Create release v0.5.0-rc.5.

CMakeLists.txt

@@ -19,7 +19,7 @@ set(CMAKE_OSX_DEPLOYMENT_TARGET 10.15 CACHE STRING "Minimum OS X deployment vers
 set(PROJECT_NAME libCellML)
 set(PROJECT_URL https://libcellml.org)
 set(_PROJECT_VERSION 0.5.0)
-set(PROJECT_DEVELOPER_VERSION -rc.4)
+set(PROJECT_DEVELOPER_VERSION -rc.5)
 project(${PROJECT_NAME} VERSION ${_PROJECT_VERSION} LANGUAGES CXX)
 
 # Set policies that affect the build.

docs/changelogs/changelog_v0.5.0-rc.4.rst → docs/changelogs/changelog_v0.5.0-rc.5.rst

@@ -1,10 +1,12 @@
-libCellML v0.5.0-rc.4 Changelog
+libCellML v0.5.0-rc.5 Changelog
 ===============================
 
 Analyser
 --------
 
+* AnaylserModel: Fix loss of Units definition information by `@hsorby <https://github.com/hsorby>`_ [`#1196 <https://github.com/cellml/libcellml/pull/1196>`_].
 * Analyser: add support for unknown variables that have been marked as external by `@agarny <https://github.com/agarny>`_ [`#1184 <https://github.com/cellml/libcellml/pull/1184>`_].
+* AnalyserVariable: hold onto the owning component reference by `@agarny <https://github.com/agarny>`_ [`#1185 <https://github.com/cellml/libcellml/pull/1185>`_].
 * Analyser: don't optimise the order of variables and equations by `@agarny <https://github.com/agarny>`_ [`#1090 <https://github.com/cellml/libcellml/pull/1090>`_].
 * Analyser: reworked the analysis of a model with external variables by `@agarny <https://github.com/agarny>`_ [`#1077 <https://github.com/cellml/libcellml/pull/1077>`_].
 * Analyser: allow for the unknown variable to be either on the LHS or RHS of an equation by `@agarny <https://github.com/agarny>`_ [`#1071 <https://github.com/cellml/libcellml/pull/1071>`_].
@@ -79,11 +81,6 @@ Miscellaneous
 * Analyser/Generator: replace if...else statements with switch ones wherever possible by `@agarny <https://github.com/agarny>`_ [`#1135 <https://github.com/cellml/libcellml/pull/1135>`_].
 * Tests: added support for libXml2 2.9.11+ by `@agarny <https://github.com/agarny>`_ [`#1069 <https://github.com/cellml/libcellml/pull/1069>`_].
 
-No category
------------
-
-* AnalyserVariable: hold onto the owning component reference by `@agarny <https://github.com/agarny>`_ [`#1185 <https://github.com/cellml/libcellml/pull/1185>`_].
-
 Validation
 ----------
 

docs/changelogs/index.rst

@@ -4,7 +4,7 @@ Changelogs
 
 .. toctree::
 
-   changelog_v0.5.0-rc.4
+   changelog_v0.5.0-rc.5
    changelog_v0.4.0
    changelog_v0.3.104
    changelog_v0.3.103

docs/conf.in.py

@@ -51,7 +51,7 @@
 extlinks = {
     # NB for deployment outside of the libcellml.org domain, you will need to include the root of the href for the
     # :api: shortcut here.  This only works internally.
-    'api': ('/documentation/api/latest/classlibcellml_1_1%s', ''),  
+    'api': ('/documentation/api/latest/classlibcellml_1_1%s', ''),
     'buildbot': ('https://buildbot.net/%s',''),
     'cellml': ('https://www.cellml.org/%s',''),
     'cellml2spec': ('https://www.cellml.org/specifications/cellml_2.0%s', ''),

docs/index.rst

@@ -39,7 +39,7 @@ Changelogs
 
 .. toctree::
 
-   changelogs/changelog_v0.5.0-rc.4
+   changelogs/changelog_v0.5.0-rc.5
    changelogs/changelog_v0.4.0
    changelogs/changelog_v0.3.104
    changelogs/changelog_v0.3.103

src/analyser.cpp

@@ -2324,7 +2324,7 @@ void Analyser::AnalyserImpl::analyseModel(const ModelPtr &model)
     // Reset a few things in case this analyser was to be used to analyse more
     // than one model.
 
