `Pull Request 18740`_ +* Backend handling of setting user-role, user-group, and group-role associations + (thanks to `@jdavcs `__). + `Pull Request 18777`_ +* Refactor migration testing setup code + (thanks to `@jdavcs `__). + `Pull Request 18886`_ +* Enable ``ignore-without-code`` mypy error code + (thanks to `@nsoranzo `__). + `Pull Request 18898`_ +* Raise exception if CompressedFile used on incompatible file + (thanks to `@mvdbeek `__). + `Pull Request 18888`_ +* Type annotations and fixes + (thanks to `@nsoranzo `__). + `Pull Request 18911`_ +* Remove outdated fimo wrapper and galaxy-sequence-utils dependency + (thanks to `@nsoranzo `__). + `Pull Request 18937`_ +* Migrate Library Contents API to FastAPI + (thanks to `@arash77 `__). + `Pull Request 18838`_ +* Fix extra files path type hint + (thanks to `@davelopez `__). + `Pull Request 18958`_ +* Move TRS import into WorkflowContentManager + (thanks to `@mvdbeek `__). + `Pull Request 19070`_ +* More concise, readable tool execution testing + (thanks to `@jmchilton `__). + `Pull Request 18977`_ +* Libraries Modernisation: Directory Dataset Picker + (thanks to `@itisAliRH `__). + `Pull Request 18638`_ + + +Fixes +------------------------------- + +.. major_bug + + +.. bug_tag_viz + +* Install npm-package viz to the package prefix explicitly + (thanks to `@dannon `__). + `Pull Request 18950`_ +* Restore access to saved visualizations + (thanks to `@guerler `__). + `Pull Request 19136`_ +.. bug_tag_datatypes + +* Add gtf to auto_compressed_types + (thanks to `@mvdbeek `__). + `Pull Request 19175`_ +.. bug_tag_tools + +* Drop "Send to cloud" tool and associated cloudauthz code + (thanks to `@jdavcs `__). + `Pull Request 18196`_ +* Fix commas that shouldn't be in biotools_mappings.tsv + (thanks to `@jmchilton `__). + `Pull Request 18919`_ +.. bug_tag_workflows + +* Fix collection type drag and drop validation + (thanks to `@mvdbeek `__). + `Pull Request 18623`_ +* Fix very slow workflow editor loading + (thanks to `@mvdbeek `__). + `Pull Request 19068`_ +.. bug_tag_ui + +* Bump requirejs from 2.3.6 to 2.3.7 in /client + (thanks to `@dependabot[bot] `__). + `Pull Request 18610`_ +* Bump axios from 1.6.2 to 1.7.4 in /client + (thanks to `@dependabot[bot] `__). + `Pull Request 18717`_ +* Bump webpack from 5.89.0 to 5.94.0 in /client + (thanks to `@dependabot[bot] `__). + `Pull Request 18768`_ +* Bump express from 4.19.2 to 4.21.0 in /client + (thanks to `@dependabot[bot] `__). + `Pull Request 18808`_ +* Bump dompurify from 3.0.6 to 3.1.3 in /client + (thanks to `@dependabot[bot] `__). + `Pull Request 18821`_ +* Bump http-proxy-middleware from 2.0.6 to 2.0.7 in /client + (thanks to `@dependabot[bot] `__). + `Pull Request 19060`_ +* Bump dompurify from 2.3.10 to 3.1.6 in /client + (thanks to `@dependabot[bot] `__). + `Pull Request 18880`_ +.. bug_tag_jobs + +* Fixes random job failures in kubernetes + (thanks to `@mapk-amazon `__). + `Pull Request 19001`_ +.. bug_tag_admin + +.. bug + +* Return generic message for password reset email + (thanks to `@ahmedhamidawan `__). + `Pull Request 18479`_ +* Raise Message Exception when displaying binary data + (thanks to `@mvdbeek `__). + `Pull Request 18503`_ +* Handle all requests error in ``ApiBiotoolsMetadataSource._raw_get_metadata`` + (thanks to `@nsoranzo `__). + `Pull Request 18510`_ +* Follow-up on `#18212 `__ + (thanks to `@nsoranzo `__). + `Pull Request 18516`_ +* Fix "worklfow" typo here and there + (thanks to `@abretaud `__). + `Pull Request 18523`_ +* Fix MessageException handling in get_edit + (thanks to `@mvdbeek `__). + `Pull Request 18529`_ +* Fix bugs in tool shed tool API + (thanks to `@jmchilton `__). + `Pull Request 18558`_ +* Fix Archive header encoding + (thanks to `@arash77 `__). + `Pull Request 18583`_ +* Fix for not-null in 'column_list' object + (thanks to `@hujambo-dunia `__). + `Pull Request 18553`_ +* Fix API key reveals on mouse hover + (thanks to `@itisAliRH `__). + `Pull Request 18593`_ +* Fix for Numeric form field to allow Null min/max values in validation methods + (thanks to `@hujambo-dunia `__). + `Pull Request 18585`_ +* xsd: allow `change_format` and `actions` also in statically defined collection elements, and break recursion + (thanks to `@bernt-matthias `__). + `Pull Request 18605`_ +* Fixes for errors reported by mypy 1.11.0 + (thanks to `@nsoranzo `__). + `Pull Request 18608`_ +* Bug