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v0.3.3
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@y1zhou y1zhou released this 31 Mar 02:49
· 123 commits to main since this release
v0.3.3
7066e4d

What's New

  • feat: Link reaction nodes connecting related pathways by @y1zhou in #28
  • refactor: BRENDA-related code by @y1zhou in #29
  • feat: FBA analysis and major refactor by @y1zhou in #30

Full Changelog: v0.3.2...v0.3.3

Breaking changes

  • Support for Python 3.6 is dropped as it's EOL in December 2021. Now Python>=3.8 is required because of the use of walrus operators.
  • SBML parsing and database-related methods are extracted to their own classes.
  • All hasLeft relationships point to reactants, and all hasRight relationships point to products of reactions. There might be a mismatch between reaction Gibbs 0 and direction for reversible Reaction nodes.
  • Name of the database is now part of the config file. It's no longer needed to be passed to the CLI function setup().

Dependency changes

  • pyarrow is no longer required as parsed BRENDA files are now serialized to a JSON file instead of a parquet file.
  • orjson is an added dependency for faster (de)serialization.
  • pandas>=1.0.0 is required because of the use of pd.NA.
  • neo4j>=4.3.4 is required as recommended in this article.

Contributors

y1zhou
Assets 2
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