Add GitHub Action job to run MATLAB tests

.github/workflows/matlab.yml

@@ -0,0 +1,93 @@
+name: MATLAB Tests Workflow
+
+on:
+  push:
+  pull_request:
+  schedule:
+  # * is a special character in YAML so you have to quote this string
+  # Execute a "nightly" build at 2 AM UTC 
+  - cron:  '0 2 * * *'
+
+jobs:
+  build-matlab-tests:    
+    name: '[matlab:${{ matrix.matlab_version }}:${{ matrix.os }}]'
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        build_type: [Release]
+        os: [ubuntu-20.04]
+        matlab_version: [R2020a, R2020b, R2021a, latest]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        miniforge-variant: Mambaforge
+        miniforge-version: latest
+        channels: conda-forge,robotology
+
+    - name: Setup MATLAB
+      uses: matlab-actions/setup-matlab@v1
+      with:
+        release: ${{ matrix.matlab_version }}
+
+    # workaround for https://github.com/robotology/robotology-superbuild/issues/64
+    - name: Do not use MATLAB's stdc++ to avoid incompatibilities with other libraries
+      if: contains(matrix.os, 'ubuntu')
+      run:
+          echo 'LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6' >> $GITHUB_ENV
+
+    - name: Dependencies
+      shell: bash -l {0}
+      run: |
+        # Workaround for https://github.com/conda-incubator/setup-miniconda/issues/186
+        conda config --remove channels defaults
+        # Compilation related dependencies 
+        mamba install cmake compilers make ninja pkg-config
+        # Actual dependencies
+        mamba install eigen libxml2 assimp ipopt qt irrlicht osqp-eigen
+
+    # Additional dependencies useful only on Linux
+    - name: Dependencies [Conda/Linux]
+      if: contains(matrix.os, 'ubuntu') 
+      shell: bash -l {0}
+      run: |
+        # Additional dependencies only useful on Linux
+        # See https://github.com/robotology/robotology-superbuild/issues/477
+        mamba install expat-cos6-x86_64 freeglut libselinux-cos6-x86_64 libxau-cos6-x86_64 libxcb-cos6-x86_64 libxdamage-cos6-x86_64 libxext-cos6-x86_64 libxfixes-cos6-x86_64 libxxf86vm-cos6-x86_64 mesalib mesa-libgl-cos6-x86_64
+
+    - name: Configure
+      if: contains(matrix.os, 'macos') || contains(matrix.os, 'ubuntu')
+      shell: bash -l {0}
+      run: |
+        mkdir build
+        cd build
+        cmake -GNinja -DCMAKE_INSTALL_PREFIX=${CONDA_PREFIX} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DMATLAB_FIND_DEBUG:BOOL=ON -DIDYNTREE_USES_MATLAB:BOOL=ON -DIDYNTREE_COMPILE_TESTS:BOOL=ON -DIDYNTREE_USES_QT5:BOOL=ON -DIDYNTREE_USES_ASSIMP:BOOL=ON -DIDYNTREE_USES_IPOPT:BOOL=ON -DIDYNTREE_USES_IRRLICHT:BOOL=ON -DIDYNTREE_USES_YARP:BOOL=OFF -DIDYNTREE_USES_ICUB_MAIN:BOOL=OFF -DIDYNTREE_USES_OSQPEIGEN:BOOL=ON ..
+
+    - name: Build
+      shell: bash -l {0}
+      run: |
+        cd build
+        cmake --build . --config ${{ matrix.build_type }}
+
+    - name: Inspect libraries linked by iDynTreeMEX.mexa64 [Conda/Linux]
+      if: contains(matrix.os, 'ubuntu')
+      shell: bash -l {0}
+      run: |
+        cd build
+        ldd ./lib/iDynTreeMEX.mexa64
+
+    - name: Test [Conda]
+      shell: bash -l {0}
+      run: |
+        cd build
+        # Only run matlab tests as the rest of tests are already run by other jobs
+        ctest --output-on-failure -C ${{ matrix.build_type }} -R "matlab" -VV . 
+
+    - name: Install [Conda]
+      shell: bash -l {0}
+      run: |
+        cd build
+        cmake --install . --config ${{ matrix.build_type }}

bindings/matlab/tests/CMakeLists.txt

@@ -11,7 +11,7 @@ if (IDYNTREE_USES_MATLAB AND NOT IDYNTREE_DISABLE_MATLAB_TESTS)
   find_package(Matlab REQUIRED
                COMPONENTS MAIN_PROGRAM)
   add_test(NAME matlab_idyntree_tests
-           COMMAND ${Matlab_MAIN_PROGRAM} -nodisplay -nodesktop -nojvm -r "addpath('$<TARGET_FILE_DIR:${mexname}>');addpath('${MEX_BINDINGS_SOURCE_DIR}');addpath('${MATLAB_WRAPPERS_BINDINGS_SOURCE_DIR}');addpath('${CMAKE_CURRENT_SOURCE_DIR}/');addpath(genpath('${IDYNTREE_INTERNAL_MOXUNIT_PATH}'));success=moxunit_runtests('${CMAKE_CURRENT_SOURCE_DIR}','-verbose');exit(~success);")
+           COMMAND ${Matlab_MAIN_PROGRAM} -nodisplay -nodesktop -nojvm -batch "addpath('$<TARGET_FILE_DIR:${mexname}>');addpath('${MEX_BINDINGS_SOURCE_DIR}');addpath('${MATLAB_WRAPPERS_BINDINGS_SOURCE_DIR}');addpath('${CMAKE_CURRENT_SOURCE_DIR}/');addpath(genpath('${IDYNTREE_INTERNAL_MOXUNIT_PATH}'));success=moxunit_runtests('${CMAKE_CURRENT_SOURCE_DIR}','-verbose');exit(~success);")
 endif()
 
