Merge pull request #352 from sbmlteam/development

Pull from develop

CMakeLists.txt

@@ -175,6 +175,7 @@ set (LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindLIBSBML.
 
 # Whether to compile examples
 option(WITH_EXAMPLES "Compile the libSBML example programs."  OFF)
+option(WITH_CHECK "Enable testing of libSBML."  OFF)
 
 # Which language bindings should be built
 option(WITH_CSHARP   "Generate the C# language interface for libSBML."     OFF)

CMakeModules/FindBZ2.cmake

@@ -1,3 +1,5 @@
+include(CheckLibraryExists)
+
 string(TOUPPER ${PROJECT_NAME} _UPPER_PROJECT_NAME)
 set(_PROJECT_DEPENDENCY_DIR ${_UPPER_PROJECT_NAME}_DEPENDENCY_DIR)
 

CMakeModules/FindLIBXML.cmake

@@ -1,4 +1,5 @@
 include(CheckLibraryExists)
+include(CheckCSourceCompiles)
 
 string(TOUPPER ${PROJECT_NAME} _UPPER_PROJECT_NAME)
 set(_PROJECT_DEPENDENCY_DIR ${_UPPER_PROJECT_NAME}_DEPENDENCY_DIR)

NEWS.txt

@@ -1,7 +1,42 @@
            libSBML NEWS -- History of user-visible changes
 
 ====================================================================
-5.20.0
+5.20.2
+====================================================================
+
+This is mostly a bug fix release enhancing stability when validating
+and converting models.
+
+* New features / improvements
+
+  - Access to error logs from the C API  
+
+  - Attributes of the ModelHistory can now be accessed from 
+    const objects. 
+
+  - The FBC V3 package has been updated to reflect the latest
+    specification. There are now optional attributes `fbc:reaction2` 
+    on the FluxObjective and `fbc:variable2` on the 
+    UserDefinedConstraintComponent.
+
+* Bug fixes
+
+  - A bug converting / validating models with the 'comp' package
+    has been fixed.
+
+  - A crash when inferring units has been resolved. 
+
+  - A fix to the CMake Build system ensures that check for dependencies
+    is more robust. Thanks to first time contributor @adelhpour
+
+  - The type of the FBC V3 `coefficient` attribute on the 
+    UserDefinedConstraintComponent has been corrected, it was mistakenly
+    a double before, now it has been corrected to be a SIdRef as 
+    described in the specification.
+
+
+====================================================================
+5.20.0 (2023-04-03)
 ====================================================================
 
 Given the length of time since our last release the list of changes

VERSION.txt

@@ -1 +1 @@
-5.20.0
+5.20.2

configure

@@ -1,7 +1,7 @@
 #! /bin/sh
 # From configure.ac Revision.
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.71 for libSBML 5.20.0.
+# Generated by GNU Autoconf 2.71 for libSBML 5.20.2.
 #
 # Report bugs to <[email protected]>.
 #
@@ -766,8 +766,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='libSBML'
 PACKAGE_TARNAME='libsbml'
-PACKAGE_VERSION='5.20.0'
-PACKAGE_STRING='libSBML 5.20.0'
+PACKAGE_VERSION='5.20.2'
+PACKAGE_STRING='libSBML 5.20.2'
 PACKAGE_BUGREPORT='[email protected]'
 PACKAGE_URL='http://sbml.org/Software/libSBML'
 
@@ -1662,7 +1662,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures libSBML 5.20.0 to adapt to many kinds of systems.
+\`configure' configures libSBML 5.20.2 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1728,7 +1728,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of libSBML 5.20.0:";;
+     short | recursive ) echo "Configuration of libSBML 5.20.2:";;
    esac
   cat <<\_ACEOF
 
@@ -1885,7 +1885,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-libSBML configure 5.20.0
+libSBML configure 5.20.2
 generated by GNU Autoconf 2.71
 
