CI fixes: Mac runner upgrade and Doxygen installations

.github/workflows/continuous_integration.yml

@@ -21,12 +21,12 @@ jobs:
     runs-on: windows-2019
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install Doxygen
       # choco install doxygen.portable # <-- too unreliable.
       run: |
-        (New-Object System.Net.WebClient).DownloadFile("https://sourceforge.net/projects/myosin/files/doxygen-1.8.14.windows.x64.bin.zip/download", "doxygen.zip")
+        (New-Object System.Net.WebClient).DownloadFile("https://github.com/doxygen/doxygen/releases/download/Release_1_12_0/doxygen-1.12.0.windows.x64.bin.zip", "doxygen.zip")
         7z x $env:GITHUB_WORKSPACE/doxygen.zip -odoxygen
         echo "$env:GITHUB_WORKSPACE\\doxygen" >> $GITHUB_PATH
 
@@ -159,14 +159,14 @@ jobs:
     runs-on: windows-2022
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         ref: ${{ github.event.pull_request.base.ref }}
 
     - name: Install Doxygen
       # choco install doxygen.portable # <-- too unreliable.
       run: |
-        (New-Object System.Net.WebClient).DownloadFile("https://sourceforge.net/projects/myosin/files/doxygen-1.8.14.windows.x64.bin.zip/download", "doxygen.zip")
+        (New-Object System.Net.WebClient).DownloadFile("https://github.com/doxygen/doxygen/releases/download/Release_1_12_0/doxygen-1.12.0.windows.x64.bin.zip", "doxygen.zip")
         7z x $env:GITHUB_WORKSPACE/doxygen.zip -odoxygen
         echo "$env:GITHUB_WORKSPACE\\doxygen" >> $GITHUB_PATH
 
@@ -269,12 +269,12 @@ jobs:
       version: ${{ steps.configure.outputs.version }}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install Doxygen
       # choco install doxygen.portable # <-- too unreliable.
       run: |
-        (New-Object System.Net.WebClient).DownloadFile("https://sourceforge.net/projects/myosin/files/doxygen-1.8.14.windows.x64.bin.zip/download", "doxygen.zip")
+        (New-Object System.Net.WebClient).DownloadFile("https://github.com/doxygen/doxygen/releases/download/Release_1_12_0/doxygen-1.12.0.windows.x64.bin.zip", "doxygen.zip")
         7z x $env:GITHUB_WORKSPACE/doxygen.zip -odoxygen
         echo "$env:GITHUB_WORKSPACE\\doxygen" >> $GITHUB_PATH
 
@@ -370,12 +370,12 @@ jobs:
   mac_target:
     name: Mac [target]
 
-    runs-on: macos-12
+    runs-on: macos-14
 
     if: ${{ contains(github.event.pull_request.title, '[perf-mac]') || contains(github.event.pull_request.body, '[perf-mac]') }}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         ref: ${{ github.event.pull_request.base.ref }} 
 
@@ -498,15 +498,15 @@ jobs:
 
   mac_source:
 
-    runs-on: macos-12
+    runs-on: macos-14
 
     name: ${{ (contains(github.event.pull_request.title, '[perf-mac]') || contains(github.event.pull_request.body, '[perf-mac]')) && 'Mac [source]' || 'Mac' }}
 
     outputs:
       version: ${{ steps.configure.outputs.version }}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install Python packages
       uses: actions/setup-python@v4
@@ -635,7 +635,7 @@ jobs:
       - windows2022_target
       - windows2022_source
 
-    runs-on: macos-12
+    runs-on: ubuntu-latest
 
     if: ${{ contains(github.event.pull_request.title, '[perf-win]') || contains(github.event.pull_request.body, '[perf-win]') }}
 
@@ -719,7 +719,7 @@ jobs:
       - mac_target
       - mac_source
 
-    runs-on: macos-12
+    runs-on: ubuntu-latest
 
     if: ${{ contains(github.event.pull_request.title, '[perf-mac]') || contains(github.event.pull_request.body, '[perf-mac]') }}
 
@@ -798,7 +798,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install Python packages
       uses: actions/setup-python@v4
@@ -912,7 +912,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install Python packages
       uses: actions/setup-python@v4
@@ -1060,7 +1060,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Check for tabs
       # Ensure that there are no tabs in source code.

OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp

@@ -597,13 +597,16 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
             CHECK(muscle.getFiberVelocityAlongTendon(state) == -1 * Vmax);
             CHECK(muscle.getPennationAngularVelocity(state) == 0);
             CHECK(muscle.getTendonVelocity(state) == 0);
-            CHECK(muscle.getForceVelocityMultiplier(state) == 0);
+            CHECK_THAT(muscle.getForceVelocityMultiplier(state),
+                    Catch::Matchers::WithinAbs(0.0, SimTK::Eps));
 
             model.realizeDynamics(state);
             const auto Fmax = muscle.getMaxIsometricForce();
             const auto fpass = muscle.calcPassiveForceMultiplier(1.0);
-            CHECK(muscle.getActiveFiberForce(state) == 0);
-            CHECK(muscle.getActiveFiberForceAlongTendon(state) == 0);
+            CHECK_THAT(muscle.getActiveFiberForce(state),
+                    Catch::Matchers::WithinAbs(0.0, SimTK::Eps));
+            CHECK_THAT(muscle.getActiveFiberForceAlongTendon(state),
+                    Catch::Matchers::WithinAbs(0.0, SimTK::Eps));
             CHECK(muscle.getPassiveFiberForce(state) == Approx(Fmax * fpass));
             CHECK(muscle.getPassiveFiberForceAlongTendon(state) ==
                     Approx(Fmax * fpass));
@@ -630,16 +633,17 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
             SimTK::Real fiberStiffnessAlongTendon =
                     diffFiberStiffnessAlongTendon.calcDerivative(
                             muscle.get_optimal_fiber_length());
-            CHECK(muscle.getFiberStiffnessAlongTendon(state) ==
-                    Approx(fiberStiffnessAlongTendon));
+            CHECK_THAT(muscle.getFiberStiffnessAlongTendon(state),
+                    Catch::Matchers::WithinRel(fiberStiffnessAlongTendon, 1e-6));
 
