galaxy-app 26.1.1

Bump cryptography from 46.0.4 to 46.0.5 in /lib/galaxy/dependencies by @dependabot in #21815

Bump pillow from 12.1.0 to 12.1.1 in /lib/galaxy/dependencies by @dependabot in #21825

Disallow gunicorn 25.1.0 by @nsoranzo in #21905

Fix dbkey filter returning no options when dbkey unset by @jmchilton in #21916

Fix workflow implicit mapping of flat collections over paired_or_unpaired by @jmchilton in #21933

Fix silently ignored <idphint> in oidc_backends_config.xml so kc_idp_hint reaches Keycloak by @gkr0110 in #21992

Bump black from 26.3.0 to 26.3.1 in /lib/galaxy/dependencies by @dependabot in #22090

Fix transient CI failures by @mvdbeek in #22102

Fix tag duplication when copying datasets/collections between histories by @dannon in #22109

Fix anonymous_user_concurrent_jobs to not allow jobs when 0 by @ccoulombe in #22110

Convert math.inf to None in JSON-serialized tool dicts by @dannon in #22152

Use correct binary unit prefixes (KiB/MiB/GiB) by @dannon in #22153

Bump pyasn1 from 0.6.2 to 0.6.3 in /lib/galaxy/dependencies by @dependabot in #22160

Bump pydicom from 3.0.1 to 3.0.2 in /lib/galaxy/dependencies by @dependabot in #22199

Bump requests from 2.32.5 to 2.33.0 in /lib/galaxy/dependencies by @dependabot in #22270

Bump cryptography from 46.0.5 to 46.0.6 in /lib/galaxy/dependencies by @dependabot in #22289

Bump pygments from 2.19.2 to 2.20.0 in /lib/galaxy/dependencies by @dependabot in #22308

Bump fastmcp from 3.1.0 to 3.2.0 in /lib/galaxy/dependencies by @dependabot in #22334

Bump aiohttp from 3.13.3 to 3.13.4 in /lib/galaxy/dependencies by @dependabot in #22363

Bump cryptography from 46.0.6 to 46.0.7 in /lib/galaxy/dependencies by @dependabot in #22424

Bump mako from 1.3.10 to 1.3.11 in /lib/galaxy/dependencies by @dependabot in #22509

Bump authlib from 1.6.9 to 1.6.11 in /lib/galaxy/dependencies by @dependabot in #22510

Bump lxml from 6.0.4 to 6.1.0 in /lib/galaxy/dependencies by @dependabot in #22540

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

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

Honor group-derived roles in unprivileged tool access check by @mvdbeek in #22623

Bump default max_tokens for AI agents by @dannon in #22630

Bump mistune from 3.2.0 to 3.2.1 in /lib/galaxy/dependencies by @dependabot in #22651

Bump mako from 1.3.11 to 1.3.12 in /lib/galaxy/dependencies by @dependabot in #22653

Bump python-multipart from 0.0.26 to 0.0.27 in /lib/galaxy/dependencies by @dependabot in #22654

Fix SQL compatibility in kombu message pruning by @davelopez in #22655

Defer dynamic destination evaluation across resubmits by @nuwang in #22670

Don’t install data table entries for non-DM tool installs by @natefoo in #22679

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

Harden access control for user-defined tools by @mvdbeek in #22704

Fix galaxy_task DI injection on Python 3.14 by @mvdbeek in #22727

Fix shed install column mismatch from synthesized name alias by @mvdbeek in #22733

Bump pydantic-ai from 1.97.0 to 1.99.0 in /lib/galaxy/dependencies by @dependabot in #22736

Framework test for UDTs in Format 2 Workflows by @jmchilton in #22756

Add fallback at read location in dynamic options by @guerler in #22779

Fix composite uploads ignoring substitute_name_with_metadata by @mvdbeek in #22788

Route ChatGXY on the current message, and ask when uncertain by @dannon in #22791

Fix on_string containing redundant datasets by @bernt-matthias in #22801

Add fixed color set from webcolors package by @guerler in #22869

Use the correct default value for job_id_prefix by @ksuderman in #22871

Create notebooks from invocation reports instead of a new page/report by @ahmedhamidawan in #22872

Match tpv in conditional dependency requirement to pinned version by @mvdbeek in #22874

Fix memory-unit conversion and polling_interval bugs in the GCP Batch runner by @ksuderman in #22880

Address arch-review issues from #22807: move business logic out of chat controller by @mvdbeek in #22885

Bump up gravity to 1.2.3 by @mvdbeek in #22886

Cut GTN training agent token usage by capping its search loop by @dannon in #22890

Fix input mangling when conditional parameter name ends in `_N` by @mvdbeek in #22891

Always attempt to build tool request for new API endpoint by @mvdbeek in #22894

Make GalaxyAI agent retry budget configurable (fix “Exceeded maximum output retries”) by @dannon in #22896

Fix GalaxyAI router context loss and agent response attribution by @dannon in #22904

Fix upload_file_from_url passing decoded id to FetchDataPayload by @jmchilton in #22905

Make GalaxyAI route IWC workflow imports more reliably by @dannon in #22908

Make unowned but accessible pages uneditable by @ahmedhamidawan in #22911

Keep collection-operation outputs as workflow steps in extraction by @jmchilton in #22912

Speed up workflow Run form: memoize and skip redundant history scans (#22927) by @mvdbeek in #22932

Release request-scoped DB connection during streams via GalaxyStreamingResponse (alternative to #22939) by @mvdbeek in #22940

Ground ChatGXY’s “what can you do” answer in enabled agents by @dannon in #22944

Keep the standalone SSE monitor out of the control-queue routing table by @mvdbeek in #22958

Fix tool shed state serving for stock tools by @jmchilton in #22963

Make the user-defined tool schema robust for LLM authoring (CustomToolAgent) by @mvdbeek in #22968

Include hidden intermediates in workflow extraction summary (#22967) by @jmchilton in #22970

Route ChatGXY follow-ups using the previous conversation turn by @dannon in #22975

Custom-tool agent: verified container resolution + authoring safeguards (with a reusable mulled-recommend CLI) by @mvdbeek in #22981

Resolve user-defined tools in by-ids workflow extraction by @mvdbeek in #22992

Log SSE dispatch task and addressed webapp workers by @mvdbeek in #22995

Fix SSE dispatch cache unit tests: give queue mocks a string .name by @mvdbeek in #23035

Fix celery worker cold-start thundering herd (build app once, scope tool-data walk to load pass) by @mvdbeek in #23048

Fix NameError, move assignation of days prior to get_failed_jobs call by @ccoulombe in #23053

Add configurable activation for OIDC accounts by @mvdbeek in #23109

Fix clean jwd task by @davelopez in #23121

Fix activation email lookup regression by @davelopez in #23130

Fix `set_history` committing None `galaxy_session` by @ahmedhamidawan in #23156

Fix AssertionError remapping malformed galaxy markdown blocks by @mvdbeek in #23176

Fix broken calls to ``InteractiveToolManager`` methods by @nsoranzo in #23216

Show persistent best practice results in workflow editor by @mvdbeek in #19546

Allow OIDC to update EMAIL and username (if mapped) by @uwwint in #21386

Add a new “htcondor” job runner that uses the Python HTCondor version 2 bindings by @bgruening in #21528

Add support for test credentials in tools by @arash77 in #21643

Improvements for ssh file sources by @bernt-matthias in #21646

Break dereference_input into HDA and HDCA variants by @mvdbeek in #21694

Allow admin to override `$GALAXY_MEMORY_MB` by @natefoo in #21700

Update Python dependencies by @galaxybot in #21707

Implement workflow extraction backend typing by @jmchilton in #21749

Update Python dependencies by @galaxybot in #21787

Various YAML Tool Hardening and Progress toward Tool State Goals by @jmchilton in #21828

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

Update Python dependencies by @galaxybot in #21853

Use (also) case-insensitive comparison for user email by @nsoranzo in #21885

Support URL and TRS references for subworkflows in workflow import by @mvdbeek in #21887

Update Python dependencies by @galaxybot in #21899

Fix tool.parameters initialization by @mvdbeek in #21914

Allow tools to specify time limits by @jmchilton in #21927

Allow per-job max_run_duration for GCP Batch runner by @ksuderman in #21928

Add `delete_completed_jobs` option to GCP Batch runner by @ksuderman in #21929

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

First pass in unifying and clarifying collection operation interfaces and help sections by @nekrut in #21939

Add composite dataset upload method to Upload Activity by @davelopez in #21944

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

Update Python dependencies by @galaxybot in #21951

Eliminate Twill from Tool Shed tests by @jmchilton in #21953

Use ``os.path.join()`` or ``pathlib.Path`` instead of f-strings for filesystem paths by @nsoranzo in #21954

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

More concise test logging by @jmchilton in #21983

Model subcollection mapping (map_over_type) and DCE in tool parameter schema by @jmchilton in #21991

Update Python dependencies by @galaxybot in #22003

Refactor Agent Registry Wiring and Fix Config Options by @jmchilton in #22011

Replace mocked agent tests with static YAML backend for deterministic API/E2E testing by @jmchilton in #22070

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

Add GTN training agent to ChatGXY by @dannon in #22097

Update Python dependencies by @galaxybot in #22118

Improve celery rate limit and concurrency handling by @mvdbeek in #22189

Update Python dependencies by @galaxybot in #22206

Test against psycopg3 by @mvdbeek in #22210

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

Add `pick_value` Workflow Module by @jmchilton in #22222

Upgrade Sentry JS SDK to v10, add opt-in session replay by @dannon in #22233

Support IEC units in ``size_to_bytes()``, add ``QuotaManager`` unit tests by @nsoranzo in #22237

Simplify gxformat2 contract - drop ImporterGalaxyInterface, convert_and_import_workflow by @jmchilton in #22241

Add Hashicorp Vault token renewal support by @mvdbeek in #22281

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

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

Add OneDrive file source by @PlushZ in #22367

Add IIIF File Source Support by @davelopez in #22420

Better Auth0 OIDC support by @marius-mather in #22426

Parameterize GCP Batch job naming for better tracking by @ksuderman in #22434

Require logging in again when OIDC tokens can’t be refreshed by @marius-mather in #22449

Update Python dependencies by @galaxybot in #22459

Clean up legacy SQLAlchemy patterns that emit deprecation warnings by @mvdbeek in #22462

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

Migrate WebDAV file source to fsspec/webdav4 by @PlushZ in #22477

Allow attaching OIDC access token to DRS requests by @marius-mather in #22484

Narrow YAML schema by @jmchilton in #22507

Server-Sent Events for history + notification updates by @mvdbeek in #22513

Update Python dependencies by @galaxybot in #22517

Add legacy job submission fallback by @guerler in #22555

Update Python dependencies by @galaxybot in #22559

Overhaul and synchronize collection type algebra verbs by @jmchilton in #22565

Use now() wrapper instead of datetime.now() by @bgruening in #22579

Add bulk dataset storage migration by @davelopez in #22606

Pass chat history to agents as structured messages by @dannon in #22607

Pass orchestration state between agents as a typed object by @dannon in #22608

Replace agent structured-output denylist with capability table by @dannon in #22609

