Merge c2e8949 into 9f90a3b

clean

@@ -1,3 +1,3 @@
 #!/bin/sh
 
-"$(cd "$(dirname "$0")"; pwd)/scripts/genericclean"
+$(cd $(dirname $0); pwd)/scripts/genericclean

clean.bat

@@ -1,3 +1,3 @@
 @ECHO OFF
 
-CALL "%~dp0scripts\genericclean"
+CALL %~dp0scripts\genericclean

cleanall

@@ -1,3 +1,3 @@
 #!/bin/sh
 
-"$(cd "$(dirname "$0")"; pwd)/scripts/genericclean" all
+$(cd $(dirname $0); pwd)/scripts/genericclean all

cleanall.bat

@@ -1,3 +1,3 @@
 @ECHO OFF
 
-CALL "%~dp0scripts\genericclean" all
+CALL %~dp0scripts\genericclean all

distrib/windows/application.vbs.in

@@ -1,9 +1,9 @@
-args = ""
+Args = ""
 
-For Each arg in WScript.Arguments
-    args = args&" "&arg
+For Each Arg in WScript.Arguments
+    Args = Args&" "&Arg
 Next
 
-cmd = Left(Wscript.ScriptFullName, Len(Wscript.ScriptFullName)-Len(Wscript.ScriptName))&"bin\${CMAKE_PROJECT_NAME}.exe"&args
+cmd = Left(Wscript.ScriptFullName, Len(Wscript.ScriptFullName)-Len(Wscript.ScriptName))&"bin\${CMAKE_PROJECT_NAME}.exe"&Args
 
 CreateObject("WScript.Shell").Run cmd, 1, False

distrib/windows/jupyterlab.vbs

@@ -1,9 +1,9 @@
-Set shell = CreateObject("WScript.Shell")
-appDir = CreateObject("Scripting.FileSystemObject").GetParentFolderName(WScript.ScriptFullName)
-updatePythonPath = appDir&"\Python\bin\Python.exe "&appDir&"\Python\Scripts\set_python_path.py "&appDir&"\Python -s"
+Set Shell = CreateObject("WScript.Shell")
+AppDir = CreateObject("Scripting.FileSystemObject").GetParentFolderName(WScript.ScriptFullName)
+UpdatePythonPath = AppDir&"\Python\bin\Python.exe "&AppDir&"\Python\Scripts\set_python_path.py "&AppDir&"\Python -s"
 
-shell.Run updatePythonPath, 0, True
+Shell.Run UpdatePythonPath, 0, True
 
-cmd = appDir&"\Python\bin\Python.exe "&appDir&"\Python\Scripts\start_jupyter.py lab --ip 127.0.0.1"
+Cmd = AppDir&"\Python\bin\Python.exe "&AppDir&"\Python\Scripts\start_jupyter.py lab --ip 127.0.0.1"
 
-shell.Run cmd, 1, False
+Shell.Run Cmd, 1, False

distrib/windows/jupyternotebook.vbs

@@ -1,9 +1,9 @@
-Set shell = CreateObject("WScript.Shell")
-appDir = CreateObject("Scripting.FileSystemObject").GetParentFolderName(WScript.ScriptFullName)
-updatePythonPath = appDir&"\Python\bin\Python.exe "&appDir&"\Python\Scripts\set_python_path.py "&appDir&"\Python -s"
+Set Shell = CreateObject("WScript.Shell")
+AppDir = CreateObject("Scripting.FileSystemObject").GetParentFolderName(WScript.ScriptFullName)
+UpdatePythonPath = AppDir&"\Python\bin\Python.exe "&AppDir&"\Python\Scripts\set_python_path.py "&AppDir&"\Python -s"
 
-shell.Run updatePythonPath, 0, True
+Shell.Run UpdatePythonPath, 0, True
 
-cmd = appDir&"\Python\bin\Python.exe "&appDir&"\Python\Scripts\start_jupyter.py notebook --ip 127.0.0.1"
+Cmd = AppDir&"\Python\bin\Python.exe "&AppDir&"\Python\Scripts\start_jupyter.py notebook --ip 127.0.0.1"
 