 Copyright (C) 2021 Free Software Foundation, Inc.
@@ -2484,7 +2484,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by libSBML $as_me 5.20.0, which was
+It was created by libSBML $as_me 5.20.2, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   $ $0$ac_configure_args_raw
@@ -3469,7 +3469,7 @@ ac_config_headers="$ac_config_headers src/sbml/common/libsbml-package.h"
 ac_config_headers="$ac_config_headers src/sbml/common/libsbml-namespace.h"
 
 
-LIBSBML_VERSION_NUMERIC=52000
+LIBSBML_VERSION_NUMERIC=52002
 
 
 
@@ -28902,7 +28902,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by libSBML $as_me 5.20.0, which was
+This file was extended by libSBML $as_me 5.20.2, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -28967,7 +28967,7 @@ ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config='$ac_cs_config_escaped'
 ac_cs_version="\\
-libSBML config.status 5.20.0
+libSBML config.status 5.20.2
 configured by $0, generated by GNU Autoconf 2.71,
   with options \\"\$ac_cs_config\\"
 

dev/packages/deviser-fbc_v3.xml

@@ -168,6 +168,7 @@
             <attribute name="id" required="false" type="SId" abstract="false"/>
             <attribute name="name" required="false" type="string" abstract="false"/>
             <attribute name="reaction" required="true" type="SIdRef" element="Reaction" abstract="false"/>
+            <attribute name="reaction2" required="false" type="SIdRef" element="Reaction" abstract="false"/>
             <attribute name="coefficient" required="true" type="double" abstract="false"/>
             <attribute name="variableType" required="true" type="enum" element="FbcVariableType" abstract="false"/>
           </attributes>
@@ -226,8 +227,9 @@
           <attributes>
             <attribute name="id" required="false" type="SId" abstract="false"/>
             <attribute name="name" required="false" type="string" abstract="false"/>
-            <attribute name="coefficient" required="true" type="double" abstract="false"/>
+            <attribute name="coefficient" required="true" type="SIdRef" element="Parameter" abstract="false"/>
             <attribute name="variable" required="true" type="SIdRef" element="Reaction,Parameter" abstract="false"/>
+            <attribute name="variable2" required="false" type="SIdRef" element="Reaction,Parameter" abstract="false"/>
             <attribute name="variableType" required="true" type="enum" element="FbcVariableType" abstract="false"/>
           </attributes>
         </element>

src/bindings/matlab/getDefaultValues.m

@@ -3330,14 +3330,15 @@
         '', ...
         '', ...
         '', ...
+        '', ...
         0/0, ...
         int32(0), ...
         '', ...
         int32(3), ...
         int32(version), ...
         int32(3), ...
         };
-        nNumberFields = 15;
+        nNumberFields = 16;
       end
     end
   end
@@ -3565,8 +3566,8 @@
         int32(-1), ...
         '', ...
         '', ...
-        0/0, ...
-        int32(0), ...
+        '', ...
+        '', ...
         '', ...
         '', ...
         int32(3), ...

src/bindings/matlab/getStructureEnum.m

@@ -3005,14 +3005,15 @@
         {'fbc_id', 'id', 'fbc', 1, 20}, ...
         {'fbc_name', 'name', 'fbc', 1, 20}, ...
         {'fbc_reaction', 'reaction', 'fbc', 1, 20}, ...
+        {'fbc_reaction2', 'reaction2', 'fbc', 1, 20}, ...
         {'fbc_coefficient', 'coefficient', 'fbc', 1, 20}, ...
         {'isSetfbc_coefficient', 'coefficient', 'fbc', 0, 7}, ...
         {'fbc_variableType', 'variableType', 'fbc', 1, 20}, ...
         {'level', '', '', 0, 0}, ...
         {'version', '', '', 0, 0}, ...
         {'fbc_version', 'version', 'fbc', 1, 20}, ...
         };
-        nNumberFields = 15;
+        nNumberFields = 16;
       end
     end
   end
@@ -3241,8 +3242,8 @@
         {'fbc_id', 'id', 'fbc', 1, 20}, ...
         {'fbc_name', 'name', 'fbc', 1, 20}, ...
         {'fbc_coefficient', 'coefficient', 'fbc', 1, 20}, ...
-        {'isSetfbc_coefficient', 'coefficient', 'fbc', 0, 7}, ...
         {'fbc_variable', 'variable', 'fbc', 1, 20}, ...
+        {'fbc_variable2', 'variable2', 'fbc', 1, 20}, ...
         {'fbc_variableType', 'variableType', 'fbc', 1, 20}, ...
         {'level', '', '', 0, 0}, ...
         {'version', '', '', 0, 0}, ...