Give the chat router fast-path tools for browsing and inventory by @dannon in #22610

Add producer/critic reflection loops to CustomToolAgent by @dannon in #22612

Push UserToolSource semantic validation onto the pydantic model by @mvdbeek in #22615

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

Improve type annotation of workflow management methods by @nsoranzo in #22637

Paginate /api/tools/{tool_id}/build history options by @mvdbeek in #22643

Migrate Dropbox file source to fsspec by @PlushZ in #22682

Add real-LLM evaluation harness for Galaxy agents by @dannon in #22692

Migrate the Google Drive file source to fsspec by @PlushZ in #22696

Update Python dependencies by @galaxybot in #22702

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

Rebrand ChatGXY to GalaxyAI by @dannon in #22707

More structured HistoryGraph API references by @jmchilton in #22732

Refresh agent-ops data (GTN database + IWC manifest) on a celery beat schedule by @dannon in #22783

Backport of iRODS file source by @davelopez in #22816

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

Emit SSE/queue metrics as gauges, sample SSE counts in web workers by @mvdbeek in #22960

Update pulsar-galaxy-client dependency to 0.15.15 by @mvdbeek in #23108

Bump pydantic-ai from 1.44.0 to 1.56.0 in /lib/galaxy/dependencies by @dependabot in #21782

Add a shared operations layer for internal and external AI agents by @dannon in #21942

SSE update enhancements for multi-history view and published histories by @mvdbeek in #22614

Backport “Always install ``fastmcp``” by @nsoranzo in #23119

Add debug middleware and regression tests for blocked main event loop by @mvdbeek in #22207

Hide hidden tools in the tool form by @bgruening in #22215

Fix IndexError in SplitPairedAndUnpairedTool for unpaired elements by @ernestprovo23 in #22282

Respect workflow object store preference for mapped step outputs by @mvdbeek in #22409

Fix `get_structure` when it is passed a DCE with nested elements by @mvdbeek in #22453

Move job-level filters inside CTE in job cache query by @mvdbeek in #22454

Enforce file source access during dataset materialization by @mvdbeek in #22486

Fix data manager URL for managers with ‘+’ version suffix by @mvdbeek in #22525

Treat paused inputs as not-ready in DatabaseOperationTool by @mvdbeek in #22529

Fix TypeError when generating tour for tool with boolean conditional case by @ahmedhamidawan in #22532

Backport rocrate<0.15.0 pin by @nsoranzo in #22537

Fix crash merging structurally invalid nested collections by @mvdbeek in #22546

Fix silent OIDC failure when pkce is missing by @mvdbeek in #22547

Raise ToolInputsNotReady for unpopulated structured_like target by @mvdbeek in #22552

Fix notification channels not processed correctly by @davelopez in #22556

Fixes looks_like_flattened_repeat_key helper by @guerler in #22578

Raises error if decoding fails during relabeling from file by @guerler in #22595

Fix job access check for collection-only outputs by @mvdbeek in #22603

Reject malformed dataset ids in data tool parameter by @mvdbeek in #22617

Exclude user defined tools from requiring galaxy env by @mvdbeek in #22628

Ensure workflow editor always inserts latest tool version by @ahmedhamidawan in #22693

Fix HDA leak in tool form for data managers (#22674) by @mvdbeek in #22724

Backport FastAPI/Starlette upgrade for BadHost (CVE-2026-48710) by @mvdbeek in #22778

Fix ConnectedValue leak for omitted optional inputs inside groups by @mvdbeek in #22820

Replace per-term joins in workflow search with EXISTS subqueries by @mvdbeek in #22548

Fix workflow report time handling by @dannon in #19292

Bump python-ldap from 3.4.0 to 3.4.5 in /lib/galaxy/dependencies by @dependabot[bot] in #21042

Cross product tools: Fix typos in help section by @RZ9082 in #21061

Bump urllib3 from 2.5.0 to 2.6.0 in /lib/galaxy/dependencies by @dependabot[bot] in #21399

Don’t set OAUTHLIB_INSECURE_TRANSPORT setting in user_data by @nuwang in #21451

Bump filelock from 3.20.0 to 3.20.1 in /lib/galaxy/dependencies by @dependabot[bot] in #21476

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

Restrict collection of dynamic working dir output to specified directory in pulsar by @mvdbeek in #21515

Fix input tags not being copied when using copy_inputs_to_history by @mvdbeek in #21529

Bump aiohttp from 3.13.2 to 3.13.3 in /lib/galaxy/dependencies by @dependabot[bot] in #21538

Bump urllib3 from 2.6.2 to 2.6.3 in /lib/galaxy/dependencies by @dependabot[bot] in #21546

Bump werkzeug from 3.1.4 to 3.1.5 in /lib/galaxy/dependencies by @dependabot[bot] in #21549

Overhaul ChatGXY Routing approach by @dannon in #21580

Bump pyasn1 from 0.6.1 to 0.6.2 in /lib/galaxy/dependencies by @dependabot[bot] in #21605

Fix toolshed tests on Python 3.14 by @mvdbeek in #21617

Bump python-multipart from 0.0.21 to 0.0.22 in /lib/galaxy/dependencies by @dependabot[bot] in #21663

Fix storing origin for workflow landing requests by @mvdbeek in #21696

Handle TPV floating point memory values by @ksuderman in #21763

Deserialize json string for export_metadata from old records by @mvdbeek in #21772

Fix passing invalid job_destination dict to JobState constructor by @mvdbeek in #21798

Update get_definitions() to FastAPI 0.128.8 by @nsoranzo in #21834

Backport paired or unpaired mapping fix by @mvdbeek in #21936

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

Fix dataset collection tag duplication when copying a history by @mvdbeek in #21984

Restore file doesn’t match sniffed datatype message by @mvdbeek in #21988

Fix uncaught ImplicitConversionRequired by @mvdbeek in #22027

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

AttributeError when history is None during tool execution by @mvdbeek in #22031

Fix AttributeError when export_metadata is a string instead of dict by @mvdbeek in #22033

Fix TypeError when column_names metadata is None by @mvdbeek in #22057

Fail job gracefully when output name exceeds 255 character DB limit by @mvdbeek in #22059

Fix FileNotFoundError when workflow references purged HDA by @mvdbeek in #22060

Add check_database_connection to workflow scheduling path by @mvdbeek in #22063

Model hidden_data params as optional data in tool meta-models. by @jmchilton in #22116

Fix unhandled exceptions in tool form model population by @guerler in #22129

Backport transient CI fixes from #22102 to release_26.0 by @mvdbeek in #22135

Do not queue paused jobs by @martenson in #22156

Fix AmbiguousColumn error in job search for tools with long input names by @mvdbeek in #22167

Fixes for gxformat2 by @jmchilton in #22179

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

Include missing tools in stock_tool_paths. by @jmchilton in #22181

Throw ParameterValueError instead of generic error by @guerler in #22188

Fix event loop blocking in async API routes by @mvdbeek in #22202

Update fastmcp requirement to 3.0.2 by @nsoranzo in #22221

Add optional dataset collection mode to harmonize tool by @mvdbeek in #22236

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

Fix file source removal by @davelopez in #22246

Validate replacement_params values are strings before storing by @mvdbeek in #22250

Fix N+1 queries in fetch_job_states for jobs_summary endpoints by @mvdbeek in #22251

Fix oauth2 template validation by @davelopez in #22253

Drop stored workflow menu entries from user serialization by @mvdbeek in #22254

Batch-prefetch HDCA job_state_summary in history contents listing by @mvdbeek in #22256

Fix HDCA lost in tool form on rerun by @mvdbeek in #22258

Fix purge for anon histories by @mvdbeek in #22275

Raise error when API client sends invalid parameter keys by @mvdbeek in #22277

Raise MessageException instead of generic Exception in rules_dsl by @mvdbeek in #22285

Fix toolshed static image url encoding by @mvdbeek in #22286

Fix nested DatasetCollectionElement in dynamic options by @mvdbeek in #22287

Fix flaky job search for HDCA inputs on PostgreSQL by @mvdbeek in #22290

Fix HDCA shown as unavailable on tool form rerun by @mvdbeek in #22291

Fix AttributeError when anonymous user searches workflows with is:bookmarked by @mvdbeek in #22296

Downgrade authnz OAuth callback errors from ERROR/EXCEPTION to WARNING by @mvdbeek in #22300

Delay workflow scheduling when collection has unresolved ‘auto’ extension by @mvdbeek in #22303

Fix slow get_private_role_user_emails_dict query by @mvdbeek in #22307

Mark dataset collections as deleted when purging a history by @mvdbeek in #22315

Harden API parameter validation by @mvdbeek in #22351

Remove broken serialize_urls from HDASerializer by @mvdbeek in #22358

Fix HideDatasetAction not applied for cached workflow jobs by @mvdbeek in #22360

Don’t retry JobNotReadyException in job destination mapping by @mvdbeek in #22377

Fix workflow extract NoneType on LDDA leaf in implicit collection by @jmchilton in #22381

Serialize data provider errors as MessageException subclasses by @mvdbeek in #22398

Handle MaxDiscoveredFilesExceededError for dynamic collections by @mvdbeek in #22402

Unwrap HDCAs/DCEs nested in multi data input lists by @mvdbeek in #22405

Reject HDCA submitted to single data parameter by @mvdbeek in #22406

Refactor display application handling by @guerler in #15076

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

Remove Trackster by @guerler in #20974

Integrate ‘uv’ for enhanced package management by @arash77 in #21002

Update Python dependencies by @galaxybot in #21043

Improve type annotation of job runners by @nsoranzo in #21050

Remove Job.params by @jdavcs in #21075

Update Python dependencies by @galaxybot in #21104

Pulsar relay implementation by @mvdbeek in #21118

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

Fix various bugs/hacks with tool_data_table handling. by @jmchilton in #21163

Add type annotations to job handling code by @nsoranzo in #21171

Replace tuswsgi with tuspyserver by @mvdbeek in #21201

Update Python dependencies by @galaxybot in #21229

Reimplement keycloak/cilogon as PSA providers and remove custos by @nuwang in #21234

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

Move js-client bootstrapping to FastAPI by @guerler in #21264

Update Python dependencies by @galaxybot in #21301

Implement GA4GH WES API by @jmchilton in #21335

Update Python dependencies by @galaxybot in #21345

Link to an external profile when user accounts are managed by a single OIDC provider by @marius-mather in #21356

