Remove class SingletonFamily and MF attribute id

[CunliangGeng]

Singleton molecular families can be well represented with the class MolecularFamily, and it's not needed to keep a specific class SingletonFamily for them, so this PR removed it.

As for the family id, the class SingleFamily automatically set it (i.e."singleton-" + uuid), while the class MolecularFamily requires users to provide the family id during initiation. It makes more sense to let users or loaders of molecular family to decide how to set family id. So in the GNPSMolecularFamilyLoader class, the name of singleton MF was updated to "singleton-" + spectrum_id.

The attribute id of MolecularFamily is unused by anywhere, so it's removed too.

[CunliangGeng]

Current dependencies on/for this PR:

• dev
  • PR refactor filtering of user specified strains #178
    • PR Enable GCF loader to filter singleton GCFs #181
      • PR return list for get_bgcs methods of BGC loaders #182
        • PR rename strains.py to strain.py #183
          • PR remove deprecated functions of loading genomics data #184
            • PR update the process of loading genomics data #185
              • PR rename genomics.py to utils.py #186
                • PR remove deprecated functions of loading metabolomics data #187
                  • PR refactor class MolecularFamily #188
                  • PR refactor class GCF #189
                  • PR enable parallel testing using pytest-xdist #190
                  • PR Enable filtering of singleton molecular families #191
                  • PR Remove class SingletonFamily and MF attribute id #192 👈
                  • PR refactor Spectrum class #193
                  • PR remove unused mgf.py and its test file #194
                  • PR Update logics of loading metabolomics data #196
                  • PR Update loading of genomics data #197
                  • PR deprecate the method _load_class_info #198
                  • PR remove loading of optional data #199
                  • PR remove filtering of common strains during loading #200
                  • PR update logics of loading mibig data #201
                  • PR refactor initiation of paths to metabolomics files #202
                  • PR Update logics of loading metabolomics data #195

This stack of pull requests is managed by Graphite.

[CunliangGeng]

Merge activity

• Dec 19, 8:24 AM: @@CunliangGeng started a stack merge that includes this pull request via Graphite.
• Dec 19, 8:27 AM: Graphite rebased this pull request as part of a merge.
• Dec 19, 8:28 AM: @@CunliangGeng merged this pull request with Graphite.