galaxy-schema 26.1.1

Fix mapOver terminology typo and minor polish by @martenson in #22226

Fix RST syntax and other small bugs in help Markdown term YAML by @jmchilton in #22374

Fix tool id handling for shed-installed tools by @guerler in #22553

Skip missing history item ids in job exports by @guerler in #22563

Fix workflow extraction not including user-defined tool steps by @ahmedhamidawan in #22694

Migrate tool execution request from api/tools to api/jobs by @guerler in #21842

Add the History Graph API by @guerler in #21932

Add Workflow Report generator agent by @ahmedhamidawan in #21934

Convert workflow extraction interface to Vue by @ahmedhamidawan in #21935

ChatGXY UI improvements and exchange management by @dannon in #21950

Update Python dependencies by @galaxybot in #21951

Migrate Python packages to `src` layout and pure namespace packages by @mr-c in #21977

More concise test logging by @jmchilton in #21983

Add persistent docked ChatGXY panel with context awareness by @dannon in #22096

Extend the favorite tool panel concept by @bgruening in #22212

Search and paginate user and roles api by @mvdbeek in #22311

Use a help popover for TRS search field by @ahmedhamidawan in #22330

Galaxy Notebooks: Persistent Narrative for Human-AI Collaborative Science in Galaxy by @jmchilton in #22361

Clean up Pydantic v2 deprecation warnings by @mvdbeek in #22463

Add bulk dataset storage migration by @davelopez in #22606

Update Python dependencies by @galaxybot in #22619

Add user-defined-tool operations to the agent-operations layer by @dannon in #22625

Re-introduce IWC tools in agent-operations layer by @dannon in #22626

Enhance workflow extraction by IDs with deduplication and UI improvements by @jmchilton in #22706

More structured HistoryGraph API references by @jmchilton in #22732

Further polish/bugfixes for notebooks created from invocations by @ahmedhamidawan in #22873

Provide more accurate step hints for failing subworkflow steps by @mvdbeek in #21514

Add missing types to visualization model by @guerler in #21672

Fix Pydantic UnsupportedFieldAttributeWarning for Field defaults in Annotated by @mvdbeek in #21923

Fix dict leaking to process_dataset() during workflow execution by @mvdbeek in #21982

Fix AttributeError when fetching citations for missing tools by @mvdbeek in #22029

Add batch celery task for history dataset purging by @mvdbeek in #22180

Fix batch history purge not updating user’s update_time by @mvdbeek in #22238

Validate workflow invocation parameters values are dicts by @mvdbeek in #22388

Replace Copy Dataset Mako with Vue Component by @guerler in #17507

Add Support for HTTP Headers in URL Fetch Requests with Secure Storage for Landing Requests by @davelopez in #20924

Tool Request API by @jmchilton in #20935

Update Python dependencies by @galaxybot in #21043

Remove legacy Visualization Mako and Controllers by @guerler in #21133

Allow filtering job searches by history ID by @nsoranzo in #21257

Implement GA4GH WES API by @jmchilton in #21335

Add AI Agent Framework and ChatGXY 2.0 by @dannon in #21434

Enable attaching sample sheet to landing requests by @mvdbeek in #21489

Include subworkflow jobs in invocation metrics by @mvdbeek in #21511

Add support for workflow landing requests using simple URLs by @mvdbeek in #21525

Implement workflow completion monitoring with extensible hooks by @mvdbeek in #21532

Clean up code with pyupgrade by @nsoranzo in #21540

Add discarded_data option to model store import API by @mvdbeek in #21582

Drop support for Python 3.9 by @nsoranzo in #21583

Standardize agent API schemas and response metadata by @dannon in #21692

Backport chat API improvements by @dannon in #21973

Merge 25.1 into dev, fix openapi schema generation for TypedDict by @mvdbeek in #21168

Collection API related spelling fix. by @jmchilton in #20470

Don’t serialize view of item in delete/purge request by @mvdbeek in #18732

Support credentials(secrets/variables) in tool requirements by @arash77 in #19084

