Create release v0.3.103.

cellml · Sep 14, 2022 · fe5afe2 · fe5afe2
1 parent dbfc97b
commit fe5afe2
Show file tree

Hide file tree

Showing 154 changed files with 470 additions and 255 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -16,7 +16,7 @@ cmake_minimum_required(VERSION 3.10.2)
 
 set(PROJECT_NAME libCellML)
 set(PROJECT_URL https://libcellml.org)
-set(_PROJECT_VERSION 0.3.102)
+set(_PROJECT_VERSION 0.3.103)
 set(PROJECT_DEVELOPER_VERSION )
 project(${PROJECT_NAME} VERSION ${_PROJECT_VERSION} LANGUAGES CXX)
 

diff --git a/cmake/add_rpath_for_python.cmake b/cmake/add_rpath_for_python.cmake
@@ -3,6 +3,8 @@
 string(REPLACE "${LIST_SEPARATOR}" ";" SHARED_OBJECT_MODULES "${SHARED_OBJECT_MODULES}")
 foreach(_M ${SHARED_OBJECT_MODULES})
   execute_process(COMMAND ${INSTALL_NAME_TOOL_EXE} -change "/Library/Frameworks/Python.framework/Versions/${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}/Python" @rpath/Python.framework/Versions/${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}/Python ${_M})
+  execute_process(COMMAND ${INSTALL_NAME_TOOL_EXE} -add_rpath /Library/Frameworks ${_M})
+  execute_process(COMMAND ${INSTALL_NAME_TOOL_EXE} -add_rpath /usr/local/Frameworks ${_M})
   execute_process(COMMAND ${INSTALL_NAME_TOOL_EXE} -add_rpath /opt/homebrew/Frameworks ${_M})
 endforeach()
 
diff --git a/docs/changelogs/changelog_v0.3.103.rst b/docs/changelogs/changelog_v0.3.103.rst
@@ -0,0 +1,20 @@
+libCellML v0.3.103 Changelog
+============================
+
+Bug
+---
+
+* Fix segfault when printing complete MathML document by `@hsorby <https://github.com/hsorby>`_ [`#1026 <https://github.com/cellml/libcellml/pull/1026>`_].
+
+Python bindings
+---------------
+
+* Add more search paths for macOS python bindings by `@hsorby <https://github.com/hsorby>`_ [`#1037 <https://github.com/cellml/libcellml/pull/1037>`_].
+
+Contributors
+------------
+
+.. image:: https://avatars.githubusercontent.com/u/778048?v=4
+   :target: https://github.com/hsorby
+   :height: 32
+   :width: 32
diff --git a/docs/changelogs/index.rst b/docs/changelogs/index.rst
@@ -4,6 +4,7 @@ Changelogs
 
 .. toctree::
 
+   changelog_v0.3.103
    changelog_v0.3.102
    changelog_v0.3.101
    changelog_v0.3.100

diff --git a/docs/index.rst b/docs/index.rst
@@ -37,6 +37,7 @@ Changelogs
 
 .. toctree::
 
+   changelogs/changelog_v0.3.103
    changelogs/changelog_v0.3.102
    changelogs/changelog_v0.3.101
    changelogs/changelog_v0.3.100

diff --git a/src/api/libcellml/issue.h b/src/api/libcellml/issue.h
@@ -34,6 +34,7 @@ class LIBCELLML_EXPORT Issue
     friend class Annotator;
     friend class Importer;
     friend class Parser;
+    friend class Printer;
     friend class Validator;
 
 public:

diff --git a/src/api/libcellml/parser.h b/src/api/libcellml/parser.h
@@ -21,7 +21,6 @@ limitations under the License.
 #include "libcellml/logger.h"
 #include "libcellml/model.h"
 #include "libcellml/types.h"
-#include "libcellml/units.h"
 
 namespace libcellml {
 

diff --git a/src/api/libcellml/printer.h b/src/api/libcellml/printer.h
@@ -19,6 +19,7 @@ limitations under the License.
 #include <string>
 
 #include "libcellml/exportdefinitions.h"
+#include "libcellml/logger.h"
 #include "libcellml/types.h"
 
 namespace libcellml {
@@ -28,7 +29,7 @@ namespace libcellml {
  *
  * The Printer class is for representing a CellML Printer.
  */
-class LIBCELLML_EXPORT Printer
+class LIBCELLML_EXPORT Printer: public Logger
 {
 public:
     ~Printer(); /**< Destructor, @private. */
@@ -59,13 +60,13 @@ class LIBCELLML_EXPORT Printer
      *
      * @return The @c std::string representation of the @ref Model.
      */
-    std::string printModel(const ModelPtr &model, bool autoIds = false) const;
+    std::string printModel(const ModelPtr &model, bool autoIds = false);
 
 private:
     Printer(); /**< Constructor, @private. */
 
-    struct PrinterImpl; /**< Forward declaration for pImpl idiom, @private. */
-    PrinterImpl *mPimpl; /**< Private member to implementation pointer, @private. */
+    class PrinterImpl; /**< Forward declaration for pImpl idiom, @private. */
+    PrinterImpl *pFunc(); /**< Getter for private implementation pointer, @private. */
 };
 
