Embrace std::optional

source/auto_generated_file_list.cmake

@@ -1878,6 +1878,7 @@ set(
 set(
 	TESTSOURCES_CT_COMMON_CATH_COMMON_STRING
 		ct_common/cath/common/string/booled_to_string_test.cpp
+		ct_common/cath/common/string/cath_to_string_test.cpp
 		ct_common/cath/common/string/string_parse_tools_test.cpp
 		ct_common/cath/common/string/sub_string_parser_test.cpp
 )
@@ -1924,7 +1925,6 @@ set(
 		${TESTSOURCES_CT_COMMON_CATH_COMMON_STRING}
 		ct_common/cath/common/temp_check_offset_1_test.cpp
 		${TESTSOURCES_CT_COMMON_CATH_COMMON_TUPLE}
-		ct_common/cath/common/tuple_insertion_operator_test.cpp
 		ct_common/cath/common/type_to_string_test.cpp
 		${TESTSOURCES_CT_COMMON_CATH_COMMON_TYPE_TRAITS}
 )

source/ct_biocore/cath/biocore/biocore_type_aliases.hpp

@@ -22,11 +22,10 @@
 #define _CATH_TOOLS_SOURCE_CT_BIOCORE_CATH_BIOCORE_BIOCORE_TYPE_ALIASES_HPP
 
 #include <map>
+#include <optional>
 #include <set>
 #include <vector>
 
-#include <boost/optional/optional_fwd.hpp>
-
 // clang-format off
 namespace cath { class chain_label; }
 namespace cath { class residue_id; }
@@ -42,10 +41,10 @@ namespace cath {
 	using chain_label_set                 = ::std::set<chain_label>;
 
 	/// \brief TODOCUMENT
-	using chain_label_opt                 = ::boost::optional<chain_label>;
+	using chain_label_opt                 = ::std::optional<chain_label>;
 
 	/// \brief TODOCUMENT
-	using residue_name_opt                = ::boost::optional<residue_name>;
+	using residue_name_opt                = ::std::optional<residue_name>;
 
 	/// \brief TODOCUMENT
 	using residue_name_set                = ::std::set<residue_name>;

source/ct_biocore/cath/biocore/residue_id.cpp

@@ -20,21 +20,22 @@
 
 #include "residue_id.hpp"
 
+#include <iostream>
+#include <optional>
+#include <string>
+
 #include <boost/algorithm/cxx11/any_of.hpp>
 
 #include "cath/common/cpp14/cbegin_cend.hpp"
 #include "cath/common/exception/invalid_argument_exception.hpp"
-
-#include <iostream>
-#include <string>
+#include "cath/common/optional/make_optional_if.hpp"
 
 using namespace ::cath;
 using namespace ::cath::common;
 
 using ::boost::algorithm::any_of;
-using ::boost::make_optional;
-using ::boost::none;
 using ::std::istream;
+using ::std::nullopt;
 using ::std::ostream;
 using ::std::string;
 
@@ -114,18 +115,18 @@ chain_label_residue_id_vec_map cath::get_residue_id_by_chain_label(const residue
 }
 
 /// \brief Return a chain label that is used consistently in all of the specified residue_ids
-///        or none otherwise
+///        or nullopt otherwise
 ///
-/// Returns none if `prm_residue_ids.empty()`
+/// Returns nullopt if `prm_residue_ids.empty()`
 ///
 /// \relates residue_id
 chain_label_opt cath::consistent_chain_label(const residue_id_vec &prm_residue_ids ///< The vector of residue_ids to query
                                              ) {
 	if ( prm_residue_ids.empty() ) {
-		return none;
+		return nullopt;
 	}
 	const auto &front_chain_label = prm_residue_ids.front().get_chain_label();
-	return make_optional(
+	return make_optional_if(
 		all_of(
 			next( common::cbegin( prm_residue_ids ) ),
 			common::cend( prm_residue_ids ),

source/ct_biocore/cath/biocore/residue_name.cpp

@@ -20,6 +20,8 @@
 
 #include "residue_name.hpp"
 
+#include <optional>
+
 #include <boost/algorithm/string/classification.hpp>
 #include <boost/lexical_cast.hpp>
 
@@ -31,8 +33,8 @@ using namespace ::cath::common;
 using ::boost::algorithm::is_alnum;
 using ::boost::algorithm::is_digit;
 using ::boost::lexical_cast;
-using ::boost::optional;
 using ::std::istream;
+using ::std::optional;
 using ::std::ostream;
 using ::std::string;
 

source/ct_biocore/cath/biocore/residue_name.hpp

@@ -21,8 +21,9 @@
 #ifndef _CATH_TOOLS_SOURCE_CT_BIOCORE_CATH_BIOCORE_RESIDUE_NAME_HPP
 #define _CATH_TOOLS_SOURCE_CT_BIOCORE_CATH_BIOCORE_RESIDUE_NAME_HPP
 
