Fixes for package installed Galaxy. by @jmchilton in #23360

Fix failing API tests on release_26.1 by @mvdbeek in #23405

Document unique server names for multi-instance Gunicorn deployments by @mvdbeek in #23488

Fix built-in converter registration during toolbox reload by @mvdbeek in #23797

Fix OIDC PKCE login by carrying the code verifier in a cookie by @bgruening in #23836

Apply max_discovered_files to collection operation tools that multiply inputs by @mvdbeek in #23859

Return users to their destination after login, add allowed_login_redirect_hosts by @mvdbeek in #24111

Ignore stale user and history object store preferences by @davelopez in #24280

Match tool shed GUIDs when looking up job resource parameters by @monsterlag in #24355

Backport RMSX datatype registration and viewer 0.0.4 to Galaxy 26.1 by @Finn2400 in #23531

Add TensorBoardEvents datatype and sample file for tfevents by @IvoLeist in #23553

Add Montreal Forced Aligner datatypes by @IvoLeist in #23893

Add datatypes sniffer: alto/page/abbyy XML and hOCR (HTML) by @IvoLeist in #23916

backport #23353 (mzlite datatype) by @bernt-matthias in #24000

Backport test CI time fixes: pytest-xdist and parallel docs build by @mvdbeek in #24336

add embl.gz as auto compress embl by @bernt-matthias in #24403

Ignore stale user and history object store preferences by @davelopez in #24280

Match tool shed GUIDs when looking up job resource parameters by @monsterlag in #24355

Add new datatypes for the tool vg by @Maed0x in #23111

Ignore stale user and history object store preferences by @davelopez in #24280

Match tool shed GUIDs when looking up job resource parameters by @monsterlag in #24355

Remove unused enable_beta_workflow_modules config option by @jmchilton in #22050

Remove dual load of cutWrapper.xml by @natefoo in #22266

Revert ``galaxy.yml.sample`` changes by @nsoranzo in #22569

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

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

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

Disable tool request by default by @guerler in #23113

Support multipart upload for Invenio-based file sources by @martenson in #23118

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

Add ASCII Raster (.asc) datatype by @tStehling in #21937

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

Update config sample files after `make config-rebuild` by @davelopez in #21940

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

More concise test logging by @jmchilton in #21983

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 GTN training agent to ChatGXY by @dannon in #22097

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

Test against psycopg3 by @mvdbeek in #22210

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

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

Add egapx_local_cache datatype, a subclass of Directory by @richard-burhans in #22268

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

Add bwa_index datatype by @Delphine-L in #22310

Add IIIF File Source Support by @davelopez in #22420

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

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

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

Add legacy job submission fallback by @guerler in #22555

Add bulk dataset storage migration by @davelopez in #22606

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

Add rmd filetype by @jdavcs in #22746

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

Add namespace stripping to ``CachedExplicitSingularityContainerResolver`` by @mvdbeek in #22878

Add new datatypes for the tool vg giraffe by @Maed0x in #22935

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

Add PAGE XML, AbbyyXML, hOCR, mlmodel and Apache Arrow IPC datatype support in datatypes_conf.xml.sample by @IvoLeist in #23088

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

Add `enable_statsd_middleware` option to send backend execution timing to statsd without enabling web request timing by @natefoo in #22557

add TEI XML datatype by @bgruening in #22718

Infer type from extension for mzml by @bgruening in #21033

Update config samples from schema by @davelopez in #21053

remove a tool from sample that is no longer included in dist by @martenson in #21371

Various fixes around ascp file source by @mvdbeek in #21372

Add tool_shed_url config for explicit hostname setting by @jmchilton in #21499

Use inference_services config for plugin chat proxy by @dannon in #21986

Silence social_core’s noisy handle_http_errors logging by @mvdbeek in #22403

Improve docs for invalidjobexception_state and _retry of DRMAA runners by @bernt-matthias in #20612

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

Remove Trackster by @guerler in #20974

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

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

Slight improvement of mztab2 datatype by @nguilhot in #21258

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

Ascp plugin by @d-callan in #21357

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

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

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

Drop support for Python 3.9 by @nsoranzo in #21583

Update to gravity 1.2.0 by @nsoranzo in #21608

Add new datatypes: .taf and .taf.gz by @Maed0x in #22242

Backport of 21939 by @jdavcs in #22265

Add missing enable_beta_tool_formats config option by @bernt-matthias in #21190

Add Deacon idx format by @SantaMcCloud in #21632

Add amnis cif flow cytometry data type by @bernt-matthias in #21829

Use quotes for Galaxy citation bibtex by @bernt-matthias in #21563

Add split paired or unpaired tool to sample tool conf by @bernt-matthias in #21647