-shell.Run cmd, 1, False
+Shell.Run Cmd, 1, False

doc/downloads/index.js

@@ -37,8 +37,8 @@ var jsonData = { "versions": [
                        }
                      ],
                      "changes": [
-                       { "change": "<strong>General:</strong> added (initial) support for <a href=\"https://python.org/\">Python</a> (see issue <a href=\"https://github.com/opencor/opencor/issues/1255\">#1255</a>). Replaced our use of <a href=\"https://developer.apple.com/library/archive/documentation/DeveloperTools/Conceptual/PackageMakerUserGuide/Introduction/Introduction.html\">PackageMaker</a> with that of productbuild on <a href=\"https://en.wikipedia.org/wiki/MacOS\">macOS</a> (see issue <a href=\"https://github.com/opencor/opencor/issues/2210\">#2210</a>). A selectable plugin cannot be needed by another plugin (see issue <a href=\"https://github.com/opencor/opencor/issues/2247\">#2247</a>)." },
-                       { "change": "<strong>Python support:</strong> now update the environment variable <code>PATH</code> using <code>\\</code> rather than <code>/</code> on Windows (see issue <a href=\"https://github.com/opencor/opencor/issues/2219\">#2219</a>). Merged our duplicated code (see issue <a href=\"https://github.com/opencor/opencor/issues/2225\">#2225</a>). Don't make our JupyterKernel and PythonShell plugins selectable (see issue <a href=\"https://github.com/opencor/opencor/issues/2245\">#2245</a>). Make sure that \"implementation\" and \"implementation_version\" are properly set in the JupyterKernel plugin (see issue <a href=\"https://github.com/opencor/opencor/issues/2250\">#2250</a>)." },
+                       { "change": "<strong>General:</strong> Replaced our use of <a href=\"https://developer.apple.com/library/archive/documentation/DeveloperTools/Conceptual/PackageMakerUserGuide/Introduction/Introduction.html\">PackageMaker</a> with that of productbuild on <a href=\"https://en.wikipedia.org/wiki/MacOS\">macOS</a> (see issue <a href=\"https://github.com/opencor/opencor/issues/2210\">#2210</a>). A selectable plugin cannot be needed by another plugin (see issue <a href=\"https://github.com/opencor/opencor/issues/2247\">#2247</a>)." },
+                       { "change": "<strong>Python support:</strong> added (initial) support for <a href=\"https://python.org/\">Python</a> (see issue <a href=\"https://github.com/opencor/opencor/issues/1255\">#1255</a>). Added some <a href=\"https://python.org/\">Python</a>-based tests (see issue <a href=\"https://github.com/opencor/opencor/issues/2178\">#2178</a>). Now update the environment variable <code>PATH</code> using <code>\\</code> rather than <code>/</code> on Windows (see issue <a href=\"https://github.com/opencor/opencor/issues/2219\">#2219</a>). Merged our duplicated code (see issue <a href=\"https://github.com/opencor/opencor/issues/2225\">#2225</a>). Don't make our JupyterKernel and PythonShell plugins selectable (see issue <a href=\"https://github.com/opencor/opencor/issues/2245\">#2245</a>). Make sure that \"implementation\" and \"implementation_version\" are properly set in the JupyterKernel plugin (see issue <a href=\"https://github.com/opencor/opencor/issues/2250\">#2250</a>)." },
                        { "change": "<strong>CellML support:</strong> fixed an issue with the CellML API wrongly allowing code generation for non-runnable models (see issue <a href=\"https://github.com/opencor/opencor/issues/2240\">#2240</a>)." },
                        { "change": "<strong>SED-ML support:</strong> added support left and right triangle symbols (see issue <a href=\"https://github.com/opencor/opencor/issues/2173\">#2173</a>)." },
                        { "change": "<strong>Simulation support:</strong> don't require all our solvers to be installed anymore (see issue <a href=\"https://github.com/opencor/opencor/issues/2234\">#2234</a>)." },

format

@@ -1,12 +1,12 @@
 #!/bin/sh
 
-appDir="$(cd "$(dirname "$0")"; pwd)"
+appDir=$(cd $(dirname $0); pwd)
 
-if [ -d "${appDir}/src" ]; then
+if [ -d $appDir/src ]; then
     echo "\033[44;37;1mFormatting OpenCOR...\033[0m"
 
     if [ "`hash clang-format 2>&1`" = "" ]; then
-        for i in `find ${appDir}/src -name "*.cpp" -o -name "*.h" | sort | egrep -v "(3rdparty|\/ext\/|\/qzip)"`; do
+        for i in `find $appDir/src -name "*.cpp" -o -name "*.h" | sort | egrep -v "(3rdparty|\/ext\/|\/qzip)"`; do
             echo "Formatting $i..."
 
             clang-format -i -style=file $i

format.bat

@@ -3,15 +3,15 @@
 SET AppDir=%~dp0
 SET OrigDir=%CD%
 
-IF EXIST "%AppDir%src" (
+IF EXIST %AppDir%src (
     TITLE Formatting OpenCOR...
 