+#include <optional>
+
 #include <boost/operators.hpp>
-#include <boost/optional.hpp>
 
 namespace cath {
 
@@ -35,7 +36,7 @@ namespace cath {
 		int res_num = 0;
 
 		/// \brief The (optional insert code)
-		boost::optional<char> insert;
+		::std::optional<char> insert;
 
 		/// \brief Whether this is a null residue
 		bool is_null_residue_name = true;
@@ -51,7 +52,7 @@ namespace cath {
 
 		const bool & is_null() const;
 		const int & residue_number() const;
-		const boost::optional<char> & opt_insert() const;
+		const ::std::optional<char> & opt_insert() const;
 	};
 
 
@@ -72,8 +73,8 @@ namespace cath {
 
 	int residue_number_or_value_if_null(const residue_name &,
 	                                    const int &);
-	boost::optional<char> opt_insert_or_value_if_null(const residue_name &,
-	                                                  const boost::optional<char> &);
+	::std::optional<char> opt_insert_or_value_if_null(const residue_name &,
+	                                                  const ::std::optional<char> &);
 	bool has_insert(const residue_name &);
 	bool has_insert_or_value_if_null(const residue_name &,
 	                                 const bool &);

source/ct_cath_assign_domains/cath/cath_assign_domains/options/cath_assign_domains_options.cpp

@@ -54,8 +54,8 @@ using namespace ::cath::file;
 using namespace ::cath::opts;
 using namespace ::cath::sup;
 
-using ::boost::none;
 using ::std::filesystem::path;
+using ::std::nullopt;
 using ::std::string;
 
 /// \brief The name of the program that uses this executable_options
@@ -89,7 +89,7 @@ str_opt cath_assign_domains_options::do_get_error_or_help_string() const {
 		return "Please specify a superfamily of domain file"s;
 	}
 
-	return none;
+	return nullopt;
 }
 
 /// \brief Get a string to prepend to the standard help

source/ct_cath_assign_domains/cath/cath_assign_domains/options/cath_assign_domains_options_block.cpp

@@ -24,7 +24,6 @@
 
 #include <boost/algorithm/cxx11/all_of.hpp>
 #include <boost/algorithm/string/join.hpp>
-#include <boost/optional.hpp>
 
 #include "cath/acquirer/pdbs_acquirer/file_list_pdbs_acquirer.hpp"
 #include "cath/acquirer/pdbs_acquirer/istream_pdbs_acquirer.hpp"
@@ -39,11 +38,11 @@ using namespace ::std;
 
 using ::boost::algorithm::all_of;
 using ::boost::algorithm::join;
-using ::boost::none;
 using ::boost::program_options::options_description;
 using ::boost::program_options::value;
 using ::boost::program_options::variables_map;
 using ::std::filesystem::path;
+using ::std::nullopt;
 
 /// \brief The long option specifying the SVM-light RBF model file
 const string cath_assign_domains_options_block::PO_SVMLIGHT_RBF_FILE( "svmlight-rbf-file" );
@@ -104,7 +103,7 @@ str_opt cath_assign_domains_options_block::do_invalid_string(const variables_map
 	if ( ! all_of( forbidden_nodes, is_valid_cath_node_id{} ) ) {
 		return "Forbidden nodes list " + join( forbidden_nodes, ", ") + " is not a list of valid CATH nodes";
 	}
-	return none;
+	return nullopt;
 }
 
 /// \brief Return all options names for this block

source/ct_cath_cluster/cath/cath_cluster/cath_clusterer.cpp

@@ -44,9 +44,9 @@ using namespace ::cath::clust;
 using namespace ::cath::common;
 using namespace ::cath::opts;
 
-using ::boost::make_optional;
 using ::std::ifstream;
 using ::std::istream;
+using ::std::make_optional;
 using ::std::ostream;
 
 /// \brief Perform clustering according to the specified arguments strings with the specified i/o streams

source/ct_cath_cluster/cath/cath_cluster/options/cath_cluster_options.cpp

@@ -23,8 +23,8 @@
 using namespace ::cath;
 using namespace ::cath::clust;
 
-using ::boost::none;
 using ::boost::program_options::positional_options_description;
+using ::std::nullopt;
 using ::std::string;
 
