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build(deps): Update snakemake requirement from <=7.32.4 to <=8.11.1 #288

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@dependabot dependabot bot commented on behalf of github May 1, 2024

Updates the requirements on snakemake to permit the latest version.

Release notes

Sourced from snakemake's releases.

v8.11.1

8.11.1 (2024-04-29)

Bug Fixes

  • check template rendering output for leaked input file paths (#2850) (433302e)
  • do not distinguish between local and remote rules in dryrun (74b99ec)
  • omit norun jobs when determining remote storage input file retrieval (#2854) (37a7c7f)
  • Prevent binary log files to crash snakemake execution with show-failed-logs (#2827) (8a80bda)
  • replace pkg_resources for python 3.12 (#2831) (ac144fc)
  • return set instead of list when just --quiet (#2829) (eeb57e2)
  • small typo in error (#2853) (325a715)
  • use keyword arguments in _IOFile.open (#2847) (50c84dc)

Documentation

Changelog

Sourced from snakemake's changelog.

8.11.1 (2024-04-29)

Bug Fixes

  • check template rendering output for leaked input file paths (#2850) (433302e)
  • do not distinguish between local and remote rules in dryrun (74b99ec)
  • omit norun jobs when determining remote storage input file retrieval (#2854) (37a7c7f)
  • Prevent binary log files to crash snakemake execution with show-failed-logs (#2827) (8a80bda)
  • replace pkg_resources for python 3.12 (#2831) (ac144fc)
  • return set instead of list when just --quiet (#2829) (eeb57e2)
  • small typo in error (#2853) (325a715)
  • use keyword arguments in _IOFile.open (#2847) (50c84dc)

Documentation

8.11.0 (2024-04-25)

Features

  • allow for more extensive benchmark file in jsonl format (#2691) (de12463)

Bug Fixes

  • only download input for local jobs in the main process, not within remote groups (#2842) (97f428b)
  • remove non-empty local copies of remote storage dirs (#2845) (71b2b87)
  • retrieve files from storage if necessary when calling their open method (e.g. when accessing output files from a checkpoint) (#2839) (5448208)

8.10.8 (2024-04-19)

Bug Fixes

  • extend workflow test suite by wildcards with slashes (in order to detect bugs that can occur in executors) (#2810) (fc9971b)
  • invalid extensions with multixt and cache (#1808) (#2823) (a845b1c)
  • module prefix added twice on expand (#2814) (27416f4)
  • retrieve inputs of local rules from storage even if they are intermediate results (#2811) (d158aa8)

Documentation

  • add snakemake and reportplugins to req.txt to show all cli options (#2817) (aaa9065)

8.10.7 (2024-04-12)

... (truncated)

Commits
  • fc70c90 chore(main): release 8.11.1 (#2849)
  • 50c84dc fix: use keyword arguments in _IOFile.open (#2847)
  • 37a7c7f fix: omit norun jobs when determining remote storage input file retrieval (#2...
  • 8a80bda fix: Prevent binary log files to crash snakemake execution with `show-failed-...
  • ac144fc fix: replace pkg_resources for python 3.12 (#2831)
  • eeb57e2 fix: return set instead of list when just --quiet (#2829)
  • cec0041 docs: fix typo and link for RO Crate (#2851)
  • 325a715 fix: small typo in error (#2853)
  • 433302e fix: check template rendering output for leaked input file paths (#2850)
  • 74b99ec fix: do not distinguish between local and remote rules in dryrun
  • Additional commits viewable in compare view

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Updates the requirements on [snakemake](https://github.com/snakemake/snakemake) to permit the latest version.
- [Release notes](https://github.com/snakemake/snakemake/releases)
- [Changelog](https://github.com/snakemake/snakemake/blob/main/CHANGELOG.md)
- [Commits](snakemake/snakemake@v2.4.8...v8.11.1)

---
updated-dependencies:
- dependency-name: snakemake
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot dependabot bot added the dependencies Pull requests that update a dependency file label May 1, 2024
@alsmith151
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@dependabot rebase

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dependabot bot commented on behalf of github Jun 25, 2024

Superseded by #291.

@dependabot dependabot bot closed this Jun 25, 2024
@dependabot dependabot bot deleted the dependabot/pip/snakemake-lte-8.11.1 branch June 25, 2024 10:06
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