     FOR %%X IN (clang-format.exe) DO (
         SET ClangFormatFound=%%~$PATH:X
     )
 
     IF DEFINED ClangFormatFound (
-        CD "%AppDir%src"
+        CD %AppDir%src
 
         FOR /R %%I IN (*.cpp *.h) DO (
             ECHO.%%I | FINDSTR /V "3rdparty \ext\ \qzip">NUL && (
@@ -21,7 +21,7 @@ IF EXIST "%AppDir%src" (
             )
         )
 
-        CD "%OrigDir%"
+        CD %OrigDir%
     ) ELSE (
         ECHO Clang-Format is not installed.
     )

make

@@ -1,3 +1,3 @@
 #!/bin/sh
 
-"$(cd "$(dirname "$0")"; pwd)/scripts/genericmake" Release $*
+$(cd $(dirname $0); pwd)/scripts/genericmake Release "$@"

make.bat

@@ -1,3 +1,3 @@
 @ECHO OFF
 
-CALL "%~dp0scripts\genericmake" Release %*
+CALL %~dp0scripts\genericmake Release %*

maketests

@@ -1,3 +1,3 @@
 #!/bin/sh
 
-"$(cd "$(dirname "$0")"; pwd)/scripts/genericmake" Tests $*
+$(cd $(dirname $0); pwd)/scripts/genericmake Tests "$@"

maketests.bat

@@ -1,3 +1,3 @@
 @ECHO OFF
 
-CALL "%~dp0scripts\genericmake" Tests %*
+CALL %~dp0scripts\genericmake Tests %*

models/tests/sedml/lorenz.sedml

@@ -136,7 +136,7 @@
                             <title>x vs. t</title>
                             <line>
                                 <style>solid</style>
-                                <width>3</width>
+                                <width>2</width>
                                 <color>#0072bd</color>
                             </line>
                             <symbol>

package

@@ -1,9 +1,9 @@
 #!/bin/sh
 
-appDir="$(cd "$(dirname "$0")"; pwd)"
+appDir=$(cd $(dirname $0); pwd)
 
-${appDir}/clean
-${appDir}/make $*
+$appDir/clean
+$appDir/make $*
 
 exitCode=$?
 
@@ -15,7 +15,7 @@ echo "\033[44;37;1mPackaging OpenCOR...\033[0m"
 
 origDir=`pwd`
 
-cd ${appDir}/build
+cd $appDir/build
 
 cpack
 
@@ -24,13 +24,13 @@ exitCode=$?
 if [ "`uname -s`" = "Darwin" ]; then
     packageName="OpenCOR-`date '+%Y-%m-%d'`-macOS"
 
-    mkdir ${packageName}
+    mkdir $packageName
 
-    mv ${packageName}.pkg ${packageName}
+    mv $packageName.pkg $packageName
 
-    hdiutil create -srcfolder ${packageName} ${packageName}.dmg
+    hdiutil create -srcfolder $packageName $packageName.dmg
 
-    rm -fr ${packageName}
+    rm -fr $packageName
 fi
 
 cd $origDir

package.bat

@@ -4,8 +4,8 @@ SETLOCAL ENABLEDELAYEDEXPANSION
 
 SET AppDir=%~dp0
 
-CALL "%AppDir%clean"
-CALL "%AppDir%make" %*
+CALL %AppDir%clean
+CALL %AppDir%make %*
 
 SET ExitCode=!ERRORLEVEL!
 
@@ -14,13 +14,13 @@ IF !ExitCode! EQU 0 (
 
     SET OrigDir=%CD%
 
-    CD "%AppDir%build"
+    CD %AppDir%build
 
     cpack
 
     SET ExitCode=!ERRORLEVEL!
 
