Merge pull request #102 from sbmlteam/sk-fix-tests-other

Adding any changes

deviser/base_files/BaseCppFile.py

@@ -296,7 +296,10 @@ def update_attribute_dictionary(self, att_type, mydict, attrib_name):
         :return: nothing
         """
         # Now update the dictionary, with the set of values according
-        # to att_type:
+        # to att_type
+
+        # note util_NaN must be prefixed by language if used in other library in v2
+
         if att_type in ['SId', 'SIdRef', 'IDREF', 'ID', 'UnitSId',
                         'UnitSIdRef', 'string']:
             mydict.update({'attType': 'string', 'attTypeCode': 'std::string&',
@@ -306,7 +309,7 @@ def update_attribute_dictionary(self, att_type, mydict, attrib_name):
         elif att_type == 'double':
             mydict.update({'attType': 'double', 'attTypeCode': 'double',
                            'CType': 'double', 'isNumber': True,
-                           'default': 'util_NaN()'})
+                           'default': gv.util_NaN})
 
         elif att_type == 'int':
             mydict.update({'attType': 'integer', 'attTypeCode': 'int',

deviser/code_files/CppCodeFile.py

@@ -139,7 +139,7 @@ def write_general_includes(self):
                 self.write_line_verbatim('#include <{0}/{1}'
                                          '.h>'.format(self.language,
                                                       lo_name))
-            self.write_line_verbatim('#include <sbml/xml/XMLInputStream.h>')
+            self.write_line_verbatim('#include <xml/XMLInputStream.h>')
 
         # determine whether we need to write other headers
         write_element_filter = False
@@ -559,8 +559,9 @@ def write_document_error_log_functions(self):
         num_elements = len(self.child_elements)
         # add error log and ns to child elements
         att_tc = 'XMLNamespaces*'
-        if not global_variables.is_package:
-            att_tc = 'LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNamespaces*'
+        # not needed in v 2.0
+#        if not global_variables.is_package:
+#            att_tc = 'LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNamespaces*'
         element = dict({'name': 'Namespaces',
                         'isArray': False,
                         'attTypeCode': att_tc,

deviser/code_files/CppHeaderFile.py

@@ -281,9 +281,9 @@ def write_general_includes(self):
             include_lines += ['<{0}/{1}ErrorLog.h>'.format(self.language, global_variables.prefix)]
 
         # if we another library we need the libsbml ns qualifier
-        if not global_variables.is_package:
-            include_lines += ['<sbml/common/libsbml-namespace.h>']
-
+        # not tru in v 2.0
+#        if not global_variables.is_package:
+#            include_lines += ['<common/libsbml-namespace.h>']
 
         # write them out
         for line in include_lines:
@@ -637,8 +637,9 @@ def write_document_error_log_functions(self):
         num_elements = len(self.child_elements)
         # add error log and ns to child elements
         att_tc = 'XMLNamespaces*'
-        if not global_variables.is_package:
-            att_tc = 'LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNamespaces*'
+        # not needed in v 2.0
+#        if not global_variables.is_package:
+#            att_tc = 'LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNamespaces*'
         element = dict({'name': 'Namespaces',
                         'isArray': False,
                         'attTypeCode': att_tc,

deviser/code_files/BaseClassFiles.py → deviser/code_files/OtherLibraryFiles.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 #
-# @file    BaseClassFiles.py
+# @file    OtherLibraryFiles.py
 # @brief   class for generating base files for other library implementations
 # @author  Frank Bergmann
 # @author  Sarah Keating
@@ -50,7 +50,7 @@
 from ..base_files import BaseCMakeFile, BaseTemplateFile
 