 } // namespace libcellml
diff --git a/src/api/libcellml/types.h b/src/api/libcellml/types.h
@@ -227,6 +227,7 @@ class LIBCELLML_EXPORT AnyCellmlElement
     friend class Importer;
     friend class Issue;
     friend class Parser;
+    friend class Printer;
     friend class Validator;
 
 public:

diff --git a/src/bindings/interface/printer.i b/src/bindings/interface/printer.i
@@ -5,6 +5,7 @@
 %include <std_string.i>
 
 %import "createconstructor.i"
+%import "logger.i"
 %import "types.i"
 
 %feature("docstring") libcellml::Printer

diff --git a/src/printer.cpp b/src/printer.cpp
@@ -26,31 +26,41 @@ limitations under the License.
 
 #include "libcellml/component.h"
 #include "libcellml/importsource.h"
+#include "libcellml/issue.h"
 #include "libcellml/model.h"
 #include "libcellml/reset.h"
 #include "libcellml/units.h"
 #include "libcellml/variable.h"
 
+#include "anycellmlelement_p.h"
 #include "internaltypes.h"
+#include "issue_p.h"
+#include "logger_p.h"
 #include "utilities.h"
 #include "xmldoc.h"
 
+#include <iostream>
+
 namespace libcellml {
 
 /**
  * @brief The Printer::PrinterImpl struct.
  *
  * The private implementation for the Printer class.
  */
-struct Printer::PrinterImpl
+class Printer::PrinterImpl: public Logger::LoggerImpl
 {
-    std::string printImports(const ModelPtr &model, IdList &idList, bool autoIds);
-    std::string printUnits(const UnitsPtr &units, IdList &idList, bool autoIds);
+public:
+    Printer *mPrinter = nullptr;
+
     std::string printComponent(const ComponentPtr &component, IdList &idList, bool autoIds);
     std::string printEncapsulation(const ComponentPtr &component, IdList &idList, bool autoIds);
-    std::string printVariable(const VariablePtr &variable, IdList &idList, bool autoIds);
+    std::string printImports(const ModelPtr &model, IdList &idList, bool autoIds);
+    std::string printMath(const std::string &math);
     std::string printReset(const ResetPtr &reset, IdList &idList, bool autoIds);
     std::string printResetChild(const std::string &childLabel, const std::string &childId, const std::string &math, IdList &idList, bool autoIds);
+    std::string printUnits(const UnitsPtr &units, IdList &idList, bool autoIds);
+    std::string printVariable(const VariablePtr &variable, IdList &idList, bool autoIds);
 };
 
 std::string printMapVariables(const VariablePairPtr &variablePair, IdList &idList, bool autoIds)
@@ -127,12 +137,32 @@ std::string printConnections(const ComponentMap &componentMap, const VariableMap
     return connections;
 }
 
-std::string printMath(const std::string &math)
+std::string Printer::PrinterImpl::printMath(const std::string &math)
 {
     static const std::regex before(">[\\s\n\t]*");
     static const std::regex after("[\\s\n\t]*<");
-    auto temp = std::regex_replace(math, before, ">");
-    return std::regex_replace(temp, after, "<");
+    static const std::regex xmlDeclaration(R"|(<\?xml[[:space:]]+version=.*\?>)|");
+
+    XmlDocPtr xmlDoc = std::make_shared<XmlDoc>();
+    xmlKeepBlanksDefault(0);
+    xmlDoc->parse(math);
+    if (xmlDoc->xmlErrorCount() == 0) {
+        auto result = xmlDoc->prettyPrint();
+        // Remove any XML declarations from the string.
+        result = std::regex_replace(result, xmlDeclaration, "");
+        // Clean whitespace in the math.
+        result = std::regex_replace(result, before, ">");
+        return std::regex_replace(result, after, "<");
+    } else {
+        for (size_t i = 0; i < xmlDoc->xmlErrorCount(); ++i) {
+            auto issue = Issue::IssueImpl::create();
+            issue->mPimpl->setDescription("LibXml2 error: " + xmlDoc->xmlError(i));
+            issue->mPimpl->setReferenceRule(Issue::ReferenceRule::XML);
+            addIssue(issue);
+        }
+    }
+
+    return "";
 }
 
