Remove unused parameter tree checks

dune/copasi/common/parameter_tree_check.hh

-#ifndef DUNE_COPASI_PARAMETER_PARSER_HH
-#define DUNE_COPASI_PARAMETER_PARSER_HH
-
-#include <functional>
-
-#include <dune/common/parametertree.hh>
-
-namespace Dune::Copasi {
-
-bool
-eq(const ParameterTree& config_l, const ParameterTree& config_r)
-{
-  // absolutely not obtimal for big trees!
-  for (auto&& key : config_r.getValueKeys())
-    if (not config_l.hasKey(key))
-      return false;
-
-  for (auto&& key : config_l.getValueKeys())
-    if (not config_r.hasKey(key))
-      return false;
-
-  for (auto&& section : config_r.getSubKeys())
-    if (not eq(config_l.sub(section), config_r.sub(section)))
-      return false;
-
-  for (auto&& section : config_l.getSubKeys())
-    if (not eq(config_l.sub(section), config_r.sub(section)))
-      return false;
-
-  return true;
-}
-
-// merge parameter trees
-// config_l += config_r
-void
-add(ParameterTree& config_l,
-    const ParameterTree& config_r,
-    bool trow_on_override = true)
-{
-  for (auto&& key : config_r.getValueKeys()) {
-    if (config_l.hasKey(key))
-      DUNE_THROW(RangeError,
-                 "config file addition failed due to duplucated key: " << key);
-    config_l[key] = config_r[key];
-  }
-  for (auto&& section : config_r.getSubKeys())
-    add(config_l.sub(section), config_r.sub(section));
-}
-
-// diff parameter trees
-// config_l -= config_r
-void
-diff(ParameterTree& config_l, const ParameterTree& config_r)
-{
-  ParameterTree config_l_copy(config_l);
-  config_l = {};
-
-  for (auto&& key : config_l_copy.getValueKeys())
-    if (not config_r.hasKey(key))
-      config_l[key] = config_l_copy[key];
-
-  for (auto&& section : config_l_copy.getSubKeys()) {
-    diff(config_l_copy.sub(section), config_r.sub(section));
-    if (config_l_copy.sub(section).getValueKeys().size() > 0 or
-        config_l_copy.sub(section).getSubKeys().size() >
-          0) // remove empty sections
-      config_l.sub(section) = config_l_copy.sub(section);
-  }
-}
-
-// get keys in vector
-ParameterTree
-get_keys(const ParameterTree& config, const std::vector<std::string>& keys)
-{
-  ParameterTree new_config;
-  for (auto&& key : keys)
-    new_config[key] = config[key];
-  return new_config;
-}
-
-// get all keys (no section)
-ParameterTree
-get_keys(const ParameterTree& config)
-{
-  return get_keys(config, config.getValueKeys());
-}
-
-// get sections in vector
-ParameterTree
-get_sections(
-  const ParameterTree& config,
-  const std::vector<std::function<ParameterTree(const ParameterTree&)>>&
-    sections)
-{
-  ParameterTree new_config;
-  for (auto&& section : sections)
-    add(new_config, section(config));
-  return new_config;
-}
-
-ParameterTree
-get_grid(const ParameterTree& config)
-{
-  std::vector<std::string> grid_keys{ "file", "initial_level" };
-  auto grid_config = get_keys(config.sub("grid"), grid_keys);
-  // todo : check file is valid
-  // todo : check initial_level is > 0
-
-  ParameterTree new_config;
-  new_config.sub("grid") = grid_config;
-  return new_config;
-}
-
-ParameterTree
-get_initial(const ParameterTree& config)
-{
-  auto initial_config = get_keys(config.sub("initial"));
-  // todo : check that they are math expressions
-  // todo : keys are ordered
-
-  ParameterTree new_config;
-  new_config.sub("initial") = initial_config;
-  return new_config;
-}
-
-// check_var_consistency with respect to initial sections
-ParameterTree
-get_diffusion(const ParameterTree& config, bool check_var_consistency = true)
-{
-  ParameterTree diffusion_config;
-  if (check_var_consistency) {
-    auto initial_config = get_keys(config.sub("initial"));
-    diffusion_config =
-      get_keys(config.sub("diffusion"), initial_config.getValueKeys());
-  } else {
-    diffusion_config = get_keys(config.sub("diffusion"));
-  }
-  // todo : check that they are math expressions
-  // todo : keys are ordered
-
-  ParameterTree new_config;
-  new_config.sub("diffusion") = diffusion_config;
-  return new_config;
-}
-
-// check_var_consistency with respect to initial sections
-ParameterTree
-get_operator(const ParameterTree& config, bool check_var_consistency = true)
-{
-  ParameterTree operator_config;
-  if (check_var_consistency) {
-    auto initial_config = get_keys(config.sub("initial"));
-    operator_config =
