Switch from Boost log to spdlog

CMakeLists.txt

@@ -52,9 +52,11 @@ endif()
 
 # For useful information on getting CMake to work with Boost, type the following command: `cmake --help-module FindBoost`
 # or add `SET( Boost_DEBUG "ON" )` to this file to get helpful debug information when running CMake
-find_package( Boost 1.60 REQUIRED filesystem iostreams log program_options serialization timer unit_test_framework )
+find_package( Boost 1.60 REQUIRED filesystem iostreams program_options serialization timer unit_test_framework )
 
 find_package( RapidJSON 1.1.0 REQUIRED )
+find_package( fmt       7.1.3 REQUIRED )
+find_package( spdlog    1.8.5 REQUIRED )
 
 # Compiler options
 SET( CMAKE_CXX_STANDARD   14    )

conanfile.txt

@@ -3,9 +3,12 @@
 # Using Boost 1.72 because:
 # 
 # * the CI is using Ubuntu 20.04, which has CMake 3.16, which only knows Boost ≤1.72 and spews warnings about higher versions
-# * though it wouldn't be hard to modify the CI to use the Kitware Ubuntu CMake repos, there's little point because the code doesn't use any features after 1.60 anyway
+# * though it wouldn't be hard to modify the CI to use the Kitware Ubuntu CMake repos, there's little point because the
+#   code doesn't use any features after 1.60 anyway
 boost/1.72.0@
+fmt/7.1.3@
 rapidjson/1.1.0
+spdlog/1.8.5@
 
 [generators]
 cmake_find_package
@@ -16,34 +19,34 @@ cmake
 boost:without_exception=False
 boost:without_filesystem=False
 boost:without_iostreams=False        # Used by gnuplot-iostream.h - consider dropping
-boost:without_log=False              # Without log, could drop: container, date_time, locale, thread
 boost:without_program_options=False
 boost:without_serialization=False
 boost:without_test=False
 
 # Secondary dependencies (ie required but only by primary dependencies)
 boost:without_atomic=False
 boost:without_chrono=False
-boost:without_container=False
-boost:without_date_time=False
-boost:without_locale=False
 boost:without_math=False
 boost:without_random=False
 boost:without_regex=False
 boost:without_system=False
-boost:without_thread=False
 boost:without_timer=False
 
 # boost:without_json=True   # applies for more recent Boosts
 # boost:without_nowide=True # applies for more recent Boosts
+boost:without_container=True
 boost:without_context=True
 boost:without_contract=True
 boost:without_coroutine=True
+boost:without_date_time=True
 boost:without_fiber=True
 boost:without_graph=True
 boost:without_graph_parallel=True
+boost:without_locale=True
+boost:without_log=True
 boost:without_mpi=True
 boost:without_python=True
 boost:without_stacktrace=True
+boost:without_thread=True
 boost:without_type_erasure=True
-boost:without_wave=True
+boost:without_wave=True

source/CMakeLists.txt

@@ -89,7 +89,7 @@ target_link_libraries( ct_cath_superpose      PUBLIC ct_common ct_uni
 target_link_libraries( ct_chopping            PUBLIC ct_biocore Boost::program_options                     )
 target_link_libraries( ct_clustagglom         PUBLIC ct_common Boost::program_options                      )
 target_link_libraries( ct_cluster             PUBLIC ct_common ct_options ct_seq Boost::program_options    )
-target_link_libraries( ct_common              PUBLIC Boost::log cath_tools_gsl cath_tools_rapidjson        )
+target_link_libraries( ct_common              PUBLIC Boost::filesystem cath_tools_gsl cath_tools_rapidjson spdlog::spdlog )
 target_link_libraries( ct_display_colour      PUBLIC ct_common                                             )
 target_link_libraries( ct_options             PUBLIC ct_chopping ct_external_info                          )
 target_link_libraries( ct_resolve_hits        PUBLIC ct_display_colour ct_options ct_seq                   )

source/ct_cath_cluster/cath/cath_cluster/cath_clusterer.cpp

@@ -20,7 +20,9 @@
 
 #include "cath_clusterer.hpp"
 
-#include <boost/log/trivial.hpp>
+#include <fstream>
+
+#include <spdlog/spdlog.h>
 
