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SnapPy is a package for studying the topology and geometry of 3-manifolds, with a focus on hyperbolic structures. It is based on the SnapPea kernel written by Jeff Weeks.
Spherogram is a Python module for dealing with the kind of planar diagrams that arise in 3-dimensional topology, such as link and Heegaard diagrams. It a component of the larger SnapPy project.
CyPari is a Python3 extension module for Windows, macOS and linux. The user interface, and most of the underlying code, is the same for CyPari as for Sage's cypari2 module, but CyPari is completely self-contained.