update changelog

CMakeLists.txt

@@ -32,7 +32,7 @@ endif()
 # set the project name
 project(
 	libcifpp
-	VERSION 9.0.3
+	VERSION 9.0.4
 	LANGUAGES CXX C)
 
 list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")

changelog

@@ -1,3 +1,6 @@
+Version 9.0.4
+- Fix various stopping and reconstruction errors
+
 Version 9.0.3
 - Reconstruction fixed when some entity ids are missing
 

src/datablock.cpp

@@ -25,8 +25,11 @@
  */
 
 #include "cif++/datablock.hpp"
+
 #include "cif++/validate.hpp"
 
+#include <exception>
+
 namespace cif
 {
 
@@ -42,7 +45,16 @@ datablock::datablock(const datablock &db)
 void datablock::load_dictionary()
 {
 	if (auto *audit_conform = get("audit_conform"); audit_conform and not audit_conform->empty())
-		set_validator(&validator_factory::instance().get(*audit_conform));
+	{
+		try
+		{
+			set_validator(&validator_factory::instance().get(*audit_conform));
+		}
+		catch (const std::exception &ex)
+		{
+			std::clog << ex.what() << '\n';
+		}
+	}
 }
 
 void datablock::set_validator(const validator *v)
@@ -96,7 +108,8 @@ bool datablock::strip()
 	bool result = true;
 
 	// remove all categories that have no validator
-	erase(std::remove_if(begin(), end(), [](category &c) {
+	erase(std::remove_if(begin(), end(), [](category &c)
+			  {
 		bool result = false;
 		if (c.get_cat_validator() == nullptr)
 		{
@@ -104,8 +117,8 @@ bool datablock::strip()
 				std::clog << "Dropping category " << c.name() << '\n';
 			result = true;
 		}
-		return result;
-	}), end());
+		return result; }),
+		end());
 
 	// then strip the remaining categories
 	for (auto &cat : *this)

src/pdb/reconstruct.cpp

@@ -295,11 +295,13 @@ void createEntityIDs(datablock &db)
 					{ "id", entity_id },
 					{ "type", "water" } });
 			else
+			{
 				entity.emplace({ //
 					{ "id", entity_id },
 					{ "type", "non-polymer" } });
 
-			newEntitiesForCompound[comp_id] = entity_id;
+				newEntitiesForCompound[comp_id] = entity_id;
+			}
 		}
 
 		entity_ids[i] = entity_id;

src/validate.cpp

@@ -561,8 +561,10 @@ const validator &validator_factory::get(const category &audit_conform)
 	// If the audit conform contains only one record, this is easy
 	if (audit_conform.size() == 1)
 	{
-		const auto &[name, version] = audit_conform.front().get<std::string, std::optional<std::string>>("dict_name", "dict_version");
-		return m_validators.emplace_back(construct_validator(name, version));
+		const auto &[name, version] =
+			audit_conform.front().get<std::string, std::optional<std::string>>("dict_name", "dict_version");
+		if (not name.empty())
+			return m_validators.emplace_back(construct_validator(name, version));
 	}
 
 	// A new, merged dictionary
@@ -570,6 +572,9 @@ const validator &validator_factory::get(const category &audit_conform)
 	std::optional<validator> v;
 	for (const auto &[name, version] : audit_conform.rows<std::string, std::optional<std::string>>("dict_name", "dict_version"))
 	{
+		if (name.empty())
+			continue;
+
 		if (not v)
 			v = construct_validator(name, version);
 		else

test/CMakeLists.txt

@@ -31,7 +31,7 @@ if(NOT (Catch2_FOUND OR TARGET Catch2))
 		FetchContent_Declare(
 			Catch2
 			GIT_REPOSITORY https://github.com/catchorg/Catch2.git
-            GIT_TAG v3.8.0)
+            GIT_TAG v3.4.0)
 
 		FetchContent_MakeAvailable(Catch2)