build(deps): (deps): bump cwltool from 3.1.20230425144158 to 3.1.20230624081518

[dependabot]

Bumps cwltool from 3.1.20230425144158 to 3.1.20230624081518.

Release notes

Sourced from cwltool's releases.

3.1.20230624081518

What's Changed

• pass through QEMU_LD_PREFIX by default by @​mr-c in common-workflow-language/cwltool#1849
• dockerfile: pin graphviz to before 8.x by @​mr-c in common-workflow-language/cwltool#1863

Misc

• Remove deprecated use of Pathlib.Path as a context-mananger by @​mr-c in common-workflow-language/cwltool#1854
• gh-actions: keep running even if codecov upload fails by @​mr-c in common-workflow-language/cwltool#1857

Deps

• Update ruamel-yaml requirement from =0.16.0,<0.17.32 by @​dependabot in common-workflow-language/cwltool#1852
• Update flake8-bugbear requirement from <23.6 to <23.7 by @​dependabot in common-workflow-language/cwltool#1856
• Bump sphinx-rtd-theme from 1.2.1 to 1.2.2 by @​dependabot in common-workflow-language/cwltool#1858
• Update pytest requirement from =6.2,<7.5 by @​dependabot in common-workflow-language/cwltool#1864

Full Changelog: common-workflow-language/cwltool@3.1.20230601100705...3.1.20230624081518

3.1.20230601100705

What's Changed

• Ensure that files with identical basenames get staged to unique paths by @​mr-c in common-workflow-language/cwltool#1853

Full Changelog: common-workflow-language/cwltool@3.1.20230527103121...3.1.20230601100705

3.1.20230527103121

What's Changed

• synchronize setup.py & requirements.txt by @​mr-c in common-workflow-language/cwltool#1848 (fixes missing dependency on importlib_resources and importlib_metadata; also drop dependency on the bagit library library which is only used in the tests)

Full Changelog: common-workflow-language/cwltool@3.1.20230526180938...3.1.20230527103121

3.1.20230526180938

What's Changed

• CWLProv snapshots: capture the workflow even if the cwl:tool trick in the input object is used by @​mr-c in common-workflow-language/cwltool#1847

• Refactoring provenance.py as provenance submodule by @​RenskeW in common-workflow-language/cwltool#1775

• use importlib instead of the deprecated pkg_resources by @​mr-c in common-workflow-language/cwltool#1844

• Bump sphinx-rtd-theme from 1.2.0 to 1.2.1 by @​dependabot in common-workflow-language/cwltool#1845

• Update ruamel-yaml requirement from =0.16.0,<0.17.28 by @​dependabot in common-workflow-language/cwltool#1846

Full Changelog: common-workflow-language/cwltool@3.1.20230513155734...3.1.20230526180938

3.1.20230513155734

What's Changed

• Update ruamel-yaml requirement from =0.16.0,<0.17.27 by @​dependabot in common-workflow-language/cwltool#1838
• --leave-tmpdir includes the input staging directories by @​mr-c in common-workflow-language/cwltool#1674 common-workflow-language/cwltool#1840
• Bump mypy from 1.2.0 to 1.3.0 by @​dependabot in common-workflow-language/cwltool#1839

... (truncated)

Commits

• 15a4f64 Update pytest requirement from <7.4,>=6.2 to >=6.2,<7.5
• 9e1eb1d pin to compatible galaxy-util
• 8aecdcc dockerfile: pin graphviz to before 8.x
• ac4cd0c Bump sphinx-rtd-theme from 1.2.1 to 1.2.2 (#1858)
• d73e104 gh-actions: keep running even if codecov upload fails (#1857)
• d7cde2e Update flake8-bugbear requirement from <23.6 to <23.7 (#1856)
• 0f58a96 pass through QEMU_LD_PREFIX by default (#1849)
• 88019c8 Remove deprecated use of Pathlib.Path as a context-mananger (#1854)
• dbe5330 ruamel.yaml: pin maximum version at 0.18 (#1852)
• fd7db53 Files with identical basenames get staged to unique paths (#1853)
• Additional commits viewable in compare view

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

---

Dependabot commands and options

You can trigger Dependabot actions by commenting on this PR:

• @dependabot rebase will rebase this PR
• @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
• @dependabot merge will merge this PR after your CI passes on it
• @dependabot squash and merge will squash and merge this PR after your CI passes on it
• @dependabot cancel merge will cancel a previously requested merge and block automerging
• @dependabot reopen will reopen this PR if it is closed
• @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
• @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)

[dependabot]

Superseded by #3570.