Example results in error

[LLautenbacher]

Hi, thank you for preparing this package! When I tried to use the example from https://rustyms.readthedocs.io/en/stable/. It results in this error. I used version rustyms==0.9.0.

import rustyms

# Create a new spectrum
raw_spectrum = rustyms.RawSpectrum(
    title="spectrum_1",
    num_scans=6,
    rt=10,
    precursor_mass=436.12634,
    precursor_charge=2,
    mz_array=[72.04444, 148.06048, 175.05362, 263.08742, 290.08056, 366.09661],
    intensity_array=[100, 600, 300, 400, 500, 200],
)

# Create a new peptide from a ProForma 2.0 string
peptide = rustyms.LinearPeptide("ACDE/2")

# Annotate the spectrum with the peptide
annotated_spectrum = raw_spectrum.annotate(peptide, "cid_hcd")

TypeError                                 Traceback (most recent call last)
Cell In[3], [line 18](vscode-notebook-cell:?execution_count=3&line=18)
     [15](vscode-notebook-cell:?execution_count=3&line=15) peptide = rustyms.LinearPeptide("ACDE/2")
     [17](vscode-notebook-cell:?execution_count=3&line=17) # Annotate the spectrum with the peptide
---> [18](vscode-notebook-cell:?execution_count=3&line=18) annotated_spectrum = raw_spectrum.annotate(peptide, "cid_hcd")

TypeError: argument 'peptide': 'LinearPeptide' object cannot be converted to 'CompoundPeptidoform'

[douweschulte]

I will update the example, thank you for opening the issue. The issue here is that since 0.9 the spectrum annotation has to be done with a CompoundPeptidoform. To get your code running the easiest is to create one instead on a linear peptide rustyms.CompoundPeptidoform("ACDE/2"). I will look into how I can make the API easier to use, maybe I can make it so that any peptide like object will work.

[douweschulte]

I am not sure if I can get nice behaviour where the annotate function accepts any of the three peptidoform types. It looks like getting this to work in pyO3 is somewhat more involved then I hoped. I will keep my eyes peeled for a solution though. Otherwise I updated the documentation so with the next release it will be fixed.