 
-class BaseClassFiles(BaseTemplateFile.BaseTemplateFile):
+class OtherLibraryFiles(BaseTemplateFile.BaseTemplateFile):
     """Class for all Base files"""
 
     def __init__(self, name, elements, verbose=False):

deviser/code_files/cpp_functions/Constructors.py

@@ -789,7 +789,8 @@ def write_constructor_args(self, ns):
         else:
             sep = ','
         for attrib in self.attributes:
-            if not self.is_plugin and global_variables.language == 'sbml' and (attrib['memberName'] == 'mId' or attrib['memberName'] == 'mName'):
+            if not self.is_plugin and global_variables.language == 'sbml' and \
+                    (attrib['memberName'] == 'mId' or attrib['memberName'] == 'mName'):
                 continue
             elif global_variables.language != 'sbml' and attrib['memberName'] == 'mId':
                 continue

deviser/code_files/cpp_functions/GeneralFunctions.py

@@ -663,10 +663,11 @@ def write_write_elements(self):
         # create the function declaration
         function = 'writeElements'
         return_type = 'void'
-        if global_variables.is_package:
-            arguments = ['XMLOutputStream& stream']
-        else:
-            arguments = ['LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream& stream']
+        # no longer necessary to have libsbml namespace in v2
+#        if global_variables.is_package:
+        arguments = ['XMLOutputStream& stream']
+#        else:
+#            arguments = ['LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream& stream']
 
         # create the function implementation
         base = self.base_class
@@ -917,10 +918,11 @@ def write_write(self):
         # create the function declaration
         function = 'write'
         return_type = 'void'
-        if global_variables.is_package:
-            arguments = ['XMLOutputStream& stream']
-        else:
-            arguments = ['LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream& stream']
+        # not needed in v 2.0
+#        if global_variables.is_package:
+        arguments = ['XMLOutputStream& stream']
+#        else:
+#            arguments = ['LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream& stream']
 
         # create the function implementation
         # find the array attribute

deviser/code_files/cpp_functions/GenericAttributeFunctions.py

@@ -592,7 +592,7 @@ def write_add_object(self):
         code = []
         if not self.has_elements_with_same_xml_name():
             # create the function implementation
-            last_line = ['return LIBSBML_OPERATION_FAILED']
+            last_line = ['return {0}'.format(global_variables.ret_failed)]
             first = True
             block = []
             if_block = []

deviser/code_files/cpp_functions/ProtectedFunctions.py

@@ -174,12 +174,13 @@ def write_create_object(self):
         # create the function declaration
         function = 'createObject'
         return_type = '{0}*'.format(self.std_base)
-        if global_variables.is_package:
-            arguments = ['XMLInputStream& stream']
-            xmlns = 'XMLNamespaces'
-        else:
-            arguments = ['LIBSBML_CPP_NAMESPACE_QUALIFIER XMLInputStream& stream']
-            xmlns = 'LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNamespaces'
+        # libsbml ns not needed in v 2.0
+#        if global_variables.is_package:
+        arguments = ['XMLInputStream& stream']
+        xmlns = 'XMLNamespaces'
+#        else:
+#            arguments = ['LIBSBML_CPP_NAMESPACE_QUALIFIER XMLInputStream& stream']
+#            xmlns = 'LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNamespaces'
 
         # create the function implementation
         code = []
@@ -609,10 +610,11 @@ def write_add_expected_attributes(self):
         # create the function declaration
         function = 'addExpectedAttributes'
         return_type = 'void'
-        if global_variables.is_package:
-            arguments = ['ExpectedAttributes& attributes']
-        else:
-            arguments = ['LIBSBML_CPP_NAMESPACE_QUALIFIER ExpectedAttributes& attributes']
+        # no longer necessary to have libsbml namespace in v2
+        # if global_variables.is_package:
+        arguments = ['ExpectedAttributes& attributes']
+        # else:
+        #     arguments = ['LIBSBML_CPP_NAMESPACE_QUALIFIER ExpectedAttributes& attributes']
 