fix for invalid duplicate id in function test tools + (thanks to `@jmchilton `__). + `Pull Request 18644`_ +* Handle output parsing when tool is not available for tool-centric API + (thanks to `@jmchilton `__). + `Pull Request 18643`_ +* Restore interactive tools watcher + (thanks to `@guerler `__). + `Pull Request 18581`_ +* Strip whitespace when listifying admin users + (thanks to `@jdavcs `__). + `Pull Request 18656`_ +* Update mercurial + (thanks to `@mvdbeek `__). + `Pull Request 18686`_ +* Restore repository update in the tool shed 2.0 + (thanks to `@jmchilton `__). + `Pull Request 18655`_ +* Fix "Latest Updates" order in tool shed 2.0 + (thanks to `@jmchilton `__). + `Pull Request 16894`_ +* Replace types-pkg-resources with types-setuptools + (thanks to `@nsoranzo `__). + `Pull Request 18708`_ +* Update ruff to 0.6.1 + (thanks to `@nsoranzo `__). + `Pull Request 18716`_ +* Fix new flake8-bugbear B039 and mypy type-var errors + (thanks to `@nsoranzo `__). + `Pull Request 18755`_ +* Fixing RegisterForm.vue not appending prefix when set + (thanks to `@mcuaya1 `__). + `Pull Request 18786`_ +* Fix response if dataset requested by display application is deleted + (thanks to `@mvdbeek `__). + `Pull Request 18803`_ +* Fix alert handling in workflow label handler + (thanks to `@guerler `__). + `Pull Request 18836`_ +* Fix transiently failing selenium tooltip issues + (thanks to `@jmchilton `__). + `Pull Request 18847`_ +* Fix flaky `test/integration_selenium/test_toolbox_filters.py::TestToolboxFiltersSeleniumIntegration::test_toolbox_filters` + (thanks to `@ahmedhamidawan `__). + `Pull Request 18854`_ +* Fix migration data fixes tests + (thanks to `@jdavcs `__). + `Pull Request 18885`_ +* data_column params: offer same columns with and without use_header_names + (thanks to `@wm75 `__). + `Pull Request 18879`_ +* Allow users with 'can_modify_folder' permission to delete items in libraries + (thanks to `@npinter `__). + `Pull Request 18924`_ +* Fix `WorkflowInvocationHeader` import type and current user errors + (thanks to `@itisAliRH `__). + `Pull Request 18956`_ +* Explicitly display dataset preview in pages and workflow reports + (thanks to `@guerler `__). + `Pull Request 18968`_ +* Ignore preflight options in API schema + (thanks to `@jmchilton `__). + `Pull Request 18983`_ +* Define environment variables in ``env:`` section + (thanks to `@nsoranzo `__). + `Pull Request 18987`_ +* Fix the bioblend test failures + (thanks to `@arash77 `__). + `Pull Request 18991`_ +* Fix job directory not being cleaned up + (thanks to `@davelopez `__). + `Pull Request 18997`_ +* Fix job search statement building + (thanks to `@mvdbeek `__). + `Pull Request 19010`_ +* Fix test_stock.py unit test + (thanks to `@mvdbeek `__). + `Pull Request 19037`_ +* add data source doc to the list in index + (thanks to `@PlushZ `__). + `Pull Request 18742`_ +* Fix auto-detect metadata from Edit Dataset Attributes panel + (thanks to `@davelopez `__). + `Pull Request 19025`_ +* Fix numerous issues with tool input format "21.01" + (thanks to `@jmchilton `__). + `Pull Request 19030`_ +* Prevent purged users from logging in + (thanks to `@jdavcs `__). + `Pull Request 19094`_ +* Fixes and tests for data fetch models + (thanks to `@jmchilton `__). + `Pull Request 18834`_ +* Run ``uv lock`` under Python 3.9 + (thanks to `@nsoranzo `__). + `Pull Request 19111`_ +* Allow modes `z` and `Z` for docker volumes + (thanks to `@bernt-matthias `__). + `Pull Request 18998`_ +* Fix handling of v2 hashes + (thanks to `@bernt-matthias `__). + `Pull Request 18522`_ +* Dynamics options add library dataset + (thanks to `@gagayuan `__). + `Pull Request 18198`_ +* Add merge migration to merge 2 heads + (thanks to `@jdavcs `__). + `Pull Request 19163`_ +* Disallow /tool_runner? in robots.txt + (thanks to `@dannon `__). + `Pull Request 19020`_ +* Avoid possible negative offset in LibraryFolder + (thanks to `@martenson `__). + `Pull Request 19090`_ +* Fix backend role sharing bug + (thanks to `@jdavcs `__). + `Pull Request 18942`_ +* Update a localized word with a more appropriate one + (thanks to `@mpalmada `__). + `Pull Request 18910`_ +* Fix tag processing in library upload + (thanks to `@davelopez `__). + `Pull Request 18714`_ +* Update plausible script name in mako templates + (thanks to `@sanjaysrikakulam `__). + `Pull Request 18458`_ +* Fix issue with generating