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 successfull 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)
• only skip eval when resource depends on input (#3374) (4574c92)
• Prevent execution of conda in apptainer when not explicitly requested in software deployment method (#3388) (c43c5c0)
• print filenames with quotes around them in RuleException (#3269) (6baeda5)
• Re-evaluation of free resources (#3399) (6371293)
• ReadTheDocs layout issue due to src directory change (#3419) (695b127)
• robustly escaping quotes in generated bash scripts (v2) (#3297) (#3389) (58720bd)
• Show apptainer image URL in snakemake report (#3407) (45f0450)
• Update ReadTheDocs configuration for documentation build to use Pixi (#3433) (3f227a6)

Documentation

• Add pixi setup instructions to general use tutorial (#3382) (115e81b)
• fix contribution section heading levels, fix docs testing setup order (#3360) (051dc53)
• fix link to github.com/snakemake/poetry-snakemake-plugin (#3436) (ec6d97c)
• fix quoting (#3394) (b40f599)
• fix rerun-triggers default (#3403) (4430e23)
• fix typo 'safe' -> 'save' (#3384) (7755861)
• mention code formatting in the contribution section (#3431) (e8682b7)
• remove duplicated 'functions'. (#3356) (7c595db)
• update broken links documentation (#3437) (e3d0d88)
• Updating contributing guidelines with new pixi dev setup (#3415) (8e95a12)