PyBioPAX v0.1.5

What's Changed

• Enable passing encoding by @cthoyt in #51
• Update pc2 URL to use https by @tonywu1999 in #53

New Contributors

• @tonywu1999 made their first contribution in #53

Full Changelog: 0.1.4...0.1.5

PyBioPAX v0.1.4

What's Changed

• Add attributes to NucleicAcid reference BioPAX classes by @bgyori in #48
• Added pathway_order and next_step to a list by @tmushayahama in #49

Full Changelog: 0.1.3...0.1.4

PyBioPAX v0.1.3

What's Changed

• Add py.typed by @bgyori in #45
• Add global tqdm config by @bgyori in #46

Full Changelog: 0.1.2...0.1.3

PyBioPAX v0.1.2

What's Changed

• Add functions to get database references from a model by @bgyori in #35
• Use empty list by default if list-type is None by @bgyori in #37
• Enable passing a list of BioPaxObject to BioPaxModel by @cthoyt in #38
• Improve BioPAX class attribute documentation by @bgyori in #39
• Notebook demonstrating model construction by @bgyori in #41

Full Changelog: 0.1.1...0.1.2

PyBioPAX v0.1.1

• Add a paper describing PyBioPAX in the paper folder
• Improve some tests to be version independent

PyBioPAX v0.1.0

• Improve the BioPAX object model by implementing Xreffable, Named and Observable as mixin classes.
• Implement BioPAX object reverse links (e.g., participant_of) as property attributes populated during deserialization.
• Implement a new paths module to find objects matching a given path specification as a string from a given starting object.
• Implement new API functions to query models from the Reactome, NetPath, EcoCyc, MetaCyc, BioCycm and HumanCyc web services.
• Implement API function to process owl.gz files.
• Extend testing to Python 3.6-3.9 and migrate to pytest for testing
• Add contribution guidelines
• Add a tutorial Jupyter notebook and two case study notebooks

PyBioPAX v0.0.6

• Fix participants attribute of Interactions to be list-like

PyBioPAX v0.0.5

• Allow using custom encoding when processing OWL
• Migrate testing from Travis to GitHub Actions

PyBioPAX v0.0.4

• Export the correct custom XML-base name space associated with a model when serializing into OWL

PyBioPAX v0.0.3

• Generalize the OWL parser to serialization formats that are different from the PathwayCommons conventions (e.g., the PhosphoSitePlus BioPAX export).