Add OMERO File Source Plugin by @davelopez in #21367

Update Python dependencies by @galaxybot in #21368

Fix: tool execution typing improvements/fixes by @jmchilton in #21374

Update fastapi to 0.123.4 and get_openapi() fork by @nsoranzo in #21384

Add initial support for the DICOM format by @kostrykin in #21385

Add new Azure Flat object store file source by @guerler in #21398

Update Python dependencies by @galaxybot in #21400

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

Add Google Batch job runner by @ksuderman in #21443

Update Python dependencies by @galaxybot in #21449

Add Jupyternaut adapter for JupyterLite integration by @guerler in #21463

Add support for Python 3.14 by @nsoranzo in #21486

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

Update Python dependencies by @galaxybot in #21500

Raise ConfigurationError instead etree.ParseError by @mvdbeek in #21509

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

Update Python dependencies by @galaxybot in #21513

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

Update Python dependencies by @galaxybot in #21526

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

Clean up code with pyupgrade by @nsoranzo in #21540

Update Python dependencies by @galaxybot in #21552

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

Drop support for Python 3.9 by @nsoranzo in #21583

Switch Google Cloud Storage file source from fs-gcsfs to gcsfs (fsspec) by @mvdbeek in #21590

Update Python dependencies by @galaxybot in #21606

Update to gravity 1.2.0 by @nsoranzo in #21608

Move legacy Visualization Plugins API to FastAPI by @guerler in #21612

Apply 2026 black style by @galaxybot in #21618

Update Python dependencies by @galaxybot in #21653

Add agent based AI tool recommendation by @dannon in #21661

Type annotations and refactorings by @nsoranzo in #21673

Check file source template config files for determining conditional dependencies + add constraint for zero-ice by @bernt-matthias in #21688

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

Backport chat API improvements by @dannon in #21973

Use ParameterValueError for dataset count validation to reduce Sentry noise by @mvdbeek in #22058

Use mock test server when tests don’t target external galaxy server by @mvdbeek in #22103

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

Don’t return 404 when file name can’t be serialized by @mvdbeek in #21577

Reduce completion monitor logging by @mvdbeek in #21674

Backport: Fix dbkey filter returning no options when dbkey unset by @bernt-matthias in #21945

Show invalid tool error reasons in Tool Shed UI by @mvdbeek in #22040

Backport of 21939 by @jdavcs in #22265

Record input parameter invocation inputs by @mvdbeek in #21452

Maintain column definitions on map over by @mvdbeek in #21468

Do not update a user’s update_time when an admin archives (and purges) a history by @natefoo in #21484

Fix subworkflow runs for disconnected required inputs with defaults by @mvdbeek in #21488

Usability fixes for sample sheet selection. by @jmchilton in #21503

Fix type annotation for invocation report errors field by @mvdbeek in #21508

Filter out failed_metadata HDAs from job cache by @mvdbeek in #21544

Fix pulsar with rewrite_parameters: false by @mvdbeek in #21557

Fix Pulsar with default_file_action: none by @mvdbeek in #21578

Fix condor typo by @gsaudade99 in #21651

Fix HTCondor runner unwatching jobs when stopping containers by @kysrpex in #21656

Fix option propagation for workflow inputs connected to multiple subworkflows by @mvdbeek in #21712

Add missing filter_failed_collection_1.1.0.xml tool by @mvdbeek in #21719

Strip inline comments in conditional requirements by @mvdbeek in #21720

Add sample sheet support to many database operation tools by @mvdbeek in #21465

Add database operation tool to convert sample sheets to list collections by @mvdbeek in #21625

Workaround to numeric sorting in the local portion of tool versions if they are galaxy “build” numbers by @natefoo in #13570

Bump requests from 2.32.3 to 2.32.4 in /lib/galaxy/dependencies by @dependabot[bot] in #20422

Remove decoded ids from job/dataset error report email by @ahmedhamidawan in #20714

Fix multiple=”true” data collection map over for shell_command tools by @mvdbeek in #20859

Fix default conditional test parameters… by @jmchilton in #20942

Set minimum profile version for expression tools by @mvdbeek in #21151

Add Convert characters1 to workflow safe updates by @mvdbeek in #21160

Bump up minimal tpv version by @mvdbeek in #21166

Add missing more-itertools dependency by @nsoranzo in #21214

Fix downloading subworkflows without stored workflow by @mvdbeek in #21223

Fix fastapi package conflict by @mvdbeek in #21349

Skip mako for rendering tool help by @mvdbeek in #21428

Fix optional subworkflow input scheduling bug by @mvdbeek in #21435

Maintain columns on sample sheet map over by @mvdbeek in #21436

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

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

Add tags to output datasets from tool form by @PlushZ in #19225

Implement Sample Sheets by @jmchilton in #19305

Consider collections in on_strings for parameters accepting multiple datasets by @bernt-matthias in #19817

Remove backbone-based charts modules by @guerler in #19892

Update Python dependencies by @galaxybot in #20139

Remove legacy visualizations by @guerler in #20173

Split Login and Register, enable OIDC Registration. by @uwwint in #20287

Empower Users to More Pragmatically Import Datasets & Collections From Tables by @jmchilton in #20288

Switch Default Visualization Endpoint to script, migrate to YAML by @guerler in #20303

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

Update Python dependencies by @galaxybot in #20347

Install Visualization plugins as self-contained packages by @guerler in #20348

Prepare ToolBox.dynamic_tool_to_tool() for CWL formats by @nsoranzo in #20364

Install visualizations directly to static path, avoid duplication by @guerler in #20372

Update Python dependencies by @galaxybot in #20383

Type annotation fixes for mypy 1.16.0 by @nsoranzo in #20424

Implement dataset source requested transformations. by @jmchilton in #20435

Add username_key setting to configure python-social-auth OIDC by @marius-mather in #20497

Remove deprecated tool document cache by @nsoranzo in #20510

Fixes for invocation import. by @jmchilton in #20528

Update Python dependencies by @galaxybot in #20537

Decode OIDC access token as part of authentication pipeline by @marius-mather in #20547

Update Python dependencies by @galaxybot in #20577

Display the Galaxy Citation within the Export Tool References List by @mschatz in #20584

Implement Data Landing Requests by @jmchilton in #20592

Update Python dependencies by @galaxybot in #20601

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

Clean up code from pyupgrade by @nsoranzo in #20642

Update Python dependencies by @galaxybot in #20653

Update Python dependencies by @galaxybot in #20680

Update Python dependencies by @galaxybot in #20699

Improve cli and slurmcli runner traceability for job status and failure reasons by @selten in #20717

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

Hierarchical display collection dataset states by @mvdbeek in #20731

Update Python dependencies by @galaxybot in #20732

Update Python dependencies by @galaxybot in #20753

Consolidate visualization mako, avoid user agent styles by @guerler in #20760

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

Drop old load_workflow controller method, use API by @mvdbeek in #20774

Update Python dependencies by @galaxybot in #20779

Add Hugging Face 🤗 file source and user-defined template by @davelopez in #20805

Update Python dependencies by @galaxybot in #20812

Update pytest to v8 by @nsoranzo in #20838

Update Python dependencies by @galaxybot in #20841

Allow adding extra steps to the default pipeline of the OIDC authentication by @marius-mather in #20845

Use a streaming based parser (ijson) when setting metadata for biom1 files. by @ksuderman in #20851

Various Container Execution Enhancements (including GCP Batch support) by @jmchilton in #20862

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

Update Python dependencies by @galaxybot in #20869

Improve type annotation for job runners and InteractiveToolManager by @nsoranzo in #20871

Replace deprecated codecs.open() by @nsoranzo in #20891

Update Python dependencies by @galaxybot in #20905

Allow creation of visualizations without dataset by @guerler in #20914

Add support for picking from_work_dir directory by @mvdbeek in #20916

Add tool to add nesting level to collection by @bernt-matthias in #20926

Update Python dependencies by @galaxybot in #20930

Allow addressing user defined tools in job config by @mvdbeek in #20932

Wire up and test resource requirement via tpv by @mvdbeek in #20936

Limit admin requirement of selected tool data api endpoints by @guerler in #20949

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

Use nodejs-wheel to install node by @mvdbeek in #20963

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

Update Python dependencies by @galaxybot in #20968

Log task execution errors with log.exception by @mvdbeek in #20970

Update Python dependencies by @galaxybot in #21005

Bump up total-perspective-vortex dependency by @mvdbeek in #21014

Tighter API for tool run tagging. by @jmchilton in #21210

Optimize /api/invocations/steps/{step_id} by @mvdbeek in #21249

Optionally include column headers in sample sheet file by @mvdbeek in #21439

Merge release_25.0 into dev by @davelopez in #20484

Bump pillow from 11.2.1 to 11.3.0 in /lib/galaxy/dependencies by @dependabot[bot] in #20591

Sample Sheet Bug Fixes around Preserving Collection Metadata by @jmchilton in #20749

Validate sample sheet column definitions in workflow definitions on backend. by @jmchilton in #20880

Drop fastapi extra dep from sentry-sdk by @mvdbeek in #21156

Resolve possible symlink before establishing tool file location by @mvdbeek in #21175

Check for expiration in refresh token dictionary by @jdavcs in #20954

Deactivate user file source on unknown error by @mvdbeek in #20962

Don’t create workflow outputs to recover input parameter outputs by @mvdbeek in #20980

Fix PUT /api/workflows for user defined tools by @mvdbeek in #20987

Store pulsar job prep error messages by @mvdbeek in #21013

Require OK datasets for filtering empty datasets by @bernt-matthias in #21023

Fix InvalidRequestError when saving workflow step with dynamic tool by @mvdbeek in #21056

Run landing request state through validator by @mvdbeek in #21087

Create new datasets when creating skipped database operation tool outputs by @mvdbeek in #21142

Fix refresh token expiration retrieval logic by @nuwang in #21213

Use job cache also for implicit conversions by @mvdbeek in #21021

Fix restricting user defined tool input datasets extensions by @mvdbeek in #20545

Don’t assume cwd = job directory when running prepare dirs by @natefoo in #20571

Fix apply rules ownership check by @mvdbeek in #20582

Prevent importing workflows with invalid step UUID by @davelopez in #20596

Constraint conditional redis version to allow only minor updates by @davelopez in #20603

Fix optional unspecified input to conditional step by @mvdbeek in #20647

Avoid postgres truncation of aliases and labels by @mvdbeek in #20649

Fix deferred datasets in multiple dataset parameters. by @jmchilton in #20650

Bump up pulsar dependency to 0.15.9 by @mvdbeek in #20672

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

Update galaxy-release-util by @mvdbeek in #20727

Fix maximum workflow invocation duration test by @mvdbeek in #20729

Add redis conditional dependency by @davelopez in #20502

Improve workflow monitor loop times by @mvdbeek in #20522

Fix single data element identifier to be a regular string by @mvdbeek in #20438

Pin isa-rwval 0.10.11, drop conditional import handling by @natefoo in #20527

Fix galaxy-config script, move install to galaxy-dependencies in app package by @natefoo in #20531

Bump gravity dependency to 1.1.0 by @mvdbeek in #20520

Bump Gravity to 1.1.1 by @natefoo in #20533

Bump tornado from 6.4.1 to 6.4.2 in /lib/galaxy/dependencies by @dependabot[bot] in #19189

Don’t calculate dataset hash for datasets in non-OK state by @nsoranzo in #19191

Bump python-multipart from 0.0.17 to 0.0.18 in /lib/galaxy/dependencies by @dependabot[bot] in #19233

