Add reusable SpectraREML batch AI-REML engine

include/spectra_reml/batch_io.hpp

@@ -0,0 +1,62 @@
+#pragma once
+
+#include "spectra_reml/grm.hpp"
+#include "spectra_reml/types.hpp"
+
+#include <cstddef>
+#include <cstdint>
+#include <filesystem>
+#include <string>
+#include <vector>
+
+namespace spectra::reml {
+
+struct BatchInputPaths {
+    std::filesystem::path grm_bin;
+    std::filesystem::path grm_id;
+    std::filesystem::path base_x_f64;
+    std::filesystem::path phenotype_f64;
+    std::filesystem::path extra_covariate_f32;
+    std::filesystem::path tasks_tsv;
+    std::filesystem::path extra_offsets_i64;
+    std::filesystem::path extra_indices_i32;
+    std::filesystem::path output_directory;
+};
+
+struct BatchDimensions {
+    std::size_t sample_count = 0;
+    std::size_t base_covariate_count = 0;
+    std::size_t phenotype_row_count = 0;
+    std::size_t extra_covariate_row_count = 0;
+};
+
+struct BatchOptions {
+    std::size_t block_size = 256;
+    std::size_t outer_threads = 1;
+    bool resume = false;
+    bool overwrite = false;
+    RemlOptions reml;
+};
+
+[[nodiscard]] ColMajorMatrix read_row_major_f64_matrix(
+    const std::filesystem::path& path, std::size_t rows, std::size_t cols);
+
+[[nodiscard]] std::vector<RemlTask> read_tasks(
+    const std::filesystem::path& tasks_tsv,
+    const std::filesystem::path& extra_offsets_i64,
+    const std::filesystem::path& extra_indices_i32,
+    const BatchDimensions& dimensions);
+
+// Runs one complete task set.  The GRM and common variables are transformed
+// once; phenotypes are transformed in blocks and tasks are fitted in parallel.
+// Each completed block contains:
+//   block_NNNNNN.summary.tsv
+//   block_NNNNNN.beta.f64.bin
+//   block_NNNNNN.cov.f64.bin
+//   block_NNNNNN.complete
+// The .complete marker is renamed last and is the sole resume criterion.
+void run_task_batch(const BatchInputPaths& paths,
+                    const BatchDimensions& dimensions,
+                    const BatchOptions& options);
+
+}  // namespace spectra::reml