Specify config file explicitly for initializing NPLinker

[CunliangGeng]

Change how to initialise NPLinker class, from npl = NPLinker() to npl = NPLinker("the_config_file.toml"). The change makes sure that the use of config file is explicit, improving clarity for end users.

[CunliangGeng]

• update docs #260
• improving type hints and usage of abc #259
• add pickling #258
• fix mypy and ruff errors #257
• refactor NPLinker class #256
• rename molfam to mf to uniform the abbreviation for MolecularFamily #255
• refactor MetcalfScoring methods #254
• use uniformed attribute name id  #253
• Add LinkGraph to replace ObjectLink and LinkCollection #252
• merge DataLinks get_common_strains to ObjectLink #250
• merge DataLinks to MetcalfScoring class #249
• merge LinkFinder to MetcalfScoring class #248
• add abstract base class for scoring methods #247
• Specify config file explicitly for initializing NPLinker #246 👈
• fix empty caplog #245
• dev

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[CunliangGeng]

Merge activity

• Jun 6, 3:19 AM EDT: @CunliangGeng started a stack merge that includes this pull request via Graphite.
• Jun 6, 3:19 AM EDT: @CunliangGeng merged this pull request with Graphite.