Upgrade to new matchms release

[niekdejonge]

Upgrade to new matchms release and replace ms2query steps that are now covered by matchms:

• Use the new pubchemlookup (this could also be achieved without upgrading matchms
• Replace the cleaning steps with Pipeline

[mapio]

Fixing this would be great since now I've a WARNING:matchms:interpret_pepmass:Overwriting existing precursor_mz message for every spectrum (meaning close to 500K warnings, clogging the log and slowing the process), from matchms/filtering/metadata_processing/interpret_pepmass.py probably due to the fact that, in the used version of matchms, such warning is not guarded by the and _substantial_difference part of the if clause present at line 42 in the current version.

[niekdejonge]

The reason it takes a bit longer, is that matchms has some new dependencies. For instance pandas 2.0. We did use pickled pandas df's in the tests (now fixed with #221) and as a way of storing embeddings. We could simply store the embeddings as pickled pandas 2.0 df, but this would be double work and break backwards compatibility an extra time, since we want to upgrade to a different embedding storage format anyway. This is being implemented in #228.
Once the last issues have been resolved here, the update to matchms 0.24.0 should hopefully be more straightforward.