Allow several Galaxy Markdown directives to be embedded. by @jmchilton in #19086

Implement Sample Sheets by @jmchilton in #19305

Add short term storage expiration indicator to history items by @davelopez in #20332

Update create_time field to be required in history content items by @davelopez in #20357

Implement Data Landing Requests by @jmchilton in #20592

Add a “Debug” (email report) tab to Workflow Invocations by @ahmedhamidawan in #20624

Clean up code from pyupgrade by @nsoranzo in #20642

Refactor Files Sources Framework for stronger typing using pydantic models by @davelopez in #20728

Hierarchical display collection dataset states by @mvdbeek in #20731

Change Advanced Tool Search to a Tool Discovery View by @ahmedhamidawan in #20747

Add configfiles support and various enhancements for user defined tools by @mvdbeek in #20761

Support remote file source hashes by @davelopez in #20853

Replace tour_generator webhook with internal API and frontend by @ahmedhamidawan in #20868

Update Python dependencies by @galaxybot in #20905

Add resource docs and tweak tool source schema title generation by @mvdbeek in #20951

Allow sending and tracking landing request origin by @mvdbeek in #20957

Track landing request with invocation by @mvdbeek in #20960

Move tours schema to schema directory (to fix package structure) by @ahmedhamidawan in #20965

Use workflow-style payload in data landing request by @mvdbeek in #21107

Correct visualization response schema by @guerler in #20627

Fix dataset serializers and response models by @arash77 in #20694

Merge 24.2 into 25.0 by @ahmedhamidawan in #20681

Better handling of public pages and workflows authored by deleted users by @jdavcs in #19394

Implement tool markdown reports. by @jmchilton in #19054

Let file sources choose a path for uploaded files by @kysrpex in #19154

Calculate hash for new non-deferred datasets when finishing a job by @nsoranzo in #19181

Fix UP031 errors - Part 4 by @nsoranzo in #19235

Update pydantic to 2.10.3 by @nsoranzo in #19326

Empower Users to Build More Kinds of Collections, More Intelligently by @jmchilton in #19377

Add User-Defined Tools by @mvdbeek in #19434

Improve asynchronous tasks error handling and reporting by @davelopez in #19448

Allow to send notifications when Admins cancel jobs by @davelopez in #19547

Remove tags used by @ElectronicBlueberry in #19576

Generate correct types for Dataset source transformations on backend. by @jmchilton in #19666

Define simple models for job messages. by @jmchilton in #19688

Show workflow help (and readme?) in run form by @ahmedhamidawan in #19736

Migrate Page editing controller endpoint to API by @guerler in #19923

Update Python dependencies by @galaxybot in #19929

Enable warn_redundant_casts mypy option and drop redundant casts by @nsoranzo in #20008

Add DOI to workflow metadata by @jdavcs in #20033

Drop “Send to cloud” tool and associated cloudauthz code by @jdavcs in #18196

Fix issue with generating slug for sharing by @arash77 in #18986

Fix invocation metrics usability by providing job context. by @jmchilton in #19279

Experimental galactic wizard by @dannon in #15860

Feature - stdout live reporting by @gecage952 in #16975

Add errors fast api by @arash77 in #18093

Allow OAuth 2.0 user defined file sources (w/Dropbox integration) by @jmchilton in #18272

Improve datasets permissions API schema typing by @davelopez in #18563

Improve typing for archived histories API schema by @davelopez in #18586

Tighten user notification API response types by @davelopez in #18599

Improve update user API payload schema by @davelopez in #18602

Improve update history payload schema by @davelopez in #18618

Improve types around User in schema and client by @davelopez in #18645

Improve accept header API schema by @davelopez in #18668

Migrate Visualizations API to FastAPI by @arash77 in #18721

Backend handling of setting user-role, user-group, and group-role associations by @jdavcs in #18777

