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Merge remote-tracking branch 'opensim-org/master' into FixingSO
2 parents 26b88b9 + 3535586 commit 51ef274

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‎.clang-format‎

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# This file can be used by the clang-format tool to
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# automatically format C++ source code.
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# See https://clang.llvm.org/docs/ClangFormat.html.
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# You can either run clang-format directly, or you can use
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# Integrated Development Environments (IDEs) that support clang-format,
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# such as:
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# - Visual Studio (https://devblogs.microsoft.com/cppblog/clangformat-support-in-visual-studio-2017-15-7-preview-1/),
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# - CLion (https://www.jetbrains.com/help/clion/clangformat-as-alternative-formatter.html).
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# See the documentation for IDEs for more information.
10+
---
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Language: Cpp
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# BasedOnStyle: LLVM
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AccessModifierOffset: -4
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AlignAfterOpenBracket: DontAlign
15+
AlignConsecutiveAssignments: false
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AlignConsecutiveDeclarations: false
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AlignEscapedNewlines: Right
18+
AlignOperands: true
19+
AlignTrailingComments: true
20+
AllowAllParametersOfDeclarationOnNextLine: true
21+
AllowShortBlocksOnASingleLine: true
22+
AllowShortCaseLabelsOnASingleLine: true
23+
AllowShortFunctionsOnASingleLine: All
24+
AllowShortIfStatementsOnASingleLine: true
25+
AllowShortLoopsOnASingleLine: true
26+
AlwaysBreakAfterDefinitionReturnType: None
27+
AlwaysBreakAfterReturnType: None
28+
AlwaysBreakBeforeMultilineStrings: false
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# AlwaysBreakTemplateDeclarations: Yes
30+
BinPackArguments: true
31+
BinPackParameters: true
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BraceWrapping:
33+
AfterClass: false
34+
AfterControlStatement: false
35+
AfterEnum: false
36+
AfterFunction: false
37+
AfterNamespace: false
38+
AfterObjCDeclaration: false
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AfterStruct: false
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AfterUnion: false
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AfterExternBlock: false
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BeforeCatch: false
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BeforeElse: false
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IndentBraces: false
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SplitEmptyFunction: true
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SplitEmptyRecord: true
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SplitEmptyNamespace: true
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BreakBeforeBinaryOperators: None
49+
BreakBeforeBraces: Attach
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BreakBeforeInheritanceComma: false
51+
# BreakInheritanceList: BeforeColon
52+
BreakBeforeTernaryOperators: true
53+
BreakConstructorInitializersBeforeComma: false
54+
BreakConstructorInitializers: BeforeColon
55+
BreakAfterJavaFieldAnnotations: false
56+
BreakStringLiterals: true
57+
ColumnLimit: 80
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CommentPragmas: '^ IWYU pragma:'
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CompactNamespaces: false
60+
ConstructorInitializerAllOnOneLineOrOnePerLine: false
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ConstructorInitializerIndentWidth: 8
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ContinuationIndentWidth: 8
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Cpp11BracedListStyle: true
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DerivePointerAlignment: false
65+
DisableFormat: false
66+
ExperimentalAutoDetectBinPacking: false
67+
FixNamespaceComments: true
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ForEachMacros:
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- foreach
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- Q_FOREACH
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- BOOST_FOREACH
72+
IncludeBlocks: Regroup
73+
IncludeCategories:
74+
- Regex: '^(<SimTKcommon/)'
75+
Priority: 2
76+
- Regex: '^(<simbody/)'
77+
Priority: 3
78+
- Regex: '^(<OpenSim/)'
79+
Priority: 4
80+
- Regex: '.*'
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Priority: 1
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IncludeIsMainRegex: '(Test)?$'
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IndentCaseLabels: false
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IndentPPDirectives: AfterHash
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IndentWidth: 4
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IndentWrappedFunctionNames: false
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JavaScriptQuotes: Leave
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JavaScriptWrapImports: true
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KeepEmptyLinesAtTheStartOfBlocks: true
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MacroBlockBegin: ''
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MacroBlockEnd: ''
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MaxEmptyLinesToKeep: 1
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NamespaceIndentation: None
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# ObjCBinPackProtocolList: Auto
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ObjCBlockIndentWidth: 2
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ObjCSpaceAfterProperty: false
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ObjCSpaceBeforeProtocolList: true
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PenaltyBreakAssignment: 2
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PenaltyBreakBeforeFirstCallParameter: 19
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PenaltyBreakComment: 300
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PenaltyBreakFirstLessLess: 120
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PenaltyBreakString: 1000
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# PenaltyBreakTemplateDeclaration: 10
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PenaltyExcessCharacter: 1000000
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PenaltyReturnTypeOnItsOwnLine: 60
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PointerAlignment: Left
107+
ReflowComments: true
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SortIncludes: true
109+
SortUsingDeclarations: true
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SpaceAfterCStyleCast: false
111+
SpaceAfterTemplateKeyword: true
112+
SpaceBeforeAssignmentOperators: true
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# SpaceBeforeCpp11BracedList: false
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# SpaceBeforeCtorInitializerColon: true
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# SpaceBeforeInheritanceColon: true
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SpaceBeforeParens: ControlStatements
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# SpaceBeforeRangeBasedForLoopColon: true
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SpaceInEmptyParentheses: false
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SpacesBeforeTrailingComments: 1
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SpacesInAngles: false
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SpacesInContainerLiterals: true
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SpacesInCStyleCastParentheses: false
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SpacesInParentheses: false
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SpacesInSquareBrackets: false
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Standard: Cpp11
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TabWidth: 4
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UseTab: Never
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...
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‎.github/workflows/continuous_integration.yml‎

