phutil 0.0.3

Bug fixes

• Adjusted vendored Hera sources to explicitly include missing headers that are not pulled in transitively in latest clang versions; adapted R-CMD-check action to exercise this along the way (#62).
  • Aligned vendored sources with upstream repository at https://github.com/animetov/hera; actually currently aligned with https://github.com/astamm/hera@r-compatibility with PR awaiting approval.
  • Use a configure script to mirror the vendored Hera headers as forwarding headers in inst/include and generate Makevars from Makevars.in (via abs_srcdir) so the upstream <hera/...> includes resolve without modifying the vendored sources; a cleanup script then removes these generated artifacts, keeping them out of version control (see src/README.md).
  • Define hera’s FOR_R_TDA flag (in src/Makevars.in) to suppress the upstream std::cerr/std::cout diagnostics, satisfying R’s requirement that compiled code not write to stdout/stderr.
• as_persistence.diagram() would fail when the input was obtained through do.call(); it now continues without error, but with empty information about the engine (#58).

phutil 0.0.2

New features

• New as_diagram() generic and methods for persistence and PHom classes, enabling round-trip conversion back to the diagram class used by {TDA} (#53).

Bug fixes

• as_persistence.diagram() now correctly handles diagram objects whose Birth and Death columns appear in a different order, which can occur with some {TDA} filtrations (#52).
• Graphics options are now properly restored to the user’s original settings after being temporarily changed (#41).

Minor improvements

• {TDA} functions are now called with explicit TDA:: namespace prefixes and print.progress = FALSE for cleaner output (#41).
• Tests for {ripserr} integration are now run conditionally on {ripserr} being installed, removing it as a hard suggested dependency (#41).
• The vignette no longer requires {ggplot2} or {scales}, reducing optional dependencies for building the documentation (#46, closes #45).
• Vendored {cpp11} headers have been removed; the package now relies on the {cpp11} headers provided by the installed package, allowing it to benefit from updated versions. The NO_LEGACY_NONAPI flag is set to comply with the R API going forward (#55).
• Package description updated with references to the distance methods implemented (#41).

phutil 0.0.1

This is a new submission to CRAN.

Goals

The {phutil} package is intended to be a low-level package for hosting persistence data. It is part of the TDAverse suite of packages, which are designed to provide a collection of packages for enabling machine learning and data science tasks using persistent homology.

Current features

The package currently exposes:

• a new data structure (the persistence class) for hosting persistence data;
• a set of utility functions for coercing persistence data to and from other data structures (e.g., data.frame, tibble, list, matrix,PHom and diagram classes);
• a set of utility functions for computing Bottleneck and Wasserstein distances between two persistence diagrams (bottleneck_distance() and wasserstein_distance()) and from a sample of persistence diagrams in a pairwise manner (bottleneck_pairwise_distance() and wasserstein_pairwise_distance()).

Dependencies

Messages, warnings and errors are relayed to the user using the {rlang} package and the {cli} package which are both licensed under the MIT license and with no dependency trail.

Computation of distances is performed using the BSD-licensed Hera C++ library. The code interfacing R and C++ is generated by the header-only {cpp11} package which is MIT-licensed. Computation of pairwise distances is parallelized over the number of pairs using OpenMP.