 #include "cath/cath_cluster/options/cath_cluster_options.hpp"
 #include "cath/clustagglom/calc_complete_linkage_merge_list.hpp"
@@ -38,14 +40,11 @@
 #include "cath/common/file/path_or_istream.hpp"
 #include "cath/common/logger.hpp"
 
-#include <fstream>
-
 using namespace ::cath::clust;
 using namespace ::cath::common;
 using namespace ::cath::opts;
 
 using ::boost::filesystem::path;
-using ::boost::log::trivial::warning;
 using ::boost::make_optional;
 using ::std::ifstream;
 using ::std::istream;
@@ -88,7 +87,7 @@ void cath::clust::perform_cluster(const cath_cluster_options &prm_opts,    ///<
 	const strength      the_max_dissim = get_max_dissim         ( clust_spec, the_link_dirn );
 
 	if ( level_warning ) {
-		BOOST_LOG_TRIVIAL( warning ) << *level_warning;
+		::spdlog::warn( *level_warning );
 	}
 
 	// Organise the input stream
@@ -112,10 +111,9 @@ void cath::clust::perform_cluster(const cath_cluster_options &prm_opts,    ///<
 		if ( has_names_file ) {
 			return get_sorting_scores( the_name_ider, props );
 		}
-		BOOST_LOG_TRIVIAL( warning )
-			<< "No names file has been specified. You are recommended to specify a names file ("
-			<< cath_cluster_input_options_block::PO_NAMES_INFILE
-			<< ") to ensure singletons don't get missed.";
+		::spdlog::warn( "No names file has been specified. You are recommended to specify a names file ({}) to ensure "
+		                "singletons don't get missed.",
+		                cath_cluster_input_options_block::PO_NAMES_INFILE );
 		return get_sorting_scores( the_name_ider );
 	} ();
 

source/ct_cath_superpose/cath/cath_superpose/cath_superposer.cpp

@@ -21,9 +21,10 @@
 #include "cath_superposer.hpp"
 
 #include <boost/filesystem/path.hpp>
-#include <boost/log/trivial.hpp>
 #include <boost/ptr_container/ptr_vector.hpp>
 
+#include <spdlog/spdlog.h>
+
 #include "cath/acquirer/alignment_acquirer/alignment_acquirer.hpp"
 #include "cath/acquirer/pdbs_acquirer/pdbs_acquirer.hpp"
 #include "cath/acquirer/selection_policy_acquirer/selection_policy_acquirer.hpp"
@@ -83,7 +84,7 @@ void cath_superposer::superpose(const cath_superpose_options &prm_cath_superpose
 	}
 	else {
 		if ( ! aln_outputters.empty() ) {
-			BOOST_LOG_TRIVIAL( warning ) << "Ignoring alignment output options because there is no alignment (and the cake is a lie)";
+			::spdlog::warn( "Ignoring alignment output options because there is no alignment (and the cake is a lie)" );
 		}
 	}
 

source/ct_cath_superpose/cath/cath_superpose/cath_superposer_test.cpp

@@ -20,9 +20,13 @@
 
 #include "cath_superposer.hpp"
 
-#include <boost/log/trivial.hpp>
+#include <fstream>
+#include <sstream>
+
 #include <boost/test/unit_test.hpp>
 
+#include <spdlog/spdlog.h>
+
 #include "cath/cath_superpose/options/cath_superpose_options.hpp"
 #include "cath/chopping/domain/domain.hpp"
 #include "cath/common/argc_argv_faker.hpp"
@@ -34,9 +38,6 @@
 #include "cath/test/predicate/files_equal.hpp"
 #include "cath/test/predicate/istream_and_file_equal.hpp"
 
-#include <fstream>
-#include <sstream>
-
 using namespace ::cath;
 using namespace ::cath::common;
 using namespace ::cath::opts;
@@ -122,11 +123,9 @@ void cath::test::cath_superposer_test_suite_fixture::check_cath_superposer_use_c
 	if ( prm_outputs_to_temp_file ) {
 		const auto output_file = temp_output_filename;
 		if ( ! exists( output_file ) )  {
-			BOOST_LOG_TRIVIAL( error ) << "cath-superpose command did not produce output file. Got stdout is: \""
-			                           << test_stdout.str()
-			                           << "\". Got stderr is: \""
-			                           << test_stderr.str()
-			                           << "\"";
+			::spdlog::error( R"(cath-superpose command did not produce output file. Got stdout is: "{}". Got stderr is: "{}")",
+			                 test_stdout.str(),
+			                 test_stderr.str() );
 		}
 