Use resource_path() to access datatypes_conf.xml.sample as a package resource by @nsoranzo in #19331

Require importlib-resources also for Python 3.9-3.11 by @nsoranzo in #19358

Bump jinja2 from 3.1.4 to 3.1.5 in /lib/galaxy/dependencies by @dependabot[bot] in #19369

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

Alternative format_source fix by @mvdbeek in #19395

Avoid using custos refresh tokens which are expired by @martenson in #19411

Use fissix also when python3-lib2to3 is not installed by @nsoranzo in #19749

Fix setting env and tags on resubmission by @bernt-matthias in #19753

Fix Galaxy ignoring job object_store_id for quota check by @bernt-matthias in #19854

Fix broken optimisation introduced in #19852 by @nsoranzo in #19871

Fix various mypy issues around mapped attributes by @mvdbeek in #19883

More fixes to FormData drag and drop and typing by @ahmedhamidawan in #19900

Fix ownership check in history contents update route by @mvdbeek in #19969

Pass host url to visualizations by @guerler in #20022

Allow deferred and ok state datasets for vis by @guerler in #20143

Fix certain cases of collection parameter handling during workflow execution. by @jmchilton in #20152

Fix tapis module typing errors by @jdavcs in #20175

Fix NFDI auth by @bgruening in #20217

Add non-dev httpx dependency by @mvdbeek in #20281

Rerun workflows for the correct version/instance by @ahmedhamidawan in #20313

Fix workflow bookmark filtering by @davelopez in #20325

Generate a tenant-unique UID for tapis. by @dannon in #20370

Fix job rerun with tool version change by @mvdbeek in #20417

Update pulsar-galaxy-lib to 0.15.8 by @mvdbeek in #20419

Upgrade tensorflow conditional dependency version to 2.15.1 by @cat-bro in #20434

Dataset Display and Preferred Viz fixes by @dannon in #20439

Dynamic options: add data table filter by @bernt-matthias in #12941

Run the tool working dir backup/restore on Pulsar by @natefoo in #16696

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

Update Python dependencies by @galaxybot in #19190

Fix UP031 errors - Part 1 by @nsoranzo in #19194

Fix UP031 errors - Part 3 by @nsoranzo in #19218

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

Refactor for better reuse of workflow parameter type constants by @nsoranzo in #19260

Fix UP031 errors - Part 5 by @nsoranzo in #19282

Migrate WF Collection Input Form Definition to Client Side by @jmchilton in #19313

Fix UP031 errors - Part 6 by @nsoranzo in #19314

Update pydantic to 2.10.3 by @nsoranzo in #19326

Misc fixes 202412 by @nsoranzo in #19341

Hide outdated visualizations from visualizations activity panel by @guerler in #19353

Update Python dependencies by @galaxybot in #19366

Add Dataverse RDM repository integration by @KaiOnGitHub in #19367

Type annotation fixes for mypy 1.14.0 by @nsoranzo in #19372

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

Set safe default extraction filter for tar archives by @nsoranzo in #19406

Remove transaction helper by @jdavcs in #19407

Prevent users from reusing a banned email after account is purged by @jdavcs in #19413

Update Python dependencies by @galaxybot in #19418

Add User-Defined Tools by @mvdbeek in #19434

Type annotations improvements by @nsoranzo in #19442

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

Update Python dependencies by @galaxybot in #19464

Type annotation improvements by @nsoranzo in #19485

Update Python dependencies by @galaxybot in #19510

Add config options for tool dependency installs by @afgane in #19565

Update Python dependencies by @galaxybot in #19567

Remove tags used by @ElectronicBlueberry in #19576

Expand workflow metadata for readme. by @jmchilton in #19591

Add failed jobs working directory cleanup as a celery periodic task by @sanjaysrikakulam in #19594

Use correct plugin_kind in user file sources by @davelopez in #19622

Update Python dependencies by @galaxybot in #19623

Format code with black 25.1.0 by @nsoranzo in #19625

Type annotation improvements by @nsoranzo in #19642

Refactor dependencies for tool output actions. by @jmchilton in #19662

Add webdavclient3 to conditional-requirements.txt by @bgruening in #19671

Update Python dependencies by @galaxybot in #19682

Drop support for Python 3.8 by @nsoranzo in #19685

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

Move RequiredAppT back into galaxy packages. by @jmchilton in #19704

Use model classes from galaxy.model instead of app.model object - Part 1 by @nsoranzo in #19706

Preserve workflow labels in final invocation reports by @guerler in #19721

ToolShed 2.1 - Various bugfixes and enhancements. by @jmchilton in #19722

Use model classes from galaxy.model instead of app.model object - Part 2 by @nsoranzo in #19726

Update Python dependencies by @galaxybot in #19727

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

Improvements to package decomposition. by @jmchilton in #19759

Update Python dependencies by @galaxybot in #19772

Add visualization framework interface to cell-based markdown editor by @guerler in #19775

Update Python dependencies by @galaxybot in #19816

Populate image metadata without allocating memory for the entire image content by @kostrykin in #19830

Syntactic sugar to ease TPV configuration. by @jmchilton in #19834

Improve markdown editor modularity and structure by @guerler in #19835

Add mandatory RO-Crate metadata when exporting by @elichad in #19846

Add basic support for icons in tools by @davelopez in #19850

Improve type annotations of ModelPersistenceContext and derived classes by @nsoranzo in #19852

Drop old galaxy_session records by @jdavcs in #19872

Update Python dependencies by @galaxybot in #19874

Add Tapis auth support by @dannon in #19887

Remove unnecessary code duplications by @nsoranzo in #19921

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

Update Python dependencies by @galaxybot in #19929

Add type hints around collection copying and job things by @mvdbeek in #19961

Job cache allow different names when possible by @mvdbeek in #19962

Update Python dependencies by @galaxybot in #19964

Allow different AI providers (as long as they are openai compatible) by @uwwint in #19989

Improve type annotation of tool parameter wrapping by @nsoranzo in #19991

IT Activity Panel by @dannon in #19996

Update Python dependencies by @galaxybot in #19998

Implement dataset collection support in workflow landing requests by @mvdbeek in #20004

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

Add DOI to workflow metadata by @jdavcs in #20033

Add support for Markdown help text in visualizations by @guerler in #20043

Add sample datasets for visualizations by @guerler in #20046

Use visualization dropdown solely for examples by @guerler in #20094

Update Python dependencies by @galaxybot in #20096

Adds Example Datasets and Help Text for Visualizations by @guerler in #20097

Additional type hints for toolbox.get_tool / toolbox.has_tool by @mvdbeek in #20150

Create working dir output outside of tool evaluator by @mvdbeek in #20153

Add three AAI providers by @martenson in #20165

Add replacement_dataset option to collection filter tools by @simonbray in #20166

Implement file source to integrate Galaxy with RSpace by @kysrpex in #20167

Visualization-First Display functionality by @dannon in #20190

Improve type annotation of galaxy.model.dataset_collections by @nsoranzo in #20194

Improve performance of job cache query by @mvdbeek in #20319

Merge 24.2 into dev by @jdavcs in #19590

Fix import and update_page type signature by @mvdbeek in #19932

Fix copying job output from discovered outputs by @mvdbeek in #19999

Bump h11 from 0.14.0 to 0.16.0 in /lib/galaxy/dependencies by @dependabot[bot] in #20088

Fix job rerun for dynamic tools by @mvdbeek in #20259

Fix conditional dependency path resolution by @mvdbeek in #19723

Allow tool state changes in refactor actions by @mvdbeek in #19730

Update fs.dropboxfs conditional dependency version to 1.0.3 by @davelopez in #19741

Follow-up to #19651: Do not reassign: method modifies object in-place by @jdavcs in #19746

Add bwa_mem2_index directory datatype, framework enhancements for testing directories by @mvdbeek in #19694

Skip slow tests for manage_db, db_dev scripts by @jdavcs in #19744

Make k8s user and group ids overriddable per job by @nuwang in #19568

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

Dynamics options add library dataset by @gagayuan in #18198

Fix some deprecations by @nsoranzo in #18433

Fixes for errors reported by mypy 1.11.0 by @nsoranzo in #18608

Update mercurial by @mvdbeek in #18686

Replace types-pkg-resources with types-setuptools by @nsoranzo in #18708

Fix tag processing in library upload by @davelopez in #18714

Update ruff to 0.6.1 by @nsoranzo in #18716

Fix new flake8-bugbear B039 and mypy type-var errors by @nsoranzo in #18755

Fixes and tests for data fetch models. by @jmchilton in #18834

data_column params: offer same columns with and without use_header_names by @wm75 in #18879

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

Fix the bioblend test failures by @arash77 in #18991

Fix job directory not being cleaned up by @davelopez in #18997

Fixes random job failures in kubernetes by @mapk-amazon in #19001

Fix numerous issues with tool input format “21.01” by @jmchilton in #19030

Fix test_stock.py unit test by @mvdbeek in #19037

quota: do not complain on no-change of default by @bernt-matthias in #19045

Normalize usernames to lowercase in OIDC authentication by @arash77 in #19131

2 small uv config fixes by @nsoranzo in #19146

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

Fix import of previously-deleted TRS workflow by @mvdbeek in #19311

Fix quota usage with user object stores by @davelopez in #19323

Fix workflows with optional non-default parameter input by @mvdbeek in #19332

Backport #19001 kubernetes api client fix by @mvdbeek in #19338

Partial backport of #19331 by @nsoranzo in #19342

Use select_from_url test data from github, not usegalaxy.org by @mvdbeek in #19352

Fix to only show ChatGXY when available. by @dannon in #19389

Fix job parameter summary for inputs without label by @mvdbeek in #19427

Show Keycloak provider label in UI by @ahmedhamidawan in #19447

Expression tool format source backport by @mvdbeek in #19466

backport of defensive refresh tokens by @martenson in #19471

Improve relabel from file error if file doesn’t contain enough lines by @mvdbeek in #19480

Serialize message exceptions on execution error by @mvdbeek in #19483

Fail with error message when submitting invalid request by @mvdbeek in #19489

Fix deleting lddas in batch by @davelopez in #19506

Skip token refresh without refresh token in psa by @mvdbeek in #19514

Downgrade ‘InteractiveTools are not enabled’ to warning by @mvdbeek in #19518

Fix extracting workflows from purged and deleted histories by @mvdbeek in #19525

Fix error message when subworkflow input connection missing by @mvdbeek in #19526

Fix remap for parameter called id by @mvdbeek in #19532

Fix admin cancel job message not being displayed to the user by @davelopez in #19537

Use instance wide default real_system_username if not defined on destination by @bernt-matthias in #19544

Fix job paused on user defined object store by @davelopez in #19578

Add clean up job working directory as celery task by @sanjaysrikakulam in #15816

Experimental galactic wizard by @dannon in #15860

Feature - stdout live reporting by @gecage952 in #16975

Update Python dependencies by @galaxybot in #18226

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

More data access tests, some refactoring and cleanup by @jdavcs in #18312

Update Python dependencies by @galaxybot in #18406

Add Python 3.13 support by @nsoranzo in #18449

Add onedata templates by @bwalkowi in #18457

Support high-availability setups for the interactive tools proxy by @kysrpex in #18481

