Merge remote-tracking branch 'opensim-org/master' into FixingSO

Author: pariterre

.clang-format

@@ -0,0 +1,129 @@
+# This file can be used by the clang-format tool to 
+# automatically format C++ source code.
+# See https://clang.llvm.org/docs/ClangFormat.html.
+# You can either run clang-format directly, or you can use
+# Integrated Development Environments (IDEs) that support clang-format,
+# such as:
+#  - Visual Studio (https://devblogs.microsoft.com/cppblog/clangformat-support-in-visual-studio-2017-15-7-preview-1/),
+#  - CLion (https://www.jetbrains.com/help/clion/clangformat-as-alternative-formatter.html).
+# See the documentation for IDEs for more information.
+---
+Language:        Cpp
+# BasedOnStyle:  LLVM
+AccessModifierOffset: -4
+AlignAfterOpenBracket: DontAlign 
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlines: Right
+AlignOperands:   true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: true 
+AllowShortCaseLabelsOnASingleLine: true 
+AllowShortFunctionsOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: true 
+AllowShortLoopsOnASingleLine: true 
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+# AlwaysBreakTemplateDeclarations: Yes
+BinPackArguments: true
+BinPackParameters: true
+BraceWrapping:   
+  AfterClass:      false
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   false
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  AfterExternBlock: false
+  BeforeCatch:     false
+  BeforeElse:      false
+  IndentBraces:    false
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Attach
+BreakBeforeInheritanceComma: false
+# BreakInheritanceList: BeforeColon
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakConstructorInitializers: BeforeColon
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+ColumnLimit:     80
+CommentPragmas:  '^ IWYU pragma:'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerIndentWidth: 8
+ContinuationIndentWidth: 8
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+DisableFormat:   false
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros:   
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+IncludeBlocks:   Regroup
+IncludeCategories: 
+  - Regex:           '^(<SimTKcommon/)'
+    Priority:        2
+  - Regex:           '^(<simbody/)'
+    Priority:        3
+  - Regex:           '^(<OpenSim/)'
+    Priority:        4
+  - Regex:           '.*'
+    Priority:        1
+IncludeIsMainRegex: '(Test)?$'
+IndentCaseLabels: false
+IndentPPDirectives: AfterHash
+IndentWidth:     4
+IndentWrappedFunctionNames: false
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: true
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+# ObjCBinPackProtocolList: Auto
+ObjCBlockIndentWidth: 2
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: true
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+# PenaltyBreakTemplateDeclaration: 10
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 60
+PointerAlignment: Left
+ReflowComments:  true
+SortIncludes:    true
+SortUsingDeclarations: true
+SpaceAfterCStyleCast: false
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+# SpaceBeforeCpp11BracedList: false
+# SpaceBeforeCtorInitializerColon: true
+# SpaceBeforeInheritanceColon: true
+SpaceBeforeParens: ControlStatements
+# SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Cpp11
+TabWidth:        4
+UseTab:          Never
+...
+