slug for sharing + (thanks to `@arash77 `__). + `Pull Request 18986`_ +* Consolidate tag validation + (thanks to `@dannon `__). + `Pull Request 19166`_ +* Move invocation view running actions and improve styling of annotation section + (thanks to `@ahmedhamidawan `__). + `Pull Request 19168`_ +* Fix mulled_hash + (thanks to `@bernt-matthias `__). + `Pull Request 19199`_ +* Add requirement/resource to schema docs + (thanks to `@bernt-matthias `__). + `Pull Request 19172`_ +* Normalize usernames to lowercase in OIDC authentication + (thanks to `@arash77 `__). + `Pull Request 19131`_ + +.. include:: 24.2_prs.rst + diff --git a/doc/source/releases/24.2_announce.rst b/doc/source/releases/24.2_announce.rst index 112bddcd20d5..f3a679bcc77a 100644 --- a/doc/source/releases/24.2_announce.rst +++ b/doc/source/releases/24.2_announce.rst @@ -1,12 +1,65 @@ -:orphan: +=========================================================== +24.2 Galaxy Release (January 2025) +=========================================================== +.. include:: _header.rst + +Highlights =========================================================== -October 2024 Galaxy Release (v 24.2) + +Feature1 +-------- + +Feature description. + +Feature2 +-------- + +Feature description. + +Feature3 +-------- + +Feature description. + +Also check out the `24.2 user release notes <24.2_announce_user.html>`__. +Are you an admin? Check out `some admin relevant PRs `__. + +Get Galaxy =========================================================== +The code lives at `GitHub `__ and you should have `Git `__ to obtain it. + +To get a new Galaxy repository run: + .. code-block:: shell + + $ git clone -b release_24.2 https://github.com/galaxyproject/galaxy.git -Schedule +To update an existing Galaxy repository run: + .. code-block:: shell + + $ git fetch origin && git checkout release_24.2 && git pull --ff-only origin release_24.2 + +See the `community hub `__ for additional details on source code locations. + + +Administration Notes +=========================================================== +Add content or drop section. + +Configuration Changes =========================================================== - * Planned Freeze Date: 2024-10-07 - * Planned Release Date: 2024-10-28 +Add content or drop section. + +Deprecation Notices +=========================================================== +Add content or drop section. + +Release Notes +=========================================================== + +.. include:: 24.2.rst + :start-after: announce_start + +.. include:: _thanks.rst diff --git a/doc/source/releases/24.2_announce_user.rst b/doc/source/releases/24.2_announce_user.rst new file mode 100644 index 000000000000..786891f5d214 --- /dev/null +++ b/doc/source/releases/24.2_announce_user.rst @@ -0,0 +1,149 @@ + +=========================================================== +24.2 Galaxy Release (January 2025) +=========================================================== + +.. include:: _header.rst + +Highlights +=========================================================== + +Feature1 +-------- + +Feature description. + +Feature2 +-------- + +Feature description. + +Feature3 +-------- + +Feature description. + + +Visualizations +=========================================================== + +.. visualizations +* Fix MSA viz, new dependency specification options + (thanks to `@dannon `__). + `Pull Request 18760`_ +* Parse stored config details to script-based visualizations + (thanks to `@guerler `__). + `Pull Request 18651`_ +* Install npm-package viz to the package prefix explicitly + (thanks to `@dannon `__). + `Pull Request 18950`_ +* Migrate NGL viewer to npm package + (thanks to `@guerler `__). + `Pull Request 18946`_ +* Support deferred datasets in visualizations + (thanks to `@davelopez `__). + `Pull Request 19097`_ +* Openlayer update to npm package + (thanks to `@hujambo-dunia `__). + `Pull Request 19134`_ +* Replace static Cytoscape plugin with npm package + (thanks to `@itisAliRH `__). + `Pull Request 19127`_ +* Update tiff viewer to use script entry_point + (thanks to `@guerler `__). + `Pull Request 19151`_ +* Migrate Venn Diagram to Script-Tag + (thanks to `@guerler `__). + `Pull Request 19153`_ +* FITS file table graph visualization plugin + (thanks to `@francoismg `__). + `Pull Request 19003`_ +* Restore access to saved visualizations + (thanks to `@guerler `__). + `Pull