 if (IDYNTREE_USES_OCTAVE)

bindings/matlab/tests/EKFTest.m

@@ -1,4 +1,8 @@
 function test_suite=EKFTest
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions=localfunctions();
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
     initTestSuite
 
 function test_span

bindings/matlab/tests/InertiaUnitTest.m

@@ -1,4 +1,8 @@
 function test_suite=InertiaUnitTest
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions=localfunctions();
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
     initTestSuite
 
 function test_momentum_invariance

bindings/matlab/tests/JointUnitTest.m

@@ -1,4 +1,8 @@
 function test_suite=JointUnitTest
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions=localfunctions();
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
     initTestSuite
 
 function test_joint_constructor

bindings/matlab/tests/MatrixUnitTest.m

@@ -1,4 +1,8 @@
 function test_suite=MatrixUnitTest
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions=localfunctions();
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
     initTestSuite
 
 function test_sparse_matrices

bindings/matlab/tests/PositionUnitTest.m

@@ -1,4 +1,8 @@
 function test_suite=PositionUnitTest
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions=localfunctions();
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
     initTestSuite
     test_sum_of_positions
 

bindings/matlab/tests/TransformUnitTest.m

@@ -1,4 +1,8 @@
 function test_suite=TransformUnitTest
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions=localfunctions();
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
     initTestSuite
 
 function test_pos_twist_wrench_invariance

bindings/matlab/tests/highLevelWrappersSmokeTest.m

@@ -1,4 +1,8 @@
 function test_suite = highLevelWrappersSmokeTest
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions=localfunctions();
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
     initTestSuite
 
 function test__high_level_wrappers

extern/MOxUnit/.github/workflows/CI.yml

@@ -0,0 +1,44 @@
+name: CI
+
+# Controls when the action will run. Triggers the workflow on push or pull request
+# events but only for the master branch
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "unit-tests"
+  unit-tests:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+    # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+    - uses: actions/checkout@v2
+
+    # Use A Github Action to perform tests
+    - name: run unit tests and documentation tests, generate coverage report
+      uses: joergbrech/moxunit-action@v1.1
+      with:
+        tests: tests
+        src: MOxUnit
+        with_coverage: true
+        doc_tests: true
+        cover_xml_file: coverage.xml
+
+    # Store the coverage report as an artifact
+    - name: Store Coverage report as artifact
+      uses: actions/upload-artifact@v1
+      with:
+        name: coverage_xml_file
+        path: coverage.xml
+
+    ## Use a Github Action to publish coverage reports
+    #- name: Publish coverage report to codecov.io
+    #  uses: codecov/codecov-action@v1
+    #  with:
+    #    file: ./coverage.xml

extern/MOxUnit/.gitignore

@@ -0,0 +1,14 @@
+*.DS_Store
+*.swp
+*.css
+*.m~
+data
+datadb
+datadb.zip
+.git.bfg-report
+*.md.sw?
+octave-workspace
+git_log.txt
+git_summary.txt
+*.pyc
+*.asv

