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The three Python packages

PackageCrateInputTypical use
phlitephlite_pya chain complex you build: integer columns, CSC arrays, or your own cell objects; any filtrationcubical complexes, simplicial complexes, cell complexes, anything PHAT or LoPHAT would take
phlite_ripsphlite_ripsa distance matrixVietoris–Rips persistence, like ripser and giotto-ph
phlite_grpphphlite_grppha weighted digraph (networkx or edge list)grounded persistent path homology, like grpphati

The full API reference (every class, method and argument) is generated from the packages’ docstrings with Sphinx (docs/python). These chapters are the guide.

All three share:

  • an Algorithm class, with the same options, to choose the reduction;
  • method="cohomology" (default) or "homology";
  • representatives=True for a cycle representing each bar;
  • release of the GIL during the computation, so other Python threads keep running.

Installing

The packages are built from source with maturin. From a crate’s directory:

just develop            # builds the release extension into the current virtual environment

or with maturin directly: maturin develop --release -m phlite_py/Cargo.toml.

Barcodes at a glance

import phlite

chain = phlite.ChainComplex.from_pairs([(0, []), (0, []), (1, [0, 1])])
barcode = chain.filtration([0.0, 1.0, 2.0]).persistence()
barcode.pairings      # [(1, 2)]: the component born at cell 1 dies at cell 2
barcode.essential     # [0]
barcode.diagram(0)    # array([[0., inf], [1., 2.]])

from phlite_rips import rips
barcode = rips(distances, max_dim=1, representatives=True)
barcode.pairings[1]                  # (birth, death) values of the finite H1 bars
barcode.pairing_representatives[1]   # a cycle (list of edges) for each

phlite‘s barcode is in terms of cells (with diagram for values); phlite_rips’ and phlite_grpph’s are lists per dimension of values, with representatives as lists of simplices or paths.