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chore(deps-dev): update snakemake requirement from ^8.20.1 to >=8.20.1,<10.0.0 #33

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merged 1 commit into from
Mar 17, 2025
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chore(deps-dev): update snakemake requirement from ^8.20.1 to >=8.20.1,<10.0.0 #33

merged 1 commit into from
Mar 17, 2025

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@dependabot dependabot bot commented on behalf of github Mar 17, 2025

Updates the requirements on snakemake to permit the latest version.

Release notes

Sourced from snakemake's releases.

v9.0.1

9.0.1 (2025-03-14)

Bug Fixes

Changelog

Sourced from snakemake's changelog.

9.0.1 (2025-03-14)

Bug Fixes

9.0.0 (2025-03-14)

⚠ BREAKING CHANGES

  • Logging refactor & add LoggerPluginInterface (#3107)

Features

  • #3412 - keep shadow folder of failed job if --keep-incomplete flag is set. (#3430) (22978c3)
  • add flag --report-after-run to automatically generate the report after a successful workflow run (#3428) (b0a7f03)
  • add flatten function to IO utils (#3424) (67fa392)
  • add helper functions to parse input files (#2918) (63e45a7)
  • Add option to print redacted file names (#3089) (ba4d264)
  • add support for validation of polars dataframe and lazyframe (#3262) (c7473a6)
  • added support for rendering dag with mermaid js (#3409) (7bf8381)
  • adding --replace-workflow-config to fully replace workflow configs (from config: directive) with --configfile, instead of merging them (#3381) (47504a0)
  • Dynamic module name (#3401) (024dc32)
  • Enable saving and reloading IOCache object (#3386) (c935953)
  • files added in rule params with workflow.source_path will be available in used containers (#3385) (a6e45bf)
  • Fix keep_local in storage directive and more freedom over remote retrieval behaviour (#3410) (67b4739)
  • inherit parameters of use rule and extend/replace individual items them when using 'with' directive (#3365) (93e4b92)
  • Logging refactor & add LoggerPluginInterface (#3107) (86f1d6e)
  • Maximal file size for checksums (#3368) (b039f8a)
  • Modernize package configuration using Pixi (#3369) (77992d8)
  • multiext support for named input/output (#3372) (05e1378)
  • optionally auto-group jobs via temp files in case of remote execution (#3378) (cc9bba2)

Bug Fixes

  • --delete-all-output ignores --dry-run (#3265) (23fef82)
  • 3342 faster touch runs and warning messages for non-existing files (#3398) (cd9c3c3)
  • add default value to max-jobs-per-timespan (#3043) (2959abe)
  • checkpoints inside modules are overwritten (#3359) (fba3ac7)
  • Convert Path to IOFile (#3405) (c58684c)
  • Do not perform storage object cleanup with --keep-storage-local-copies set (#3358) (9a6d14b)
  • edgecases of source deployment in case of remote execution (#3396) (5da13be)
  • enhance error message formatting for strict DAG-building mode (#3376) (a1c39ee)
  • fix bug in checkpoint handling that led to exceptions in case checkpoint output was missing upon rerun (#3423) (8cf4a2f)
  • force check all required outputs (#3341) (495a4e7)
  • group job formatting (#3442) (f0b10a3)
  • in remote jobs, upload storage in topological order such that modification dates are preserved (e.g. in case of group jobs) (#3377) (eace08f)

... (truncated)

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@dependabot
chore(deps-dev): update snakemake requirement
9ead1aa 
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@v8.20.1...v9.0.1)

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

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update python code labels Mar 17, 2025
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@cmeesters cmeesters self-requested a review March 17, 2025 14:16
@cmeesters cmeesters merged commit 7f03338 into main Mar 17, 2025
5 checks passed
@cmeesters cmeesters deleted the dependabot/pip/snakemake-gte-8.20.1-and-lt-10.0.0 branch March 17, 2025 14:16
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