v2.0.0-alpha.2

Full Changelog

Closed issues:

• improvement on docs #232
• writing tutorials and docs for preparing data #204

Merged pull requests:

• update docs #260 (CunliangGeng)
• improving type hints and usage of abc #259 (CunliangGeng)
• add pickling #258 (CunliangGeng)
• fix mypy and ruff errors #257 (CunliangGeng)
• refactor NPLinker class #256 (CunliangGeng)
• rename molfam to mf to uniform the abbreviation for MolecularFamily #255 (CunliangGeng)
• refactor MetcalfScoring methods #254 (CunliangGeng)
• use uniformed attribute name id #253 (CunliangGeng)
• Add LinkGraph to replace ObjectLink and LinkCollection #252 (CunliangGeng)
• merge DataLinks get_common_strains to ObjectLink #250 (CunliangGeng)
• merge DataLinks to MetcalfScoring class #249 (CunliangGeng)
• merge LinkFinder to MetcalfScoring class #248 (CunliangGeng)
• add abstract base class for scoring methods #247 (CunliangGeng)
• Specify config file explicitly for initializing NPLinker #246 (CunliangGeng)
• fix empty caplog #245 (CunliangGeng)
• update docs and readme #244 (CunliangGeng)
• refactor logging control #243 (CunliangGeng)
• add default output path #241 (CunliangGeng)
• rename globals.py to defaults.py #240 (CunliangGeng)
• Fix locations of attributes docstrings #239 (CunliangGeng)
• check format and typing only on changed files #238 (CunliangGeng)
• remove static typings from Returns in docstrings #236 (CunliangGeng)
• set ruff to not check docstrings of test files #235 (CunliangGeng)
• Support Bigscape v2 data #234 (adraismawur)