 		// Blank out the version number in the superposition

source/ct_chopping/cath/chopping/region/regions_limiter.cpp

@@ -22,10 +22,11 @@
 
 #include <boost/algorithm/cxx11/any_of.hpp>
 #include <boost/algorithm/string/join.hpp>
-#include <boost/log/trivial.hpp>
 #include <boost/range/adaptor/filtered.hpp>
 #include <boost/range/adaptor/transformed.hpp>
 
+#include <spdlog/spdlog.h>
+
 #include "cath/biocore/residue_id.hpp"
 #include "cath/chopping/region/region.hpp"
 #include "cath/common/algorithm/transform_build.hpp"
@@ -205,6 +206,6 @@ void cath::chop::warn_if_specified_regions_remain_unseen(const regions_limiter &
                                                          ) {
 	const auto warn_str = warn_str_if_specified_regions_remain_unseen( prm_regions );
 	if ( warn_str ) {
-		BOOST_LOG_TRIVIAL( warning ) << *warn_str;
+		::spdlog::warn( *warn_str );
 	}
 }

source/ct_cluster/cath/cluster/file/cluster_membership_file.cpp

@@ -20,9 +20,16 @@
 
 #include "cluster_membership_file.hpp"
 
-#include <boost/log/trivial.hpp>
+#include <fstream>
+#include <iostream>
+#include <sstream>
+#include <string>
+
 #include <boost/utility/string_ref.hpp>
 
+#include <spdlog/fmt/ostr.h>
+#include <spdlog/spdlog.h>
+
 #include "cath/cluster/cluster_type_aliases.hpp"
 #include "cath/cluster/old_cluster_data.hpp"
 #include "cath/common/boost_addenda/log/log_to_ostream_guard.hpp"
@@ -33,11 +40,6 @@
 #include "cath/common/string/string_parse_tools.hpp"
 #include "cath/seq/seq_seg_run_parser.hpp"
 
-#include <fstream>
-#include <iostream>
-#include <sstream>
-#include <string>
-
 using namespace ::cath;
 using namespace ::cath::clust;
 using namespace ::cath::common;
@@ -68,26 +70,29 @@ static inline void warn_if_neccessary(const clust_entry_problem &prm_problem,
 		switch ( prm_problem ) {
 			case ( clust_entry_problem::REPEAT ) : {
 				if ( ! prm_warned_duplicate ) {
-					BOOST_LOG_TRIVIAL( warning ) << "Skipping entry "
-						<< prm_entry_name   << " (in cluster "
-						<< prm_cluster_name << ") because it duplicates a previous entry in the same cluster-membership input data. Will not warn about any further duplicate entries."
-						<< ( prm_extra_info ? " - " + *prm_extra_info : string{} );
+					::spdlog::warn(
+					  "Skipping entry {} (in cluster {}) because it duplicates a previous entry in the same "
+					  "cluster-membership input data. Will not warn about any further duplicate entries.{}",
+					  prm_entry_name,
+					  prm_cluster_name,
+					  ( prm_extra_info ? " - " + *prm_extra_info : string{} ) );
 					prm_warned_duplicate = true;
 				}
 				break;
 			}
 			case ( clust_entry_problem::CLASH ) : {
-				BOOST_LOG_TRIVIAL( warning ) << "Skipping entry "
-					<< prm_entry_name   << " (in cluster "
-					<< prm_cluster_name << ") because it clashes with a previous entry in the same cluster-membership input data"
-					<< ( prm_extra_info ? " - " + *prm_extra_info : string{} );
+				::spdlog::warn( "Skipping entry {} (in cluster {}) because it clashes with a previous entry in the "
+				                "same cluster-membership input data{}",
+				                prm_entry_name,
+				                prm_cluster_name,
+				                ( prm_extra_info ? " - " + *prm_extra_info : string{} ) );
 				break;
 			}
 			case ( clust_entry_problem::PARSE_ERROR ) : {
-				BOOST_LOG_TRIVIAL( warning ) << "Problem parsing segments from entry "
-					<< prm_entry_name   << " (in cluster "
-					<< prm_cluster_name << ")"
-					<< ( prm_extra_info ? " - " + *prm_extra_info : string{} );
+				::spdlog::warn( "Problem parsing segments from entry {} (in cluster {}){}",
+				                prm_entry_name,
+				                prm_cluster_name,
+				                ( prm_extra_info ? " - " + *prm_extra_info : string{} ) );
 				break;
 			}
 			case ( clust_entry_problem::NONE ) : {}