Update Visualization FastAPI by @arash77 in #18792

Workflow Landing Requests by @jmchilton in #18807

Migrate Library Contents API to FastAPI by @arash77 in #18838

Enable ignore-without-code mypy error code by @nsoranzo in #18898

Decouple user email from role name by @jdavcs in #18966

Workflow landing improvements by @mvdbeek in #18979

Allow recovering a normalized version of workflow request state from API by @jmchilton in #18985

Add job metrics per invocation by @mvdbeek in #19048

Implement workflow parameter validators. by @jmchilton in #19092

Access public history in job cache / job search by @mvdbeek in #19108

Always validate hashes when provided by @nsoranzo in #19110

Handle error when workflow is unowned in Invocation view by @ahmedhamidawan in #18730

Fix datatype validation of newly built collection by @mvdbeek in #18738

Fix job summary for optional unset job data inputs by @mvdbeek in #18754

Fix TypeError from Pydantic 2.9.0 by @nsoranzo in #18788

Fix wrong extension on pick data output by @mvdbeek in #18798

Make all fields optional for HelpForumPost by @davelopez in #18839

Remove the default Incoming suffix in GenericModel class by @davelopez in #19174

Include workflow invocation id in exception logs by @mvdbeek in #18594

Handle error when workflow is unowned in Invocation view by @ahmedhamidawan in #18730

Fix datatype validation of newly built collection by @mvdbeek in #18738

Fix job summary for optional unset job data inputs by @mvdbeek in #18754

Fix TypeError from Pydantic 2.9.0 by @nsoranzo in #18788

Fix wrong extension on pick data output by @mvdbeek in #18798

Make all fields optional for HelpForumPost by @davelopez in #18839

Include workflow invocation id in exception logs by @mvdbeek in #18594

Handle error when workflow is unowned in Invocation view by @ahmedhamidawan in #18730

Fix datatype validation of newly built collection by @mvdbeek in #18738

Fix job summary for optional unset job data inputs by @mvdbeek in #18754

Fix TypeError from Pydantic 2.9.0 by @nsoranzo in #18788

Fix wrong extension on pick data output by @mvdbeek in #18798

Make all fields optional for HelpForumPost by @davelopez in #18839

Include workflow invocation id in exception logs by @mvdbeek in #18594

Fix Workflow Comment Model for Pydantic 2 by @ElectronicBlueberry in #17296

Add basic model import attribute validation by @mvdbeek in #17628

Make latest_workflow_uuid optional by @mvdbeek in #17629

Fix workflow person validation by @dannon in #17636

Make WorkflowInput label, value and uuid optional by @mvdbeek in #17638

Fix step type serialization for StoredWorkflowDetailed models by @mvdbeek in #17716

Fix input parameter step type by @mvdbeek in #17767

Fix optional types in Help Forum API by @davelopez in #17832

Fix archived histories mixing with active in histories list by @davelopez in #17856

port invocation API to fastapi by @martenson in #16707

Python 3.8 as minimum by @mr-c in #16954

Toward declarative help for Galaxy markdown directives. by @jmchilton in #16979

Create pydantic model for the return of show operation - get: /api/jobs/{job_id} by @heisner-tillman in #17153

Vueifiy History Grids by @guerler in #17219

Refactor two of the missing invocation routes to FastAPI by @heisner-tillman in #17237

Migrate models to pydantic 2 by @mvdbeek in #17262

Combines legacy qv-pattern and advanced filter pattern in history index endpoint by @guerler in #17368

Update to black 2024 stable style by @nsoranzo in #17391

Allow using tool data bundles as inputs to reference data select parameters by @mvdbeek in #17435

Refactor Workflow API routes - Part 1 by @heisner-tillman in #17463

Consolidate resource grids into tab views by @guerler in #17487

Display workflow invocation counts. by @jmchilton in #17488

Filter out subworkflow invocations by @mvdbeek in #17558

Restore histories API behavior for keys query parameter by @davelopez in #17779

Fix datasets API custom keys encoding by @davelopez in #17793