.github/workflows/continuous_integration.yml

@@ -0,0 +1,129 @@
+name: continuous-integration
+
+# TODO: build master branch after PRs are merged.
+# syntax https://help.github.com/en/articles/workflow-syntax-for-github-actions
+on:
+  schedule:
+  - cron: '0 2 * * *'
+    
+jobs:
+  windows:
+    name: Windows
+
+    runs-on: windows-2016
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Install Chocolatey packages
+      run: choco install swig --version 3.0.9 --yes --limit-output 
+    - name: Build
+      run: |
+        echo %GITHUB_WORKSPACE%\\build_deps
+        mkdir %GITHUB_WORKSPACE%\\build_deps
+        chdir %GITHUB_WORKSPACE%\\build_deps
+        cmake --version
+        cmake %GITHUB_WORKSPACE%\\dependencies -G"Visual Studio 15 2017" -A x64 -DCMAKE_INSTALL_PREFIX=%GITHUB_WORKSPACE%\\opensim_dependencies_install
+        cmake --build . --config Release -- /maxcpucount:4 
+        mkdir %GITHUB_WORKSPACE%\\build 
+        chdir %GITHUB_WORKSPACE%\\build
+        cmake %GITHUB_WORKSPACE% -G"Visual Studio 15 2017" -A x64 -DCMAKE_INSTALL_PREFIX=%GITHUB_WORKSPACE%\\opensim-core-install -DOPENSIM_DEPENDENCIES_DIR=%GITHUB_WORKSPACE%\\opensim_dependencies_install -DWITH_BTK=on -DBUILD_PYTHON_WRAPPING=on -DBUILD_JAVA_WRAPPING=on
+        cmake --build . --config Release -- /maxcpucount:4 
+    - name: Test
+      run: |
+        chdir %GITHUB_WORKSPACE%\\build
+        ctest --parallel 4 --output-on-failure --build-config Release
+    - name: Install
+      run: |
+        chdir %GITHUB_WORKSPACE%\\build
+        cmake --build . --config Release --target install -- /maxcpucount:4 /verbosity:quiet
+  
+  mac:
+    name: Mac
+
+    runs-on: macOS-10.14
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Install Homebrew packages
+      run: |
+        brew install doxygen swig@3
+    - name: Build
+      run: |
+        mkdir $GITHUB_WORKSPACE/../build_deps && cd $GITHUB_WORKSPACE/../build_deps
+        DEP_CMAKE_ARGS=($GITHUB_WORKSPACE/dependencies -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/../opensim_dependencies_install -DCMAKE_BUILD_TYPE=Release)
+        DEP_CMAKE_ARGS+=(-DCMAKE_OSX_DEPLOYMENT_TARGET=10.10)
+        cmake "${DEP_CMAKE_ARGS[@]}"
+        make --jobs 4
+        mkdir $GITHUB_WORKSPACE/../build && cd $GITHUB_WORKSPACE/../build
+        OSIM_CMAKE_ARGS=($GITHUB_WORKSPACE -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/../opensim-core-install -DCMAKE_BUILD_TYPE=Release)
+        OSIM_CMAKE_ARGS+=(-DOPENSIM_DEPENDENCIES_DIR=$GITHUB_WORKSPACE/../opensim_dependencies_install)
+        OSIM_CMAKE_ARGS+=(-DCMAKE_OSX_DEPLOYMENT_TARGET=10.10)
+        OSIM_CMAKE_ARGS+=(-DWITH_BTK=on)
+        OSIM_CMAKE_ARGS+=(-DBUILD_PYTHON_WRAPPING=on -DBUILD_JAVA_WRAPPING=on -DSWIG_EXECUTABLE=/usr/local/opt/swig@3/bin/swig)
+        OSIM_CMAKE_ARGS+=(-DOPENSIM_INSTALL_UNIX_FHS=OFF)
+        OSIM_CMAKE_ARGS+=(-DOPENSIM_DOXYGEN_USE_MATHJAX=off)
+        OSIM_CMAKE_ARGS+=(-DOPENSIM_SIMBODY_DOXYGEN_LOCATION="https://simtk.org/api_docs/simbody/latest/")
+        OSIM_CMAKE_ARGS+=(-DCMAKE_CXX_FLAGS="-Werror")
+        printf '%s\n' "${OSIM_CMAKE_ARGS[@]}" 
+        cmake "${OSIM_CMAKE_ARGS[@]}"
+        make --jobs 4
+    - name: Test
+      run: |
+        cd $GITHUB_WORKSPACE/../build
+        ctest --parallel 4 --output-on-failure
+    - name: Install
+      run: |
+        cd $GITHUB_WORKSPACE/../build
+        make doxygen
+        make install
+        rm -r $GITHUB_WORKSPACE/../opensim_dependencies_install
+        cd $GITHUB_WORKSPACE/../opensim-core-install/sdk/Python
+        # Run the python tests, verbosely.
+        python3 -m unittest discover --start-directory opensim/tests --verbose
+    # TODO: deploy
+
+  linux:
+    name: Linux
+
+    runs-on: ubuntu-18.04
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Install packages
+      run: sudo apt-get install --yes liblapack-dev freeglut3-dev libxi-dev libxmu-dev doxygen python3 python3-dev python3-numpy python3-setuptools swig
+    - name: Build
+      run: |
+        mkdir $GITHUB_WORKSPACE/../build_deps && cd $GITHUB_WORKSPACE/../build_deps
+        cmake $GITHUB_WORKSPACE/dependencies -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/../opensim_dependencies_install -DCMAKE_BUILD_TYPE=Release
+        make --jobs 4
+        mkdir $GITHUB_WORKSPACE/../build && cd $GITHUB_WORKSPACE/../build
+        OSIM_CMAKE_ARGS=($GITHUB_WORKSPACE -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/../opensim-core-install -DCMAKE_BUILD_TYPE=Release)
+        OSIM_CMAKE_ARGS+=(-DOPENSIM_DEPENDENCIES_DIR=$GITHUB_WORKSPACE/../opensim_dependencies_install)
+        OSIM_CMAKE_ARGS+=(-DWITH_BTK=on)
+        OSIM_CMAKE_ARGS+=(-DBUILD_PYTHON_WRAPPING=on -DBUILD_JAVA_WRAPPING=on)
+        OSIM_CMAKE_ARGS+=(-DOPENSIM_INSTALL_UNIX_FHS=OFF)
+        OSIM_CMAKE_ARGS+=(-DOPENSIM_DOXYGEN_USE_MATHJAX=off)
+        OSIM_CMAKE_ARGS+=(-DOPENSIM_SIMBODY_DOXYGEN_LOCATION="https://simtk.org/api_docs/simbody/latest/")
+        # OSIM_CMAKE_ARGS+=(-DCMAKE_CXX_FLAGS="-Werror")
+        printf '%s\n' "${OSIM_CMAKE_ARGS[@]}"
+        cmake "${OSIM_CMAKE_ARGS[@]}"
+        make --jobs 4
+    - name: Test
+      run: |
+        cd $GITHUB_WORKSPACE/../build
+        # TODO: Temporary for python to find Simbody libraries.
+        export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$GITHUB_WORKSPACE/../opensim_dependencies_install/simbody/lib
+        ctest --parallel 4 --output-on-failure
+    - name: Install
+      run: |
+        cd $GITHUB_WORKSPACE/../build
+        make doxygen
+        make install
+        rm -r $GITHUB_WORKSPACE/../opensim_dependencies_install
+        # cd $GITHUB_WORKSPACE/../opensim-core-install/sdk/Python
+        # Run the python tests, verbosely.
+        # python3 -m unittest discover --start-directory opensim/tests --verbose
+    # TODO: deploy
+
+
+  

