Release notes

Release 3.0.0

Python 3.11 or later is required. Linux CI tests Python 3.11 through 3.14.
History paths are now relative to the history database directory, allowing runs from different working directories when the same database and files are used. Moving a project together with its database preserves checkpoints if their relative layout is unchanged.
Old histories do not record their original working directory. Their records are preserved in the ruffus_legacy_history SQLite table, and active checkpoints are rebuilt on the next history-based run. Expect a one-time rerun of affected jobs. Do not share upgraded databases with older Ruffus.
Keyword-only defaults now contribute to function checksums. Tasks with these defaults may rerun once at checksum levels 2 and 3 after upgrading.

Add @run_in_main_process() and Task.run_in_main_process() for tasks that need to create their own multiprocessing children or run in the pipeline caller’s thread. Other tasks retain pool execution. jobs_limit(1) remains a concurrency limit and does not opt into this behaviour. See run_in_main_process for limitations.
Stop resubmitting successful DRMAA jobs when retries are enabled and the scheduler provides no job information. Communication-error retry limitations remain; this change does not make resubmission safe after a lost response.
Fix keyword-only and mixed arguments in @split, and correct argument forwarding for the legacy regex form.
Modernize the test runner and add Linux GitHub Actions coverage.
Remove obsolete hosting references from the documentation.
Add a pyproject.toml build configuration using setuptools.

@transform works even when the ouput has more than one file.
@subdivide works in exactly the same way as @transform.
ruffus.drmaa_wrapper.run_job() works with python3 `(github) Fixed issue with byte and text streams.
ruffus.drmaa.wrapper.run_job() allows env (environment) to be set for jobs run locally as well as those on the cluster.
New object-orientated style syntax works seamlessly with Ruffus command line support.

pipeline_printout_graph()` incompatibility with python3 fixed.
checkpointing did not work correctly with @split and @subdivide.
@transoform has easier to understand syntax and takes care of most common use cases of ruffus (Thanks Milan Simonovic).
@transform takes an optional output_dir.
Decorators can take named parameters.