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

add new datatype for kmindex index data by @Smeds in #21429

Add Sourmash sig new datatype by @SaimMomin12 in #21469

Adds object_expires_after_days example usage to sample config by @davelopez in #21547

Add a few datatypes from the digital humanities domain by @bgruening in #21596

Add new datatype pg and hg for pangenomics by @SaimMomin12 in #21620

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

Add new datatypes required for VG tool by @SaimMomin12 in #21644

Fix typo in lib/galaxy/config/sample/job_conf.sample.yml: enviroment –> environment by @blankenberg in #20652

Implement Sample Sheets by @jmchilton in #19305

Add rerun.io web viewer by @guerler in #20202

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

Add LocusZoom Visualization by @elmedjadjirayane in #20354

Remove deprecated tool document cache by @nsoranzo in #20510

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

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

Clean up code from pyupgrade by @nsoranzo in #20642

Update location of latest tpv shared db by @nuwang in #20651

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

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

Add axt and maf to auto_compressed_types by @richard-burhans in #20875

Add Multiple Sequence Alignment Viewer 2.0 by @guerler in #20907

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

Make jupyterlite default visualization for ipynb by @guerler in #20931

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

Allow specifying a command for determining a docker host port by @natefoo in #20953

Add freq.json datatype subclass by @guerler in #21012

New datatype addition: HAL by @SaimMomin12 in #21379

Add PNTS datatype for 3D Tiles Point Cloud by @kgerb in #21414

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

Add safetensors datatype by @nilchia in #20754

Fix MIME type for LAZ datatype by @kysrpex in #21202

Add Auspice JSON datatype by @pvanheus in #20466

Add SpatialData datatype by @nilchia in #21000

Add LAS and LAZ file format by @bgruening in #21049

New datatype addition: gam for vg toolkit by @SaimMomin12 in #21096

support ZARR v3 for Spatialdata dt by @nilchia in #21265

New datatype addition: beast.trees datatype by @SaimMomin12 in #21055

Add display_in_upload to LAZ and LAS by @bgruening in #21060

Fix DOCX detection and add PPTX support by @arash77 in #20827

Add HiC datatype by @abretaud in #20874

Undo accidental push by @bernt-matthias in #20854

Merge 25.0 into dev by @ahmedhamidawan in #20911

add fasta.bz2 as auto_compressed type by @bernt-matthias in #20496

Add datatype for LexicMap index by @Smeds in #20586

Add mzMLb and MBI datatypes by @chambm in #20632

Pairtool updated format and sniffers by @Smeds in #20634

Add support for M4A audio files by @arash77 in #20667

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

Fixes for static handling and the web_client package by @natefoo in #20516

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

Remove hgv_sift from tool_conf.xml.sample by @natefoo in #19972

Add job config variable for singularity –contain by @bernt-matthias in #20400

Isolate singularity containers more thoroughly for better reproducibility. by @rhpvorderman in #18628

Implement tool markdown reports. by @jmchilton in #19054

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

eLabFTW integration via Galaxy file source by @kysrpex in #19319

Misc fixes 202412 by @nsoranzo in #19341

Add Dataverse RDM repository integration by @KaiOnGitHub in #19367

Clarify that extra_scopes is sometimes non-optional by @martenson in #19385

Change galaxy system user uid for K8s image by @afgane in #19403

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

Add IGB display support for CRAM files by @paige-kulzer in #19428

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

Support setting masthead height in a theme by @ksuderman in #19581

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

Enhance OpenAI Chat Integration by @uwwint in #19612

Data-source tool for DICED database (https://diced.lerner.ccf.org/) added. by @jaidevjoshi83 in #19689

Update RStudio IT by @afgane in #19711

Add bigbed to bed converter and tests by @d-callan in #19787

Decrease sentry_sdk.errors log level to INFO by @natefoo in #19951

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

Add vitesscejson datatype by @guerler in #20027

Add VTK Visualization Toolkit Plugin by @guerler in #20028

Add docx datatype by @bgruening in #20055

Add markdown datatype by @bgruening in #20056

Add flac audio format by @bgruening in #20057

Add rd datatype by @richard-burhans in #20060

Enhance external login interface styling by @ahmedhamidawan in #20100

Add specific datatypes for Cytoscape and Kepler.gl by @guerler in #20117

Add more metadata, esp infer_from to datatypes configuration by @bgruening in #20142