Add unique constraints to the email and username fields in the galaxy_user table by @jdavcs in #18493

Update Python dependencies by @galaxybot in #18505

Improvements for K8S deployment (especially ITs) by @almahmoud in #18514

Add Tool-Centric APIs to the Tool Shed 2.0 by @jmchilton in #18524

Improvements to Tool Test Parsing by @jmchilton in #18560

Group tool templating exceptions in sentry by @mvdbeek in #18570

Update Python dependencies by @galaxybot in #18578

Record container id and type in core job metrics by @mvdbeek in #18579

Rev pinned gxformat2. by @jmchilton in #18624

Better Typing for Tool Execution Plumbing by @jmchilton in #18626

Remove unused functions in dataset managers by @jmchilton in #18631

Parameter Model Improvements by @jmchilton in #18641

Parse stored config details to script-based visualizations by @guerler in #18651

Another round of parameter model improvements. by @jmchilton in #18673

Allow access to invocation via shared or published history by @mvdbeek in #18707

Allow specifying multi-select workflow parameters by @mvdbeek in #18715

Improvements to help terms & tool help. by @jmchilton in #18722

Add a retry when deleting a k8s job by @afgane in #18744

More typing, docs, and decomposition around tool execution by @jmchilton in #18758

Add Workflow Title and Annotation sections by @hujambo-dunia in #18762

Refactor LibraryDatasetsManager and fix type annotation issue by @nsoranzo in #18773

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

Allow using tracks and groups in visualization xml by @guerler in #18779

Workflow Landing Requests by @jmchilton in #18807

Update Mypy to 1.11.2 and fix new signature override errors by @nsoranzo in #18811

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

Update Python dependencies by @galaxybot in #18864

Implement Pydantic model for workflow test format. by @jmchilton in #18884

Remove some unused dynamic drill down options. by @jmchilton in #18892

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

Update Python dependencies by @galaxybot in #18904

Type annotations and fixes by @nsoranzo in #18911

Add filter null collection operation tool by @mvdbeek in #18928

Remove outdated fimo wrapper and galaxy-sequence-utils dependency by @nsoranzo in #18937

Update Python dependencies by @galaxybot in #18943

Allow to overwrite real_system_username per destination by @bernt-matthias in #18945

Assert that data_column parameters have a valid data_ref by @bernt-matthias in #18949

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

Workflow landing improvements by @mvdbeek in #18979

Update Python dependencies by @galaxybot in #18982

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

Enhance relabel_from_file to work with any column pair in mapping file by @wm75 in #19022

A variety of improvements around tool parameter modeling (second try) by @jmchilton in #19027

Better logging around tool loading by @jmchilton in #19029

Update Python dependencies by @galaxybot in #19031

Silence the quota manager for updates by @bernt-matthias in #19046

Add job metrics per invocation by @mvdbeek in #19048

Update Python dependencies by @galaxybot in #19062

Annotate DatasetAssociationManager as generic type by @nsoranzo in #19063

Move TRS import into WorkflowContentManager by @mvdbeek in #19070

Replace poetry with uv by @nsoranzo in #19075

Allow deferred datasets to behave as URIs by @davelopez in #19077

Implement workflow parameter validators. by @jmchilton in #19092

Allow directory_uri workflow parameters. by @jmchilton in #19093

Better cleanup of sharing roles on user purge by @jdavcs in #19096

Support deferred datasets in visualizations by @davelopez in #19097

uv: Do not recalculate dependencies when exporting by @nsoranzo in #19099

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

Test hash validation also for upload by path by @nsoranzo in #19109

Always validate hashes when provided by @nsoranzo in #19110

Add type annotations to JobRunnerMapper and related code by @nsoranzo in #19115

Update Python dependencies by @galaxybot in #19123

Allow a posix file source to prefer linking. by @jmchilton in #19132

Remove OpenLayers legacy files and add SVG logo by @guerler in #19135

Update Python dependencies by @galaxybot in #19149

Fix default value handling for parameters connected to required parameters by @mvdbeek in #19219

Workflow Inputs Activity by @ElectronicBlueberry in #19252

Fix workflow invocation accessibility check by @mvdbeek in #18746

Fix destentation typo by @mvdbeek in #19140

Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in #18428

Update mercurial to non-yanked 6.7.4 by @nsoranzo in #18434

Fix dropped when_expression on step upgrade by @mvdbeek in #18446

Improve workflow-related exception reporting by @mvdbeek in #18447

Fix subwofklow tags serialization type by @arash77 in #18456

by @laperlej in #18459

Add input extra files to get_input_fnames by @mvdbeek in #18462

Return generic message for password reset email by @ahmedhamidawan in #18479

Increase API robustness to invalid requests, improve compressed data serving by @mvdbeek in #18494

Don’t call job_runner.stop_job on jobs in new state by @mvdbeek in #18495

Prevent job submission if input collection element is deleted by @mvdbeek in #18517

Strip unicode null from tool stdio by @mvdbeek in #18527

Fix map over calculation for runtime inputs by @mvdbeek in #18535

Fix for not-null in ‘column_list’ object by @hujambo-dunia in #18553

Also fail ensure_dataset_on_disk if dataset is in new state by @mvdbeek in #18559

Fix sqlalchemy statement in tooltagmanager reset output by @dannon in #18591

Set minimum weasyprint version by @mvdbeek in #18606

Improve relabel identifiers message when number of columns is not 2 by @mvdbeek in #18634

Fix extract workflow from history when implicit collection has no jobs by @mvdbeek in #18661

Make sure we set file size also for purged outputs by @mvdbeek in #18681

File source and object store instance api fixes by @mvdbeek in #18685

Fix change datatype PJA on expression tool data outputs by @mvdbeek in #18691

Fill in missing help for cross product tools. by @jmchilton in #18698

Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by @mvdbeek in #18731

Catch and display exceptions when importing malformatted yaml workflows by @mvdbeek in #18734

Fix infinitely delayed workflow scheduling if skipped step creates HDCA by @mvdbeek in #18751

Fix directory get or create logic by @mvdbeek in #18752

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

Allow to change only the description of a quota by @bernt-matthias in #18775

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

Fix unspecified oidc_endpoint variable overwriting specified redirect_url by @bgruening in #18818

Fix wrong celery_app config on job and workflow handlers by @mvdbeek in #18819

Fix named cursor is not valid anymore by @mvdbeek in #18825

Tighten TRS url check by @mvdbeek in #18841

Fix Workflow index bookmark filter by @itisAliRH in #18842

Skip metric collection if job working directory doesn’t exist by @mvdbeek in #18845

Extend on disk checks to running, queued and error states by @mvdbeek in #18846

Raise MessageException instead of assertions on rerun problems by @mvdbeek in #18858

Fix data_column ref to nested collection by @mvdbeek in #18875

Fix loading very old workflows with data inputs by @mvdbeek in #18876

Access tool data table filters in workflow building mode by @mvdbeek in #18900

Fix username used in invocation report by @mvdbeek in #18932

Disable locking when opening h5 files, add missing with by @mvdbeek in #18976

Fix job search statement building by @mvdbeek in #19010

Put cached jobs back into queue on handler restart by @mvdbeek in #19012

Fix various invocation export issues by @mvdbeek in #19215

Create harmonized collections from correct tool outputs by @wm75 in #19222

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

Implemented the generic OIDC backend from python-social-auth into Gal… by @Edmontosaurus in #18670

Collect job metrics also when job failed by @mvdbeek in #18809

prevent “missing refresh_token” errors by supporting <extra_scopes> also with Keycloak backend by @ljocha in #18826

Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in #18428

Update mercurial to non-yanked 6.7.4 by @nsoranzo in #18434

Fix dropped when_expression on step upgrade by @mvdbeek in #18446

Improve workflow-related exception reporting by @mvdbeek in #18447

Fix subwofklow tags serialization type by @arash77 in #18456

by @laperlej in #18459

Add input extra files to get_input_fnames by @mvdbeek in #18462

Return generic message for password reset email by @ahmedhamidawan in #18479

Increase API robustness to invalid requests, improve compressed data serving by @mvdbeek in #18494

Prevent job submission if input collection element is deleted by @mvdbeek in #18517

Strip unicode null from tool stdio by @mvdbeek in #18527

Fix map over calculation for runtime inputs by @mvdbeek in #18535

Fix for not-null in ‘column_list’ object by @hujambo-dunia in #18553

Also fail ensure_dataset_on_disk if dataset is in new state by @mvdbeek in #18559

Fix sqlalchemy statement in tooltagmanager reset output by @dannon in #18591

Set minimum weasyprint version by @mvdbeek in #18606

Improve relabel identifiers message when number of columns is not 2 by @mvdbeek in #18634

Fix extract workflow from history when implicit collection has no jobs by @mvdbeek in #18661

Make sure we set file size also for purged outputs by @mvdbeek in #18681

File source and object store instance api fixes by @mvdbeek in #18685

Fix change datatype PJA on expression tool data outputs by @mvdbeek in #18691

Fill in missing help for cross product tools. by @jmchilton in #18698

Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by @mvdbeek in #18731

Catch and display exceptions when importing malformatted yaml workflows by @mvdbeek in #18734

Fix infinitely delayed workflow scheduling if skipped step creates HDCA by @mvdbeek in #18751

Fix directory get or create logic by @mvdbeek in #18752

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

Allow to change only the description of a quota by @bernt-matthias in #18775

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

Fix unspecified oidc_endpoint variable overwriting specified redirect_url by @bgruening in #18818

Fix wrong celery_app config on job and workflow handlers by @mvdbeek in #18819

Fix named cursor is not valid anymore by @mvdbeek in #18825

Tighten TRS url check by @mvdbeek in #18841

Fix Workflow index bookmark filter by @itisAliRH in #18842

Skip metric collection if job working directory doesn’t exist by @mvdbeek in #18845

Extend on disk checks to running, queued and error states by @mvdbeek in #18846

Raise MessageException instead of assertions on rerun problems by @mvdbeek in #18858

Fix data_column ref to nested collection by @mvdbeek in #18875

Fix loading very old workflows with data inputs by @mvdbeek in #18876

Access tool data table filters in workflow building mode by @mvdbeek in #18900

Fix username used in invocation report by @mvdbeek in #18932

Disable locking when opening h5 files, add missing with by @mvdbeek in #18976

Fix job search statement building by @mvdbeek in #19010

Put cached jobs back into queue on handler restart by @mvdbeek in #19012

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

Implemented the generic OIDC backend from python-social-auth into Gal… by @Edmontosaurus in #18670

Collect job metrics also when job failed by @mvdbeek in #18809

prevent “missing refresh_token” errors by supporting <extra_scopes> also with Keycloak backend by @ljocha in #18826