-      get_keys(config.sub("operator"), initial_config.getValueKeys());
-  } else {
-    operator_config = get_keys(config.sub("operator"));
-  }
-  // todo : check that they are signed integers
-  // todo : keys are ordered
-
-  ParameterTree new_config;
-  new_config.sub("operator") = operator_config;
-  return new_config;
-}
-
-ParameterTree
-get_jacobian(const ParameterTree& config,
-             std::vector<std::string> base_variables)
-{
-  auto jacobian_config = get_keys(config.sub("jacobian"));
-  std::size_t jac_size = jacobian_config.getValueKeys().size();
-  std::size_t base_size = base_variables.size();
-
-  // it's important that jacobian has the right size and is ordered
-  if (jac_size != base_size * base_size)
-    DUNE_THROW(RangeError, "jacobian section has wrong size");
-
-  std::size_t count(0);
-  for (auto&& var_i : base_variables) {
-    for (auto&& var_j : base_variables) {
-      std::string jac_key = jacobian_config.getValueKeys()[count];
-      auto found_i = jac_key.find(var_i);
-      if (found_i == std::string::npos)
-        DUNE_THROW(RangeError,
-                   "Jacobian key '" << jac_key
-                                    << "' does not contain its base key i '"
-                                    << var_i << "'");
-      auto found_j = jac_key.find(var_j);
-      if (found_j == std::string::npos)
-        DUNE_THROW(RangeError,
-                   "Jacobian key '" << jac_key
-                                    << "' does not contain its base key j '"
-                                    << var_j << "'");
-      count++;
-    }
-  }
-
-  // todo : check that they are math expressions
-  // todo : keys are ordered
-
-  ParameterTree new_config;
-  new_config.sub("jacobian") = jacobian_config;
-  return new_config;
-}
-
-ParameterTree
-get_reaction(const ParameterTree& config, bool check_var_consistency = true)
-{
-  ParameterTree reaction_config;
-  if (check_var_consistency) {
-    auto initial_config = get_keys(config.sub("initial"));
-    reaction_config =
-      get_keys(config.sub("reaction"), initial_config.getValueKeys());
-  } else {
-    reaction_config = get_keys(config.sub("reaction"));
-  }
-
-  auto jacobian_config =
-    get_jacobian(config.sub("reaction"), reaction_config.getValueKeys());
-  add(reaction_config, jacobian_config);
-  // todo : check that they are math expressions
-  // todo : keys are ordered
-
-  ParameterTree new_config;
-  new_config.sub("reaction") = reaction_config;
-  return new_config;
-}
-
-ParameterTree
-get_compartment_i(const ParameterTree& config, const std::string& name)
-{
-  std::vector<std::function<ParameterTree(const ParameterTree&)>> sections;
-  sections.push_back(get_initial);
-  sections.push_back([](auto i) { return get_diffusion(i); });
-  sections.push_back([](auto i) { return get_reaction(i); });
-  sections.push_back([](auto i) { return get_operator(i); });
-  auto compart_config = get_sections(config.sub(name), sections);
-
-  ParameterTree new_config;
-  new_config.sub(name) = compart_config;
-  return new_config;
-}
-
-ParameterTree
-get_compartments(const ParameterTree& config)
-{
-  auto compart_config = get_keys(config.sub("compartments"));
-  // todo : check that they are valid keys
-
-  ParameterTree new_config;
-  new_config.sub("compartments") = compart_config;
-  return new_config;
-}
-
-ParameterTree
-get_model(const ParameterTree& config)
-{
-  auto compartments = get_compartments(config.sub("model"));
-
-  std::vector<std::function<ParameterTree(const ParameterTree&)>> sections;
-  for (auto&& compartment : compartments.sub("compartments").getValueKeys())
-    sections.push_back(
-      [&](auto ini) { return get_compartment_i(ini, compartment); });
-
-  auto compartment_i = get_sections(config.sub("model"), sections);
-
-  add(compartments, compartment_i);
-
-  ParameterTree new_config;
-  new_config.sub("model") = compartments;
-
-  // bug in parameter tree. If keys go first, sub section is not well set!
-  std::vector<std::string> model_keys{ "begin_time", "end_time", "time_step" };
-  add(new_config.sub("model"), get_keys(config.sub("model"), model_keys));
-
-  // todo : check that they are valid keys
-  return new_config;
-}
-
-} // namespace Dune::Copasi
-
-#endif // DUNE_COPASI_PARAMETER_PARSER_HH
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