source/ct_common/cath/common/algorithm/constexpr_modulo_fns_test.cpp

@@ -18,7 +18,6 @@
 /// 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/log/trivial.hpp> // ***** TEMPORARY *****
 #include <boost/range/combine.hpp>
 #include <boost/range/irange.hpp>
 #include <boost/test/unit_test.hpp>

source/ct_common/cath/common/boost_addenda/log/log_to_ostream_guard.cpp

@@ -18,48 +18,48 @@
 /// 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 "log_to_ostream_guard.hpp"
+#include <iostream>
 
-#include <boost/core/null_deleter.hpp>
-#include <boost/shared_ptr.hpp>
+#include <spdlog/sinks/ostream_sink.h>
+
+#include "cath/common/boost_addenda/log/log_to_ostream_guard.hpp"
 
 using namespace ::cath;
-using namespace ::std;
 
-using ::boost::null_deleter;
+using ::std::make_shared;
+using ::std::ostream;
+using ::std::shared_ptr;
 
-/// \brief Ctor for log_to_ostream_guard
-log_to_ostream_guard::log_to_ostream_guard(ostream &prm_ostream ///< TODOCUMENT
-                                           ) {
-	if ( &prm_ostream != &cerr ) {
-		// Construct a sink
-		boost_log_sink_bsptr = boost::make_shared<sink_t>();
+namespace sinks = ::spdlog::sinks;
 
-		// Get a (non-deleting) shared_ptr to the ostream and add it to the sink
-		boost::shared_ptr<ostream> stream_bsptr( &prm_ostream, null_deleter() );
-		boost_log_sink_bsptr->locked_backend()->add_stream( stream_bsptr );
+/// \brief Ctor for log_to_ostream_guard
+///
+/// \param prm_ostream The ostream to which logging should temporarily be redirected for the log_to_ostream_guard's lifetime
+log_to_ostream_guard::log_to_ostream_guard( ostream &prm_ostream ) : logger_shptr{ ::spdlog::default_logger() } {
+	// The previous logger is being stored in logger_shptr
+	// So now set a new logger to log to prm_ostream
+	::spdlog::set_default_logger( make_shared<::spdlog::logger>(
+	  "", shared_ptr<::sinks::sink>( make_shared<::sinks::ostream_sink_mt>( prm_ostream ) ) ) );
 
-		// Register the sink in the logging core
-		boost::log::core::get()->add_sink( boost_log_sink_bsptr );
-	}
+	// Change the format to just contain the message
+	::spdlog::default_logger()->set_pattern( "%v" );
 }
 
 /// \brief Virtual empty dtor for log_to_ostream_guard
 log_to_ostream_guard::~log_to_ostream_guard() noexcept {
-	// If this log_to_ostream_guard has added a sink to the Boost Log core
-	// then try to remove it now
+	// If this log_to_ostream_guard has changed the default logger, reset it
 	try {
-		remove_log_sink();
+		reset_default_logger();
 	}
 	// ...but don't let any exceptions escape the destructor
-	catch (...) {
+	catch ( ... ) {
 	}
 }
 
-/// \brief TODOCUMENT
-void log_to_ostream_guard::remove_log_sink() {
-	if ( boost_log_sink_bsptr ) {
-		boost::log::core::get()->remove_sink( boost_log_sink_bsptr );
-		boost_log_sink_bsptr.reset();
+/// \brief Reset the default logger
+void log_to_ostream_guard::reset_default_logger() {
+	if ( logger_shptr ) {
+		::spdlog::set_default_logger( logger_shptr );
+		logger_shptr.reset();
 	}
 }