Return generic message for password reset email by @ahmedhamidawan in #18479

Increase API robustness to invalid requests, improve compressed data serving by @mvdbeek in #18494

Prevent job submission if input collection element is deleted by @mvdbeek in #18517

Strip unicode null from tool stdio by @mvdbeek in #18527

Fix map over calculation for runtime inputs by @mvdbeek in #18535

Fix for not-null in ‘column_list’ object by @hujambo-dunia in #18553

Also fail ensure_dataset_on_disk if dataset is in new state by @mvdbeek in #18559

Fix sqlalchemy statement in tooltagmanager reset output by @dannon in #18591

Set minimum weasyprint version by @mvdbeek in #18606

Improve relabel identifiers message when number of columns is not 2 by @mvdbeek in #18634

Fix extract workflow from history when implicit collection has no jobs by @mvdbeek in #18661

Make sure we set file size also for purged outputs by @mvdbeek in #18681

File source and object store instance api fixes by @mvdbeek in #18685

Fix change datatype PJA on expression tool data outputs by @mvdbeek in #18691

Fill in missing help for cross product tools. by @jmchilton in #18698

Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by @mvdbeek in #18731

Catch and display exceptions when importing malformatted yaml workflows by @mvdbeek in #18734

Fix infinitely delayed workflow scheduling if skipped step creates HDCA by @mvdbeek in #18751

Fix directory get or create logic by @mvdbeek in #18752

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

Allow to change only the description of a quota by @bernt-matthias in #18775

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

Fix unspecified oidc_endpoint variable overwriting specified redirect_url by @bgruening in #18818

Fix wrong celery_app config on job and workflow handlers by @mvdbeek in #18819

Fix named cursor is not valid anymore by @mvdbeek in #18825

Tighten TRS url check by @mvdbeek in #18841

Fix Workflow index bookmark filter by @itisAliRH in #18842

Skip metric collection if job working directory doesn’t exist by @mvdbeek in #18845

Extend on disk checks to running, queued and error states by @mvdbeek in #18846

Raise MessageException instead of assertions on rerun problems by @mvdbeek in #18858

Fix data_column ref to nested collection by @mvdbeek in #18875

Fix loading very old workflows with data inputs by @mvdbeek in #18876

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

Implemented the generic OIDC backend from python-social-auth into Gal… by @Edmontosaurus in #18670

Collect job metrics also when job failed by @mvdbeek in #18809

prevent “missing refresh_token” errors by supporting <extra_scopes> also with Keycloak backend by @ljocha in #18826

Unpin social-auth-core dependency by @nsoranzo in #17607

Dynamic tool fixes by @dcore94 in #18085

Fix for unexpected OIDC XML validation error by @Edmontosaurus in #18106

Revert some requests import changes by @nsoranzo in #18199

Small bug fixes for user data plugins by @jmchilton in #18246

Fix handler: access to result row items changed in SA2.0 by @jdavcs in #18274

Fix various packages’ issues by @nsoranzo in #18301

Adapt Tool prediction API to Transformer-based deep learning architecture by @anuprulez in #18305

Fix empty usernames in database + bug in username generation by @jdavcs in #18379

Add TypedDict for JobsSummary by @mvdbeek in #18418

Pin pydantic to >=2.7.4 by @nsoranzo in #18423

Update mercurial to non-yanked 6.7.4 by @nsoranzo in #18434

Fix dropped when_expression on step upgrade by @mvdbeek in #18446

Improve workflow-related exception reporting by @mvdbeek in #18447

Fix subwofklow tags serialization type by @arash77 in #18456

Disable password reset for deleted users [GCC2024_COFEST] by @laperlej in #18459

Add input extra files to get_input_fnames by @mvdbeek in #18462

Only include tool stdout/stderr in HDA info by @natefoo in #16730

Adding object store plugin for Rucio by @SergeyYakubov in #17156

Enable all-vs-all collection analysis patterns. by @jmchilton in #17366

Add onedata objectstore by @bwalkowi in #17540

Type annotation improvements by @nsoranzo in #17601

Type annotation and CWL-related improvements by @nsoranzo in #17630

Update Python dependencies by @galaxybot in #17653

Code cleanups from ruff and pyupgrade by @nsoranzo in #17654

Update Python dependencies by @galaxybot in #17764

SQLAlchemy 2.0 by @jdavcs in #17778

Update Python dependencies by @galaxybot in #17819

Update Python dependencies by @galaxybot in #17870

Add email notifications channel by @davelopez in #17914

Model edits and bug fixes by @jdavcs in #17922

Update Python dependencies by @galaxybot in #17923

Model typing and SA2.0 follow-up by @jdavcs in #17958

Error reporting unit tests by @jmchilton in #17968

Make urgent notifications mandatory by @davelopez in #17975

Update Python dependencies by @galaxybot in #17982

Enable warn_unused_ignores mypy option by @nsoranzo in #17991

Add galaxy to user agent by @mvdbeek in #18003

Add Zenodo integration by @davelopez in #18022

Update Python dependencies by @galaxybot in #18035

Add stronger type annotations in file sources + refactoring by @davelopez in #18050

Add pagination support to Files Source plugins by @davelopez in #18059

Update Python dependencies by @galaxybot in #18063

Enable flake8-implicit-str-concat ruff rules by @nsoranzo in #18067

Ensure history update_time is set when exporting by @davelopez in #18086

Overhaul Azure storage infrastructure. by @jmchilton in #18087

Update Python dependencies by @galaxybot in #18095

Update Python dependencies by @galaxybot in #18125

Revises handling of warnings in the workflow run form by @guerler in #18126

Empower users to bring their own storage and file sources by @jmchilton in #18127

Update s3fs dependency. by @jmchilton in #18135

More unit testing for object store stuff. by @jmchilton in #18136

Harden User Object Store and File Source Creation by @jmchilton in #18172

Fix boto3-stubs typecheck dependency by @nsoranzo in #18173

More structured indexing for user data objects. by @jmchilton in #18291

Onedada object store and files source stability fixes by @bwalkowi in #18372

Allow running and editing workflows for specific versions by @ahmedhamidawan in #18378

Chore: remove repetitive words by @tianzedavid in #18076

Fix #18316 (anonymous file sources) by @jmchilton in #18352

Merge 24.0 into 24.1 by @jdavcs in #18353

Merge 24.0 into 24.1 by @jdavcs in #18365

Raise exception if collection elements missing during download by @jdavcs in #18094

Allow purge query param, deprecate purge body param by @mvdbeek in #18105

Backport OIDC schema fix by @mvdbeek in #18111

Don’t log exception if cancelled slurm job doesn’t have stderr file by @mvdbeek in #18121

Downgrade missing output file in working directory to warning for failed jobs by @mvdbeek in #18123

Fix data default values not getting added to history by @mvdbeek in #18132

Drop redundant error message by @mvdbeek in #18156

Emit warning when user-cancelled job already complete by @mvdbeek in #18178

Avoid object store path lookup when constructing JobState object by @mvdbeek in #18190

Add string cast for dbkey / genome_build by @mvdbeek in #18207

Check dataset state when attempting to acces dataset contents by @mvdbeek in #18214

Don’t set dataset peek for errored jobs by @mvdbeek in #18231

Raise exception when extracting dataset from collection without datasets by @mvdbeek in #18249

Skip tests if toolshed, dx.doi not responding by @mvdbeek in #18250

Don’t attempt to download purged datasets by @mvdbeek in #18278

Check various preconditions in FeatureLocationIndexDataProvider by @davelopez in #18283

Don’t serialize display application links for deleted datasets by @mvdbeek in #18307

Downgrade doi fetch error to debug by @mvdbeek in #18330

Fix authentication error for anonymous users querying jobs by @davelopez in #18333

Fix seek in slurm memory check by @mvdbeek in #18338

Do not copy purged outputs to object store by @mvdbeek in #18342

Kill pulsar job if job stopped on galaxy side by @mvdbeek in #18348

Allow DCE as outer input to to_cwl by @mvdbeek in #18349

Fix anonymous user job retrieval logic by @davelopez in #18358

Fix update group API payload model by @davelopez in #18374

Fix user’s private role can be missing by @davelopez in #18381

Fix null inputs in database operation tools by @mvdbeek in #18385

Assign default data extension on discovered collection output by @mvdbeek in #18389

Fix get_accessible_job if called without session by @mvdbeek in #18400

Fix invocation step_job_summary for new collections by @mvdbeek in #18402

Really allow in-range validator for txt by @bernt-matthias in #18411

Fix collection map over status for dragged collections by @mvdbeek in #18416

Serialize purged flag for datasets in collections by @davelopez in #18420

Minor linting cleanup by @mvdbeek in #18421

Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in #18428

Fix tool version switch in editor by @mvdbeek in #17858

Fix workflow run form failing on certain histories by @mvdbeek in #17869

Always serialize element_count and populated when listing contents by @mvdbeek in #17890

Fix saving workflows with freehand_comments only by @mvdbeek in #17901

Always discard session after __handle_waiting_jobs is done by @mvdbeek in #17913

Fix workflow run form for workflows with null rename PJA by @mvdbeek in #17929

Revert unnecessary error change by @mvdbeek in #17948

Fix missing implicit conversion for mapped over jobs by @mvdbeek in #17952

Fix get_content_as_text for compressed text datatypes by @mvdbeek in #17976

Backport: Fix bug: call unique() on result, not select stmt by @jdavcs in #17981

Fix LengthValidator if no value passed by @mvdbeek in #17983

Raise RequestParameterInvalidException if collection element has unknown extension by @mvdbeek in #17985

Don’t attempt to commit in dry_run mode by @mvdbeek in #17987

Don’t fail if reporting invalid parameter values by @mvdbeek in #18002

Include exception info when something goes wrong while refreshing tokens by @mvdbeek in #18008

Avoid exception when opening apply rules tool and no collection in history by @mvdbeek in #18011

Don’t commit without having set a hid by @mvdbeek in #18014

Raise appropriate exception if user forces a collection that is not populated with elements as input by @mvdbeek in #18023

Fix tag regex pattern by @jdavcs in #18025

Fix History Dataset Association creation so that hid is always set by @mvdbeek in #18036

Change wrong quota_source value from KeyError to ValueError by @mvdbeek in #18040

Check database connection to issue a rollback if no connection by @jdavcs in #18070

Fix remote files sources error handling by @davelopez in #18027

Drop left-over debug statement by @mvdbeek in #17939

Reload built-in converters on toolbox reload by @bernt-matthias in #17209

Optional Reply-to SMTP header in tool error reports by @neoformit in #17243

Package tests fixes by @nsoranzo in #17301

Follow-up on #17274 and #17262 by @nsoranzo in #17302

Rollback invalidated transaction: catch them earlier by @jdavcs in #17312

Fixes for flake8-bugbear 24.1.17 by @nsoranzo in #17340

Fix data_source and data_source_async bugs by @wm75 in #17422

More efficient change_state queries, maybe fix deadlock by @mvdbeek in #17632

Don’t index tasks without task_uuid by @mvdbeek in #17646

Separate ConnectedValue from RuntimeValue by @mvdbeek in #17678

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

Fix usage of DISTINCT by @jdavcs in #17759

Also set extension and metadata on copies of job outputs when finishing job by @mvdbeek in #17777