 /// The name of the program that uses this executable_options
@@ -62,7 +62,7 @@ str_opt cath_cluster_options::do_get_error_or_help_string() const {
 			+ " output when generating more than one level of clustering";
 	}
 
-	return none;
+	return nullopt;
 }
 
 /// \brief Get a string to prepend to the standard help

source/ct_cath_cluster/cath/cath_cluster/options/options_block/cath_cluster_clustering_options_block.cpp

@@ -28,10 +28,10 @@ using namespace ::cath::clust;
 using namespace ::cath::common;
 using namespace ::cath::opts;
 
-using ::boost::none;
 using ::boost::program_options::options_description;
 using ::boost::program_options::value;
 using ::boost::program_options::variables_map;
+using ::std::nullopt;
 using ::std::string;
 using ::std::unique_ptr;
 
@@ -70,10 +70,10 @@ void cath_cluster_clustering_options_block::do_add_visible_options_to_descriptio
 }
 
 /// \brief Generate a description of any problem that makes the specified cath_cluster_clustering_options_block invalid
-///        or none otherwise
+///        or nullopt otherwise
 str_opt cath_cluster_clustering_options_block::do_invalid_string(const variables_map &/*prm_variables_map*/ ///< The variables map, which options_blocks can use to determine which options were specified, defaulted etc
                                                                  ) const {
-	return none;
+	return nullopt;
 }
 
 /// \brief Return all options names for this block

source/ct_cath_cluster/cath/cath_cluster/options/options_block/cath_cluster_output_options_block.cpp

@@ -29,11 +29,11 @@ using namespace ::cath::clust;
 using namespace ::cath::common;
 using namespace ::cath::opts;
 
-using ::boost::none;
 using ::boost::program_options::options_description;
 using ::boost::program_options::value;
 using ::boost::program_options::variables_map;
 using ::std::filesystem::path;
+using ::std::nullopt;
 using ::std::string;
 using ::std::unique_ptr;
 
@@ -131,10 +131,10 @@ void cath_cluster_output_options_block::do_add_hidden_options_to_description(opt
 }
 
 /// \brief Generate a description of any problem that makes the specified cath_cluster_output_options_block invalid
-///        or none otherwise
+///        or nullopt otherwise
 str_opt cath_cluster_output_options_block::do_invalid_string(const variables_map &/*prm_variables_map*/ ///< The variables map, which options_blocks can use to determine which options were specified, defaulted etc
                                                              ) const {
-	return none;
+	return nullopt;
 }
 
 /// \brief Return all options names for this block

source/ct_cath_cluster/cath/cath_cluster/options/spec/cath_cluster_clustering_spec.cpp

@@ -29,6 +29,7 @@
 
 #include "cath/common/boost_addenda/range/max_proj_element.hpp"
 #include "cath/common/exception/invalid_argument_exception.hpp"
+#include "cath/common/optional/make_optional_if.hpp"
 
 #include <functional>
 
@@ -42,11 +43,10 @@ using ::boost::algorithm::is_sorted;
 using ::boost::algorithm::join;
 using ::boost::algorithm::to_lower_copy;
 using ::boost::lexical_cast;
-using ::boost::make_optional;
-using ::boost::none;
 using ::boost::range::sort;
 using ::std::greater;
 using ::std::less;
+using ::std::nullopt;
 using ::std::string;
 
 /// \brief Getter for the levels at which the clustering should be performed
@@ -62,7 +62,7 @@ cath_cluster_clustering_spec & cath_cluster_clustering_spec::set_levels(const st
 }
 
 /// \brief Generate a description of any problem that makes the specified cath_cluster_clustering_spec invalid
-///        or none otherwise
+///        or nullopt otherwise
 ///
 /// \relates cath_cluster_clustering_spec
 str_opt cath::clust::get_invalid_description(const cath_cluster_clustering_spec &prm_clustering_spec ///< The cath_cluster_clustering_spec to query
@@ -71,18 +71,18 @@ str_opt cath::clust::get_invalid_description(const cath_cluster_clustering_spec
 		return "Most specify at least one clustering level"s;
 	}
 
-	return none;
+	return nullopt;
 }
 
 /// \brief Get a warning string if the specified clustering levels aren't sorted suitable for the specified link_dirn
-///        or none otherwise
+///        or nullopt otherwise
 str_opt cath::clust::get_dissim_sort_warning(const strength_vec &prm_levels,   ///< The clustering levels to check
                                              const link_dirn    &prm_link_dirn ///< Whether the links in the input file represent strengths or dissimilarities
                                              ) {
 	const bool is_correct = ( prm_link_dirn == link_dirn::STRENGTH )
 		? is_sorted( prm_levels, less   <>{} )
 		: is_sorted( prm_levels, greater<>{} );
-	return make_optional(
+	return make_optional_if(
 		! is_correct,
 		"The levels ("
 			+ join(
@@ -135,7 +135,7 @@ strength cath::clust::get_max_dissim(const strength_vec &prm_levels,   ///< The
 }
 
