Code and data: Causal Structure Sets from an Avida-like digital-evolution simulator

Code and result files behind Section 8 and Appendix H of W. van der Wijngaart, "Which Structures Carry Information? The Inverse Problem of Heredity and a Computational Test in Digital Evolution", arXiv:2407.09567, version 8.

The archive contains an Avida-like simulator that logs every executed instruction; the builder that turns a logged run into a Causal Structure Set (CSS) by one-step intervention replay; the role-blind search for replication, variation, translation, lineage and information families; the organism-level analysis with memory-content swaps; the guided checks against the simulator's withheld record; the family-level null; the preregistered held-out test on seeds 101–140, with its frozen preregistration, freeze archive and results; and the figure scripts, including the check of the recipe reconstructions of Section 7 and Appendix G.

All code is Python 3 with the standard library only. The runs are deterministic, so every log and every CSS regenerates from its seed. README.md gives the commands, and MANIFEST.txt the size and SHA-256 of every file.