What's Changed

• Build and release script updates by @mvdbeek in #1561
• Fix underscores in config option by @bernt-matthias in #1567
• Enable dependabot version updates for GitHub actions by @nsoranzo in #1566
• Bump actions/checkout from 4 to 5 by @dependabot[bot] in #1569
• Bump actions/setup-python from 5 to 6 by @dependabot[bot] in #1570
• Bump actions/setup-node from 4 to 5 by @dependabot[bot] in #1571
• Updates to pyproject.toml and CI workflows by @nsoranzo in #1572
• Wait for upload job and make sure uploads are ok by @mvdbeek in #1574
• Raise click exception where we don't need a full traceback by @mvdbeek in #1577
• Fall back to sqlite when database creation fails by @mvdbeek in #1576
• Improve command not found handling by @mvdbeek in #1575
• Delay toil import and use or fail when actually used by @mvdbeek in #1580
• Don't report failed workflow run with --no_wait by @mvdbeek in #1579
• Fail when pointing at a profile that doesn't exist by @mvdbeek in #1578

Full Changelog: 0.75.32...0.75.33

What's Changed

• Fixing 429 url error by @arash77 in #1556
• Fix subworkflow invocation tracking by @mvdbeek in #1560

New Contributors

• @arash77 made their first contribution in #1556

Full Changelog: 0.75.31...0.75.32

What's Changed

• create provided output_directory if it doesn't exist by @Smeds in #1526
• Overhaul Galaxy job config handling. by @jmchilton in #1506
• Fix job handler setup by @mvdbeek in #1538
• Workflow progress bar. by @jmchilton in #1510
• add file extension to downloaded output by @Smeds in #1531
• Enable celery tasks by @mvdbeek in #1541
• Print job errors in workflow invocation as they occur by @mvdbeek in #1540
• Bump requirements for galaxy packages to 25.0 by @ahmedhamidawan in #1542
• cmd to export an existing invocations as an archive for storage or later import. by @Smeds in #1534
• update shed categories by @bgruening in #1539
• Add the option to download the outputs of a completed workflow run by @Smeds in #1532
• Add missing module to pyproject.toml by @mvdbeek in #1545
• Add a slurm_init command. by @jmchilton in #1543
• Don't do preload in managed instance by @mvdbeek in #1546
• Terminate polling if we can't advance invocation by @mvdbeek in #1547
• Drop unnecessary autogen in cmd_slurm_init by @mvdbeek in #1549
• Load default job metrics by @mvdbeek in #1548
• Add flag to export invocation from run command by @mvdbeek in #1551
• Make no_dependency_resolution and simultaneous_upload global options by @mvdbeek in #1553
• Add ruff and isort to make format and tox, add pre-commit config by @mvdbeek in #1552
• Don't pollute working directory with tools.yaml file by @mvdbeek in #1554

New Contributors

• @ahmedhamidawan made their first contribution in #1542

Full Changelog: 0.75.30...0.75.31

What's Changed

• fix lint_shed_version if there are no installable revisions by @bernt-matthias in #1509
• Fix bumping of dev versions by @mvdbeek in #1514
• Don't escape non-ascii unicode characters in json.dumps by @mvdbeek in #1523
• Fix version linter for new repos by @bernt-matthias in #1519
• Add switch to prevent early termination of workflow runs by @kostrykin in #1518
• Add missing collection operation tools by @mvdbeek in #1524

New Contributors

• @kostrykin made their first contribution in #1518

Full Changelog: 0.75.29...0.75.30

What's Changed

• Fix dependency specification by @mvdbeek in #1507

Full Changelog: 0.75.28...0.75.29

What's Changed

• Update browser user agent string by @nsoranzo in #1495
• Loosen test assertions by @bernt-matthias in #1494
• Add postgres singularity option by @Smeds in #1492
• Add support for Python 3.12 by @nsoranzo in #1496
• Migrate mypy settings to pyproject.toml. by @jmchilton in #1500
• Fix make quick-test. by @jmchilton in #1501
• Add linter to check if tool versions are bumped by @bernt-matthias in #1502
• Build Modernization by @jmchilton in #1503
• fix: removes that spaces that aren't allowed in the singularity instance name by @Smeds in #1504
• Print stdout stderr if install command fails by @mvdbeek in #1505

New Contributors

• @Smeds made their first contribution in #1492

Full Changelog: 0.75.27...0.75.28

What's Changed

• Fix repository category update by @mvdbeek in #1481
• Use python 3.13 for deploymen by @bernt-matthias in #1488
• Bump requirements for galaxy packages to 24.2 by @jdavcs in #1491
• Add category Geo Science by @bernt-matthias in #1483
• Remove usage of defaults conda channel by @bernt-matthias in #1487

Full Changelog: 0.75.26...0.75.27

What's Changed

• Display last lines of logs by @mvdbeek in #1473
• Fix autoupdate for workflows with overlapping tool updates by @bernt-matthias in #1452
• Fix up autopygen type annotation by @mvdbeek in #1474

Full Changelog: 0.75.25...0.75.26

What's Changed

• Add extended-assertions requirements by @bernt-matthias in #1471
• Add a new single cell category by @pavanvidem in #1457

New Contributors

• @pavanvidem made their first contribution in #1457

Full Changelog: 0.75.24...0.75.25

What's Changed

• Tool linting add --skip_file and remove lxml schema validation by @bernt-matthias in #1420
• Remove myself from committer list by @simonbray in #1454
• Make sure that skip list does not get [''] (if no skip is given) by @bernt-matthias in #1453
• Add the option to provide a history id to run the workflow in by @Delphine-L in #1461
• Run CI tests against newer Galaxy versions by @bernt-matthias in #1466
• Increase worflow linting by @lldelisle in #1463
• Add option to create a minimal markdown test report by @bernt-matthias in #1462
• Update pinning for Galaxy 24.1 by @bernt-matthias in #1460
• Workflow best practices: check that creator identifiers are URIs by @elichad in #1458

New Contributors

• @Delphine-L made their first contribution in #1461
• @elichad made their first contribution in #1458

Full Changelog: v0.75.23...0.75.24