Add three AAI providers by @martenson in #20165

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

Visualization-First Display functionality by @dannon in #20190

Deprecate enable_tool_document_cache by @nsoranzo in #20433

Add Aladin as standard FITS viewer by @bgruening in #20465

Add molstar as default viewer for some molecule formats by @bgruening in #20467

Make job cache generally available by @dannon in #19798

Rename vitessce_json file_ext to vitessce.json by @mvdbeek in #20473

Reduce default framework tool test timeout to 60 seconds by @mvdbeek in #19819

Add rDock prm datatype by @nsoranzo in #19783

Fix conditional dependency path resolution by @mvdbeek in #19723

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

Updated registration warning message by @dannon in #19598

Add fastk_ktab_tar datatype required for fastk tool by @SaimMomin12 in #19615

Fix loading error for built in tool sift by @bernt-matthias in #18357

Add gtf to auto_compressed_types by @mvdbeek in #19175

Partial backport of #19331 by @nsoranzo in #19342

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

Experimental galactic wizard by @dannon in #15860

Improve usability of Directory datatype by @wm75 in #17614

Add pod5 datatype by @TomHarrop in #18419

Add onedata templates by @bwalkowi in #18457

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

Minor config documentation enhancements by @bgruening in #18499

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

Bring your own file sources: Add the WebDAV template and configuration by @sanjaysrikakulam in #18598

Add BlobToolkit to the list of interactive tools by @Delphine-L in #18630

Remove defaults channel for conda usage by @bernt-matthias in #18757

Workflow Landing Requests by @jmchilton in #18807

Jupyter Interactive Tool 1.0.1/24.07 by @natefoo in #18861

Allow setting a few global defaults for file source plugin types. by @jmchilton in #18909

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

Add hint to the tool schema about runtime conditional changes by @martenson in #18996

Irods ssl connection by @pauldg in #19014

Add some Zarr-based datatypes by @davelopez in #19040

Run installed Galaxy with no config and a simplified entry point by @natefoo in #19050

Add XML based vtk datatype by @tStehling in #19104

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

Add bcsp datatype by @SantaMcCloud in #19365

add MuData as subclass of H5 by @pavanvidem in #19416

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

Strip whitespace when listifying admin users by @jdavcs in #18656

Remove defaults channel for conda usage by @bernt-matthias in #18859

Make default_panel_view a _by_host option by @natefoo in #18471

More datatype deprecation warnings by @mvdbeek in #18612

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

Backport pod5 datatype by @TomHarrop in #18507

Backport PR 18630 “Add BlobToolkit to the list of interactive tools” to release_24.1 by @cat-bro in #18784

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

Strip whitespace when listifying admin users by @jdavcs in #18656

Remove defaults channel for conda usage by @bernt-matthias in #18859

Make default_panel_view a _by_host option by @natefoo in #18471

More datatype deprecation warnings by @mvdbeek in #18612

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

Backport pod5 datatype by @TomHarrop in #18507

Backport PR 18630 “Add BlobToolkit to the list of interactive tools” to release_24.1 by @cat-bro in #18784

Strip whitespace when listifying admin users by @jdavcs in #18656

Make default_panel_view a _by_host option by @natefoo in #18471

More datatype deprecation warnings by @mvdbeek in #18612

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

Backport pod5 datatype by @TomHarrop in #18507

Backport PR 18630 “Add BlobToolkit to the list of interactive tools” to release_24.1 by @cat-bro in #18784

Replace sample Celery result_backend in config by @davelopez in #17949

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

Fix various packages’ issues by @nsoranzo in #18301

Rebuild Galaxy config by @bgruening in #18325

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

Add onedata objectstore by @bwalkowi in #17540

Add colabfold tar file datatype by @astrovsky01 in #17567

Update Python dependencies by @galaxybot in #17653

SQLAlchemy 2.0 by @jdavcs in #17778

Add email notifications channel by @davelopez in #17914

Update config docs about Celery by @davelopez in #17918

Make urgent notifications mandatory by @davelopez in #17975

Enable warn_unused_ignores mypy option by @nsoranzo in #17991

Add Zenodo integration by @davelopez in #18022

Add support for additional media types by @arash77 in #18054

Update Python dependencies by @galaxybot in #18063

Add Net datatype by @martenson in #18080

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

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

Tighten axt sniffer by @martenson in #18204

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

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

Chore: remove repetitive words by @tianzedavid in #18076

Fix the link to the carbon config by @bgruening in #18314

Backport OIDC schema fix by @mvdbeek in #18111

Minor fix to enable external hgweb process by @mvdbeek in #18256

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

Invenio plugin fixes by @davelopez in #17997

clarify the object store relocate functionality by @martenson in #18033

Updated the datatypes name for FASTK tool by @SaimMomin12 in #18053

Added 4dn_pairs and 4dn_pairsam datatypes by @SaimMomin12 in #17875

Add middleware for logging start and end of request by @mvdbeek in #18046

Rebuild config samples by @davelopez in #17911

Backport colabfold tar file datatype by @mvdbeek in #18029

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

Fix minor oidc_backends_config comment bug by @ahmedhamidawan in #17385

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

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

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

Add support for (fast5.tar).xz binary compressed files by @tuncK in #17106

Add a3m datatype by @astrovsky01 in #17217

Convert sample object store configuration to YAML and support configuring inline by @natefoo in #17222