-    CD "%OrigDir%"
+    CD %OrigDir%
 )
 
 EXIT /B !ExitCode!

run

@@ -2,16 +2,16 @@
 
 echo "\033[44;37;1mRunning OpenCOR...\033[0m"
 
-appDir="$(cd "$(dirname "$0")"; pwd)"
+appDir=$(cd $(dirname $0); pwd)
 
 if [ "`uname -s`" = "Linux" ]; then
-    appExe=${appDir}/build/bin/OpenCOR
+    appExe=$appDir/build/bin/OpenCOR
 else
-    appExe=${appDir}/build/OpenCOR.app/Contents/MacOS/OpenCOR
+    appExe=$appDir/build/OpenCOR.app/Contents/MacOS/OpenCOR
 fi
 
-if [ -f ${appExe} ]; then
-    ${appExe} "$@"
+if [ -f $appExe ]; then
+    $appExe "$@"
 else
     echo "OpenCOR must first be built before being run."
 fi

run.bat

@@ -5,11 +5,11 @@ TITLE Running OpenCOR...
 SET AppBase=%~dp0build\bin\OpenCOR
 SET NeedInformation=
 
-IF NOT EXIST "%AppBase%.com" SET NeedInformation=Yes
-IF NOT EXIST "%AppBase%.exe" SET NeedInformation=Yes
+IF NOT EXIST %AppBase%.com SET NeedInformation=Yes
+IF NOT EXIST %AppBase%.exe SET NeedInformation=Yes
 
 IF DEFINED NeedInformation (
     ECHO OpenCOR must first be built before being run.
 ) ELSE (
-    "%AppBase%" %*
+    %AppBase% %*
 )

run.vbs

@@ -1,15 +1,15 @@
 AppExe = Left(Wscript.ScriptFullName, Len(Wscript.ScriptFullName)-Len(Wscript.ScriptName))&"build\bin\OpenCOR.exe"
 
 If CreateObject("Scripting.FileSystemObject").FileExists(AppExe) Then
-    args = ""
+    Args = ""
 
-    For Each arg in WScript.Arguments
-        args = args&" "&arg
+    For Each Arg in WScript.Arguments
+        Args = Args&" "&Arg
     Next
 
-    cmd = """"&AppExe&args&""""
+    Cmd = AppExe&Args
 
-    CreateObject("WScript.Shell").Run cmd, 1, False
+    CreateObject("WScript.Shell").Run Cmd, 1, False
 Else
     WScript.Echo "OpenCOR must first be built before being run."
 End If

runtests

@@ -2,16 +2,16 @@
 
 echo "\033[44;37;1mRunning OpenCOR's tests...\033[0m"
 
-appDir="$(cd "$(dirname "$0")"; pwd)"
+appDir=$(cd $(dirname $0); pwd)
 
 if [ "`uname -s`" = "Linux" ]; then
-    OPENCOR_TESTS_EXE=${appDir}/build/bin/runtests
+    appTestsExe=$appDir/build/bin/runtests
 else
-    OPENCOR_TESTS_EXE=${appDir}/build/OpenCOR.app/Contents/MacOS/runtests
+    appTestsExe=$appDir/build/OpenCOR.app/Contents/MacOS/runtests
 fi
 
-if [ -f ${OPENCOR_TESTS_EXE} ]; then
-    ${OPENCOR_TESTS_EXE} "$@"
+if [ -f $appTestsExe ]; then
+    $appTestsExe "$@"
 else
     echo "OpenCOR's tests must first be built before being run."
 fi

runtests.bat

@@ -7,5 +7,5 @@ SET AppTestsExe=%~dp0build\bin\runtests.exe
 IF NOT EXIST %AppTestsExe% (
     ECHO OpenCOR's tests must first be built before being run.
 ) ELSE (
-    "%AppTestsExe%"
+    %AppTestsExe% %*
 )

src/misc/furtherinitialize.cpp.inl

@@ -124,7 +124,7 @@ QString Simulation::furtherInitialize() const
                             }
 #else
 
-                            mData->addNlaSolverProperty(id, value);
+                            mData->setNlaSolverProperty(id, value);
 #endif
                         }
                     }

src/misc/initializesolver.cpp.inl

@@ -110,7 +110,7 @@ QString Simulation::initializeSolver(const libsedml::SedListOfAlgorithmParameter
         }
 #else
 
-        mData->addOdeSolverProperty(solverInterface->id(parameterKisaoId),
+        mData->setOdeSolverProperty(solverInterface->id(parameterKisaoId),
                                     QString::fromStdString(sedmlAlgorithmParameter->getValue()));
 #endif
     }