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1+
name: continuous-integration
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3+
# TODO: build master branch after PRs are merged.
4+
# syntax https://help.github.com/en/articles/workflow-syntax-for-github-actions
5+
on:
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schedule:
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- cron: '0 2 * * *'
8+
9+
jobs:
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windows:
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name: Windows
12+
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runs-on: windows-2016
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steps:
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- uses: actions/checkout@v1
17+
- name: Install Chocolatey packages
18+
run: choco install swig --version 3.0.9 --yes --limit-output
19+
- name: Build
20+
run: |
21+
echo %GITHUB_WORKSPACE%\\build_deps
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mkdir %GITHUB_WORKSPACE%\\build_deps
23+
chdir %GITHUB_WORKSPACE%\\build_deps
24+
cmake --version
25+
cmake %GITHUB_WORKSPACE%\\dependencies -G"Visual Studio 15 2017" -A x64 -DCMAKE_INSTALL_PREFIX=%GITHUB_WORKSPACE%\\opensim_dependencies_install
26+
cmake --build . --config Release -- /maxcpucount:4
27+
mkdir %GITHUB_WORKSPACE%\\build
28+
chdir %GITHUB_WORKSPACE%\\build
29+
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
30+
cmake --build . --config Release -- /maxcpucount:4
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- name: Test
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run: |
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chdir %GITHUB_WORKSPACE%\\build
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ctest --parallel 4 --output-on-failure --build-config Release
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- name: Install
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run: |
37+
chdir %GITHUB_WORKSPACE%\\build
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cmake --build . --config Release --target install -- /maxcpucount:4 /verbosity:quiet
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mac:
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name: Mac
42+
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runs-on: macOS-10.14
44+
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steps:
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- uses: actions/checkout@v1
47+
- name: Install Homebrew packages
48+
run: |
49+
brew install doxygen swig@3
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- name: Build
51+
run: |
52+
mkdir $GITHUB_WORKSPACE/../build_deps && cd $GITHUB_WORKSPACE/../build_deps
53+
DEP_CMAKE_ARGS=($GITHUB_WORKSPACE/dependencies -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/../opensim_dependencies_install -DCMAKE_BUILD_TYPE=Release)
54+
DEP_CMAKE_ARGS+=(-DCMAKE_OSX_DEPLOYMENT_TARGET=10.10)
55+
cmake "${DEP_CMAKE_ARGS[@]}"
56+
make --jobs 4
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mkdir $GITHUB_WORKSPACE/../build && cd $GITHUB_WORKSPACE/../build
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OSIM_CMAKE_ARGS=($GITHUB_WORKSPACE -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/../opensim-core-install -DCMAKE_BUILD_TYPE=Release)
59+
OSIM_CMAKE_ARGS+=(-DOPENSIM_DEPENDENCIES_DIR=$GITHUB_WORKSPACE/../opensim_dependencies_install)
