Ensure Translate/OutputSBML work on Octave and Matlab

.github/workflows/octave.yml

@@ -0,0 +1,71 @@
+name: Octave
+
+on: [push]
+
+env:
+  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
+  BUILD_TYPE: Release
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Checkout submodules
+      run: git submodule update --init --recursive
+
+    - name: update 
+      if: matrix.os == 'ubuntu-latest'
+      shell: bash
+      run: |
+           sudo apt-get update
+
+    - name: add linux dependencies
+      if: matrix.os == 'ubuntu-latest'
+      shell: bash
+      run: |
+           sudo apt-get install swig liboctave-dev
+
+    - name: Create Build Environment
+      # Some projects don't allow in-source building, so create a separate build directory
+      # We'll use this as our working directory for all subsequent commands
+      run: cmake -E make_directory ${{runner.workspace}}/build
+
+    - name: Configure
+      # build dependencies
+      working-directory: ${{runner.workspace}}/build
+      shell: bash
+      run: |
+          cmake -DCMAKE_INSTALL_PREFIX=${{runner.workspace}}/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DWITH_BZIP2=ON -DWITH_CHECK=OFF -DWITH_EXPAT=ON -DWITH_LIBXML=OFF -DWITH_OCTAVE=ON $GITHUB_WORKSPACE
+
+    - name: Build
+      working-directory: ${{runner.workspace}}/build
+      shell: bash
+      # Execute the build.  You can specify a specific target with "--target <NAME>"
+      run: cmake --build . --config $BUILD_TYPE
+
+
+    - name: Install Strip
+      working-directory: ${{runner.workspace}}/build
+      run: cmake --install . --prefix instdir --strip
+
+    - name: Pack
+      working-directory: ${{runner.workspace}}/build/instdir
+      run: cmake -E tar cvzf ../octave_${{ matrix.os }}.tar.gz .
+
+    - name: Test
+      working-directory: ${{runner.workspace}}/build/instdir/lib/octave/site/oct/x86_64-pc-linux-gnu/test
+      shell: bash
+      run: LD_LIBRARY_PATH=../../../../.. octave --eval "runTests()"
+
+    - name: Upload
+      uses: actions/upload-artifact@v1
+      with:
+        path: ${{runner.workspace}}/build/octave_${{ matrix.os }}.tar.gz
+        name: octave_${{ matrix.os }}.tar.gz

src/bindings/matlab/.gitignore

@@ -1,2 +1,7 @@
 runTests.log
 *.mex*
+testout.xml
+mytest.m
+*.asv
+test/Out-test1/*
+

src/bindings/matlab/CMakeLists.txt

@@ -92,10 +92,17 @@ endif()
 	if (EXTRA_INCLUDE_DIRS) 
 	  include_directories(${EXTRA_INCLUDE_DIRS})
 	endif(EXTRA_INCLUDE_DIRS)
+
+	SET(COMMON_FILES
+		"${CMAKE_CURRENT_SOURCE_DIR}/ModelDetails.cpp"
+		"${CMAKE_CURRENT_SOURCE_DIR}/StructureFields.cpp"
+		"${CMAKE_CURRENT_SOURCE_DIR}/CommonFunctions.cpp"
+		"${CMAKE_CURRENT_SOURCE_DIR}/Filenames.cpp"
+		"${CMAKE_CURRENT_SOURCE_DIR}/InputOutput.cpp"	)
 
 	foreach(matlab_source_file "TranslateSBML" "OutputSBML")
 
-		add_library(matlab_binding_${matlab_source_file} SHARED "${CMAKE_CURRENT_SOURCE_DIR}/${matlab_source_file}.cpp")
+		add_library(matlab_binding_${matlab_source_file} SHARED "${CMAKE_CURRENT_SOURCE_DIR}/${matlab_source_file}.cpp" ${COMMON_FILES})
 		set_target_properties(matlab_binding_${matlab_source_file} PROPERTIES OUTPUT_NAME "${matlab_source_file}")
 		set_target_properties(matlab_binding_${matlab_source_file} PROPERTIES SUFFIX ".${MATLAB_MEX_EXT}")
                 set_target_properties(matlab_binding_${matlab_source_file} PROPERTIES  PREFIX "")

