Bug or undocumented v8 breaking change: snakemake: error: unrecognized arguments: --reason=True

[corneliusroemer]

I'm trying out snakemake 8. If have reason: True in a profile. I now get:

snakemake: error: unrecognized arguments: --reason=True

This isn't documented in the migration guide so it's either a bug or it should be added to the migration guide here: https://snakemake.readthedocs.io/en/stable/getting_started/migration.html#command-line-interface

Which currently reads:

Morever, some options have been renamed:

All the execution backends have been moved into plugins. When you used e.g. --kubernetes and corresponding options before, you should now use --executor kubeternes and check the Snakemake plugin catalog for the new options. The same holds for all other execution backends, see here.

The --use-conda and --use-singularity options are deprecated. Instead you should now use --software-deployment-method conda or --software-deployment-method apptainer or --software-deployment-method conda apptainer if you need both.

This seems to be the only breaking change, no other migration necessary for the nextstrain/mpox phylogenetic workflow, so not too bad ;)

[fgvieira]

It seems the reason why a rule is being run is now always printed to screen.

[corneliusroemer]

Yes it seems to have been set to true and removed as a cli arg.

To avoid being breaking, one could accept it, print a deprecation warning and remove later.

Or document it.

[corneliusroemer]

It's been marked as deprecated for a while - but no warning has been printed which is why I was surprised it got removed.
see #1902

[ammaraziz]

Could anyone explain why this flag was depreciated? It's very handy to silence the reason: output of snakemake when building pipelines. A possible explanation is that --quiet can now handle inputs to silence specific terminal outputs.

A possible solution would be to include an option in --quiet which is similar to progress but silences reason:.

Might be worth discussing this in a separate issue/feature request?