rename genomics.py to utils.py

[CunliangGeng]

The genomics.py contains several helper functions for handling genomics data. So better rename this file to untils.py which is now located at src/nplinker/genomics/utils.py.

Major changes:

• rename files
• rename utility functions
• add docstrings and typings

[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 14, 5:52 AM: @@CunliangGeng started a stack merge that includes this pull request via Graphite.
• Dec 14, 5:57 AM: Graphite rebased this pull request as part of a merge.
• Dec 14, 5:58 AM: @@CunliangGeng merged this pull request with Graphite.