Request 19136`_ +* Remove OpenLayers legacy files and add SVG logo + (thanks to `@guerler `__). + `Pull Request 19135`_ + +Datatypes +=========================================================== + +.. datatypes +* Add pod5 datatype + (thanks to `@TomHarrop `__). + `Pull Request 18419`_ +* Handle compressed content in dataset preview for all sequence classes + (thanks to `@PlushZ `__). + `Pull Request 18776`_ +* Type annotations and fixes + (thanks to `@nsoranzo `__). + `Pull Request 18911`_ +* Improve usability of Directory datatype + (thanks to `@wm75 `__). + `Pull Request 17614`_ +* Add some Zarr-based datatypes + (thanks to `@davelopez `__). + `Pull Request 19040`_ +* Add XML based `vtk` datatype + (thanks to `@tStehling `__). + `Pull Request 19104`_ +* Add gtf to auto_compressed_types + (thanks to `@mvdbeek `__). + `Pull Request 19175`_ + +Builtin Tool Updates +=========================================================== + +.. tools +* Drop "Send to cloud" tool and associated cloudauthz code + (thanks to `@jdavcs `__). + `Pull Request 18196`_ +* Update GPU JupyterLab tool + (thanks to `@anuprulez `__). + `Pull Request 18220`_ +* Improvements to Tool Test Parsing + (thanks to `@jmchilton `__). + `Pull Request 18560`_ +* Add Tool-Centric APIs to the Tool Shed 2.0 + (thanks to `@jmchilton `__). + `Pull Request 18524`_ +* Add BlobToolkit to the list of interactive tools + (thanks to `@Delphine-L `__). + `Pull Request 18630`_ +* Enable ``ignore-without-code`` mypy error code + (thanks to `@nsoranzo `__). + `Pull Request 18898`_ +* Remove some unused dynamic drill down options + (thanks to `@jmchilton `__). + `Pull Request 18892`_ +* Fix commas that shouldn't be in biotools_mappings.tsv + (thanks to `@jmchilton `__). + `Pull Request 18919`_ +* Add filter null collection operation tool + (thanks to `@mvdbeek `__). + `Pull Request 18928`_ +* Remove outdated fimo wrapper and galaxy-sequence-utils dependency + (thanks to `@nsoranzo `__). + `Pull Request 18937`_ +* Jupyter Interactive Tool 1.0.1/24.07 + (thanks to `@natefoo `__). + `Pull Request 18861`_ +* Add Interactive Tool Ilastik + (thanks to `@lldelisle `__). + `Pull Request 16837`_ + +Release Testing Team +=========================================================== + +A special thanks to the release testing team for testing many of the new features and reporting many bugs: + + + +Release Notes +=========================================================== + +Please see the :doc:`full release notes <24.2_announce>` for more details. + +.. include:: 24.2_prs.rst + +.. include:: _thanks.rst diff --git a/doc/source/releases/24.2_prs.rst b/doc/source/releases/24.2_prs.rst new file mode 100644 index 000000000000..6d2a4867386f --- /dev/null +++ b/doc/source/releases/24.2_prs.rst @@ -0,0 +1,249 @@ + +.. github_links +.. _Pull Request 18197: https://github.com/galaxyproject/galaxy/pull/18197 +.. _Pull Request 18196: https://github.com/galaxyproject/galaxy/pull/18196 +.. _Pull Request 18220: https://github.com/galaxyproject/galaxy/pull/18220 +.. _Pull Request 18386: https://github.com/galaxyproject/galaxy/pull/18386 +.. _Pull Request 18461: https://github.com/galaxyproject/galaxy/pull/18461 +.. _Pull Request 18479: https://github.com/galaxyproject/galaxy/pull/18479 +.. _Pull Request 18503: https://github.com/galaxyproject/galaxy/pull/18503 +.. _Pull Request 18419: https://github.com/galaxyproject/galaxy/pull/18419 +.. _Pull Request 18468: https://github.com/galaxyproject/galaxy/pull/18468 +.. _Pull Request 18510: https://github.com/galaxyproject/galaxy/pull/18510 +.. _Pull Request 18516: https://github.com/galaxyproject/galaxy/pull/18516 +.. _Pull Request 18523: https://github.com/galaxyproject/galaxy/pull/18523 +.. _Pull Request 18519: https://github.com/galaxyproject/galaxy/pull/18519 +.. _Pull Request 18539: https://github.com/galaxyproject/galaxy/pull/18539 +.. _Pull Request 18469: https://github.com/galaxyproject/galaxy/pull/18469 +.. _Pull Request 18538: https://github.com/galaxyproject/galaxy/pull/18538 +.. _Pull Request 18093: https://github.com/galaxyproject/galaxy/pull/18093 +.. _Pull Request 18529: https://github.com/galaxyproject/galaxy/pull/18529 +.. _Pull Request 18558: https://github.com/galaxyproject/galaxy/pull/18558 +.. _Pull Request 18560: https://github.com/galaxyproject/galaxy/pull/18560 +.. _Pull Request 18551: https://github.com/galaxyproject/galaxy/pull/18551 +.. _Pull Request 18563: https://github.com/galaxyproject/galaxy/pull/18563 +.. _Pull Request 18568: https://github.com/galaxyproject/galaxy/pull/18568 +.. _Pull Request 18524: https://github.com/galaxyproject/galaxy/pull/18524 +.. _Pull Request 18583: https://github.com/galaxyproject/galaxy/pull/18583 +.. _Pull Request 18570: https://github.com/galaxyproject/galaxy/pull/18570 +.. _Pull Request 18575: https://github.com/galaxyproject/galaxy/pull/18575 +.. _Pull Request 18553: https://github.com/galaxyproject/galaxy/pull/18553 +.. _Pull Request 18589: https://github.com/galaxyproject/galaxy/pull/18589 +.. _Pull Request 18593: https://github.com/galaxyproject/galaxy/pull/18593 +.. _Pull Request 18599: https://github.com/galaxyproject/galaxy/pull/18599 +.. _Pull Request 18265: https://github.com/galaxyproject/galaxy/pull/18265 +.. _Pull Request 18602: https://github.com/galaxyproject/galaxy/pull/18602 +.. _Pull Request 18590: https://github.com/galaxyproject/galaxy/pull/18590 +.. _Pull Request 18579: https://github.com/galaxyproject/galaxy/pull/18579 +.. _Pull Request 18610: https://github.com/galaxyproject/galaxy/pull/18610 +.. _Pull Request 18623: https://github.com/galaxyproject/galaxy/pull/18623 +.. _Pull Request 18618: https://github.com/galaxyproject/galaxy/pull/18618 +.. _Pull Request 18624: https://github.com/galaxyproject/galaxy/pull/18624 +.. _Pull Request 18585: https://github.com/galaxyproject/galaxy/pull/18585 +.. _Pull Request 18605: https://github.com/galaxyproject/galaxy/pull/18605 +.. _Pull Request 18608: https://github.com/galaxyproject/galaxy/pull/18608 +.. _Pull Request 18586: https://github.com/galaxyproject/galaxy/pull/18586 +.. _Pull Request 18632: https://github.com/galaxyproject/galaxy/pull/18632 +.. _Pull Request 18644: https://github.com/galaxyproject/galaxy/pull/18644 +.. _Pull Request 18631: https://github.com/galaxyproject/galaxy/pull/18631 +.. _Pull Request 18643: https://github.com/galaxyproject/galaxy/pull/18643 +.. _Pull Request 18645: https://github.com/galaxyproject/galaxy/pull/18645 +.. _Pull Request 18647: https://github.com/galaxyproject/galaxy/pull/18647 +.. _Pull Request 18626: https://github.com/galaxyproject/galaxy/pull/18626 +.. _Pull Request 18581: https://github.com/galaxyproject/galaxy/pull/18581 +.. _Pull Request 18656: https://github.com/galaxyproject/galaxy/pull/18656 +.. _Pull Request 18668: https://github.com/galaxyproject/galaxy/pull/18668 +.. _Pull Request 18673: https://github.com/galaxyproject/galaxy/pull/18673 +.. _Pull Request 18676: https://github.com/galaxyproject/galaxy/pull/18676 +.. _Pull Request 18674: https://github.com/galaxyproject/galaxy/pull/18674 +.. _Pull Request 18686: https://github.com/galaxyproject/galaxy/pull/18686 +.. _Pull Request 18655: https://github.com/galaxyproject/galaxy/pull/18655 +.. _Pull Request 18706: https://github.com/galaxyproject/galaxy/pull/18706 +.. _Pull Request 16894: https://github.com/galaxyproject/galaxy/pull/16894 +.. _Pull Request 18708: https://github.com/galaxyproject/galaxy/pull/18708 +.. _Pull Request 18716: https://github.com/galaxyproject/galaxy/pull/18716 +.. _Pull Request 18717: https://github.com/galaxyproject/galaxy/pull/18717 +.. _Pull Request 18678: https://github.com/galaxyproject/galaxy/pull/18678 +.. _Pull Request 18679: https://github.com/galaxyproject/galaxy/pull/18679 +.. _Pull Request 18715: https://github.com/galaxyproject/galaxy/pull/18715 +.. _Pull Request 18728: https://github.com/galaxyproject/galaxy/pull/18728 +.. _Pull Request 18746: https://github.com/galaxyproject/galaxy/pull/18746 +.. _Pull Request 18707: https://github.com/galaxyproject/galaxy/pull/18707 +.. _Pull Request 18755: https://github.com/galaxyproject/galaxy/pull/18755 +.. _Pull Request 18768: https://github.com/galaxyproject/galaxy/pull/18768 +.. _Pull Request 18457: https://github.com/galaxyproject/galaxy/pull/18457 +.. _Pull Request 18630: https://github.com/galaxyproject/galaxy/pull/18630 +.. _Pull Request 18776: https://github.com/galaxyproject/galaxy/pull/18776 +.. _Pull Request 18758: https://github.com/galaxyproject/galaxy/pull/18758 +.. _Pull Request 18789: https://github.com/galaxyproject/galaxy/pull/18789 +.. _Pull Request 18488: https://github.com/galaxyproject/galaxy/pull/18488 +.. _Pull Request 18721: https://github.com/galaxyproject/galaxy/pull/18721 +.. _Pull Request 18786: https://github.com/galaxyproject/galaxy/pull/18786 +.. _Pull Request 18794: https://github.com/galaxyproject/galaxy/pull/18794 +.. _Pull Request 18773: https://github.com/galaxyproject/galaxy/pull/18773 +.. _Pull Request 18760: https://github.com/galaxyproject/galaxy/pull/18760 +.. _Pull Request 18792: https://github.com/galaxyproject/galaxy/pull/18792 +.. _Pull Request 18613: https://github.com/galaxyproject/galaxy/pull/18613 +.. _Pull Request 18722: https://github.com/galaxyproject/galaxy/pull/18722 +.. _Pull Request 18803: https://github.com/galaxyproject/galaxy/pull/18803 +.. _Pull Request 18651: https://github.com/galaxyproject/galaxy/pull/18651 +.. _Pull Request 18811: https://github.com/galaxyproject/galaxy/pull/18811 +.. _Pull Request 18578: https://github.com/galaxyproject/galaxy/pull/18578 +.. _Pull Request 18787: https://github.com/galaxyproject/galaxy/pull/18787 +.. _Pull Request 18740: https://github.com/galaxyproject/galaxy/pull/18740 +.. _Pull Request 18836: https://github.com/galaxyproject/galaxy/pull/18836 +.. _Pull Request 18595: https://github.com/galaxyproject/galaxy/pull/18595 +.. _Pull Request 18808: https://github.com/galaxyproject/galaxy/pull/18808 +.. _Pull Request 18847: https://github.com/galaxyproject/galaxy/pull/18847 +.. _Pull Request 18796: https://github.com/galaxyproject/galaxy/pull/18796 +.. _Pull Request 18743: https://github.com/galaxyproject/galaxy/pull/18743 +.. _Pull Request 18844: https://github.com/galaxyproject/galaxy/pull/18844 +.. _Pull Request 18852: https://github.com/galaxyproject/galaxy/pull/18852 +.. _Pull Request 18860: https://github.com/galaxyproject/galaxy/pull/18860 +.. _Pull Request 18864: https://github.com/galaxyproject/galaxy/pull/18864 +.. _Pull Request 18854: https://github.com/galaxyproject/galaxy/pull/18854 +.. _Pull Request 18821: https://github.com/galaxyproject/galaxy/pull/18821 +.. _Pull Request 18757: https://github.com/galaxyproject/galaxy/pull/18757 +.. _Pull Request 18777: https://github.com/galaxyproject/galaxy/pull/18777 +.. _Pull Request 18493: https://github.com/galaxyproject/galaxy/pull/18493 +.. _Pull Request 18885: https://github.com/galaxyproject/galaxy/pull/18885 +.. _Pull Request 18879: https://github.com/galaxyproject/galaxy/pull/18879 +.. _Pull Request 18884: https://github.com/galaxyproject/galaxy/pull/18884 +.. _Pull Request 18886: https://github.com/galaxyproject/galaxy/pull/18886 +.. _Pull Request 18898: https://github.com/galaxyproject/galaxy/pull/18898 +.. _Pull Request 18888: https://github.com/galaxyproject/galaxy/pull/18888 +.. _Pull Request 18889: https://github.com/galaxyproject/galaxy/pull/18889 +.. _Pull Request 18518: https://github.com/galaxyproject/galaxy/pull/18518 +.. _Pull Request 18911: https://github.com/galaxyproject/galaxy/pull/18911 +.. _Pull Request 18779: https://github.com/galaxyproject/galaxy/pull/18779 +.. _Pull Request 18904: https://github.com/galaxyproject/galaxy/pull/18904 +.. _Pull Request 18923: https://github.com/galaxyproject/galaxy/pull/18923 +.. _Pull Request 18892: https://github.com/galaxyproject/galaxy/pull/18892 +.. _Pull Request 18919: https://github.com/galaxyproject/galaxy/pull/18919 +.. _Pull Request 18928: https://github.com/galaxyproject/galaxy/pull/18928 +.. _Pull Request 18891: https://github.com/galaxyproject/galaxy/pull/18891 +.. _Pull Request 18937: https://github.com/galaxyproject/galaxy/pull/18937 +.. _Pull Request 18943: https://github.com/galaxyproject/galaxy/pull/18943 +.. _Pull Request 18909: https://github.com/galaxyproject/galaxy/pull/18909 +.. _Pull Request 18838: https://github.com/galaxyproject/galaxy/pull/18838 +.. _Pull Request 18924: https://github.com/galaxyproject/galaxy/pull/18924 +.. _Pull Request 18950: https://github.com/galaxyproject/galaxy/pull/18950 +.. _Pull Request 18956: https://github.com/galaxyproject/galaxy/pull/18956 +.. _Pull Request 18958: https://github.com/galaxyproject/galaxy/pull/18958 +.. _Pull Request 18963: https://github.com/galaxyproject/galaxy/pull/18963 +.. _Pull Request 18975: https://github.com/galaxyproject/galaxy/pull/18975 +.. _Pull Request 18968: https://github.com/galaxyproject/galaxy/pull/18968 +.. _Pull Request 18970: https://github.com/galaxyproject/galaxy/pull/18970 +.. _Pull Request 18983: https://github.com/galaxyproject/galaxy/pull/18983 +.. _Pull Request 18982: https://github.com/galaxyproject/galaxy/pull/18982 +.. _Pull Request 18598: https://github.com/galaxyproject/galaxy/pull/18598 +.. _Pull Request 18987: https://github.com/galaxyproject/galaxy/pull/18987 +.. _Pull Request 18988: https://github.com/galaxyproject/galaxy/pull/18988 +.. _Pull Request 18991: https://github.com/galaxyproject/galaxy/pull/18991 +.. _Pull Request 18997: https://github.com/galaxyproject/galaxy/pull/18997 +.. _Pull Request 18835: https://github.com/galaxyproject/galaxy/pull/18835 +.. _Pull Request 19010: https://github.com/galaxyproject/galaxy/pull/19010 +.. _Pull Request 19019: https://github.com/galaxyproject/galaxy/pull/19019 +.. _Pull Request 19001: https://github.com/galaxyproject/galaxy/pull/19001 +.. _Pull Request 18946: https://github.com/galaxyproject/galaxy/pull/18946 +.. _Pull Request 19037: https://github.com/galaxyproject/galaxy/pull/19037 +.. _Pull Request 19031: https://github.com/galaxyproject/galaxy/pull/19031 +.. _Pull Request 18887: https://github.com/galaxyproject/galaxy/pull/18887 +.. _Pull Request 18979: https://github.com/galaxyproject/galaxy/pull/18979 +.. _Pull Request 18742: https://github.com/galaxyproject/galaxy/pull/18742 +.. _Pull Request 19041: https://github.com/galaxyproject/galaxy/pull/19041 +.. _Pull Request 19062: https://github.com/galaxyproject/galaxy/pull/19062 +.. _Pull Request 19025: https://github.com/galaxyproject/galaxy/pull/19025 +.. _Pull Request 19063: https://github.com/galaxyproject/galaxy/pull/19063 +.. _Pull Request 19029: https://github.com/galaxyproject/galaxy/pull/19029 +.. _Pull Request 19055: https://github.com/galaxyproject/galaxy/pull/19055 +.. _Pull Request 19060: https://github.com/galaxyproject/galaxy/pull/19060 +.. _Pull Request 19002: https://github.com/galaxyproject/galaxy/pull/19002 +.. _Pull Request 19068: https://github.com/galaxyproject/galaxy/pull/19068 +.. _Pull Request 19076: https://github.com/galaxyproject/galaxy/pull/19076 +.. _Pull Request 19070: https://github.com/galaxyproject/galaxy/pull/19070 +.. _Pull Request 17614: https://github.com/galaxyproject/galaxy/pull/17614 +.. _Pull Request 19075: https://github.com/galaxyproject/galaxy/pull/19075 +.. _Pull Request 18449: https://github.com/galaxyproject/galaxy/pull/18449 +.. _Pull Request 19030: https://github.com/galaxyproject/galaxy/pull/19030 +.. _Pull Request 19077: https://github.com/galaxyproject/galaxy/pull/19077 +.. _Pull Request 19097: https://github.com/galaxyproject/galaxy/pull/19097 +.. _Pull Request 19099: https://github.com/galaxyproject/galaxy/pull/19099 +.. _Pull Request 19094: https://github.com/galaxyproject/galaxy/pull/19094 +.. _Pull Request 19109: https://github.com/galaxyproject/galaxy/pull/19109 +.. _Pull Request 19073: https://github.com/galaxyproject/galaxy/pull/19073 +.. _Pull Request 19047: https://github.com/galaxyproject/galaxy/pull/19047 +.. _Pull Request 18834: https://github.com/galaxyproject/galaxy/pull/18834 +.. _Pull Request 19111: https://github.com/galaxyproject/galaxy/pull/19111 +.. _Pull Request 19113: https://github.com/galaxyproject/galaxy/pull/19113 +.. _Pull Request 19108: https://github.com/galaxyproject/galaxy/pull/19108 +.. _Pull Request 19110: https://github.com/galaxyproject/galaxy/pull/19110 +.. _Pull Request 19114: https://github.com/galaxyproject/galaxy/pull/19114 +.. _Pull Request 19123: https://github.com/galaxyproject/galaxy/pull/19123 +.. _Pull Request 19128: https://github.com/galaxyproject/galaxy/pull/19128 +.. _Pull Request 18998: https://github.com/galaxyproject/galaxy/pull/18998 +.. _Pull Request 19046: https://github.com/galaxyproject/galaxy/pull/19046 +.. _Pull Request 19115: https://github.com/galaxyproject/galaxy/pull/19115 +.. _Pull Request 19040: https://github.com/galaxyproject/galaxy/pull/19040 +.. _Pull Request 18522: https://github.com/galaxyproject/galaxy/pull/18522 +.. _Pull Request 18945: https://github.com/galaxyproject/galaxy/pull/18945 +.. _Pull Request 18198: https://github.com/galaxyproject/galaxy/pull/18198 +.. _Pull Request 19134: https://github.com/galaxyproject/galaxy/pull/19134 +.. _Pull Request 19022: https://github.com/galaxyproject/galaxy/pull/19022 +.. _Pull Request 19014: https://github.com/galaxyproject/galaxy/pull/19014 +.. _Pull Request 18880: https://github.com/galaxyproject/galaxy/pull/18880 +.. _Pull Request 18861: https://github.com/galaxyproject/galaxy/pull/18861 +.. _Pull Request 19101: https://github.com/galaxyproject/galaxy/pull/19101 +.. _Pull