 void buildMapsForComponentsVariables(const ComponentPtr &component, ComponentMap &componentMap, VariableMap &variableMap)
@@ -255,7 +285,13 @@ std::string Printer::PrinterImpl::printComponent(const ComponentPtr &component,
                 repr += printReset(component->reset(i), idList, autoIds);
             }
             if (!component->math().empty()) {
+                size_t startIssueCount = mPrinter->issueCount();
                 repr += printMath(component->math());
+                size_t endIssueCount = mPrinter->issueCount();
+                for (size_t current = startIssueCount; current < endIssueCount; ++current) {
+                    auto issue = mPrinter->issue(current);
+                    issue->mPimpl->mItem->mPimpl->setComponent(component);
+                }
             }
 
             repr += "</component>";
@@ -376,6 +412,7 @@ std::string Printer::PrinterImpl::printReset(const ResetPtr &reset, IdList &idLi
         repr += " id=\"" + makeUniqueId(idList) + "\"";
     }
 
+    size_t startIssueCount = mPrinter->issueCount();
     std::string testValue = printResetChild("test_value", reset->testValueId(), reset->testValue(), idList, autoIds);
     if (!testValue.empty()) {
         repr += ">" + testValue;
@@ -390,6 +427,11 @@ std::string Printer::PrinterImpl::printReset(const ResetPtr &reset, IdList &idLi
         hasChild = true;
     }
     if (hasChild) {
+        size_t endIssueCount = mPrinter->issueCount();
+        for (size_t current = startIssueCount; current < endIssueCount; ++current) {
+            auto issue = mPrinter->issue(current);
+            issue->mPimpl->mItem->mPimpl->setReset(reset);
+        }
         repr += "</reset>";
     } else {
         repr += "/>";
@@ -453,22 +495,28 @@ std::string Printer::PrinterImpl::printImports(const ModelPtr &model, IdList &id
     return repr;
 }
 
+Printer::PrinterImpl *Printer::pFunc()
+{
+    return reinterpret_cast<Printer::PrinterImpl *>(Logger::pFunc());
+}
+
 Printer::Printer()
-    : mPimpl(new PrinterImpl())
+    : Logger(new PrinterImpl())
 {
+    pFunc()->mPrinter = this;
 }
 
 Printer::~Printer()
 {
-    delete mPimpl;
+    delete pFunc();
 }
 
 PrinterPtr Printer::create() noexcept
 {
     return std::shared_ptr<Printer> {new Printer {}};
 }
 
-std::string Printer::printModel(const ModelPtr &model, bool autoIds) const
+std::string Printer::printModel(const ModelPtr &model, bool autoIds)
 {
     if (model == nullptr) {
         return "";
@@ -497,21 +545,21 @@ std::string Printer::printModel(const ModelPtr &model, bool autoIds) const
     }
 
     if (model->hasImports()) {
-        repr += mPimpl->printImports(model, idList, autoIds);
+        repr += pFunc()->printImports(model, idList, autoIds);
     }
 
     for (size_t i = 0; i < model->unitsCount(); ++i) {
-        repr += mPimpl->printUnits(model->units(i), idList, autoIds);
+        repr += pFunc()->printUnits(model->units(i), idList, autoIds);
     }
 
     std::string componentEncapsulation;
     // Serialise components of the model, imported components have already been dealt with at this point,
     //  ... but their locally-defined children have not.
     for (size_t i = 0; i < model->componentCount(); ++i) {
         ComponentPtr component = model->component(i);
-        repr += mPimpl->printComponent(component, idList, autoIds);
+        repr += pFunc()->printComponent(component, idList, autoIds);
         if (component->componentCount() > 0) {
-            componentEncapsulation += mPimpl->printEncapsulation(component, idList, autoIds);
+            componentEncapsulation += pFunc()->printEncapsulation(component, idList, autoIds);
         }
     }
 

diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
@@ -176,7 +176,7 @@ if(LIBCELLML_LLVM_COVERAGE)
     COMMENT "Running LLVM coverage tests")
 
   add_custom_target(llvm_coverage_report
-    COMMAND ${LLVM_COV_EXE} show $<TARGET_FILE:cellml> -instr-profile=${DATA_PROFILE_FILENAME} -format=html -Xdemangler c++filt -Xdemangler -n -o coverage_report
+    COMMAND ${LLVM_COV_EXE} show $<TARGET_FILE:cellml> -instr-profile=${DATA_PROFILE_FILENAME} -format=html -Xdemangler c++filt -Xdemangler -n -o coverage_report --show-branches=count
     DEPENDS prepare_llvm_coverage
     WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     COMMENT "Running LLVM coverage missing lines command")

diff --git a/tests/bindings/javascript/version.test.js b/tests/bindings/javascript/version.test.js
@@ -22,6 +22,6 @@ describe("Version tests", () => {
     libcellml = await libCellMLModule();
   });
   test('Checking version string.', () => {
-    expect(libcellml.versionString()).toBe('0.3.102');
+    expect(libcellml.versionString()).toBe('0.3.103');
   });
 })