.travis.yml

@@ -5,6 +5,7 @@ language: cpp
 
 # Use container-based infrastructure to allow caching (for ccache).
 sudo: false
+dist: trusty
 
 # For thread_local support on macOS, we require xcode8 or greater.
 # Before 2018, xcode7 was the default. Now that xcode8.3 is the default,
@@ -32,7 +33,7 @@ matrix:
     - if: type != cron
       os: osx
       compiler: clang
-      env: BTYPE=Release WRAP=on  DOXY=on  NPROC=2 DEPLOY=yes OSX_TARGET=10.10
+      env: BTYPE=Release WRAP=on  DOXY=off  NPROC=2 DEPLOY=yes OSX_TARGET=10.10
 
 branches:
   except:
@@ -82,6 +83,9 @@ addons:
       - valgrind
       # To build doxygen documentation.
       # TOO OLD; see below. - doxygen
+      # python3 as linux and osx are still on python2
+      - python3
+      - python3-pip
   # To avoid being prompted when ssh'ing into sourceforge.
   ssh_known_hosts:
       # For uploading doxygen.
@@ -217,11 +221,13 @@ install:
 
   # Dependencies.
   - OSIM_CMAKE_ARGS+=(-DSIMBODY_HOME=~/simbody -DOPENSIM_DEPENDENCIES_DIR=$OPENSIM_DEPENDENCIES_INSTALL_DIR -DWITH_BTK:BOOL=ON)
-  
+  # Build applications
+  - OSIM_CMAKE_ARGS+=(-DOPENSIM_BUILD_INDIVIDUAL_APPS=ON)
+
   # Bindings.
   - OSIM_CMAKE_ARGS+=(-DBUILD_PYTHON_WRAPPING=$WRAP -DBUILD_JAVA_WRAPPING=$WRAP -DSWIG_EXECUTABLE=$HOME/swig/bin/swig)
   # On Mac, use system python instead of Homebrew python.
-  - if [ "$TRAVIS_OS_NAME" = "osx" ]; then OSIM_CMAKE_ARGS+=(-DPYTHON_EXECUTABLE=/usr/bin/python); fi
+  #- if [ "$TRAVIS_OS_NAME" = "osx" ]; then OSIM_CMAKE_ARGS+=(-DPYTHON_EXECUTABLE=/usr/bin/python3); fi
 
   # Doxygen.
   - OSIM_CMAKE_ARGS+=(-DOPENSIM_DOXYGEN_USE_MATHJAX=off -DOPENSIM_SIMBODY_DOXYGEN_LOCATION="https://simtk.org/api_docs/simbody/latest/")
@@ -264,7 +270,7 @@ script:
   # Go to the python wrapping package directory.
   - if [ "$WRAP" = "on" ]; then cd $OPENSIM_HOME/sdk/Python; fi
   # Run the python tests, verbosely.
-  - if [ "$WRAP" = "on" ]; then /usr/bin/python -m unittest discover --start-directory opensim/tests --verbose; fi
+  - if [ "$WRAP" = "on" ]; then python3 -m unittest discover --start-directory opensim/tests --verbose; fi
 