extern/MOxUnit/.travis.yml

@@ -0,0 +1,82 @@
+# vim ft=yaml
+# travis-ci.org definition for MOxUnit build (based on CoSMoMVPA,
+# which is based on PyMVPA, which is based on nipype configuration, 
+# which in turn was based on nipy)
+
+language: minimal
+os: linux
+
+cache:
+  - apt
+
+env:
+  matrix:
+    - WITH_COVERAGE=
+    - WITH_COVERAGE=true
+    - RUN_DOC_TEST=true
+
+before_install:
+  # to prevent IPv6 being used for APT
+  - sudo bash -c "echo 'Acquire::ForceIPv4 \"true\";' > /etc/apt/apt.conf.d/99force-ipv4"
+  - travis_retry sudo apt-get -y -qq update
+  - travis_retry sudo apt-get install -y -qq software-properties-common python-software-properties
+  - travis_retry sudo apt-add-repository -y ppa:octave/stable
+  - travis_retry sudo apt-get -y -qq update
+  # get Octave 4,0
+  - travis_retry sudo apt-get -y -qq install octave liboctave-dev
+  # install MOcov
+  - cd ..
+  - rm -rf MOcov
+  - git clone https://github.com/MOcov/MOcov.git
+  - make -C MOcov install
+  # retrieve MOdox
+  - rm -rf MOdox
+  - travis_retry git clone -v git://github.com/MOdox/MOdox.git
+  - make -C MOdox install
+  # go back to original directory
+  - cd MOxUnit
+  # prevent shippable from re-using old test results
+  - if [[  "$SHIPPABLE" == "true"  ]]; then
+      if [[  "$WITH_COVERAGE" != "true" ]]; then
+          rm -f ${SHIPPABLE_BUILD_DIR}/shippable/testresults/*.xml;
+      fi;
+    fi
+
+script:
+  - if [[  "$WITH_COVERAGE" == "true" ]]; then
+      TEST_ARGS=WITH_COVERAGE=true;
+      COVER_ARGS=COVER=`pwd`/MOxUnit;
+
+      if [[  "$SHIPPABLE" == "true"  ]]; then
+        OUTPUT_ARGS=COVER_XML_FILE=${SHIPPABLE_BUILD_DIR}/shippable/codecoverage/coverage.xml;
+        AFTER_SCRIPT="find ${SHIPPABLE_BUILD_DIR}/shippable/;cat ${SHIPPABLE_BUILD_DIR}/shippable/codecoverage/coverage.xml;which reports";
+      elif [[  "$TRAVIS" == "true"  ]]; then
+        OUTPUT_ARGS=COVER_JSON_FILE=`pwd`/coveralls.json;
+        AFTER_SCRIPT="curl --verbose -F json_file=@`pwd`/coveralls.json https://coveralls.io/api/v1/jobs";
+      fi;
+    elif [[  "$SHIPPABLE" == "true"  ]]; then
+      RESULT_ARGS=JUNIT_XML_FILE=${SHIPPABLE_BUILD_DIR}/shippable/testresults/test_results.xml;
+    elif [[  "$RUN_DOC_TEST" == "true" ]]; then
+      TEST_ARGS=RUN_DOC_TEST=true;
+    fi;
+
+  - echo Test arguments $TEST_ARGS $COVER_ARGS $OUTPUT_ARGS $RESULT_ARGS
+  - make test $TEST_ARGS $COVER_ARGS $OUTPUT_ARGS $RESULT_ARGS
+  - eval $AFTER_SCRIPT
+
+jobs:
+  include:
+    - language: matlab
+      matlab: R2020a
+
+      # No need to do anything, but the 'before_install' key is inherited from teh enclosing scope and has to be reset to something insubstantial
+      before_install:
+        - echo 'noop'
+      # Could also clear 'env' but, as is, the only environment variable inhereted fromthe scope is $WITH_COVERAGE which does nothing here
+
+      script:
+        - if [[  "$SHIPPABLE" == "true"  ]]; then
+            echo 'No Matlab testing on Shippable';
+          else
+            matlab -batch 'back=cd("./MOxUnit/"); moxunit_set_path(); cd(back); moxunit_runtests tests -verbose; exit(double(~ans))';
+          fi;

extern/MOxUnit/COPYING

@@ -1,6 +1,6 @@
 (The MIT License)
 
-Copyright (c) 2015 Nikolaas N. Oosterhof
+Copyright (c) 2015-2017 Nikolaas N. Oosterhof
 
 Permission is hereby granted, free of charge, to any person obtaining 
 a copy of this software and associated documentation files (the 

extern/MOxUnit/MOxUnit/@MOxUnitFunctionHandleTestCase/run.m

@@ -16,12 +16,19 @@
 %
 % NNO 2015
 
+    original_warning_state=warning('query');
+    warning_state_resetter=onCleanup(@()warning(original_warning_state));
+
     start_tic = tic;
 
     try
         passed=false;
         try
-            obj.function_handle();
+            if nargin(obj.function_handle) > 0
+                obj.function_handle(obj);
+            else
+                obj.function_handle();
+            end
             passed=true;
         catch
             e=lasterror();
@@ -39,7 +46,11 @@
                 test_outcome_args={reason};
             else
                 test_outcome_constructor=@MOxUnitFailedTestOutcome;
-                test_outcome_args={e};
+
+                % trim the stack so that all test case machinery is
+                % removed from the stack
+                e_trimmed=trim_stack(e);
+                test_outcome_args={e_trimmed};
             end
         end
 
@@ -56,4 +67,29 @@
     test_outcome = test_outcome_constructor(obj, toc(start_tic), ...
                             test_outcome_args{:});
 
-    report = reportTestOutcome(report, test_outcome);
+    report = reportTestOutcome(report, test_outcome);
+
+
+function e_trimmed=trim_stack(e)
+% trim the stack from e.stack, so that everything up to and including the
+% first (nearest to the calling root) entry is removed
+    stack=e.stack;
+
+    n_stack=numel(stack);
+
+    this_file=sprintf('%s.m',mfilename('fullpath'));
+
+    for pos=n_stack:-1:1
+        if strcmp(stack(pos).file,this_file)
+            % found first match with this filename, now trim this function
+            % and their callig functions
+            trimmed_stack=stack(1:(pos-1));
+
+            e_trimmed=e;
+            e_trimmed.stack=trimmed_stack;
+            return;
+        end
+    end
+
+    assert(false,'This should not happen');
+