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chore(deps): update snakemake requirement from <8,>=7.32.0 to >=7.32.0,<9 #588

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@dependabot dependabot bot commented on behalf of github Dec 30, 2024

Updates the requirements on snakemake to permit the latest version.

Release notes

Sourced from snakemake's releases.

v8.26.0

8.26.0 (2024-12-23)

Features

  • add helpers for deferred input/output etc. item access (#2927) (2cca9bc)

Bug Fixes

  • convert parameters so they can be serialized (#2925) (9e653fb)
  • correct formatting of R preamble (#2425) (5380cae)
  • fix modification checks for scripts and and notebooks containing wildcards or params in their paths (#2751) (773568d)
  • Improved handling of missing output files in group job postprocessing, accounting for temporary files. (#1765) (bac06ba)
  • mtime of script or notebook not triggering workflow without metadata (#3148) (e8a0b83)
  • Pass host attribute to GitlabFile instantiation within class methods (#3155) (9ef52de)
  • problem with spaces in path (#3236) (2d08c63)
  • require current yte release which contains an important bug fix for cases where numpy/pandas data is passed to templates (#3227) (c3339da)
  • rerun jobs if previously failed but rule was changed afterwards (thanks to @​laf070810 for bringing this up) (#3237) (1dc0084)
  • use relpath for configfiles added to the source archive (thanks to @​sposadac for the initial solution) (#3240) (bff3844)
Changelog

Sourced from snakemake's changelog.

8.26.0 (2024-12-23)

Features

  • add helpers for deferred input/output etc. item access (#2927) (2cca9bc)

Bug Fixes

  • convert parameters so they can be serialized (#2925) (9e653fb)
  • correct formatting of R preamble (#2425) (5380cae)
  • fix modification checks for scripts and and notebooks containing wildcards or params in their paths (#2751) (773568d)
  • Improved handling of missing output files in group job postprocessing, accounting for temporary files. (#1765) (bac06ba)
  • mtime of script or notebook not triggering workflow without metadata (#3148) (e8a0b83)
  • Pass host attribute to GitlabFile instantiation within class methods (#3155) (9ef52de)
  • problem with spaces in path (#3236) (2d08c63)
  • require current yte release which contains an important bug fix for cases where numpy/pandas data is passed to templates (#3227) (c3339da)
  • rerun jobs if previously failed but rule was changed afterwards (thanks to @​laf070810 for bringing this up) (#3237) (1dc0084)
  • use relpath for configfiles added to the source archive (thanks to @​sposadac for the initial solution) (#3240) (bff3844)

8.25.5 (2024-11-29)

Bug Fixes

  • expand environment variables in --remote-job-local-storage-prefix within the remote job, not the main snakemake job (#3222) (59c86a4)

8.25.4 (2024-11-27)

Bug Fixes

  • clean env vars in apptainer (#3199) (76d5329)
  • ensure that intermediate files in job groups do not cause spurious mtime errors when checking for consistency with output files (#3220) (4ba2bdf)
  • Remove incomplete marker also when drop-metadata is active (#3215) (a4f2e5c)
  • Remove incomplete marker for job finished only after metadata is written (#3197) (6567e5f)
  • Support versioned URLs in Asset class and fix missing versions in Snakemake report (#3203) (f086f6c)
  • update rust-script usage to recent version (v0.35.0) #3183 (#3208) (43885d7)

Documentation

  • clarify continuously updated input section (#3219) (72a6994)
  • Fix typo in CHANGELOG.md (#3198) (0e445ed)
  • refer to Merkle trees instead of "blockchain" in caching.rst (#3216) (282e5d9)
  • remove twitter in favor of bluesky and mastodon (#3217) (231c6df)
  • use "dictionary" not "array" wording in config docs (#3156) (17aed41)

8.25.3 (2024-11-11)

... (truncated)

Commits
  • 2cf0fbc chore(main): release 8.26.0 (#3229)
  • bff3844 fix: use relpath for configfiles added to the source archive (thanks to @​spos...
  • bac06ba fix: Improved handling of missing output files in group job postprocessing, a...
  • 9ef52de fix: Pass host attribute to GitlabFile instantiation within class methods...
  • 773568d fix: fix modification checks for scripts and and notebooks containing wildcar...
  • 5380cae fix: correct formatting of R preamble (#2425)
  • 9e653fb fix: convert parameters so they can be serialized (#2925)
  • 1dc0084 fix: rerun jobs if previously failed but rule was changed afterwards (thanks ...
  • 46d7d0c fix: Cannot change working directory when R script hosted on GitHub with sour...
  • e8a0b83 fix: mtime of script or notebook not triggering workflow without metadata (#3...
  • 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@v7.32.0...v8.26.0)

---
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 Dec 30, 2024
@coveralls
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Coverage Status

coverage: 85.765%. remained the same
when pulling cbcb551 on dependabot/pip/snakemake-gte-7.32.0-and-lt-9
into dbeb3ed on main.

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