biodivine

The Python interface of the Biodivine libraries. Every library is a submodule of the biodivine package, and every submodule is an idiomatic Python layer over a Rust implementation:

pip install biodivine
# or
conda install -c conda-forge -c daemontus biodivine

Example

The following builds a small namespaced document, checks that it is valid, and serializes it:

import biodivine.xml_dom as xml

document = xml.Document()
ex = xml.Namespace("http://example.com", "ex")

root = document.create_element(("root", ex))
root.declare_namespace(ex)
document.set_root(root)

child = document.create_element(("child", ex))
child.append_child(document.create_text("Hello, World!"))
root.append_child(child)

assert document.is_valid()
assert document.write() == (
    '<ex:root xmlns:ex="http://example.com"><ex:child>Hello, World!</ex:child></ex:root>'
)

How it fits together

The Rust code of all libraries is compiled into one native extension, distributed as the biodivine-sys package and installed automatically as a dependency. Because every library shares that extension, the objects of one library (say, an XML document) can be handed to another library directly. You never need to import biodivine_sys yourself: the classes of biodivine accept Python values in several convenient forms, follow Python protocols (len, iteration, indexing, equality, hashing) and never return a native object.

Documentation

• The API reference documents every submodule, class and function, with examples. It describes the latest release; the reference of an earlier version X.Y.Z is at https://biodivine.fi.muni.cz/docs/biodivine-py/vX.Y.Z/.
• The Biodivine book teaches every library with examples in both Python and Rust.
• The source code, the issue tracker and the development workflow are in the biodivine-py repository.