pyflagser

Almost everything else in this corpus starts from a distance, and a distance is symmetric. That is usually harmless and occasionally fatal: in a connectome, a gene regulatory network, or any signed flow, the fact that A drives B and B does not drive A is the biology, and a Vietoris–Rips complex discards it in the first step.

The directed flag complex keeps it. Given a directed graph, a k-simplex is a set of k+1 vertices whose edges are all present and all consistent with a single ordering of them — a directed clique with an unambiguous source and sink. Reciprocal edges and cycles do not produce simplices the way an undirected clique would, so the complex genuinely responds to orientation rather than symmetrizing and hoping. pyflagser computes the homology of that complex, along with cell counts and Euler characteristics, over a filtration built from edge or vertex weights.

The motivation is not hypothetical. This construction came out of neuroscience, where the directed graph is a wiring diagram and the question is whether its higher-order structure differs from what a random graph with the same statistics would give.

Two licenses stacked

pyflagser is a wrapper. The engine underneath is luetge/flagser, written by Daniel Lütgehetmann, and flagser is itself built on Ripser — the repository ships a copy of Bauer’s program modified only to support flagser’s features. So the second of this family’s two compute engines also descends from ripser-cpp, by a different route than giotto-ph took.

The licenses do not descend together. flagser is MIT (with an added clause about modifications released without written agreement); pyflagser, the wrapper, is AGPL-3.0. The stricter license is the giotto-side contribution, not the engine’s.

That is worth stating because it is the mirror image of gudhi‘s situation, and reading either one from its top-level license alone gets it wrong. GUDHI is permissive code that behaves as copyleft because of what it depends on; pyflagser is copyleft code wrapping a permissive engine. Anyone who needs the directed flag complex without the AGPL has a real option — the engine is MIT and usable directly — and anyone who takes the Python API takes the AGPL.

In this corpus

pyflagser-environment stages pyflagser-recipe, verified green on linux-64 and capping the fixture at L1. It shares giotto-ph‘s build problem for the same reason — the C++ engine is a submodule, so the build needs git and the network — plus the force-included <cstdint> and a version import repointed from pkg_resources.extern to the standalone packaging distribution. giotto-tda declares it as a dependency and discusses the AGPL’s network clause. The technique is persistent-homology, applied to a complex the usual Rips route cannot build.