fix ms2.py update sliced fragment dataframe bug

[CRYoushiwo]

Before Revise
in ms2.py:
628 update_sliced_fragment_dataframe(
629 self.predict_df,
630 self.predict_df.to_numpy(copy=True),
631 predicts.reshape((-1, len(self.charged_frag_types))),
632 batch_df[["frag_start_idx", "frag_stop_idx"]].values,
633 )

running:

pdeep.train(psm_df, fragment_inten_df, 
    warmup_epoch=1, epoch=2, batch_size=512, lr=1e-4,
    verbose=True,
    verbose_each_epoch=True
)
predict_inten_df = pdeep.predict(psm_df, reference_frag_df=fragment_inten_df, verbose=True)
df, metrics = calc_ms2_similarity(psm_df, predict_inten_df, fragment_inten_df, pdeep.charged_frag_types, verbose=True)

metrics =

	PCC	COS	SA	SPC
count	741510.00	741510.00	741510.00	741510.00
mean	0.00	0.00	0.00	-0.022181
std	0.00	0.00	0.00	0.195575
min	0.00	0.00	0.00	-0.821355
25%	0.00	0.00	0.00	-0.176919
50%	0.00	0.00	0.00	-0.009774
75%	0.00	0.00	0.00	0.134845
max	0.00	0.00	0.00	0.669911
>0.90	0.00	0.00	0.00	0.000000
>0.75	0.00	0.00	0.00	0.000000

After Revise
in ms2.py:
628 update_sliced_fragment_dataframe(
629 self.predict_df,
630 self.predict_df.to_numpy(),
631 predicts.reshape((-1, len(self.charged_frag_types))),
632 batch_df[["frag_start_idx", "frag_stop_idx"]].values,
633 )

running:

pdeep.train(psm_df, fragment_inten_df, 
    warmup_epoch=1, epoch=2, batch_size=512, lr=1e-4,
    verbose=True,
    verbose_each_epoch=True
)
predict_inten_df = pdeep.predict(psm_df, reference_frag_df=fragment_inten_df, verbose=True)
df, metrics = calc_ms2_similarity(psm_df, predict_inten_df, fragment_inten_df, pdeep.charged_frag_types, verbose=True)

metrics =

	PCC	COS	SA	SPC
count	741510.00	741510.00	741510.00	741510.00
mean	0.572111	0.613076	0.442540	-0.135041
std	0.237287	0.216775	0.186603	0.193894
min	-0.085739	0.003055	0.001945	-1.331361
25%	0.394702	0.453877	0.299919	-0.262786
50%	0.597644	0.640260	0.442347	-0.131268
75%	0.756201	0.780827	0.570404	0.003786
max	0.997808	0.997729	0.957086	0.451942
>0.90	0.071483	0.082213	0.004655	0.000000
>0.75	0.258934	0.308326	0.053810	0.000000

[mschwoer]

related to MannLabs/alphadia#409