 /// \brief Get a warning string if the specified cath_cluster_clustering_spec's clustering levels aren't
-///        sorted suitable for the specified link_dirn or none otherwise
+///        sorted suitable for the specified link_dirn or nullopt otherwise
 ///
 /// \relates cath_cluster_clustering_spec
 str_opt cath::clust::get_dissim_sort_warning(const cath_cluster_clustering_spec &prm_spec,     ///< The cath_cluster_clustering_spec to check

source/ct_cath_cluster/cath/cath_cluster/options/spec/cath_cluster_clustering_spec.hpp

@@ -21,8 +21,6 @@
 #ifndef _CATH_TOOLS_SOURCE_CT_CATH_CLUSTER_CATH_CATH_CLUSTER_OPTIONS_SPEC_CATH_CLUSTER_CLUSTERING_SPEC_HPP
 #define _CATH_TOOLS_SOURCE_CT_CATH_CLUSTER_CATH_CATH_CLUSTER_OPTIONS_SPEC_CATH_CLUSTER_CLUSTERING_SPEC_HPP
 
-#include <boost/optional.hpp>
-
 #include "cath/clustagglom/clustagglom_type_aliases.hpp"
 #include "cath/clustagglom/link_dirn.hpp"
 #include "cath/common/path_type_aliases.hpp"

source/ct_cath_cluster/cath/cath_cluster/options/spec/cath_cluster_clustering_spec_test.cpp

@@ -18,21 +18,21 @@
 /// You should have received a copy of the GNU General Public License
 /// along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-#include <boost/optional/optional_io.hpp>
+#include <string>
+
 #include <boost/test/unit_test.hpp>
 
 #include "cath/cath_cluster/options/spec/cath_cluster_clustering_spec.hpp"
-
-#include <string>
+#include "cath/test/boost_test_print_type.hpp"
 
 namespace cath { namespace test { } }
 
 using namespace ::cath::clust;
 using namespace ::cath::test;
 using namespace ::std::literals::string_literals;
 
-using ::boost::none;
 using ::boost::test_tools::per_element;
+using ::std::nullopt;
 
 namespace cath {
 	namespace test {
@@ -69,12 +69,12 @@ BOOST_FIXTURE_TEST_SUITE(cath_cluster_clustering_spec_test_suite, cath_cluster_c
 
 BOOST_AUTO_TEST_CASE(levels_processing_is_correct) {
 	BOOST_TEST( get_dissim_sort_warning  ( jumbled_strength_levels, link_dirn::STRENGTH      ) == "The levels (35, 95, 60, 100) are not sorted to be increasing as would be expected with a strength link direction"s );
-	BOOST_TEST( get_dissim_sort_warning  ( valid_strength_levels,   link_dirn::STRENGTH      ) == none                                           );
+	BOOST_TEST( get_dissim_sort_warning  ( valid_strength_levels,   link_dirn::STRENGTH      ) == nullopt                                        );
 	BOOST_TEST( make_dissim_and_sort_copy( valid_strength_levels,   link_dirn::STRENGTH      ) == expected_strength_levels_result, per_element{} );
 	BOOST_TEST( get_max_dissim           ( valid_strength_levels,   link_dirn::STRENGTH      ) == -35                                            );
 
 	BOOST_TEST( get_dissim_sort_warning  ( jumbled_distance_levels, link_dirn::DISSIMILARITY ) == "The levels (4, 2, 3, 1) are not sorted to be decreasing as would be expected with a distance link direction"s );
-	BOOST_TEST( get_dissim_sort_warning  ( valid_distance_levels,   link_dirn::DISSIMILARITY ) == none                                           );
+	BOOST_TEST( get_dissim_sort_warning  ( valid_distance_levels,   link_dirn::DISSIMILARITY ) == nullopt                                        );
 	BOOST_TEST( make_dissim_and_sort_copy( valid_distance_levels,   link_dirn::DISSIMILARITY ) == expected_distance_levels_result, per_element{} );
 	BOOST_TEST( get_max_dissim           ( valid_distance_levels,   link_dirn::DISSIMILARITY ) == 4                                              );
 }