src/bindings/matlab/getStructureFieldnames.m

@@ -3382,14 +3382,15 @@
         'fbc_id', ...
         'fbc_name', ...
         'fbc_reaction', ...
+        'fbc_reaction2', ...
         'fbc_coefficient', ...
         'isSetfbc_coefficient', ...
         'fbc_variableType', ...
         'level', ...
         'version', ...
         'fbc_version', ...
         };
-        nNumberFields = 15;
+        nNumberFields = 16;
       end
     end
   end
@@ -3618,8 +3619,8 @@
         'fbc_id', ...
         'fbc_name', ...
         'fbc_coefficient', ...
-        'isSetfbc_coefficient', ...
         'fbc_variable', ...
+        'fbc_variable2', ...
         'fbc_variableType', ...
         'level', ...
         'version', ...

src/bindings/matlab/getValueType.m

@@ -3333,14 +3333,15 @@
         'char', ...
         'char', ...
         'char', ...
+        'char', ...
         'double', ...
         'bool', ...
         'char', ...
         'uint', ...
         'uint', ...
         'uint', ...
         };
-        nNumberFields = 15;
+        nNumberFields = 16;
       end
     end
   end
@@ -3568,8 +3569,8 @@
         'int', ...
         'char', ...
         'char', ...
-        'double', ...
-        'bool', ...
+        'char', ...
+        'char', ...
         'char', ...
         'char', ...
         'uint', ...

src/bindings/matlab/test/test-data/fbcV3.xml

@@ -75,7 +75,7 @@
     <fbc:listOfUserDefinedConstraints>
       <fbc:userDefinedConstraint sboTerm="SBO:0000001" fbc:id="uc2" fbc:lowerBound="uc2lb" fbc:upperBound="uc2ub">
         <fbc:listOfUserDefinedConstraintComponents>
-          <fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:id="dd" fbc:name="string" fbc:coefficient="2" fbc:variable="R2" fbc:variableType="linear"/>
+          <fbc:userDefinedConstraintComponent metaid="_udc1" sboTerm="SBO:0000001" fbc:id="dd" fbc:name="string" fbc:coefficient="uc2ub" fbc:variable="R2" fbc:variableType="linear"/>
         </fbc:listOfUserDefinedConstraintComponents>
       </fbc:userDefinedConstraint>
     </fbc:listOfUserDefinedConstraints>

src/bindings/matlab/test/testReadFromFileFbc2.m

@@ -80,7 +80,7 @@
   Totalfail = Totalfail + fail_unless( strcmp(m.fbc_objective(1).fbc_fluxObjective(1).typecode, 'SBML_FBC_FLUXOBJECTIVE'));
   Totalfail = Totalfail + fail_unless( strcmp(m.fbc_objective(1).fbc_fluxObjective(1).fbc_reaction, 'R1'));
   Totalfail = Totalfail + fail_unless( m.fbc_objective(1).fbc_fluxObjective(1).fbc_coefficient == 1);
-  Totalfail = Totalfail + fail_unless( m.fbc_objective(1).fbc_fluxObjective(1).isSetfbc_coefficient == 1);
+
 