src/bindings/matlab/CommonFunctions.cpp

@@ -0,0 +1,114 @@
+#include "CommonFunctions.h"
+
+
+//
+// report error/free memory and exit when error encountered
+
+void 
+FreeMem(GV& gv)
+{
+  /* destroy arrays created */
+  mxDestroyArray(gv.modelArray);
+  gv.modelArray = NULL;
+}
+
+void
+reportError(const std::string&id, const std::string& message, GV& gv)
+{
+  if (gv.freeMemory)
+  {
+    FreeMem(gv);
+  }
+
+  mexErrMsgIdAndTxt(id.c_str(), message.c_str());
+}
+
+
+void
+displayLine(const std::string& line)
+{
+  mxArray* mxErrors[1];
+  mxErrors[0] = mxCreateString(line.c_str());
+  mexCallMATLAB(0, NULL, 1, mxErrors, "disp");
+  mxDestroyArray(mxErrors[0]);
+}
+
+
+mxArray *
+CreateIntScalar (int nValue)
+{
+  mxArray * pArray;
+  int * panData;
+
+  pArray = mxCreateNumericMatrix(1,1,mxINT32_CLASS, mxREAL);
+  panData = (int *)mxGetData(pArray);
+  panData[0] = nValue;
+
+  return pArray;
+}
+
+const char* FIELDTYPE_STRINGS[] =
+{
+      "bool"
+    , "char"
+    , "double"
+    , "int"
+    , "structure"
+    , "uint"
+};
+
+
+FieldType_t
+getFieldType(const char* type)
+{
+  if (type != NULL)
+  {
+    const FieldType_t lo = TYPE_BOOL;
+    const FieldType_t hi = (const FieldType_t)(TYPE_UNKNOWN - 1);
+
+    return (FieldType_t)util_bsearchStringsI(FIELDTYPE_STRINGS, type, lo, hi);
+  }
+  else
+    return TYPE_UNKNOWN;
+}
+
+// only used by OutputSBML
+bool getRequiredStatus(const std::string& prefix, GV& gv)
+{
+  bool required = false;
+
+  if (gv.reqdPkgPrefixes.contains(prefix))
+  {
+    required = true;
+  }
+
+  return required;
+}
+
+void populatePackageLists(GV& gv)
+{
+  //reqdPkgPrefixes.append("comp");
+  //reqdPkgPrefixes.append("spatial");
+
+  gv.unreqdPkgPrefixes.append("fbc");
+  gv.unreqdPkgPrefixes.append("qual");
+  gv.unreqdPkgPrefixes.append("groups");
+}
+
+// only used by OutputSBML
+bool
+isUnknownType(std::string tc)
+{
+  // TO DO 
+  if (tc == "(Unknown SBML Type)")
+    return true;
+  else if (tc == "(Unknown SBML Fbc Type)")
+    return true;
+  else if (tc == "(Unknown SBML Groups Type)")
+    return true;
+  else if (tc == "(Unknown SBML Qual Type)")
+    return true;
+  else
+    return false;
+}
+

src/bindings/matlab/CommonFunctions.h

@@ -0,0 +1,24 @@
+#ifndef COMMON_FUNTICONS_INCLUDED
+#define COMMON_FUNTICONS_INCLUDED
+
+#include <string>
+
+#include "Variables.h"
+
+void FreeMem(GV& gv);
+
+void reportError(const std::string&id, const std::string& message, GV& gv);
+
+void displayLine(const std::string& line);
+
+mxArray * CreateIntScalar (int nValue);
+
+FieldType_t getFieldType(const char* type);
+
+bool getRequiredStatus(const std::string& prefix, GV& gv);
+
+void populatePackageLists(GV& gv);
+
+bool isUnknownType(std::string tc);
+
+#endif // COMMON_FUNTICONS_INCLUDED

src/bindings/matlab/ConvertFormulaToMathML.m

@@ -119,7 +119,7 @@
     j = j+1;
     x = SubFormula(j:length(SubFormula)-1);
 
-    if (exist('OCTAVE_VERSION', 'var'))
+    if (exist('OCTAVE_VERSION'))
       ReplaceFormula = myRegexprep(SubFormula, n, x, 'once');
       ReplaceFormula = myRegexprep(ReplaceFormula,regexptranslate('escape',x),n,2);
       ReplaceFormula = myRegexprep(ReplaceFormula, 'nthroot', 'root', 'once');