Bump cwltool from 3.2.20260413085819 to 3.3.20260925135507

[dependabot]

Fixes #5545

Bumps cwltool from 3.2.20260413085819 to 3.3.20260925135507.

Release notes

Sourced from cwltool's releases.

3.3.20260925135507

What's Changed

• Warn when 'baseCommand' is a single string with whitespace (#2240) by @​arimu1 in common-workflow-language/cwltool#2292
• Handle list-valued doc when rendering --tool-help by @​arimu1 in common-workflow-language/cwltool#2304
• Give a meaningful error for an empty job order file by @​Sanjays2402 in common-workflow-language/cwltool#2316
• Fix float/double inputs below 1e-6 truncating to 0 on the command line (#2104) by @​arimu1 in common-workflow-language/cwltool#2310
• version support: add initial Py3.13-3.15 dates by @​mr-c in common-workflow-language/cwltool#2330
• python 3.15 by @​mr-c in common-workflow-language/cwltool#2329
• Delete "dirname" also for type Directory by @​adrabent in common-workflow-language/cwltool#2281
• Defer spython imports in singularity.py to where they're used by @​markjschreiber in common-workflow-language/cwltool#2344
• Fix loadContents for file array in step input (#2339) by @​CGuichard in common-workflow-language/cwltool#2340
• Fix workflow File defaults by @​Guflly in common-workflow-language/cwltool#2323
• Clearer error when a job hits a full disk (ENOSPC) (#1899) by @​arimu1 in common-workflow-language/cwltool#2293
• Sync up unique cache paths for Singularity images with cwl-utils by @​adamnovak in common-workflow-language/cwltool#2284
• bump minor version: changes in Singularity caching by @​mr-c in common-workflow-language/cwltool#2360

