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deps(python): bump snakemake from 8.5.3 to 8.9.0 in /dependencies/python #5425

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@dependabot dependabot bot commented on behalf of github Mar 22, 2024

Bumps snakemake from 8.5.3 to 8.9.0.

Release notes

Sourced from snakemake's releases.

v8.9.0

8.9.0 (2024-03-18)

Features

  • add function 'exists' for checking the prior existence of files or dirs before workflow execution while considering any remote storage settings. In addition: some bug fixes for error handling and the update/before_update functionality. (ee96393)

v8.8.0

8.8.0 (2024-03-15)

Features

Bug Fixes

  • various error handling improvements, fixed logging/error behavior (stdout from dryrun, stderr otherwise) (#2759) (d0d1f48)

v8.7.0

8.7.0 (2024-03-13)

Features

  • add flag for marking output as being updated instead of rewritten (update("test.txt")) (#2754) (9ba5d95)
  • allow default storage provider to be explicitly set to none (#2746) (ce519d7)

v8.6.0

8.6.0 (2024-03-11)

Features

  • add setting for defining separate local storage prefix for remote jobs; improved ergonomics for semantic helper functions (#2743) (5007e5c)
  • allow passing of lists of functions or single functions to expand (#2741) (32e65df)

Bug Fixes

  • fix error message for invalid storage provider queries (977951e)
  • fix premature deletion of temp files in combination with checkpoints (#2737) (b22ba5f)

v8.5.5

8.5.5 (2024-03-07)

Bug Fixes

... (truncated)

Changelog

Sourced from snakemake's changelog.

8.9.0 (2024-03-18)

Features

  • add function 'exists' for checking the prior existence of files or dirs before workflow execution while considering any remote storage settings. In addition: some bug fixes for error handling and the update/before_update functionality. (ee96393)

8.8.0 (2024-03-15)

Features

Bug Fixes

  • various error handling improvements, fixed logging/error behavior (stdout from dryrun, stderr otherwise) (#2759) (d0d1f48)

8.7.0 (2024-03-13)

Features

  • add flag for marking output as being updated instead of rewritten (update("test.txt")) (#2754) (9ba5d95)
  • allow default storage provider to be explicitly set to none (#2746) (ce519d7)

8.6.0 (2024-03-11)

Features

  • add setting for defining separate local storage prefix for remote jobs; improved ergonomics for semantic helper functions (#2743) (5007e5c)
  • allow passing of lists of functions or single functions to expand (#2741) (32e65df)

Bug Fixes

  • fix error message for invalid storage provider queries (977951e)
  • fix premature deletion of temp files in combination with checkpoints (#2737) (b22ba5f)

8.5.5 (2024-03-07)

Bug Fixes

  • less frightering message when telling about missing output files as reason for running a job (7b6c9d4)

8.5.4 (2024-03-06)

... (truncated)

Commits
  • 1a9515a chore(main): release 8.9.0 (#2764)
  • 491bb33 add missing test files
  • 26cebcf fixes and tests
  • ee96393 feat: add function 'exists' for checking the prior existence of files or dirs...
  • 6f53d4b chore(main): release 8.8.0 (#2760)
  • d52c1b1 feat: Allow smart_open 7.x (#2745)
  • d0d1f48 fix: various error handling improvements, fixed logging/error behavior (stdou...
  • 05ee812 chore(main): release 8.7.0 (#2747)
  • 9ba5d95 feat: add flag for marking output as being updated instead of rewritten (upda...
  • ce519d7 feat: allow default storage provider to be explicitly set to none (#2746)
  • Additional commits viewable in compare view

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Bumps [snakemake](https://github.com/snakemake/snakemake) from 8.5.3 to 8.9.0.
- [Release notes](https://github.com/snakemake/snakemake/releases)
- [Changelog](https://github.com/snakemake/snakemake/blob/main/CHANGELOG.md)
- [Commits](snakemake/snakemake@v8.5.3...v8.9.0)

---
updated-dependencies:
- dependency-name: snakemake
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot requested a review from zkoppert as a code owner March 22, 2024 10:21
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Mar 22, 2024
@github-actions github-actions bot enabled auto-merge March 22, 2024 10:21
@github-actions github-actions bot added this pull request to the merge queue Mar 22, 2024
Merged via the queue into main with commit 3ec9980 Mar 22, 2024
87 checks passed
@dependabot dependabot bot deleted the dependabot/pip/dependencies/python/snakemake-8.9.0 branch March 22, 2024 13:15
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