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

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

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

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

Use short link for TPV shared database by @nuwang in #17467

Feature SBOL datatypes by @guillaume-gricourt in #17482

Add documentation on how to use vault keys in file sources by @bernt-matthias in #17498

add npy datatype by @astrovsky01 in #17517

Enhance Avivator display app to support regular Tiffs by @davelopez in #17554

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

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

MINERVA display application: enable cors, add for tabular by @hexylena in #16737

chore: fix typos by @afuetterer in #16851

Add back 1.1.0 version of Filtering1 tool by @mvdbeek in #16883

Set webdav file source to use temp files by default by @davelopez in #17388

Update cellxgene interactive tool to 1.1.1 by @pcm32 in #15313

Tool Shed 2.0 by @jmchilton in #15639

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

Add carbon emissions admin configuration options by @Renni771 in #16307

Add Invenio RDM repository integration by @davelopez in #16381

Add new datatype: STL by @TanguyGen in #16478

add new tabular file formats cns,cnr and cnn to datatypes_conf.xml.sample file as they are neaded for cnvkit galaxy tools by @khaled196 in #16503

Tweak tool memory use and optimize shared memory when using preload by @mvdbeek in #16536

Implement datatype upload warnings by @jmchilton in #16564

Support new genome browser chain file format by @claudiofr in #16576

Update Python dependencies by @galaxybot in #16577

Implement instance URLs in Galaxy markdown. by @jmchilton in #16675

Use fs.onedatarestfs for Onedata files source plugin implementation by @lopiola in #16690

Update datatypes_conf.xml.sample with docx type by @yvanlebras in #16713

Replace ELIXIR AAI button with Life Science login by @sebastian-schaaf in #16762

Add EGI Check-in as OIDC authentication option by @enolfc in #16782

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

Remove record access handling for Invenio RDM plugin by @davelopez in #16900

optimize object store cache operations by @SergeyYakubov in #17025

Support configuring job metrics inline, update documentation by @natefoo in #17178

Add binary datatypes for intermediate output of fastk tools by @astrovsky01 in #17265

Add magres datatype by @martenson in #17499

Merge 23.1 into dev by @mvdbeek in #16534

Remove xml remnant in sample yml job conf by @bernt-matthias in #16609

Prevent Singular external auth users from disconnecting identity by @ahmedhamidawan in #16961

Set correct tool_path for packaged galaxy by @mvdbeek in #17102

Add support for larch datatypes by @patrick-austin in #17080

Fix some drs handling issues by @nuwang in #15777

Improve container resolver documentation by @mvdbeek in #16280

Limit tool document cache to tool configs with explicit cache path by @mvdbeek in #16537

Backport tool mem fixes by @mvdbeek in #16601

Fix allowlist deserialization in file sources by @mvdbeek in #16729

External Login Flow: Redirect users if account already exists by @ahmedhamidawan in #15019

Add slack error reporting plugin by @hexylena in #15025

Documents use of k8s_extra_job_envs in job_conf sample advanced by @pcm32 in #15110

Expose additional beaker caching backends by @claudiofr in #15349

Unify url handling with filesources by @nuwang in #15497

Handle “email_from” config option consistently, as per schema description by @jdavcs in #15557

Drop workflow exports to myexperiment.org by @dannon in #15576

Container resolvers: add docs, typing and tests by @bernt-matthias in #15614

Add suggested Training material to Tool Form by @ElectronicBlueberry in #15628

Deprecate tools/evolution by @bernt-matthias in #15656

Add Galaxy Notification System by @davelopez in #15663

More object store documentation. by @jmchilton in #15707

Drop use_legacy_history from config by @dannon in #15861

FITS data format by @volodymyrss in #15905

Export tool citations configurable message by @minh-biocommons in #15998

Rename object stores in config. by @jmchilton in #16029

Add hdf4 datatype by @TheoMathurin in #16105

Improved Cache Monitoring for Object Stores by @jmchilton in #16110

Refactor caching object stores ahead of adding task-based store. by @jmchilton in #16144

Add zipped mongodb and genenotebook datatypes by @abretaud in #16173

Add Visium datatype for squidpy and spatialomics tools by @astrovsky01 in #16255

Implement some initial object store selection end-to-end tests. by @jmchilton in #15785

Minor bug fix for default mail templates by @neoformit in #16362

Change default watchdog inotify_buffer log level to info by @mvdbeek in #15967

Add ca_certs option for sentry client by @mvdbeek in #15943