Deps

• build(deps): bump zizmorcore/zizmor-action from 0.5.3 to 0.5.6 by @​dependabot[bot] in common-workflow-language/cwltool#2274
• build(deps): bump docker/build-push-action from 7.1.0 to 7.2.0 by @​dependabot[bot] in common-workflow-language/cwltool#2277
• build(deps): bump docker/setup-buildx-action from 4.0.0 to 4.1.0 by @​dependabot[bot] in common-workflow-language/cwltool#2279
• build(deps): bump docker/login-action from 4.1.0 to 4.2.0 by @​dependabot[bot] in common-workflow-language/cwltool#2278
• build(deps): bump codecov/codecov-action from 6.0.1 to 7.0.0 by @​dependabot[bot] in common-workflow-language/cwltool#2309
• build(deps): bump zizmorcore/zizmor-action from 0.5.6 to 0.6.0 by @​dependabot[bot] in common-workflow-language/cwltool#2306
• build(deps): bump actions/setup-python from 6.2.0 to 6.3.0 by @​dependabot[bot] in common-workflow-language/cwltool#2308
• build(deps): bump docker/setup-qemu-action from 4.0.0 to 4.2.0 by @​dependabot[bot] in common-workflow-language/cwltool#2307
• build(deps): bump actions/cache from 5.0.5 to 6.1.0 by @​dependabot[bot] in common-workflow-language/cwltool#2305
• build(deps): bump docker/login-action from 4.2.0 to 4.4.0 by @​dependabot[bot] in common-workflow-language/cwltool#2315
• build(deps): bump pypa/cibuildwheel from 3.4.1 to 4.1.0 by @​dependabot[bot] in common-workflow-language/cwltool#2313
• build(deps): bump docker/setup-buildx-action from 4.1.0 to 4.2.0 by @​dependabot[bot] in common-workflow-language/cwltool#2314
• build(deps): bump actions/checkout from 6.0.2 to 7.0.1 by @​dependabot[bot] in common-workflow-language/cwltool#2311
• build(deps): bump docker/build-push-action from 7.2.0 to 7.3.0 by @​dependabot[bot] in common-workflow-language/cwltool#2312
• build(deps): bump actions/setup-python from 6.3.0 to 7.0.0 by @​dependabot[bot] in common-workflow-language/cwltool#2318
• build(deps): bump docker/login-action from 4.4.0 to 4.5.1 by @​dependabot[bot] in common-workflow-language/cwltool#2321
• build(deps): bump pypa/cibuildwheel from 4.1.0 to 4.1.1 by @​dependabot[bot] in common-workflow-language/cwltool#2322
• build(deps): bump zizmorcore/zizmor-action from 0.6.0 to 0.6.1 by @​dependabot[bot] in common-workflow-language/cwltool#2319
• build(deps): bump docker/login-action from 4.5.1 to 4.6.0 by @​dependabot[bot] in common-workflow-language/cwltool#2326
• build(deps): bump pypa/cibuildwheel from 4.1.1 to 4.2.0 by @​dependabot[bot] in common-workflow-language/cwltool#2328
• build(deps): bump zizmorcore/zizmor-action from 0.6.1 to 0.6.2 by @​dependabot[bot] in common-workflow-language/cwltool#2327
• build(deps): bump actions/cache from 5.1.0 to 6.1.0 by @​dependabot[bot] in common-workflow-language/cwltool#2331
• build(deps): bump mypy from 2.1.0 to 2.3.0 by @​dependabot[bot] in common-workflow-language/cwltool#2336
• build(deps): update galaxy-tool-util requirement from !=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<26.1,>=22.1.2 to >=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<26.2 by @​dependabot[bot] in common-workflow-language/cwltool#2335
• build(deps): update pytest requirement from <9.1,>=6.2 to >=6.2,<9.2 by @​dependabot[bot] in common-workflow-language/cwltool#2333
• build(deps): update galaxy-util requirement from <26.1 to <26.2 by @​dependabot[bot] in common-workflow-language/cwltool#2334
• build(deps): bump docker/setup-buildx-action from 4.2.0 to 4.3.0 by @​dependabot[bot] in common-workflow-language/cwltool#2341
• build(deps): bump mypy from 2.3.0 to 2.3.1 by @​dependabot[bot] in common-workflow-language/cwltool#2342
• build(deps): bump hendrikmuhs/ccache-action from 1.2.23 to 1.2.24 by @​dependabot[bot] in common-workflow-language/cwltool#2347
• build(deps): bump zizmorcore/zizmor-action from 0.6.2 to 0.6.3 by @​dependabot[bot] in common-workflow-language/cwltool#2346
• build(deps): bump docker/setup-qemu-action from 4.2.0 to 4.3.0 by @​dependabot[bot] in common-workflow-language/cwltool#2348
• build(deps): bump pypa/cibuildwheel from 4.2.0 to 4.2.1 by @​dependabot[bot] in common-workflow-language/cwltool#2350
• build(deps): bump zizmorcore/zizmor-action from 0.6.3 to 0.6.4 by @​dependabot[bot] in common-workflow-language/cwltool#2351

... (truncated)

Commits

• 9515acb bump minor version: changes in Singularity caching (#2360)
• 90f7c35 build(deps): bump codecov/codecov-action from 7.1.0 to 7.1.1 (#2358)
• 72ae2df build(deps): bump docker/setup-buildx-action from 4.3.0 to 4.4.1 (#2356)
• c1b8b43 build(deps): bump docker/setup-qemu-action from 4.3.0 to 4.4.0 (#2355)
• 56261eb build(deps): bump docker/build-push-action from 7.3.0 to 7.4.0 (#2357)
• 964d135 Sync up unique cache paths for Singularity images with cwl-utils (#2284)
• b6d2c6e build(deps): bump codecov/codecov-action from 7.0.0 to 7.1.0 (#2354)
• 3d0956c build(deps): update flake8-bugbear requirement from <25.12 to <26.10 (#2352)
• 254c7f9 build(deps): bump zizmorcore/zizmor-action from 0.6.3 to 0.6.4 (#2351)
• 2655097 Clearer error when a job hits a full disk (ENOSPC) (#1899) (#2293)
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[mr-c]

Finally!