Request 19142: https://github.com/galaxyproject/galaxy/pull/19142 +.. _Pull Request 19127: https://github.com/galaxyproject/galaxy/pull/19127 +.. _Pull Request 19141: https://github.com/galaxyproject/galaxy/pull/19141 +.. _Pull Request 18762: https://github.com/galaxyproject/galaxy/pull/18762 +.. _Pull Request 18949: https://github.com/galaxyproject/galaxy/pull/18949 +.. _Pull Request 16837: https://github.com/galaxyproject/galaxy/pull/16837 +.. _Pull Request 19150: https://github.com/galaxyproject/galaxy/pull/19150 +.. _Pull Request 19151: https://github.com/galaxyproject/galaxy/pull/19151 +.. _Pull Request 19104: https://github.com/galaxyproject/galaxy/pull/19104 +.. _Pull Request 19153: https://github.com/galaxyproject/galaxy/pull/19153 +.. _Pull Request 18936: https://github.com/galaxyproject/galaxy/pull/18936 +.. _Pull Request 19003: https://github.com/galaxyproject/galaxy/pull/19003 +.. _Pull Request 19163: https://github.com/galaxyproject/galaxy/pull/19163 +.. _Pull Request 19136: https://github.com/galaxyproject/galaxy/pull/19136 +.. _Pull Request 19020: https://github.com/galaxyproject/galaxy/pull/19020 +.. _Pull Request 19170: https://github.com/galaxyproject/galaxy/pull/19170 +.. _Pull Request 15860: https://github.com/galaxyproject/galaxy/pull/15860 +.. _Pull Request 18272: https://github.com/galaxyproject/galaxy/pull/18272 +.. _Pull Request 19048: https://github.com/galaxyproject/galaxy/pull/19048 +.. _Pull Request 18977: https://github.com/galaxyproject/galaxy/pull/18977 +.. _Pull Request 18966: https://github.com/galaxyproject/galaxy/pull/18966 +.. _Pull Request 18807: https://github.com/galaxyproject/galaxy/pull/18807 +.. _Pull Request 18481: https://github.com/galaxyproject/galaxy/pull/18481 +.. _Pull Request 18312: https://github.com/galaxyproject/galaxy/pull/18312 +.. _Pull Request 18542: https://github.com/galaxyproject/galaxy/pull/18542 +.. _Pull Request 19135: https://github.com/galaxyproject/galaxy/pull/19135 +.. _Pull Request 19090: https://github.com/galaxyproject/galaxy/pull/19090 +.. _Pull Request 18996: https://github.com/galaxyproject/galaxy/pull/18996 +.. _Pull Request 18942: https://github.com/galaxyproject/galaxy/pull/18942 +.. _Pull Request 18910: https://github.com/galaxyproject/galaxy/pull/18910 +.. _Pull Request 18866: https://github.com/galaxyproject/galaxy/pull/18866 +.. _Pull Request 18714: https://github.com/galaxyproject/galaxy/pull/18714 +.. _Pull Request 18638: https://github.com/galaxyproject/galaxy/pull/18638 +.. _Pull Request 18548: https://github.com/galaxyproject/galaxy/pull/18548 +.. _Pull Request 18499: https://github.com/galaxyproject/galaxy/pull/18499 +.. _Pull Request 18458: https://github.com/galaxyproject/galaxy/pull/18458 +.. _Pull Request 19050: https://github.com/galaxyproject/galaxy/pull/19050 +.. _Pull Request 19027: https://github.com/galaxyproject/galaxy/pull/19027 +.. _Pull Request 18985: https://github.com/galaxyproject/galaxy/pull/18985 +.. _Pull Request 18641: https://github.com/galaxyproject/galaxy/pull/18641 +.. _Pull Request 18532: https://github.com/galaxyproject/galaxy/pull/18532 +.. _Pull Request 17927: https://github.com/galaxyproject/galaxy/pull/17927 +.. _Pull Request 18615: https://github.com/galaxyproject/galaxy/pull/18615 +.. _Pull Request 18986: https://github.com/galaxyproject/galaxy/pull/18986 +.. _Pull Request 19096: https://github.com/galaxyproject/galaxy/pull/19096 +.. _Pull Request 16975: https://github.com/galaxyproject/galaxy/pull/16975 +.. _Pull Request 19166: https://github.com/galaxyproject/galaxy/pull/19166 +.. _Pull Request 17600: https://github.com/galaxyproject/galaxy/pull/17600 +.. _Pull Request 19168: https://github.com/galaxyproject/galaxy/pull/19168 +.. _Pull Request 19199: https://github.com/galaxyproject/galaxy/pull/19199 +.. _Pull Request 19175: https://github.com/galaxyproject/galaxy/pull/19175 +.. _Pull Request 19172: https://github.com/galaxyproject/galaxy/pull/19172 +.. _Pull Request 19131: https://github.com/galaxyproject/galaxy/pull/19131 diff --git a/doc/source/releases/25.0_announce.rst b/doc/source/releases/25.0_announce.rst new file mode 100644 index 000000000000..4f1ce6ad6478 --- /dev/null +++ b/doc/source/releases/25.0_announce.rst @@ -0,0 +1,6 @@ + +:orphan: + +=========================================================== +25.0 Galaxy Release +===========================================================