60+
OSIM_CMAKE_ARGS+=(-DCMAKE_OSX_DEPLOYMENT_TARGET=10.10)
61+
OSIM_CMAKE_ARGS+=(-DWITH_BTK=on)
62+
OSIM_CMAKE_ARGS+=(-DBUILD_PYTHON_WRAPPING=on -DBUILD_JAVA_WRAPPING=on -DSWIG_EXECUTABLE=/usr/local/opt/swig@3/bin/swig)
63+
OSIM_CMAKE_ARGS+=(-DOPENSIM_INSTALL_UNIX_FHS=OFF)
64+
OSIM_CMAKE_ARGS+=(-DOPENSIM_DOXYGEN_USE_MATHJAX=off)
65+
OSIM_CMAKE_ARGS+=(-DOPENSIM_SIMBODY_DOXYGEN_LOCATION="https://simtk.org/api_docs/simbody/latest/")
66+
OSIM_CMAKE_ARGS+=(-DCMAKE_CXX_FLAGS="-Werror")
67+
printf '%s\n' "${OSIM_CMAKE_ARGS[@]}"
68+
cmake "${OSIM_CMAKE_ARGS[@]}"
69+
make --jobs 4
70+
- name: Test
71+
run: |
72+
cd $GITHUB_WORKSPACE/../build
73+
ctest --parallel 4 --output-on-failure
74+
- name: Install
75+
run: |
76+
cd $GITHUB_WORKSPACE/../build
77+
make doxygen
78+
make install
79+
rm -r $GITHUB_WORKSPACE/../opensim_dependencies_install
80+
cd $GITHUB_WORKSPACE/../opensim-core-install/sdk/Python
81+
# Run the python tests, verbosely.
82+
python3 -m unittest discover --start-directory opensim/tests --verbose
83+
# TODO: deploy
84+
85+
linux:
86+
name: Linux
87+
88+
runs-on: ubuntu-18.04
89+
90+
steps:
91+
- uses: actions/checkout@v1
92+
- name: Install packages
93+
run: sudo apt-get install --yes liblapack-dev freeglut3-dev libxi-dev libxmu-dev doxygen python3 python3-dev python3-numpy python3-setuptools swig
94+
- name: Build
95+
run: |
96+
mkdir $GITHUB_WORKSPACE/../build_deps && cd $GITHUB_WORKSPACE/../build_deps
97+
cmake $GITHUB_WORKSPACE/dependencies -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/../opensim_dependencies_install -DCMAKE_BUILD_TYPE=Release
98+
make --jobs 4
99+
mkdir $GITHUB_WORKSPACE/../build && cd $GITHUB_WORKSPACE/../build
100+
OSIM_CMAKE_ARGS=($GITHUB_WORKSPACE -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/../opensim-core-install -DCMAKE_BUILD_TYPE=Release)
101+
OSIM_CMAKE_ARGS+=(-DOPENSIM_DEPENDENCIES_DIR=$GITHUB_WORKSPACE/../opensim_dependencies_install)
102+
OSIM_CMAKE_ARGS+=(-DWITH_BTK=on)
103+
OSIM_CMAKE_ARGS+=(-DBUILD_PYTHON_WRAPPING=on -DBUILD_JAVA_WRAPPING=on)
104+
OSIM_CMAKE_ARGS+=(-DOPENSIM_INSTALL_UNIX_FHS=OFF)
105+
OSIM_CMAKE_ARGS+=(-DOPENSIM_DOXYGEN_USE_MATHJAX=off)
106+
OSIM_CMAKE_ARGS+=(-DOPENSIM_SIMBODY_DOXYGEN_LOCATION="https://simtk.org/api_docs/simbody/latest/")
107+
# OSIM_CMAKE_ARGS+=(-DCMAKE_CXX_FLAGS="-Werror")
108+
printf '%s\n' "${OSIM_CMAKE_ARGS[@]}"
109+
cmake "${OSIM_CMAKE_ARGS[@]}"
110+
make --jobs 4
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- name: Test
112+
run: |
113+
cd $GITHUB_WORKSPACE/../build
114+
# TODO: Temporary for python to find Simbody libraries.
115+
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$GITHUB_WORKSPACE/../opensim_dependencies_install/simbody/lib
116+
ctest --parallel 4 --output-on-failure
117+
- name: Install
118+
run: |
119+
cd $GITHUB_WORKSPACE/../build
120+
make doxygen
121+
make install
122+
rm -r $GITHUB_WORKSPACE/../opensim_dependencies_install
123+
# cd $GITHUB_WORKSPACE/../opensim-core-install/sdk/Python
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# Run the python tests, verbosely.
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# python3 -m unittest discover --start-directory opensim/tests --verbose
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# TODO: deploy
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‎.travis.yml‎