   ## Set up ssh for sourceforge.
   - if [[ "$DEPLOY" = "yes" || ("$DOXY" = "on" && "$TRAVIS_OS_NAME" = "linux" && "$TRAVIS_PULL_REQUEST" != "false") ]]; then PREP_SOURCEFORGE_SSH=0; else PREP_SOURCEFORGE_SSH=1; fi

Applications/Analyze/test/subject02_Setup_IAA_02_232.xml

@@ -75,7 +75,7 @@
 					<compute_potentials_only> false </compute_potentials_only>
 					<!--Report individual contributions to constraint reactions in addition to
 					    accelerations.-->
-					<report_constraint_reactions> false </report_constraint_reactions>
+					<report_constraint_reactions> true </report_constraint_reactions>
 				</InducedAccelerations>
 			</objects>
 			<groups/>

Applications/Analyze/test/testAnalyzeTool.cpp

@@ -133,15 +133,11 @@ void testTugOfWar(const string& dataFileName, const double& defaultAct) {
     analyze.run();
 
     // Load the AnalyzTool results for the muscle's force through time
-    TimeSeriesTable_<double> results =
-        STOFileAdapter_<double>::
-        read("Analyze_Tug_of_War/Tug_of_War_Millard_Iso_ForceReporter_forces.sto");
+    TimeSeriesTable_<double> results("Analyze_Tug_of_War/Tug_of_War_Millard_Iso_ForceReporter_forces.sto");
     assert(results.getNumColumns() == 1);
     SimTK::Vector forces = results.getDependentColumnAtIndex(0);
 
-    TimeSeriesTable_<double> outputs_table =
-        STOFileAdapter_<double>::
-        read("Analyze_Tug_of_War/Tug_of_War_Millard_Iso_Outputs.sto");
+    TimeSeriesTable_<double> outputs_table("Analyze_Tug_of_War/Tug_of_War_Millard_Iso_Outputs.sto");
     SimTK::Vector tf_output = outputs_table.getDependentColumnAtIndex(1);
 
     // Load input data as StatesTrajectory used to perform the Analysis

Applications/Analyze/test/testStaticOptimization.cpp

@@ -38,6 +38,8 @@ using namespace std;
 */
 void testArm26(const string& muscleModelClassName, double atol, double ftol);
 
+void testArm26DisabledMuscles();
+
 void testLapackErrorDLASD4();
 
 void testModelWithPassiveForces();
@@ -95,6 +97,14 @@ int main()
         failures.push_back("testRelativePathInExternalLoads");
     }
 
+    try {
+        testArm26DisabledMuscles();
+    }
+    catch (const std::exception& e) {
+        cout << e.what() << endl;
+        failures.push_back("testArm26DisabledMuscles");
+    }
+
     if (!failures.empty()) {
         cout << "Done, with failure(s): " << failures << endl;
         return 1;
@@ -238,3 +248,21 @@ void testRelativePathInExternalLoads() {
     analyze.setResultsDir("Results_UsingRelativePaths");
     analyze.run();
 }
+
+void testArm26DisabledMuscles() {
+    AnalyzeTool analyze("arm26_Setup_StaticOptimization.xml");
+    analyze.setResultsDir("Results_arm26_StaticOptimization_Disabled");
+    Model& model=analyze.getModel();
+    model.updComponent<Actuator>("/forceset/TRIlat").set_appliesForce(false);
+    model.updComponent<Actuator>("/forceset/TRImed").set_appliesForce(false);
+    analyze.run();
+    Storage activations(analyze.getResultsDir() + "/arm26_StaticOptimization_activation.sto");
+    ASSERT_EQUAL(activations.getColumnLabels().size(), 5);
+    ASSERT_EQUAL(activations.getColumnLabels().findIndex("TRIlat"), -1);
+    ASSERT_EQUAL(activations.getColumnLabels().findIndex("TRImed"), -1);
+    Storage forces(analyze.getResultsDir() + "/arm26_StaticOptimization_force.sto");
+    ASSERT_EQUAL(forces.getColumnLabels().size(), 5);
+    ASSERT_EQUAL(forces.getColumnLabels().findIndex("TRIlat"), -1);
+    ASSERT_EQUAL(forces.getColumnLabels().findIndex("TRImed"), -1);
+
+}

Applications/CMakeLists.txt

@@ -8,6 +8,7 @@ add_subdirectory(IK)
 add_subdirectory(ID)
 add_subdirectory(CMC)
 add_subdirectory(RRA)
+add_subdirectory(opensense)
 add_subdirectory(versionUpdate)
 
 add_subdirectory(opensim-cmd)