Use hg clone --stream to clone repos by @mvdbeek in #17786

Defer job attributes that are usually not needed by @mvdbeek in #17795

Fix change_datatype PJA for dynamic collections by @mvdbeek in #17803

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

Normalize extensions when loading tool by @mvdbeek in #17868

Ignore user data table errors for now by @mvdbeek in #17880

Add harmonize collections tool (or whatever other name) by @lldelisle in #16662

Add support for Python 3.12 by @tuncK in #16796

SQLAlchemy 2.0 upgrades (part 5) by @jdavcs in #16932

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

Support for OIDC API Auth and OIDC integration tests by @nuwang in #16977

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

Extend regex groups in stdio regex matches by @bernt-matthias in #17016

Vueify Admin User Grid by @guerler in #17030

Remove web framework dependency from tools by @davelopez in #17058

Add select parameter with options from remote resources by @mvdbeek in #17087

Expose more tool information / navigability in UI. by @jmchilton in #17105

Vueify Admin Roles Grid by @guerler in #17118

SA2.0 updates: handling “object is being merged into a Session along the backref cascade path” by @jdavcs in #17122

Update Python dependencies by @galaxybot in #17123

Vueify Admin Groups Grid by @guerler in #17126

Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning by @jdavcs in #17132

Vueify Admin Forms and Quota grids by @guerler in #17141

Update Python dependencies by @galaxybot in #17157

Update Python dependencies by @galaxybot in #17201

Vendorize fastapi-utls.cbv by @jdavcs in #17205

Fix usage of graphene-sqlalchemy, bump to 3.0.0rc1 by @jdavcs in #17216

Vueifiy History Grids by @guerler in #17219

Update Python dependencies by @galaxybot in #17230

Update Python dependencies by @galaxybot in #17235

Allow job files to consume TUS uploads by @jmchilton in #17242

Update Python dependencies by @galaxybot in #17247

Migrate models to pydantic 2 by @mvdbeek in #17262

Consider Null inputs by @bernt-matthias in #17271

Add OIDC backend configuration schema and validation by @uwwint in #17274

Adds delete, purge and undelete batch operations to History Grid by @guerler in #17282

Add __KEEP_SUCCESS_DATASETS__ by @lldelisle in #17294

Improve ModelManager type hints by @mvdbeek in #17299

API endpoint that allows “changing” the objectstore for “safe” scenarios. by @jmchilton in #17329

Update Python dependencies by @galaxybot in #17333

Add element_identifier and ext to inputs config file export by @bernt-matthias in #17357

Remove unused statements in job search function by @mvdbeek in #17361

Enable warn_unreachable mypy option by @mvdbeek in #17365

Fix type annotation of code using XML etree by @nsoranzo in #17367

More specific type annotation for BaseJobExec.parse_status() by @nsoranzo in #17381

Cancel all active jobs when the user is deleted by @davelopez in #17390

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

Purge groups and roles from DB (for real) by @davelopez in #17411

Update Python dependencies by @galaxybot in #17420

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

Adds published histories to grid list by @guerler in #17449

Allow filtering history datasets by object store ID and quota source. by @jmchilton in #17460

data_column parameter: use column_names metadata if present by @bernt-matthias in #17478

Update Python dependencies by @galaxybot in #17486

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

Update k8s docker python to 3.12 by @nuwang in #17494

add encode ID API endpoint by @mira-miracoli in #17510

Fixing data_source tools and incrementing tool profile by @wm75 in #17515

Update Python dependencies by @galaxybot in #17541

Add image_diff comparison method for test output verification using images by @kostrykin in #17556

Filter out subworkflow invocations by @mvdbeek in #17558

Update Python dependencies by @galaxybot in #17580

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

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

Improved error messages for runtime sharing problems. by @jmchilton in #17794

Allow admin to sharpen language about selected object stores. by @jmchilton in #17806

consistently compare profile versions by @bernt-matthias in #16492

pin fs.dropboxfs to >=1 by @bernt-matthias in #16451

Remove unnecessary check: item cannot be None by @jdavcs in #16550

Fix: serialize tool_shed_urls directly from the API by @davelopez in #16561

Fix dependency update GitHub workflow by @nsoranzo in #16639

Ensure Job belongs to current SA session by @jdavcs in #16647

Account for shared usage between TS and galaxy apps by @jdavcs in #16746

move the email and username redacting from the role loop by @martenson in #16805

Fix shed unit test by @mvdbeek in #16811

chore: fix typos by @afuetterer in #16851

Fix bug in SQLAlchemy statement by @jdavcs in #16881

Ruff and flake8 fixes by @nsoranzo in #16884

Update help in relabel_from_file.xml by @lldelisle in #16891

Fix subtle bug in listify function + simplify list munging by @jdavcs in #16904

prep for updated h5py and typos by @mr-c in #16963

Enhancement to Tool Form page, Repeating form fields implement parameter instructions by @hujambo-dunia in #17018

Expose file_name property in DatasetFilenameWrapper by @jdavcs in #17107

Fix to_cwl for nested collections by @mvdbeek in #17276

Rollback invalidated transaction by @jdavcs in #17280

Install newer celery on python 3.8+ by @mvdbeek in #17309

Backport Rollback invalidated transaction: catch them earlier by @mvdbeek in #17315

Discard sqlalchemy session after task completion by @mvdbeek in #17317

Scope session for job runner monitor loop by @mvdbeek in #17319

Fix History contents genome_build filter postgresql bug by @ahmedhamidawan in #17384

Update python-multipart to 0.0.7 by @nsoranzo in #17429

Build param dict before creating entrypoint by @mvdbeek in #17440

Fix bug: true >> True by @jdavcs in #17446

Set metadata states on dataset association, not dataset by @mvdbeek in #17474

Remove two print statements by @bernt-matthias in #17480

Provide working routes.url_for every ASGI request by @mvdbeek in #17497

Implement default locations for data and collection parameters. by @jmchilton in #14955

Enable job resubmissions in k8s runner by @pcm32 in #15238

Add parameter name to validation errors by @bernt-matthias in #15440

Tool Shed 2.0 by @jmchilton in #15639

Add ability to assert metadata properties on input dataset parameters by @bernt-matthias in #15825

Limit number of celery task executions per second per user by @claudiofr in #16232

Delete non-terminal jobs and subworkflow invocations when cancelling invocation by @mvdbeek in #16252

Towards SQLAlchemy 2.0 (upgrades to SA Core usage) by @jdavcs in #16264

Update Python dependencies by @galaxybot in #16305

Add carbon emissions admin configuration options by @Renni771 in #16307

Migrate a part of the users API to Fast API by @heisner-tillman in #16341

Update Python dependencies by @galaxybot in #16360

Add Invenio RDM repository integration by @davelopez in #16381

Update Python dependencies by @galaxybot in #16389

Update Python dependencies by @galaxybot in #16409

Refactor FilesDialog + Remote Files API schema improvements by @davelopez in #16420

Towards SQLAlchemy 2.0 (upgrades to SA ORM usage in /test) by @jdavcs in #16431

SQLAlchemy 2.0 upgrades to ORM usage in /lib by @jdavcs in #16434

Update Python dependencies by @galaxybot in #16436

Update Python dependencies by @galaxybot in #16485

Rename MetadataEqualsValidator by @bernt-matthias in #16489

Add support for CILogon deployments in different regions than the US by @uwwint in #16490

Refactor/OIDC custos by @uwwint in #16497

Update Python dependencies by @galaxybot in #16521

Move database access code out of galaxy.util by @jdavcs in #16526

Tweak tool memory use and optimize shared memory when using preload by @mvdbeek in #16536

Update Python dependencies by @galaxybot in #16577

Vueify Tool Form Data Selector by @guerler in #16578

Workflow Comments 💬 by @ElectronicBlueberry in #16612

Switch out conditional requirement parser by @mvdbeek in #16636

Add scroll pagination and username filter to HistoryPublishedList by @ahmedhamidawan in #16642

Bump samtools converters by @bernt-matthias in #16668

Galaxy Markdown - add workflow image and license to Galaxy markdown. by @jmchilton in #16672

Implement instance URLs in Galaxy markdown. by @jmchilton in #16675

Change Sentry error reporting plug-in by @kysrpex in #16686

Use fs.onedatarestfs for Onedata files source plugin implementation by @lopiola in #16690

Enhance task monitor composable by @davelopez in #16695

Misc. edits/refactorings to session handling by @jdavcs in #16712

SQLAlchemy 2.0 upgrades (part 2) by @jdavcs in #16724

Update Python dependencies by @galaxybot in #16735

Convert ISO to UTC for Date/Time in workflow reports by @assuntad23 in #16758

Replace ELIXIR AAI button with Life Science login by @sebastian-schaaf in #16762

Update Python dependencies by @galaxybot in #16770

Migrate a part of the jobs API to Fast API by @heisner-tillman in #16778

Add EGI Check-in as OIDC authentication option by @enolfc in #16782

Replace file_name property with get_file_name function by @SergeyYakubov in #16783

Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf by @sveinugu in #16795

Galaxy help forum integration by @ElectronicBlueberry in #16798

Update Python dependencies by @galaxybot in #16807

Another batch of SA2.0 edits in TS2.0 (part 3) by @jdavcs in #16833

Remove remaining legacy backbone form input elements by @guerler in #16834

SQLAlchemy 2.0 upgrades (part 4) by @jdavcs in #16852

Update Python dependencies by @galaxybot in #16853

Drop unused HistoryContentManager code and related tests by @jdavcs in #16882

Vueify Visualizations Grid by @guerler in #16892

Update Python dependencies by @galaxybot in #16896

Enable some flake8-logging-format rules in ruff by @nsoranzo in #16915

Remove “Create Workflow” form and allow workflow creation in editor by @ahmedhamidawan in #16938

Update Python dependencies by @galaxybot in #16939

Add helper to get dataset or collection via src and id by @mr-c in #16953

Allow non-optional integer/float params without value attribute by @nsoranzo in #16966

Update Python dependencies by @galaxybot in #16978

Fix invocation report to target correct workflow version. by @jmchilton in #17008

Update Python dependencies by @galaxybot in #17011

Upgrade job manager’s index_query method to SA2.0 by @jdavcs in #17020

optimize object store cache operations by @SergeyYakubov in #17025

Require name for workflows on save, set default to Unnamed Workflow by @ahmedhamidawan in #17038

Update Python dependencies by @galaxybot in #17050

Migrate groups API to fastAPI by @arash77 in #17051

Migrate ItemTags API to FastAPI by @arash77 in #17064

Update Python dependencies by @galaxybot in #17084

Use python-isal for fast zip deflate compression in rocrate export by @mvdbeek in #17342

Merge 23.1 into dev by @mvdbeek in #16534

Revert “[23.1] Enable job resubmissions in k8s runner” by @nuwang in #17323

Fix succces typo by @mvdbeek in #17481

Fix unbound runner variable when there is an error in the job config by @mvdbeek in #16906

