Skip to content

chore(deps-dev): update snakemake requirement from ^8.18.0 to >=8.18,<10.0 #44

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 1 commit into
base: main
Choose a base branch
from

Conversation

dependabot[bot]
Copy link
Contributor

@dependabot dependabot bot commented on behalf of github Apr 7, 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)

Commits

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 show <dependency name> ignore conditions will show all of the ignore conditions of the specified dependency
  • @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)

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@v8.18.0...v9.0.1)

---
updated-dependencies:
- dependency-name: snakemake
  dependency-version: 9.0.1
  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 Apr 7, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
dependencies Pull requests that update a dependency file python Pull requests that update python code
Projects
None yet
Development

Successfully merging this pull request may close these issues.

0 participants