Experimental/exact gradient workspace

examples/NMFS/afsc_walleye_pollock/outputs/.gitignore

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+*.log

examples/NMFS/pifsc_opakapaka/data/opakapaka_io.hpp

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+#pragma once
+
+#include "../quadra/opakapaka_model.hpp"
+
+#include <cmath>
+#include <fstream>
+#include <sstream>
+#include <stdexcept>
+#include <string>
+#include <vector>
+
+namespace opakapaka_example {
+
+std::vector<std::string> split_csv_line_simple(const std::string &line) {
+  std::vector<std::string> fields;
+  std::stringstream ss(line);
+  std::string item;
+  while (std::getline(ss, item, ',')) {
+    fields.push_back(item);
+  }
+  return fields;
+}
+
+bool finite_double_from_string(const std::string &x, double &out) {
+  try {
+    std::size_t pos = 0;
+    out = std::stod(x, &pos);
+    return pos > 0 && std::isfinite(out);
+  } catch (...) {
+    out = std::numeric_limits<double>::quiet_NaN();
+    return false;
+  }
+}
+
+std::vector<Observation> read_opakapaka_history_csv(const std::string &path) {
+  std::ifstream in(path);
+  if (!in) {
+    throw std::runtime_error("Could not open Opakapaka CSV: " + path);
+  }
+
+  std::string line;
+  if (!std::getline(in, line)) {
+    throw std::runtime_error("Opakapaka CSV is empty: " + path);
+  }
+
+  const auto header = split_csv_line_simple(line);
+  int year_col = -1;
+  int phase_col = -1;
+  int catch_col = -1;
+  int index_col = -1;
+
+  for (int i = 0; i < static_cast<int>(header.size()); ++i) {
+    if (header[i] == "year")
+      year_col = i;
+    if (header[i] == "phase")
+      phase_col = i;
+    if (header[i] == "catch_mt")
+      catch_col = i;
+    if (header[i] == "index")
+      index_col = i;
+  }
+
+  if (year_col < 0 || phase_col < 0 || catch_col < 0 || index_col < 0) {
+    throw std::runtime_error(
+        "Opakapaka CSV must contain year, phase, catch_mt, and index columns");
+  }
+
+  std::vector<opakapaka_example::Observation> out;
+
+  while (std::getline(in, line)) {
+    if (line.empty())
+      continue;
+    const auto fields = split_csv_line_simple(line);
+    const int max_col =
+        std::max(std::max(year_col, phase_col), std::max(catch_col, index_col));
+    if (static_cast<int>(fields.size()) <= max_col)
+      continue;
+
+    if (fields[phase_col] != "history")
+      continue;
+
+    double year_d = 0.0;
+    double catch_mt = 0.0;
+    double index = 0.0;
+
+    if (!finite_double_from_string(fields[year_col], year_d))
+      continue;
+    if (!finite_double_from_string(fields[catch_col], catch_mt))
+      continue;
+    if (!finite_double_from_string(fields[index_col], index))
+      continue;
+
+    opakapaka_example::Observation obs;
+    obs.year = static_cast<int>(year_d);
+    obs.catch_mt = catch_mt;
+    obs.index = index;
+    out.push_back(obs);
+  }
+
+  if (out.empty()) {
+    throw std::runtime_error(
+        "No usable historical rows found in Opakapaka CSV");
+  }
+
+  return out;
+}
+
+} // namespace opakapaka_example
+
+// Compatibility aliases for the current Opakapaka driver.
+using opakapaka_example::finite_double_from_string;
+using opakapaka_example::read_opakapaka_history_csv;
+using opakapaka_example::split_csv_line_simple;