Restore root path support for FTP file sources by @davelopez in #23497

Fix remote files ctime crash and eLabFTW listing and sorting by @mvdbeek in #23770

Fix deferred materialization fd double close and wait for gx-it-proxy in tests by @mvdbeek in #23793

Serve deferred materialization test data from the mock HTTP server by @mvdbeek in #23794

Don’t resolve DNS in HTTP file source and URI validation unit tests by @mvdbeek in #23982

Fix CI failures and flaky tests by @mvdbeek in #24028

Run the ftp file source tests against a local ftp server by @mvdbeek in #24044

Percent-encode unsafe characters in HTTP file source URLs by @itisAliRH in #24071

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

Backport flaky test fixes by @mvdbeek in #24251

Improve Dataverse file source search by @davelopez in #24324

Fix uploading files to Dataverse by @davelopez in #24327

Prevent selecting the root of RDM repositories as a directory by @davelopez in #24358

Run FTP user file source Selenium test against a local server by @mvdbeek in #24360

Name DRS-fetched datasets from DRS metadata instead of the URI basename by @dannon in #23275

Use requests rather than urllib for Invenio authenticated downloads by @martenson in #23096

Don’t resolve DNS in HTTP file source and URI validation unit tests by @mvdbeek in #23982

Fix CI failures and flaky tests by @mvdbeek in #24028

Run the ftp file source tests against a local ftp server by @mvdbeek in #24044

Backport flaky test fixes by @mvdbeek in #24251

Improve Dataverse file source search by @davelopez in #24324

Fix uploading files to Dataverse by @davelopez in #24327

Prevent selecting the root of RDM repositories as a directory by @davelopez in #24358

Run FTP user file source Selenium test against a local server by @mvdbeek in #24360

Don’t resolve DNS in HTTP file source and URI validation unit tests by @mvdbeek in #23982

Fix CI failures and flaky tests by @mvdbeek in #24028

Run the ftp file source tests against a local ftp server by @mvdbeek in #24044

Backport flaky test fixes by @mvdbeek in #24251

Improve Dataverse file source search by @davelopez in #24324

Fix uploading files to Dataverse by @davelopez in #24327

Run FTP user file source Selenium test against a local server by @mvdbeek in #24360

Add request_checksum_calculation support for s3fs by @lldelisle in #21993

Fix broken log format string in validate_non_local by @jmchilton in #22004

Restore WebDAV template v0; add v1 for url -> base_url rename by @mvdbeek in #22570

Default S3 request checksum to when_required for non-AWS endpoints by @mvdbeek in #23034

Stop the ssh file source from using local keys or the SSH agent by @bernt-matthias in #23066

Use requests rather than urllib for Invenio authenticated downloads by @martenson in #23096

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

Always use context managers in py2filesystem file sources by @bernt-matthias in #21645

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

Add support for file hash in Dataverse datasets by @davelopez in #21890

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

Update Python dependencies by @galaxybot in #22003

Update Python dependencies by @galaxybot in #22206

Unify path adaptation for remote file sources by @davelopez in #22336

Add OneDrive file source by @PlushZ in #22367

Add IIIF File Source Support by @davelopez in #22420

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

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

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

Add support for file checksums in Zenodo/Invenio by @davelopez in #22691

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

Backport of iRODS file source by @davelopez in #22816

Strip whitespace from URIs in get_file_source_path by @mvdbeek in #22506

Fix UnicodeError on empty-label URLs in fetch validation by @mvdbeek in #22526

Adds missing TLS support for FTP configurations in templates by @davelopez in #22657

Fix webdav file download by @davelopez in #22683

Fix Zenodo/Invenio browsing of own records by @davelopez in #22690

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

Better error message for unencoded/unresolvable filesource uri by @dannon in #21562

Fix OMERO file source download multi channel TIFF by @davelopez in #21856

Fix ascp download retries by @mvdbeek in #21857

Fixes some more optional fields in templates by @davelopez in #21891

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

Fix OMERO temp directory handling by @davelopez in #22262

Harden API parameter validation by @mvdbeek in #22351

Add DRS compact identifier support by @dannon in #20410

Add service account support for Google Cloud Storage client initialization by @dannon in #21027

Update Python dependencies by @galaxybot in #21043

Add Custom Validation for User-Configured Templates by @davelopez in #21155

Ascp plugin by @d-callan in #21357

Add OMERO File Source Plugin by @davelopez in #21367

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

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

Clean up code with pyupgrade by @nsoranzo in #21540

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

Unify extensions of file source templates by @bernt-matthias in #21594

Various fixes to file source template’s validation system by @davelopez in #21704

