Niek de Jonge

Add option for progress bars.

3

Currently calculate_scores does not show any progress bar. Since, Scores checks for the type to be List, tuple or np.array. It is also not possible to use tqdm() on the...

save_spectra_in_fast_import_file_type

12

Problem: Loading in entire libraries (>100.000) takes time for file types like mgf. Currently I often store large cleaned spectra files as pickled list of matchms objects, which is much...

make structure similarity scoring easier to run

1

Currently tanimoto scores can be calculated by first adding fingerprints, followed by calculating fingerprint similarity Suggested change: Select each inchikey only once (to prevent calculating too many comparisons) Per unique...

spectrum typing does not work with IDE's

1

The Spectrum type object is not the same as setting the type to Spectrum. This results in IDE highlighting typing errors, when a Spectrum object is expected and a Spectrumtype...

multi_inputs is not automatically detected

2

I am running the new multi_inputs pipeline, when running MS2Deepscore, you require to add multi_inputs=True. The error you get when forgetting to set this to True is confusing: /ms2deepscore/MS2DeepScore.py", line...

The dependencies for MS2Query 1.3 have changed, therefore I have updated the recipe here.

Fix repair parent mass is mol wt

2

Repair parent mass is mol wt should not repair the precursor mz as discussed in #616

We had an option to repair the adduct and a mistakenly added mol_wt at the same time. But this does not make any sense, so I removed the option. It...

We had two functions that had very similar functionality. require_precursor_mz and require_precursor_mz_below_mz. I have merged the two functions. In addition some assert statements were replaced with warnings, to not break...