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Original file line numberDiff line numberDiff line change
@@ -5,6 +5,7 @@ language: cpp
55

66
# Use container-based infrastructure to allow caching (for ccache).
77
sudo: false
8+
dist: trusty
89

910
# For thread_local support on macOS, we require xcode8 or greater.
1011
# Before 2018, xcode7 was the default. Now that xcode8.3 is the default,
@@ -32,7 +33,7 @@ matrix:
3233
- if: type != cron
3334
os: osx
3435
compiler: clang
35-
env: BTYPE=Release WRAP=on DOXY=on NPROC=2 DEPLOY=yes OSX_TARGET=10.10
36+
env: BTYPE=Release WRAP=on DOXY=off NPROC=2 DEPLOY=yes OSX_TARGET=10.10
3637

3738
branches:
3839
except:
@@ -82,6 +83,9 @@ addons:
8283
- valgrind
8384
# To build doxygen documentation.
8485
# TOO OLD; see below. - doxygen
86+
# python3 as linux and osx are still on python2
87+
- python3
88+
- python3-pip
8589
# To avoid being prompted when ssh'ing into sourceforge.
8690
ssh_known_hosts:
8791
# For uploading doxygen.
@@ -217,11 +221,13 @@ install:
217221

218222
# Dependencies.
219223
- OSIM_CMAKE_ARGS+=(-DSIMBODY_HOME=~/simbody -DOPENSIM_DEPENDENCIES_DIR=$OPENSIM_DEPENDENCIES_INSTALL_DIR -DWITH_BTK:BOOL=ON)
220-
224+
# Build applications
225+
- OSIM_CMAKE_ARGS+=(-DOPENSIM_BUILD_INDIVIDUAL_APPS=ON)
226+
221227
# Bindings.
222228
- OSIM_CMAKE_ARGS+=(-DBUILD_PYTHON_WRAPPING=$WRAP -DBUILD_JAVA_WRAPPING=$WRAP -DSWIG_EXECUTABLE=$HOME/swig/bin/swig)
223229
# On Mac, use system python instead of Homebrew python.
224-
- if [ "$TRAVIS_OS_NAME" = "osx" ]; then OSIM_CMAKE_ARGS+=(-DPYTHON_EXECUTABLE=/usr/bin/python); fi
230+
#- if [ "$TRAVIS_OS_NAME" = "osx" ]; then OSIM_CMAKE_ARGS+=(-DPYTHON_EXECUTABLE=/usr/bin/python3); fi
225231

226232
# Doxygen.
227233
- OSIM_CMAKE_ARGS+=(-DOPENSIM_DOXYGEN_USE_MATHJAX=off -DOPENSIM_SIMBODY_DOXYGEN_LOCATION="https://simtk.org/api_docs/simbody/latest/")
@@ -264,7 +270,7 @@ script:
264270
# Go to the python wrapping package directory.
265271
- if [ "$WRAP" = "on" ]; then cd $OPENSIM_HOME/sdk/Python; fi
266272
# Run the python tests, verbosely.
267-
- if [ "$WRAP" = "on" ]; then /usr/bin/python -m unittest discover --start-directory opensim/tests --verbose; fi
273+
- if [ "$WRAP" = "on" ]; then python3 -m unittest discover --start-directory opensim/tests --verbose; fi
268274

269275
## Set up ssh for sourceforge.
270276
- 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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -75,7 +75,7 @@
7575
<compute_potentials_only> false </compute_potentials_only>
7676
<!--Report individual contributions to constraint reactions in addition to
7777
accelerations.-->
78-
<report_constraint_reactions> false </report_constraint_reactions>
78+
<report_constraint_reactions> true </report_constraint_reactions>
7979
</InducedAccelerations>
8080
</objects>
8181
<groups/>