         # create the function implementation
         if self.base_class:
@@ -679,12 +681,13 @@ def write_read_attributes(self):
         # create function declaration
         function = 'readAttributes'
         return_type = 'void'
-        if global_variables.is_package:
-            arguments = ['const XMLAttributes& attributes',
-                         'const ExpectedAttributes& expectedAttributes']
-        else:
-            arguments = ['const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLAttributes& attributes',
-                         'const LIBSBML_CPP_NAMESPACE_QUALIFIER ExpectedAttributes& expectedAttributes']
+        # no longer necessary to have libsbml namespace in v2
+#        if global_variables.is_package:
+        arguments = ['const XMLAttributes& attributes',
+                     'const ExpectedAttributes& expectedAttributes']
+#        else:
+#            arguments = ['const LIBSBML_CPP_NAMESPACE_QUALIFIER XMLAttributes& attributes',
+#                         'const LIBSBML_CPP_NAMESPACE_QUALIFIER ExpectedAttributes& expectedAttributes']
 
         # create the function implementation
         implementation = ['unsigned int level = getLevel()',
@@ -934,10 +937,11 @@ def write_write_attributes(self):
         # create function declaration
         function = 'writeAttributes'
         return_type = 'void'
-        if global_variables.is_package:
-            arguments = ['XMLOutputStream& stream']
-        else:
-            arguments = ['LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream& stream']
+        # no longer necessary to have libsbml namespace in v2
+#        if global_variables.is_package:
+        arguments = ['XMLOutputStream& stream']
+#        else:
+#            arguments = ['LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream& stream']
 
         # create the function implementation
         if self.base_class:
@@ -1006,10 +1010,11 @@ def write_write_version_attributes(self, version):
         pkg_version = self.lv_info[version]['pkg_version']
         function = 'writeL{0}V{1}V{2}Attributes'.format(level_val, version_val, pkg_version)
         return_type = 'void'
-        if global_variables.is_package:
-            arguments = ['XMLOutputStream& stream']
-        else:
-            arguments = ['LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream& stream']
+        # not needed in v 2.0
+#        if global_variables.is_package:
+        arguments = ['XMLOutputStream& stream']
+#        else:
+#            arguments = ['LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream& stream']
 
         # create the function implementation
         code = []
@@ -1055,12 +1060,13 @@ def write_write_xmlns(self):
         # create the function declaration
         function = 'writeXMLNS'
         return_type = 'void'
-        if global_variables.is_package:
-            arguments = ['XMLOutputStream& stream']
-            xmlns = 'XMLNamespaces'
-        else:
-            arguments = ['LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream& stream']
-            xmlns = 'LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNamespaces'
+        # not needed for v 2.0
+#        if global_variables.is_package:
+        arguments = ['XMLOutputStream& stream']
+        xmlns = 'XMLNamespaces'
+#        else:
+#            arguments = ['LIBSBML_CPP_NAMESPACE_QUALIFIER XMLOutputStream& stream']
+#            xmlns = 'LIBSBML_CPP_NAMESPACE_QUALIFIER XMLNamespaces'
 
         # create the function implementation
         implementation = ['{0} xmlns'.format(xmlns),

deviser/code_files/cpp_functions/SetGetFunctions.py

@@ -1591,8 +1591,7 @@ def get_c_attribute(self, attribute):
                                          self.cap_language)]
         elif attribute['attType'] == 'double':
             line = ['return ({0} != NULL) ? {0}->get{1}() : '
-                    'util_NaN()'.format(self.abbrev_parent,
-                                        attribute['capAttName'])]
+                    '{2}'.format(self.abbrev_parent, attribute['capAttName'], global_variables.util_NaN)]
         elif attribute['attType'] == 'boolean':
             line = ['return ({0} != NULL) ? static_cast<int>({0}->get{1}()) : '
                     '0'.format(self.abbrev_parent,
@@ -1608,9 +1607,10 @@ def get_c_attribute(self, attribute):
                 use_name = 'static_cast<const ' \
                            '{0}*>({1})'.format(self.class_name,
                                                self.abbrev_parent)
-            line = ['return {0}->get{1}().empty() ? NULL : safe_strdup({0}'
+            line = ['return {0}->get{1}().empty() ? NULL : {2}({0}'
                     '->get{1}().c_str())'.format(use_name,
-                                                 attribute['capAttName'])]
+                                                 attribute['capAttName'],
+                                                 global_variables.safe_strdup)]
         code.append(self.create_code_block('line', line))
         return code