-    mModel = AnalyserModel::AnalyserModelImpl::create();
+    mModel = AnalyserModel::AnalyserModelImpl::create(model);
 
     mInternalVariables.clear();
     mInternalEquations.clear();

src/analysermodel.cpp

@@ -21,13 +21,18 @@ limitations under the License.
 
 namespace libcellml {
 
-AnalyserModelPtr AnalyserModel::AnalyserModelImpl::create()
+AnalyserModelPtr AnalyserModel::AnalyserModelImpl::create(const ModelPtr &model)
 {
-    return std::shared_ptr<AnalyserModel> {new AnalyserModel {}};
+    return std::shared_ptr<AnalyserModel> {new AnalyserModel(model)};
 }
 
-AnalyserModel::AnalyserModel()
-    : mPimpl(new AnalyserModelImpl())
+AnalyserModel::AnalyserModelImpl::AnalyserModelImpl(const ModelPtr &model)
+    : mModel(model)
+{
+}
+
+AnalyserModel::AnalyserModel(const ModelPtr &model)
+    : mPimpl(new AnalyserModelImpl(model))
 {
 }
 

src/analysermodel_p.h

@@ -27,6 +27,8 @@ namespace libcellml {
  */
 struct AnalyserModel::AnalyserModelImpl
 {
+    ModelPtr mModel;
+
     AnalyserModel::Type mType = Type::UNKNOWN;
 
     bool mHasExternalVariables = false;
@@ -65,7 +67,9 @@ struct AnalyserModel::AnalyserModelImpl
 
     std::map<uintptr_t, bool> mCachedEquivalentVariables;
 
-    static AnalyserModelPtr create();
+    static AnalyserModelPtr create(const ModelPtr &model = nullptr);
+
+    AnalyserModelImpl(const ModelPtr &model);
 };
 
 } // namespace libcellml

src/api/libcellml/analysermodel.h

@@ -510,7 +510,7 @@ class LIBCELLML_EXPORT AnalyserModel
                                 const VariablePtr &variable2);
 
 private:
-    AnalyserModel(); /**< Constructor, @private. */
+    AnalyserModel(const ModelPtr &model); /**< Constructor, @private. */
 
     struct AnalyserModelImpl;
     AnalyserModelImpl *mPimpl; /**< Private member to implementation pointer, @private. */

src/importer.cpp

@@ -787,14 +787,12 @@ void retrieveUnitsDependencies(const ModelPtr &flatModel, const ModelPtr &model,
             auto childUnits = model->units(reference);
             if (childUnits->isImport()) {
                 size_t flatModelUnitsIndex = flatModel->unitsCount();
-                UnitsPtr clonedChildUnits = childUnits->clone();
-                flatModel->addUnits(clonedChildUnits);
-                flattenUnitsImports(flatModel, clonedChildUnits, flatModelUnitsIndex, component);
+                flatModel->addUnits(childUnits);
+                flattenUnitsImports(flatModel, childUnits, flatModelUnitsIndex, component);
             } else {
-                auto clonedChildUnits = childUnits->clone();
-                transferUnitsRenamingIfRequired(model, flatModel, clonedChildUnits, component);
-                u->setUnitAttributeReference(unitIndex, clonedChildUnits->name());
-                retrieveUnitsDependencies(flatModel, model, clonedChildUnits, component);
+                transferUnitsRenamingIfRequired(model, flatModel, childUnits, component);
+                u->setUnitAttributeReference(unitIndex, childUnits->name());
+                retrieveUnitsDependencies(flatModel, model, childUnits, component);
             }
         }
     }
@@ -803,12 +801,11 @@ void retrieveUnitsDependencies(const ModelPtr &flatModel, const ModelPtr &model,
 void flattenUnitsImports(const ModelPtr &flatModel, const UnitsPtr &units, size_t index, const ComponentPtr &component)
 {
     auto importSource = units->importSource();
-    auto importingModel = importSource->model();
-    auto importedUnits = importingModel->units(units->importReference());
-    auto importedUnitsCopy = importedUnits->clone();
-    importedUnitsCopy->setName(units->name());
-    flatModel->replaceUnits(index, importedUnitsCopy);
-    retrieveUnitsDependencies(flatModel, importingModel, importedUnitsCopy, component);
+    auto importingModelCopy = importSource->model()->clone();
+    auto importedUnits = importingModelCopy->units(units->importReference());
+    importedUnits->setName(units->name());
+    flatModel->replaceUnits(index, importedUnits);
+    retrieveUnitsDependencies(flatModel, importingModelCopy, importedUnits, component);
 }
 
 ComponentPtr flattenComponent(const ComponentEntityPtr &parent, ComponentPtr &component, size_t index)

tests/generator/generator.cpp

@@ -1840,19 +1840,22 @@ TEST(Generator, variableInitialisedUsingAConstant)
 
 TEST(Generator, modelOutOfScope)
 {
-    auto analyser = libcellml::Analyser::create();
+    libcellml::AnalyserModelPtr analyserModel;
+
     {
+        auto analyser = libcellml::Analyser::create();
         auto parser = libcellml::Parser::create();
         auto model = parser->parseModel(fileContents("generator/ode_multiple_dependent_odes/model.cellml"));
 