‎Applications/Analyze/test/testAnalyzeTool.cpp‎

Lines changed: 2 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -133,15 +133,11 @@ void testTugOfWar(const string& dataFileName, const double& defaultAct) {
133133
analyze.run();
134134

135135
// Load the AnalyzTool results for the muscle's force through time
136-
TimeSeriesTable_<double> results =
137-
STOFileAdapter_<double>::
138-
read("Analyze_Tug_of_War/Tug_of_War_Millard_Iso_ForceReporter_forces.sto");
136+
TimeSeriesTable_<double> results("Analyze_Tug_of_War/Tug_of_War_Millard_Iso_ForceReporter_forces.sto");
139137
assert(results.getNumColumns() == 1);
140138
SimTK::Vector forces = results.getDependentColumnAtIndex(0);
141139

142-
TimeSeriesTable_<double> outputs_table =
143-
STOFileAdapter_<double>::
144-
read("Analyze_Tug_of_War/Tug_of_War_Millard_Iso_Outputs.sto");
140+
TimeSeriesTable_<double> outputs_table("Analyze_Tug_of_War/Tug_of_War_Millard_Iso_Outputs.sto");
145141
SimTK::Vector tf_output = outputs_table.getDependentColumnAtIndex(1);
146142

147143
// Load input data as StatesTrajectory used to perform the Analysis

‎Applications/Analyze/test/testStaticOptimization.cpp‎

Lines changed: 28 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -38,6 +38,8 @@ using namespace std;
3838
*/
3939
void testArm26(const string& muscleModelClassName, double atol, double ftol);
4040

41+
void testArm26DisabledMuscles();
42+
4143
void testLapackErrorDLASD4();
4244

4345
void testModelWithPassiveForces();
@@ -95,6 +97,14 @@ int main()
9597
failures.push_back("testRelativePathInExternalLoads");
9698
}
9799

100+
try {
101+
testArm26DisabledMuscles();
102+
}
103+
catch (const std::exception& e) {
104+
cout << e.what() << endl;
105+
failures.push_back("testArm26DisabledMuscles");
106+
}
107+
98108
if (!failures.empty()) {
99109
cout << "Done, with failure(s): " << failures << endl;
100110
return 1;
@@ -238,3 +248,21 @@ void testRelativePathInExternalLoads() {
238248
analyze.setResultsDir("Results_UsingRelativePaths");
239249
analyze.run();
240250
}
251+
252+
void testArm26DisabledMuscles() {
253+
AnalyzeTool analyze("arm26_Setup_StaticOptimization.xml");
254+
analyze.setResultsDir("Results_arm26_StaticOptimization_Disabled");
255+
Model& model=analyze.getModel();
256+
model.updComponent<Actuator>("/forceset/TRIlat").set_appliesForce(false);
257+
model.updComponent<Actuator>("/forceset/TRImed").set_appliesForce(false);
258+
analyze.run();
259+
Storage activations(analyze.getResultsDir() + "/arm26_StaticOptimization_activation.sto");
260+
ASSERT_EQUAL(activations.getColumnLabels().size(), 5);
261+
ASSERT_EQUAL(activations.getColumnLabels().findIndex("TRIlat"), -1);
262+
ASSERT_EQUAL(activations.getColumnLabels().findIndex("TRImed"), -1);
263+
Storage forces(analyze.getResultsDir() + "/arm26_StaticOptimization_force.sto");
264+
ASSERT_EQUAL(forces.getColumnLabels().size(), 5);
265+
ASSERT_EQUAL(forces.getColumnLabels().findIndex("TRIlat"), -1);
266+
ASSERT_EQUAL(forces.getColumnLabels().findIndex("TRImed"), -1);
267+
268+
}

‎Applications/CMakeLists.txt‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -8,6 +8,7 @@ add_subdirectory(IK)
88
add_subdirectory(ID)
99
add_subdirectory(CMC)
1010
add_subdirectory(RRA)
11+
add_subdirectory(opensense)
1112
add_subdirectory(versionUpdate)
1213

1314
add_subdirectory(opensim-cmd)

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