Added features to grouping.py and update tutorial notebook to heuristic grouping

[vbrennsteiner]

• Added some explanatory comments
• Changed tutorial notebook so it runs with heuristic grouping mode
• add options to grouping_and_parsimony, as well as perform_grouping to keep the max-parsimony groups

[GeorgWa]

Hi Vincenth, can you change the target to development?

[vbrennsteiner]

I'm on it 👍 Thanks!

On Sat 25. May 2024 at 10:47, Georg Wallmann @.***> wrote:

@.**** approved this pull request.

Looks good!

In .gitignore https://github.com/MannLabs/alphadia/pull/171#discussion_r1614470127:

@@ -139,6 +139,7 @@ dmypy.json

Data

testdata/ +nbs/debug/dev_grouping_comparison_data/

can you move the test data to testdata/?

In alphadia/grouping.py https://github.com/MannLabs/alphadia/pull/171#discussion_r1614471103:

@@ -14,27 +14,21 @@ def group_and_parsimony( precursor_idx: NDArray[np.int64], precursor_ids: NDArray[Any],

• return_groups: bool = False,

Can we use the same argument name like in perform_grouping() ? e.g. return_parsimony_groups

In alphadia/grouping.py https://github.com/MannLabs/alphadia/pull/171#discussion_r1614471462:

• precursor_ids : np.array[str]
• array of variable length semicolon separated str belonging to a given peptide precursor id
• Args:

Please use Numpy style docstrings

https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_numpy.html#example-numpy

On nbs/debug/dev_grouping_comparison.ipynb https://github.com/MannLabs/alphadia/pull/171#discussion_r1614472607:

(nit) can you clean the notebook before comitting?

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[GeorgWa]

As soon as the notebook is clean we are good to go 👍🏻