v0.5.0

What's Changed

• Route search functions by @y1zhou in #34
  • Get relevant information from the Neo4j database
  • Route search starting from a given Compound node
  • Map gene expression (or differential expression) data to the graph, and aggregate to reaction-level metrics
  • Support end metabolite structure similarity calculation
  • A simple streamlit app for easier queries

Full Changelog: v0.4.1...v0.5.0

v0.4.1

To test this version, run:

pip install -U -i https://test.pypi.org/simple/ metabolike==0.4.1

This is a maintenance release that focus on testing. Turns out that's something you should have 😄. The core parsing code is now unit-tested.

What's Changed

• Test all parser code by @y1zhou in #33
• fix: remove quoted compound IDs in pathway links.
• refactor: put all database methods into *_to_graph() methods.

Full Changelog: v0.4.0...v0.4.1

v0.4.0

Release v0.4.0 outperforms previous releases by a lot. With tests on my local server, parsing HumanCyc takes ~2min (previously ~7min). Parsing the entire MetaCyc, which used to be something I run overnight, now takes ~1h. This is achieved by batch updating nodes in the database.

What's New

• perf: Submit queries with batches of nodes by @y1zhou in #32
• fix: metaId property for composite reaction nodes were names, and not following the SBML specification.
• feat: Progress bars when submitting the queries.
• reafactor: the parser and database classes are mostly separated. This makes testing parser code much easier.

Full Changelog: v0.3.3...v0.4.0

Breaking changes

• displayName changed to name, and mcId changed to metaId.
• All relationships pointing to RDF nodes now have type hasRDF. This makes querying RDF entities more consistent. The bio-qualifier terms (which used to be the relationship types) are now under the bioQualifier property of the relationship.

v0.3.3

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.

v0.3.2

What's Changed

• Normalize the direction of reaction nodes by @y1zhou in #26

BREAKING CHANGE: Removes the property from reaction nodes.

Full Changelog: v0.3.1...v0.3.2

v0.3.1

This is mainly a bug fix version, also testing the auto-release to PyPI from GitHub CI.

What's Changed

• build: now uses flit to build the package.
• fix: metacyc reaction nodes could have multiple EC numbers 1fb0030
• feat: reaction nodes are now linked to compartment nodes 66ee744
• fix: canonical ID in reaction nodes are now back 4684a0b

Full Changelog: v0.3.0...v0.3.1

v0.3.0

This marks the first release of metabolike, a tool for exploring BioCyc and BRENDA data in a graph database. The current version can parse data files from MetaCyc or BioCyc and construct a graph in Neo4j. It also includes a CLI tool that builds the database (metabolike setup) and spinning up an API backend to query the database (metabolike serve). The API is still under active development and is missing a lot of functionality.

What's Changed

• Config file changes in #2
• Parse MetaCyc SBML file into graph database in #4

New Contributors

• @y1zhou made their first contribution in #3

Full Changelog: v0.1.0...v0.3.0