Spectrum feature generator

[ArthurDeclercq]

[paretje]

It might be worth considering setting these by default when running mumble through ms2rescore, given that these are kind of required for it to work, so at least it should be documented:

[ms2rescore.psm_generator.mumble]
keep_original = true
generate_modified_decoys = true

[paretje]

I had a quick look at the python 3.9 failure: this is because of mumble, which requires python 3.10. I think we could probably lower the requirement in mumble, as I don't think we actually use any new features, unless some of the dependencies do. And otherwise, we could of course just consider dropping python 3.9 for ms2rescore.

For the record, I used poetry to get a more useful error from the dependency resolver (adding the version to pyproject.toml, it seems dynamic version fields aren't supported):

The current project's supported Python range (>=3.9) is not compatible with some of the required packages Python requirement:
  - mumble-mod requires Python >=3.10, so it will not be satisfied for Python >=3.9,<3.10

Because ms2rescore depends on mumble-mod (0.2.0) @ git+https://github.com/compomics/mumble.git@114ad7d which requires Python >=3.10, version solving failed.

  * Check your dependencies Python requirement: The Python requirement can be specified via the `python` or `markers` properties

    For mumble-mod, a possible solution would be to set the `python` property to ">=3.10"

    https://python-poetry.org/docs/dependency-specification/#python-restricted-dependencies,
    https://python-poetry.org/docs/dependency-specification/#using-environment-markers