galaxy-config 24.1.1

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

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

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