Update to latest SSSOM(v0.4.x)

[hrshdhgd]

• Update sssom, semsimian and kgcl-schema dependency
• add linkml dependency in tox for pytest
• Addresses 0.4 Release mapping-commons/sssom-py#441 (comment)
  • **Merge this ONLY when sssom==0.4.0 is released.

Refactors done:

• from sssom.context import get_default_metadata => from sssom.constants import get_default_metadata
• from sssom.typehints import Metadata => from sssom.constants import MetadataType
  • Older Metadata had the metadata attribute which is now collapsed
    • e.g. meta: Metadata

              mapping_set_id = meta.metadata[MAPPING_SET_ID]
              license = meta.metadata[LICENSE]
      

      is now meta: MetadataType

              mapping_set_id = meta[MAPPING_SET_ID]
              license = meta[LICENSE]
      

• doc = MappingSetDocument(prefix_map=metadata[PREFIX_MAP_KEY], mapping_set=mset)

  •   converter = curies.chain([
         Converter.from_prefix_map(metadata.pop(CURIE_MAP_KEY, {})),
         ensure_converter(prefix_map, use_defaults=False)
     ])
      doc = MappingSetDocument(converter=converter, mapping_set=mset)
    

• metadata = get_metadata_and_prefix_map(MATCHER_META_YML) => converter, metadata = get_metadata_and_prefix_map(MATCHER_META_YML)

[matentzn]

Thanks! Looks sane, so far!

[codecov-commenter]

Codecov Report

Attention: 2 lines in your changes are missing coverage. Please review.

Comparison is base (c069273) 76.48% compared to head (4329934) 76.49%.

Files	Patch %	Lines
src/oaklib/utilities/mapping/sssom_utils.py	50.00%	2 Missing ⚠️

❗ Your organization needs to install the Codecov GitHub app to enable full functionality.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #681      +/-   ##
==========================================
+ Coverage   76.48%   76.49%   +0.01%     
==========================================
  Files         252      252              
  Lines       29385    29387       +2     
==========================================
+ Hits        22474    22480       +6     
+ Misses       6911     6907       -4     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[cthoyt]

@hrshdhgd did you miss all the effort I put into doing this? #666

[hrshdhgd]

Apparently I did, sorry about that. Should have been mentioned in mapping-commons/sssom-py#441

[hrshdhgd]

Duplication of effort with #666 . Closing for that reason.

[cthoyt]

Apparently I did, sorry about that. Should have been mentioned in mapping-commons/sssom-py#441

It was - see mapping-commons/sssom-py#441 (comment)