galaxy-util 26.1.0

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

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

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

Allow etree.XMLParser to resolve external entities by @jancrichter in #17504

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

Update Python dependencies by @galaxybot in #21707

Handle missing `future` package in galaxy-util by @mr-c in #21924

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 precise ``metric_prefix()`` implementation by @nsoranzo in #22155

Test against psycopg3 by @mvdbeek in #22210

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

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

Add ``RetrySession`` to automatically retry idempotent HTTP requests by @nsoranzo in #22567

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

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

Update version to 26.1.rc1 by @mvdbeek in #22764

Fixes looks_like_flattened_repeat_key helper by @guerler in #22578

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

Plumbing for tracking potential fixes for transient failures (and a fix demonstrating it) by @jmchilton in #21243

Remove unused handle_tool_shed_url_protocol by @mvdbeek in #21925

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

Improve timeout and error handling in /api/proxy endpoint by @mvdbeek in #22297

Skip WorkflowHub tests when workflowhub.eu is down by @mvdbeek in #22302

Discard rest of line in chunks in iter_start_of_line by @mvdbeek in #22332

Fix Content-Disposition header with trailing whitespace by @mvdbeek in #22379

Update Python dependencies by @galaxybot in #21043

Add Playwright Backend Support to Galaxy Browser Automation Framework by @jmchilton in #21102

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

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

Richer tracking of transient failures. by @jmchilton in #21227

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

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

Fix use of function, method and argument names deprecated in pyparsing 3.0.0 by @nsoranzo in #21517

Apply 2026 black style by @galaxybot in #21618

Add tests for oidc usernames by @nuwang in #21655

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

Extract: do not use common prefix dir by @bernt-matthias in #20929

Test and fix CORS on exceptions by @mvdbeek in #21105

Implement Sample Sheets by @jmchilton in #19305

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

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

Remove deprecated tool document cache by @nsoranzo in #20510

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

Support remote file source hashes by @davelopez in #20853

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

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

Fix test_in_directory on osx by @mvdbeek in #19943

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

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

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

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

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

Format code with black 25.1.0 by @nsoranzo in #19625

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

Allow PathLike parameters in make_fast_zipfile() by @nsoranzo in #19955

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

Add DOI to workflow metadata by @jdavcs in #20033

Improve type annotation of galaxy.util submodules by @nsoranzo in #20104

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

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

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

Partial backport of #19331 by @nsoranzo in #19342

Fix config template validation for file sources and object store templates by @davelopez in #19414

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

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

Add Python 3.13 support by @nsoranzo in #18449

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

Rip repository_registry out of tool shed 2.0 by @jmchilton in #18647

Workflow Landing Requests by @jmchilton in #18807

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

Raise exception if CompressedFile used on incompatible file by @mvdbeek in #18888

Type annotations and fixes by @nsoranzo in #18911

Workflow landing improvements by @mvdbeek in #18979

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

Enhance UTF-8 support for filename handling in downloads by @arash77 in #19161

Fix Archive header encoding by @arash77 in #18583

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

Use smtplib send_message to support utf-8 chars in to and from by @mvdbeek in #18805

Fix Archive header encoding by @arash77 in #18583

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

Use smtplib send_message to support utf-8 chars in to and from by @mvdbeek in #18805

Fix Archive header encoding by @arash77 in #18583

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

Use smtplib send_message to support utf-8 chars in to and from by @mvdbeek in #18805

Fix bug in image_util.py by @kostrykin in #17749

Revert some requests import changes by @nsoranzo in #18199

Better display of estimated line numbers and add number of columns for tabular by @bernt-matthias in #17492

Update Python dependencies by @galaxybot in #17653

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

SQLAlchemy 2.0 by @jdavcs in #17778

Error reporting unit tests by @jmchilton in #17968

Enable warn_unused_ignores mypy option by @nsoranzo in #17991

Add galaxy to user agent by @mvdbeek in #18003

Update Python dependencies by @galaxybot in #18063

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

Overhaul Azure storage infrastructure. by @jmchilton in #18087

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

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

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

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

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

Add support for Python 3.12 by @tuncK in #16796

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

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

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

Reuse test instance during non-integration tests by @mvdbeek in #17234

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

Enable warn_unreachable mypy option by @mvdbeek in #17365

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

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

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

Ruff and flake8 fixes by @nsoranzo in #16884

Tool Shed 2.0 by @jmchilton in #15639

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

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

Allow partial matches in workflow name tag search and search all tags for unquoted query by @ahmedhamidawan in #16860

Use python-isal for fast zip deflate compression in rocrate export by @mvdbeek in #17342

Merge 23.1 into dev by @mvdbeek in #16534

Fix bad auto-merge of dev. by @jmchilton in #15386

Fix some drs handling issues by @nuwang in #15777

Enable strict_equality mypy option by @nsoranzo in #15808

Ensure session is request-scoped for legacy endpoints by @jdavcs in #16207

Fix form builder value handling by @guerler in #16304

Backport tool mem fixes by @mvdbeek in #16601

Workaround for XML nodes of job resource parameters losing their children by @kysrpex in #16728

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

Exclude on_opened and on_closed from watcher events by @mvdbeek in #16850

Various Tool Shed Cleanup by @jmchilton in #15247

Protection against problematic boolean parameters. by @jmchilton in #15493

Unify url handling with filesources by @nuwang in #15497

Explore tool remote test data by @davelopez in #15510

Drop database views by @jdavcs in #15876

Update Python dependencies by @galaxybot in #15890

Record input datasets and collections at full parameter path by @mvdbeek in #15978

Code cleanups from ruff and pyupgrade by @nsoranzo in #16035

Vendorise packaging.versions.LegacyVersion by @nsoranzo in #16058

Improve histories and datasets immutability checks by @davelopez in #16143

Merge Target class with CondaTarget by @nsoranzo in #16181