Move from alpharaw

[mschwoer]

Move code over from alpharaw (cf. MannLabs/alpharaw#116)

[GeorgWa]

Looks good! Could we get rid of the NormalDIAGrouper?
It's not used anywhere to my knowledge.

[jalew188]

Looks good! Could we get rid of the NormalDIAGrouper? It's not used anywhere to my knowledge.

Greet, now we have alphadia to do this

[mschwoer]

@GeorgWa @jalew188 unfortunately, not:

Yes, NormalDIAGrouper is actively used. Here's the full call chain:

  1. NormalDIAGrouper — defined in match/normal_dia.py:11, instantiated in match/psm_match.py:529
  2. PepSpecMatch_DIA._match_ms2_one_raw_numba (match/psm_match.py:497) — the method that creates the NormalDIAGrouper
  3. PepSpecMatch._match_ms2_one_raw_numba is called at match/psm_match.py:429 (polymorphic call via self, dispatches to the DIA override)
  4. This is called from match_psms() (pipeline_api.py:152), which creates PepSpecMatch_DIA at line 212 when the PSM type is not DDA
  5. match_psms() is called from transfer_learn() (pipeline_api.py:360)
  6. transfer_learn() is called from:
    - cli.py:133 and cli.py:170 (CLI entry points)
    - webui/server.py:57 (web UI)

  So NormalDIAGrouper is actively in use — it's part of the DIA PSM matching pipeline, reachable from both the CLI and the web UI via transfer_learn -> match_psms -> PepSpecMatch_DIA._match_ms2_one_raw_numba.