Adds ImageJ metadata support to TIFF export by @davelopez in #21882

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

Add missing dependencies to galaxy-files package by @nsoranzo in #21518

Supports Dataverse file access via both persistent and database IDs by @davelopez in #21569

Harden Dataverse integration by @davelopez in #21624

Change wording of the client side storage handling by @bgruening in #19815

Fix GCS file source to handle virtual directories without marker objects by @dannon in #21051

Fix Huggingface timestamp parsing when last_commit is missing by @davelopez in #21072

Fixes download for restricted Zenodo records by @davelopez in #21274

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

Add Dataverse template by @davelopez in #20551

Clean up code from pyupgrade by @nsoranzo in #20642

Add fsspec base implementation for File Source plugins by @davelopez in #20698

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

Adapt S3 file source to fsspec by @davelopez in #20794

Fix fsspec fs path handling by @davelopez in #20799

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

Support remote file source hashes by @davelopez in #20853

Fix Invenio file downloads for published records with draft by @davelopez in #20685

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

Fix wrong URI written to ExportObjectResultMetadata when exporting histories to eLabFTW by @kysrpex in #19541

Update webdav user file source template help text by @sanjaysrikakulam in #19784

Change wording in the google drive user file source template by @sanjaysrikakulam in #19927

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

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

Add Dataverse RDM repository integration by @KaiOnGitHub in #19367

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

Handles S3 listing errors by @itisAliRH in #19446

Add eLabFTW file source from file source templates by @kysrpex in #19493

Add InvenioRDM file source template by @davelopez in #19619

Use discriminated unions in object stores and file source template configs by @davelopez in #19621

Add Zenodo file source template by @davelopez in #19638

Drop support for Python 3.8 by @nsoranzo in #19685

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

Add ZIP explorer to import individual files from local or remote ZIP archives by @davelopez in #20054

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

Fix Invenio file source downloads not working with some Invenio instances by @davelopez in #19930

Fix private role name performance issue by @jdavcs in #19679

Fix RDM token access for user-defined file sources by @davelopez in #19768

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

Add onedata templates by @bwalkowi in #18457

Add missing version in the file sources and object store templates by @sanjaysrikakulam in #18497

Add a new version of the production s3fs file source template with the writable configuration variable added by @sanjaysrikakulam in #18575

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

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

Type annotations and fixes by @nsoranzo in #18911

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

Fix production_aws_private_bucket.yml by @mvdbeek in #19155

Fix file source search query with empty string value by @davelopez in #18191

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

Fix check for anonymous by @jdavcs in #18364

Add onedata objectstore by @bwalkowi in #17540

Update Python dependencies by @galaxybot in #17653

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

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

More typing in galaxy.files. by @jmchilton in #18037

Refactor galaxy.files plugin loading + config handling. by @jmchilton in #18049

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

Overhaul Azure storage infrastructure. by @jmchilton in #18087

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

Display DOIs in Archived Histories by @davelopez in #18134

Update s3fs dependency. by @jmchilton in #18135

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

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

Fix listing possibly untitled records in Invenio Plugin by @davelopez in #18130

Raise RequestParameterInvalidException when url is invalid by @mvdbeek in #18155

Fix error message when accessing restricted Zenodo records by @davelopez in #18169

Raise RequestParameterInvalidException if url can’t be verified by @mvdbeek in #18230

Fix Invenio credentials handling by @davelopez in #18255

Invenio plugin fixes by @davelopez in #17997

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

Add support for Python 3.12 by @tuncK in #16796

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

Update Python dependencies by @galaxybot in #17235

fix s3fs templating by @bgruening in #17311

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

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

Write to a temp filename in posix file source plugin by @natefoo in #17350

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

More defensive access of extra props in filesources by @nuwang in #17445

Add Invenio RDM repository integration by @davelopez in #16381

Refactor FilesDialog + Remote Files API schema improvements by @davelopez in #16420

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

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

Enhance Invenio RDM integration by @davelopez in #16964

Separate collection and non-collection data element by @mvdbeek in #17236

Implement missing upload for S3 file sources by @davelopez in #17100

Fix some drs handling issues by @nuwang in #15777

Fix filesource file url support by @nuwang in #15794

Fix unittest mocks to support us checking geturl() by @dannon in #16726

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

Unify url handling with filesources by @nuwang in #15497

Fix dropbox import to support newer versions by @nuwang in #16239