#pragma once

#include "spectra_reml/types.hpp"

#include <cstddef>
#include <filesystem>
#include <vector>

namespace spectra::reml {

struct SpectralGrm {
    std::vector<double> eigenvalues;
    ColMajorMatrix eigenvectors;
    double minimum_eigenvalue = 0.0;
    double maximum_eigenvalue = 0.0;
};

// GCTA stores the lower triangle, row by row, as IEEE-754 float32 values:
// (0,0), (1,0), (1,1), (2,0), ... .  The returned matrix is full symmetric,
// double precision and column-major.
[[nodiscard]] ColMajorMatrix read_gcta_grm_lower_triangle(
    const std::filesystem::path& grm_bin, std::size_t sample_count);

// Reads and diagonalizes a GRM once.  Eigenvalues are deliberately not
// clipped: preserving the supplied GRM is required for numerical equivalence.
// The REML evaluator rejects parameter trials for which sigma_g^2 lambda_i +
// sigma_e^2 is not positive.
[[nodiscard]] SpectralGrm read_and_diagonalize_gcta_grm(
    const std::filesystem::path& grm_bin, std::size_t sample_count);

// Optional structural check for a GCTA .grm.id file.  The Python driver owns
// sample-ID alignment; this guard catches wrong dimensions at the CLI boundary.
void validate_grm_id_count(const std::filesystem::path& grm_id,
                           std::size_t expected_sample_count);

}  // namespace spectra::reml