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@dependabot dependabot bot commented on behalf of github Sep 17, 2025

Bumps toil[cwl] from 9.0.0 to 9.1.0.

Release notes

Sourced from toil[cwl]'s releases.

9.1.0

Highlighted Features Added

  • Toil's AWS job store now depends only on the S3 API; Amazon SimpleDB is no longer required. (#5123)
  • Toil's autoscaler should again be able to add AWS spot market nodes. (#5368)
  • Toil now checks scontrol first for Slurm jobs, and then pages through constrained time ranges of data from sacct, instead of first asking sacct about all of history. (#5381)

Breaking Changes

Because of the new AWS job store implementation (#5123), Toil 9.1 can no longer read, delete, or resume AWS job stores created with Toil 9.0 or earlier. If you need to destroy an old job store, use toil clean from toil[aws]==9.0. In general, Toil doesn't consider losing compatibility with an older Toil's job store data on disk to be a major-version-worthy change, since it might happen any time Toil revises its internal data structures, but in this case the lack of delete support for the old format is a tripping hazard that we want to call out.

Misc

  • Toil now has limited patience when registering with Mesos and will fail the workflow if Mesos never responds. (#5345)
  • CI tests that sniff logs will no longer crash when a Toil job log containing % is logged (#5353)
  • File staging tutorial script now runs from any location (#5305)
  • Node launch times in the provisioner are now always timezone-aware (#5365)
  • Toil doctests are now actually run in CI and via make test or make doctest (#5367)
  • Toil AWS spot provisioning and integrated autoscaler are now under periodic integration testing (#5370)
  • Toil now logs Slurm job numbers for debugging workflows (#5359)
  • toil debug-file should be able to fetch files again (#5382)
  • Toil will now detect and warn about jobs that use more CPU than they requested. (#5366)
  • toil stats will no longer report negative CPU Wait values when jobs use more CPU than they requested. (#5366)

Thank you to our contributors:

Commits
  • e341bb6 Set version for 9.1.0 release
  • 0dc7624 Update AWS instance list (#5388)
  • 5c67a86 Update pytest-randomly requirement from <4,>=3.16.0 to >=3.16.0,<5 (#5386)
  • cc9b645 Update pytest-cov requirement from <7,>=2.12.1 to >=2.12.1,<8 (#5384)
  • c79e280 Banish negative wait and detect exceeding CPU requirements (#5385)
  • 8a25370 Bump mypy from 1.17.1 to 1.18.1 (#5387)
  • 807ef36 Update docutils requirement from <0.22,>=0.16 to >=0.16,<0.23 (#5363)
  • afb9a17 Update requests requirement from <=2.32.4 to <=2.32.5 (#5374)
  • 88bb7a7 Avoid making slow Slurm queries (#5383)
  • be7f9ac Enable plain and static tests to exercise the Toil-integrated autoscaler (#5371)
  • Additional commits viewable in compare view

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Bumps [toil[cwl]](https://github.com/DataBiosphere/toil) from 9.0.0 to 9.1.0.
- [Release notes](https://github.com/DataBiosphere/toil/releases)
- [Commits](DataBiosphere/toil@releases/9.0.0...releases/9.1.0)

---
updated-dependencies:
- dependency-name: toil[cwl]
  dependency-version: 9.1.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update python code labels Sep 17, 2025
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codecov bot commented Sep 17, 2025

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 71.61%. Comparing base (154b832) to head (6f94526).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #150      +/-   ##
==========================================
+ Coverage   71.09%   71.61%   +0.51%     
==========================================
  Files           4        4              
  Lines         391      391              
==========================================
+ Hits          278      280       +2     
+ Misses        113      111       -2     

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@mr-c mr-c merged commit 0c9af64 into main Sep 17, 2025
20 checks passed
@mr-c mr-c deleted the dependabot/pip/toil-cwl--9.1.0 branch September 17, 2025 08:08
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