   Totalfail = Totalfail + fail_unless( strcmp(m.fbc_activeObjective, 'c'));
 

src/bindings/matlab/test/testReadFromFileFbc3.m

@@ -51,7 +51,7 @@
   Totalfail = Totalfail + fail_unless( strcmp(m.fbc_objective(1).fbc_fluxObjective(1).typecode, 'SBML_FBC_FLUXOBJECTIVE'));
   Totalfail = Totalfail + fail_unless( strcmp(m.fbc_objective(1).fbc_fluxObjective(1).fbc_reaction, 'R1'));
   Totalfail = Totalfail + fail_unless( m.fbc_objective(1).fbc_fluxObjective(1).fbc_coefficient == 1);
-  Totalfail = Totalfail + fail_unless( m.fbc_objective(1).fbc_fluxObjective(1).isSetfbc_coefficient == 1);
+
 
   Totalfail = Totalfail + fail_unless( strcmp(m.fbc_activeObjective, 'c'));
 
@@ -77,8 +77,8 @@
 
   Totalfail = Totalfail + fail_unless( strcmp(m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).typecode, 'SBML_FBC_USERDEFINEDCONSTRAINTCOMPONENT'));
   Totalfail = Totalfail + fail_unless( strcmp(m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).fbc_id, 'dd'));
-  Totalfail = Totalfail + fail_unless( m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).fbc_coefficient == 2);
-  Totalfail = Totalfail + fail_unless( m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).isSetfbc_coefficient == 1);
+
+  Totalfail = Totalfail + fail_unless( strcmp(m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).fbc_coefficient, 'uc2ub'));
   Totalfail = Totalfail + fail_unless( strcmp(m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).fbc_variable, 'R2'));
   Totalfail = Totalfail + fail_unless( strcmp(m.fbc_userDefinedConstraint(1).fbc_userDefinedConstraintComponent(1).fbc_variableType, 'linear'));
 

src/sbml/AlgebraicRule.cpp

@@ -371,7 +371,7 @@ AlgebraicRule_create(unsigned int level, unsigned int version)
     AlgebraicRule* obj = new AlgebraicRule(level,version);
     return obj;
   }
-  catch (SBMLConstructorException)
+  catch (SBMLConstructorException &)
   {
     return NULL;
   }
@@ -387,7 +387,7 @@ AlgebraicRule_createWithNS (SBMLNamespaces_t* sbmlns)
     AlgebraicRule* obj = new AlgebraicRule(sbmlns);
     return obj;
   }
-  catch (SBMLConstructorException)
+  catch (SBMLConstructorException &)
   {
     return NULL;
   }

src/sbml/AssignmentRule.cpp

@@ -450,7 +450,7 @@ AssignmentRule_create(unsigned int level, unsigned int version)
     AssignmentRule* obj = new AssignmentRule(level,version);
     return obj;
   }
-  catch (SBMLConstructorException)
+  catch (SBMLConstructorException &)
   {
     return NULL;
   }
@@ -466,7 +466,7 @@ AssignmentRule_createWithNS (SBMLNamespaces_t* sbmlns)
     AssignmentRule* obj = new AssignmentRule(sbmlns);
     return obj;
   }
-  catch (SBMLConstructorException)
+  catch (SBMLConstructorException &)
   {
     return NULL;
   }

src/sbml/Compartment.cpp

@@ -1999,7 +1999,7 @@ ListOfCompartments::createObject (XMLInputStream& stream)
     {
       object = new Compartment(getSBMLNamespaces());
     }
-    catch (SBMLConstructorException*)
+    catch (SBMLConstructorException &)
     {
       object = new Compartment(SBMLDocument::getDefaultLevel(),
         SBMLDocument::getDefaultVersion());
@@ -2029,7 +2029,7 @@ Compartment_create (unsigned int level, unsigned int version)
     Compartment* obj = new Compartment(level,version);
     return obj;
   }
-  catch (SBMLConstructorException)
+  catch (SBMLConstructorException &)
   {
     return NULL;
   }
@@ -2045,7 +2045,7 @@ Compartment_createWithNS (SBMLNamespaces_t* sbmlns)
     Compartment* obj = new Compartment(sbmlns);
     return obj;
   }
-  catch (SBMLConstructorException)
+  catch (SBMLConstructorException &)
   {
     return NULL;
   }