Fix discarded dataset ordering in Storage Dashboard by @davelopez in #16929

Include owner’s annotation when exporting workflow by @dannon in #16930

Skip state filtering in __MERGE_COLLECTION__ tool by @mvdbeek in #16937

Prevent Singular external auth users from disconnecting identity by @ahmedhamidawan in #16961

Prevent workflow submission with missing input values by @mvdbeek in #17048

Fix extra files collection if using store_by="id" and outputs_to_working_directory by @mvdbeek in #17067

Remove rollback from __check_jobs_at_startup by @mvdbeek in #17085

Improve invocation error reporting by @mvdbeek in #16917

read job_conf directly from config_dir instead of computing it again from config_file by @bernt-matthias in #15596

Fix some drs handling issues by @nuwang in #15777

Fix filesource file url support by @nuwang in #15794

Fix revision scripts, run migrations in CI, add repair option, improve migrations utils by @jdavcs in #15811

Change confusing pulsar logs message by @kysrpex in #16038

Fix and test startup with Python 3.11 on macOS by @nsoranzo in #16082

Fix : Ignore error messages for admin created accounts by @jvanbraekel in #16132

Ensure session is request-scoped for legacy endpoints by @jdavcs in #16207

Fix “database is locked” error (occurring in the context of workflow testing under SQLite) by @jdavcs in #16208

Fix ordering of data libraries from API by @martenson in #16300

qualify querying for an api-key by @martenson in #16320

Fix tags ownership by @davelopez in #16339

Job cache fixes for DCEs by @mvdbeek in #16384

Fix histories count by @davelopez in #16400

Fix select statement syntax for SQLAlchemy 2.0 by @jdavcs in #16421

Fix up unit tests for local use by @mvdbeek in #16483

Run through tmp_dir_creation_statement only once by @mvdbeek in #16529

Fix double-encoding notification content by @mvdbeek in #16530

Limit tool document cache to tool configs with explicit cache path by @mvdbeek in #16537

Fix multiple remote test data by @davelopez in #16542

Ignore errors with user-set job resources by @mvdbeek in #16579

Fix replacement parameters for subworkflows. by @jmchilton in #16592

make sure that TMP, TEMP, and TMPDIR are set by @bernt-matthias in #16594

Bump minimum tpv version to 2.3.2 by @mvdbeek in #16597

Backport tool mem fixes by @mvdbeek in #16601

Reload toolbox after forking when using –preload by @mvdbeek in #16620

Account for expires/expires_in when refreshing token by @mvdbeek in #16621

Fixes for conditional subworkflow steps by @mvdbeek in #16632

Fix nested conditional workflow steps by @mvdbeek in #16641

Ensure Job belongs to current SA session by @mvdbeek in #16655

Fix expression evaluation for nested state by @mvdbeek in #16656

Make sort_collection tool require terminal datasets by @mvdbeek in #16661

Push to object store even if set_meta fails by @mvdbeek in #16667

Fix metadata setting in extended metadata + outputs_to_working_directory mode by @mvdbeek in #16678

Fix regex validation for global inline flags by @mvdbeek in #16683

Fix closed transaction error on galaxy startup/check jobs by @jdavcs in #16687

Add missing join condition in job search by @mvdbeek in #16710

Fix job search query by @mvdbeek in #16714

Copy the collection contents by default when copying a collection by @mvdbeek in #16717

Fix collection id encoding by @davelopez in #16718

Workaround for XML nodes of job resource parameters losing their children by @kysrpex in #16728

move the email and username redacting from the role loop by @martenson in #16820

Fix parameter display in job info page for tools with sections by @mvdbeek in #16821

Fix workflow preview display if tool state does not contain all parameter values by @mvdbeek in #16829

Fix up local tool version handling by @mvdbeek in #16836

Fix and prevent persisting null file_size by @mvdbeek in #16855

Allow referring to steps by label only in markdown editor by @mvdbeek in #16861

Fix safe update version handling in run form by @mvdbeek in #16865

Remove more flushes in database operation tools by @mvdbeek in #16875

Fix tag ownership check by @mvdbeek in #16877

Empower Users to Select Storage Destination by @jmchilton in #14073

External Login Flow: Redirect users if account already exists by @ahmedhamidawan in #15019

Add slack error reporting plugin by @hexylena in #15025

Various Tool Shed Cleanup by @jmchilton in #15247

Add Storage Management API by @davelopez in #15295

OIDC tokens by @SergeyYakubov in #15300

Expose additional beaker caching backends by @claudiofr in #15349

Add support for visualizing HDF5 datasets. by @jarrah42 in #15394

Towards SQLAlchemy 2.0: drop session autocommit setting by @jdavcs in #15421

Update Python dependencies by @galaxybot in #15435

Fix for new style conda packages by @bernt-matthias in #15446

Move database access code out of tool_util by @jdavcs in #15467

Protection against problematic boolean parameters. by @jmchilton in #15493

Use connection instead of session for ItemGrabber by @jdavcs in #15496

Unify url handling with filesources by @nuwang in #15497

Move TS to Alembic by @jdavcs in #15509

Explore tool remote test data by @davelopez in #15510

Handle “email_from” config option consistently, as per schema description by @jdavcs in #15557

Update Python dependencies by @galaxybot in #15564

Drop workflow exports to myexperiment.org by @dannon in #15576

Update database_heartbeat for SA 2.0 compatibility by @jdavcs in #15611

Add suggested Training material to Tool Form by @ElectronicBlueberry in #15628

Wrap check_jobs_at_startup operation in a transaction (SA 2.0 compatibility) by @jdavcs in #15643

Add Galaxy Notification System by @davelopez in #15663

Unpin Beaker requirement by @nsoranzo in #15665

Add transactional state to JobHandlerStopQueue by @jdavcs in #15671

Verify that activation and reset emails are properly generated by @guerler in #15681

Add transactional state to workflow scheduling manager by @jdavcs in #15683

Remove DELETED_NEW job state from code base by @jdavcs in #15690

Fix/Enhance recalculate disk usage API endpoint by @davelopez in #15739

Add API test and refactor code for related:hid history filter by @ahmedhamidawan in #15786

Migrate to MyST-Parser for Markdown docs by @nsoranzo in #15844

Drop use_legacy_history from config by @dannon in #15861

Drop database views by @jdavcs in #15876

Update Python dependencies by @galaxybot in #15890

Allow pending inputs in some collection operation tools by @mvdbeek in #15892

Updated doc and tests for attribute value filter by @tuncK in #15929

Update Python dependencies by @galaxybot in #15942

Record input datasets and collections at full parameter path by @mvdbeek in #15978

Export tool citations configurable message by @minh-biocommons in #15998

Add History Archival feature by @davelopez in #16003

Code cleanups from ruff and pyupgrade by @nsoranzo in #16035

Add missing fields to HistorySummary schema model by @davelopez in #16041

Vendorise packaging.versions.LegacyVersion by @nsoranzo in #16058

Add Repository owner field to ToolSearch by @ahmedhamidawan in #16061

Add count support for listing filters by @davelopez in #16075

Update Python dependencies by @galaxybot in #16086

Improved Cache Monitoring for Object Stores by @jmchilton in #16110

Integrate accessibility testing into Selenium testing by @jmchilton in #16122

Update Python dependencies by @galaxybot in #16123

Improve histories and datasets immutability checks by @davelopez in #16143

Update Python dependencies by @galaxybot in #16153

Migrate display applications API to Fast API by @heisner-tillman in #16156

adjust grid sharing indicators by @martenson in #16163

Update Python dependencies by @galaxybot in #16182

Drop workarounds for old ro-crate-py and docutils versions by @mvdbeek in #16198

Remove various fallback behaviors by @mvdbeek in #16199

bring grids for (published) pages on par with workflows by @martenson in #16209

Update Python dependencies by @galaxybot in #16227

Update Python dependencies by @galaxybot in #16267

Fix tool remote test data by @davelopez in #16311

Hide conditionally skipped output by @mvdbeek in #16356

Fix Storage Dashboard missing archived histories by @davelopez in #16473

Bump bx-python to 0.10.0 by @mvdbeek in #16484

Drop expunge_all() call in WebTransactionRequest by @mvdbeek in #16606

Follow up on object store selection PR. by @jmchilton in #15654

merge release_23.0 into dev by @martenson in #15830

Move axe-selenium-python to dev dependencies by @nsoranzo in #16162

Bump msal version by @mvdbeek in #16285

Fix error_reports linting by @mvdbeek in #16465

Fix upload paramfile handling (for real user setups) by @bernt-matthias in #16504

Fix extra files path handling by @mvdbeek in #16541

Make sure job_wrapper uses a consistent metadata strategy by @mvdbeek in #16569

Fix conditional step evaluation with datasets in repeats by @mvdbeek in #16584

Don’t read request body into memory by @mvdbeek in #16585

Fixes for extra files handling and cached object stores by @mvdbeek in #16595

Lazy load tool data tables in celery worker by @mvdbeek in #16640

Force __DUPLICATE_FILE_TO_COLLECTION__ ‘size’ param to integer by @simonbray in #16659

Update pulsar client library to 0.15.5 by @mvdbeek in #16701

Bump galaxy-release-util version to 0.1.2 by @mvdbeek in #16241

When importing tool data bundles, use the first loc file for the matching table by @natefoo in #16247

Forward port of slugify username received from oidc by @nuwang in #16271

Fix Text File Busy errors at the source by @mvdbeek in #16212

Point release deps fixes and docs by @mvdbeek in #16214

Use galaxy-release-util to upload python packages by @mvdbeek in #16240

Display DCE in job parameter component, allow rerunning with DCE input by @mvdbeek in #15744

Fix mixed outputs_to_working_directory pulsar destinations by @mvdbeek in #15927

Update Gravity to 1.0.3 by @natefoo in #15939

Various fixes to path prefix handling by @mvdbeek in #16033

Fix case sensitive filtering by name in histories by @davelopez in #16036

Fix gcsfs test discovery by @mvdbeek in #16039

Replace httpbin service with pytest-httpserver by @mvdbeek in #16042

Update pulsar to 0.15.2 by @mvdbeek in #16050

Anonymous User tool link bug fix by @ahmedhamidawan in #16065

Fix BCO export by updating gxformat2 by @mvdbeek in #16081

Fix job failure handling when condor indicates job failure by @mvdbeek in #16096

Fix dataype_change not updating HDCA update_time by @mvdbeek in #16099

Extract HDA for code_file validate_input hook by @mvdbeek in #16120

Fix sort error when re-running job with DCE collection input by @mvdbeek in #16126

Fix related-hid in bulk contents API by @mvdbeek in #16128

Fix rank calculation for jobs waiting to be run by anonymous users by @jdavcs in #16137

Tool warnings can either be None or a Dictionary but not a String by @guerler in #16183

Pin minimum tpv version by @mvdbeek in #16201

Startup fix when tool removed between reboot by @mvdbeek in #16175