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CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Overview

hsnf is a Python library for computing Hermite normal form (HNF) and Smith normal form (SNF) of integer matrices, with transformation matrices. It also provides utilities for integer lattice operations and solving integer/modular linear systems.

Development Commands

# Install in development mode
pip install -e .[dev,docs]

# Run all tests with coverage
python -m pytest -v --cov=hsnf --cov-config=setup.cfg --cov-report=xml tests/

# Run a single test file
python -m pytest tests/test_normal_form.py -v

# Run a single test function
python -m pytest tests/test_normal_form.py::test_smith_normal_form -v

# Linting/formatting (via pre-commit)
pre-commit run --all-files

# Individual tools
black --line-length 99 hsnf/ tests/
flake8 hsnf/ tests/
mypy hsnf/
isort --profile black hsnf/ tests/

Architecture

The library has four modules under hsnf/:

  • Z_module.py -- Core algorithms. ZmoduleHomomorphism class implements SNF and row-style HNF via elementary row/column operations on Z-module homomorphisms. Public API functions (smith_normal_form, row_style_hermite_normal_form, column_style_hermite_normal_form) are thin wrappers that construct a ZmoduleHomomorphism with standard basis and call the corresponding method.
  • utils.py -- Low-level helpers: pivot selection (get_nonzero_min_abs*), extended GCD, Sieve of Eratosthenes for prime factorization, Chinese Remainder Theorem, and the NDArrayInt type alias.
  • integer_system.py -- Solvers built on top of SNF/HNF: solve_integer_linear_system (Ax=b over Z), solve_frobenius_congruent (Ax=b mod R/Z), and solve_modular_integer_linear_system (Ax=b mod q). The modular solver uses prime-power decomposition + CRT.
  • lattice.py -- Lattice operations: equivalence checking, union, intersection, and dual lattice computation. Uses the identity dual(L1 intersect L2) = union(dual(L1), dual(L2)).

Public API is re-exported from hsnf/__init__.py: smith_normal_form, row_style_hermite_normal_form, column_style_hermite_normal_form.

Key Conventions

  • Line length: 99 (black + flake8)
  • Import sorting: isort with black profile
  • Type annotations use NDArrayInt (alias for npt.NDArray[np.int_]) from hsnf/utils.py
  • Version is inferred at build time via setuptools_scm (git tags)
  • Python 3.8+ compatibility: uses from __future__ import annotations and typing_extensions.TypeAlias
  • Default branch is develop; CI runs on push to master/develop and PRs to master