         EXPECT_EQ(size_t(0), parser->issueCount());
 
         analyser->analyseModel(model);
-    }
 
-    EXPECT_EQ(size_t(0), analyser->errorCount());
+        EXPECT_EQ(size_t(0), analyser->errorCount());
+
+        analyserModel = analyser->model();
+    }
 
-    auto analyserModel = analyser->model();
     auto generator = libcellml::Generator::create();
 
     generator->setModel(analyserModel);
@@ -1893,3 +1896,37 @@ TEST(Generator, unknownVariableMarkedAsExternalVariable)
 
     EXPECT_EQ(fileContents("generator/unknown_variable_as_external_variable/model.py"), generator->implementationCode());
 }
+
+TEST(Generator, modelWithComplexUnitsOutOfScope)
+{
+    libcellml::AnalyserModelPtr analyserModel;
+
+    {
+        auto analyser = libcellml::Analyser::create();
+        auto parser = libcellml::Parser::create();
+        auto importer = libcellml::Importer::create();
+        auto model = parser->parseModel(fileContents("generator/cellml_slc_example/slc_model.cellml"));
+
+        EXPECT_EQ(size_t(0), parser->issueCount());
+
+        importer->resolveImports(model, resourcePath("generator/cellml_slc_example"));
+        EXPECT_FALSE(model->hasUnresolvedImports());
+
+        model = importer->flattenModel(model);
+
+        analyser->analyseModel(model);
+        EXPECT_EQ(size_t(0), analyser->errorCount());
+
+        analyserModel = analyser->model();
+    }
+
+    auto generator = libcellml::Generator::create();
+
+    generator->setModel(analyserModel);
+
+    auto profile = libcellml::GeneratorProfile::create(libcellml::GeneratorProfile::Profile::PYTHON);
+
+    generator->setProfile(profile);
+
+    EXPECT_EQ(fileContents("generator/cellml_slc_example/model.py"), generator->implementationCode());
+}

tests/importer/model_flattening.cpp

@@ -1863,3 +1863,39 @@ TEST(ModelFlattening, resolveImportsInvalidInput)
     EXPECT_EQ(size_t(1), importer->issueCount());
     EXPECT_EQ("Cannot resolve imports for null model.", importer->issue(0)->description());
 }
+
+TEST(ModelFlattening, flatteningImportedUnitsThatNeedEquivalence)
+{
+    const std::string e =
+        "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
+        "<model xmlns=\"http://www.cellml.org/cellml/2.0#\" name=\"test_model\">\n"
+        "  <units name=\"per_fmol\">\n"
+        "    <unit exponent=\"-1\" units=\"fmol\"/>\n"
+        "  </units>\n"
+        "  <units name=\"fmol\">\n"
+        "    <unit prefix=\"femto\" units=\"mole\"/>\n"
+        "  </units>\n"
+        "  <units name=\"per_fmol_sec4\">\n"
+        "    <unit units=\"per_fmol\"/>\n"
+        "    <unit exponent=\"4\" units=\"per_sec\"/>\n"
+        "  </units>\n"
+        "  <units name=\"per_sec\">\n"
+        "    <unit exponent=\"-1\" units=\"second\"/>\n"
+        "  </units>\n"
+        "</model>\n";
+
+    auto parser = libcellml::Parser::create();
+    auto importer = libcellml::Importer::create();
+
+    auto model = parser->parseModel(fileContents("generator/cellml_slc_example/slc_model_units_only.cellml"));
+
+    EXPECT_EQ(size_t(0), parser->issueCount());
+
+    importer->resolveImports(model, resourcePath("generator/cellml_slc_example"));
+    EXPECT_FALSE(model->hasUnresolvedImports());
+
+    auto flatModel = importer->flattenModel(model);
+
+    auto printer = libcellml::Printer::create();
+    EXPECT_EQ(e, printer->printModel(flatModel));
+}