             SimTK::Real tendonStiffness = SimTK::Infinity;
             CHECK(muscle.getTendonStiffness(state) == SimTK::Infinity);
-            CHECK(muscle.getMuscleStiffness(state) ==
-                    Approx(muscle.calcMuscleStiffness(
-                            tendonStiffness, fiberStiffnessAlongTendon)));
-
-            CHECK(muscle.getFiberActivePower(state) == Approx(0.0));
+            SimTK::Real muscleStiffness = muscle.calcMuscleStiffness(
+                    tendonStiffness, fiberStiffnessAlongTendon);
+            CHECK_THAT(muscle.getMuscleStiffness(state),
+                    Catch::Matchers::WithinRel(muscleStiffness, 1e-6));
+            CHECK_THAT(muscle.getFiberActivePower(state),
+                    Catch::Matchers::WithinAbs(0.0, SimTK::Eps));
             CHECK(muscle.getFiberPassivePower(state) ==
                     Approx(Vmax * Fmax * fpass));
             CHECK(muscle.getTendonPower(state) == Approx(0.0));

OpenSim/Analyses/Test/testOutputReporter.cpp

@@ -197,16 +197,9 @@ void simulateMuscle(
     state.setTime(initialTime);
     manager.initialize(state);
 
-    cout << "\nIntegrating from " << initialTime << " to " << finalTime << endl;
-
-    // Start timing the simulation
-    const clock_t start = clock();
     // simulate
     state = manager.integrate(finalTime);
 
-    // how long did it take?
-    double comp_time = (double)(clock() - start) / CLOCKS_PER_SEC;
-
     //==========================================================================
     // 4. Print the results
     //==========================================================================
@@ -221,13 +214,19 @@ void simulateMuscle(
 
     double val_t0 = tableD.getIndependentColumn()[0];
     const SimTK::Real& val_ke0 = tableD.getRowAtIndex(0)[0];
-    const Vec3& val_omega0 = tableV3.getRowAtIndex(01)[1];
+    const Vec3& val_omega0 = tableV3.getRowAtIndex(0)[1];
     const SimTK::SpatialVec& val_jrf0 = tableSV.getRowAtIndex(0)[1];
 
-    ASSERT_EQUAL(t0, val_t0, SimTK::Eps);
-    ASSERT_EQUAL(ke0, val_ke0, SimTK::Eps);
-    ASSERT_EQUAL(ang_acc0, val_omega0, SimTK::Eps);
-    ASSERT_EQUAL(reaction0, val_jrf0, SimTK::Eps);
+    CHECK_THAT(t0, Catch::Matchers::WithinAbs(val_t0, SimTK::Eps));
+    CHECK_THAT(ke0, Catch::Matchers::WithinAbs(val_ke0, SimTK::Eps));
+    for (int i = 0; i < 3; ++i) {
+        CHECK_THAT(ang_acc0[i], 
+                Catch::Matchers::WithinAbs(val_omega0[i], SimTK::Eps));
+        for (int j = 0; j < 2; ++j) {
+            CHECK_THAT(reaction0[j][i], 
+                    Catch::Matchers::WithinAbs(val_jrf0[j][i], SimTK::Eps));
+        }
+    }
 
     double val_tf = tableD.getIndependentColumn()[tableD.getNumRows() - 1];
     const SimTK::Real& val_ke = tableD.getRowAtIndex(tableD.getNumRows() - 1)[0];
@@ -240,10 +239,16 @@ void simulateMuscle(
     auto ang_acc = ball->getAngularAccelerationInGround(state);
     auto reaction = slider->calcReactionOnChildExpressedInGround(state);
 
-    ASSERT_EQUAL(state.getTime(), val_tf, SimTK::Eps);
-    ASSERT_EQUAL(ke, val_ke, SimTK::Eps);
-    ASSERT_EQUAL(ang_acc, val_omega, SimTK::Eps);
-    ASSERT_EQUAL(reaction, val_jrf, SimTK::Eps);
+    CHECK_THAT(state.getTime(), Catch::Matchers::WithinAbs(val_tf, SimTK::Eps));
+    CHECK_THAT(ke, Catch::Matchers::WithinAbs(val_ke, 1e-10));
+    for (int i = 0; i < 3; ++i) {
+        CHECK_THAT(ang_acc[i], 
+                Catch::Matchers::WithinAbs(val_omega[i], SimTK::Eps));
+        for (int j = 0; j < 2; ++j) {
+            CHECK_THAT(reaction[j][i], 
+                    Catch::Matchers::WithinAbs(val_jrf[j][i], SimTK::Eps));
+        }
+    }
 }
 
 TEST_CASE("Output Reporter")

Vendors/tropter/tests/test_derivatives.cpp

@@ -656,8 +656,9 @@ TEST_CASE("User-supplied sparsity of Hessian of Lagrangian")
                 const auto& i = hes_sparsity.row[inz];
                 const auto& j = hes_sparsity.col[inz];
                 INFO(inz << " (" << i << " " << j << ")");
-                REQUIRE(analytical_hessian(i, j) ==
-                        Approx(actual_hessian_values[inz]).epsilon(1e-5));
+                REQUIRE_THAT(analytical_hessian(i, j), 
+                        Catch::Matchers::WithinAbs(
+                                actual_hessian_values[inz], 1e-5));
             }
         }
         {