tests/resources/generator/cellml_slc_example/model.py

@@ -0,0 +1,54 @@
+# The content of this file was generated using the Python profile of libCellML 0.5.0.
+
+from enum import Enum
+from math import *
+
+
+__version__ = "0.4.0"
+LIBCELLML_VERSION = "0.5.0"
+
+VARIABLE_COUNT = 10
+
+
+class VariableType(Enum):
+    CONSTANT = 0
+    COMPUTED_CONSTANT = 1
+    ALGEBRAIC = 2
+
+
+VARIABLE_INFO = [
+    {"name": "v", "units": "fmol_per_sec", "component": "SLC_template3_ss", "type": VariableType.COMPUTED_CONSTANT},
+    {"name": "E", "units": "fmol", "component": "SLC_template3_ss", "type": VariableType.CONSTANT},
+    {"name": "P_0", "units": "per_fmol_sec4", "component": "SLC_template3_ss", "type": VariableType.CONSTANT},
+    {"name": "q_Ao", "units": "fmol", "component": "SLC_template3_ss", "type": VariableType.CONSTANT},
+    {"name": "P_1", "units": "per_fmol_sec4", "component": "SLC_template3_ss", "type": VariableType.CONSTANT},
+    {"name": "q_Ai", "units": "fmol", "component": "SLC_template3_ss", "type": VariableType.CONSTANT},
+    {"name": "P_2", "units": "per_fmol_sec3", "component": "SLC_template3_ss", "type": VariableType.CONSTANT},
+    {"name": "P_5", "units": "per_sec3", "component": "SLC_template3_ss", "type": VariableType.CONSTANT},
+    {"name": "P_4", "units": "per_fmol2_sec3", "component": "SLC_template3_ss", "type": VariableType.CONSTANT},
+    {"name": "P_3", "units": "per_fmol_sec3", "component": "SLC_template3_ss", "type": VariableType.CONSTANT}
+]
+
+
+def create_variables_array():
+    return [nan]*VARIABLE_COUNT
+
+
+def initialise_variables(variables):
+    variables[1] = 1.1
+    variables[2] = 21262500.0
+    variables[3] = 150.0
+    variables[4] = 3402000.0
+    variables[5] = 2.0
+    variables[6] = 2902500.0
+    variables[7] = 810000.0
+    variables[8] = 247140.0
+    variables[9] = 2902500.0
+
+
+def compute_computed_constants(variables):
+    variables[0] = variables[1]*(variables[2]*variables[3]-variables[4]*variables[5])/(variables[6]*variables[5]+variables[9]*variables[3]+variables[8]*variables[5]*variables[3]+variables[7])
+
+
+def compute_variables(variables):
+    pass

tests/resources/generator/cellml_slc_example/slc_model.cellml

@@ -0,0 +1,71 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<model xmlns="http://www.cellml.org/cellml/2.0#" name="test_model">
+  <import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="units_BG.cellml">
+    <units units_ref="per_sec" name="per_sec"/>
+    <units units_ref="fmol_per_sec" name="fmol_per_sec"/>
+    <units units_ref="per_fmol" name="per_fmol"/>
+    <units units_ref="fmol" name="fmol"/>
+    <units units_ref="per_fmol_sec4" name="per_fmol_sec4"/>
+    <units units_ref="per_fmol_sec3" name="per_fmol_sec3"/>
+    <units units_ref="per_fmol2_sec3" name="per_fmol2_sec3"/>
+    <units units_ref="per_sec3" name="per_sec3"/>
+  </import>
+  <component name="SLC_template3_ss">
+    <variable name="v" units="fmol_per_sec" />
+    <variable name="E" units="fmol" initial_value="1.1" />
+    <variable name="q_Ai" units="fmol" initial_value="2"/>
+    <variable name="q_Ao" units="fmol" initial_value="150" />
+    <variable name="P_0" units="per_fmol_sec4" initial_value="21262500" id="b4da6c"/>
+    <variable name="P_1" units="per_fmol_sec4" initial_value="3402000"  id="b4da6d"/>
+    <variable name="P_2" units="per_fmol_sec3"  initial_value="2902500"  id="b4da6e"/>
+    <variable name="P_3" units="per_fmol_sec3"  initial_value="2902500" interface="public" id="b4da6f"/>
+    <variable name="P_4" units="per_fmol2_sec3" initial_value="247140"  id="b4da70"/>
+    <variable name="P_5" units="per_sec3" initial_value="810000"  id="b4da71"/>
+    <math xmlns="http://www.w3.org/1998/Math/MathML" xmlns:cellml="http://www.cellml.org/cellml/2.0#">
+      <apply>
+        <eq/>
+        <ci>v</ci>
+        <apply>
+          <divide/>
+          <apply>
+            <times/>
+            <ci>E</ci>
+            <apply>
+              <minus/>
+              <apply>
+                <times/>
+                <ci>P_0</ci>
+                <ci>q_Ao</ci>
+              </apply>
+              <apply>
+                <times/>
+                <ci>P_1</ci>
+                <ci>q_Ai</ci>
+              </apply>
+            </apply>
+          </apply>
+          <apply>
+            <plus/>
+            <apply>
+              <times/>
+              <ci>P_2</ci>
+              <ci>q_Ai</ci>
+            </apply>
+            <apply>
+              <times/>
+              <ci>P_3</ci>
+              <ci>q_Ao</ci>
+            </apply>
+            <apply>
+              <times/>
+              <ci>P_4</ci>
+              <ci>q_Ai</ci>
+              <ci>q_Ao</ci>
+            </apply>
+            <ci>P_5</ci>
+          </apply>
+        </apply>
+      </apply>
+    </math>
+  </component>
+</model>