From e02d16c590d69e01c598c53854edaf48a6d3ec3f Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Mon, 30 Sep 2024 16:10:24 -0700
Subject: [PATCH 01/24] Replace Doxygen download with choco install; upgrade
 Mac runners to macOS 14 now that 12 is deprecated

---
 .github/workflows/continuous_integration.yml | 29 +++++++++++---------
 1 file changed, 16 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml
index f8c222f5d7..1668f367aa 100644
--- a/.github/workflows/continuous_integration.yml
+++ b/.github/workflows/continuous_integration.yml
@@ -26,9 +26,10 @@ jobs:
     - 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")
-        7z x $env:GITHUB_WORKSPACE/doxygen.zip -odoxygen
-        echo "$env:GITHUB_WORKSPACE\\doxygen" >> $GITHUB_PATH
+        choco install doxygen.portable
+        # (New-Object System.Net.WebClient).DownloadFile("https://sourceforge.net/projects/myosin/files/doxygen-1.8.14.windows.x64.bin.zip/download", "doxygen.zip")
+        # 7z x $env:GITHUB_WORKSPACE/doxygen.zip -odoxygen
+        # echo "$env:GITHUB_WORKSPACE\\doxygen" >> $GITHUB_PATH
 
     - name: Install Python packages
       uses: actions/setup-python@v4
@@ -166,9 +167,10 @@ jobs:
     - 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")
-        7z x $env:GITHUB_WORKSPACE/doxygen.zip -odoxygen
-        echo "$env:GITHUB_WORKSPACE\\doxygen" >> $GITHUB_PATH
+        choco install doxygen.portable
+        # (New-Object System.Net.WebClient).DownloadFile("https://sourceforge.net/projects/myosin/files/doxygen-1.8.14.windows.x64.bin.zip/download", "doxygen.zip")
+        # 7z x $env:GITHUB_WORKSPACE/doxygen.zip -odoxygen
+        # echo "$env:GITHUB_WORKSPACE\\doxygen" >> $GITHUB_PATH
 
     - name: Install Python packages
       uses: actions/setup-python@v4
@@ -274,9 +276,10 @@ jobs:
     - 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")
-        7z x $env:GITHUB_WORKSPACE/doxygen.zip -odoxygen
-        echo "$env:GITHUB_WORKSPACE\\doxygen" >> $GITHUB_PATH
+        choco install doxygen.portable
+        # (New-Object System.Net.WebClient).DownloadFile("https://sourceforge.net/projects/myosin/files/doxygen-1.8.14.windows.x64.bin.zip/download", "doxygen.zip")
+        # 7z x $env:GITHUB_WORKSPACE/doxygen.zip -odoxygen
+        # echo "$env:GITHUB_WORKSPACE\\doxygen" >> $GITHUB_PATH
 
     - name: Install Python packages
       uses: actions/setup-python@v4
@@ -370,7 +373,7 @@ 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]') }}
 
@@ -498,7 +501,7 @@ 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' }}
 
@@ -635,7 +638,7 @@ jobs:
       - windows2022_target
       - windows2022_source
 
-    runs-on: macos-12
+    runs-on: macos-14
 
     if: ${{ contains(github.event.pull_request.title, '[perf-win]') || contains(github.event.pull_request.body, '[perf-win]') }}
 
@@ -719,7 +722,7 @@ jobs:
       - mac_target
       - mac_source
 
-    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]') }}
 

From 394fad0471ccc9bc180c7f11f1fbbdde98188fc2 Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Tue, 1 Oct 2024 09:55:52 -0700
Subject: [PATCH 02/24] Use ubuntu-latest for perf jobs

---
 .github/workflows/continuous_integration.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml
index 1668f367aa..c47540f39e 100644
--- a/.github/workflows/continuous_integration.yml
+++ b/.github/workflows/continuous_integration.yml
@@ -638,7 +638,7 @@ jobs:
       - windows2022_target
       - windows2022_source
 
-    runs-on: macos-14
+    runs-on: ubuntu-latest
 
     if: ${{ contains(github.event.pull_request.title, '[perf-win]') || contains(github.event.pull_request.body, '[perf-win]') }}
 
@@ -722,7 +722,7 @@ jobs:
       - mac_target
       - mac_source
 
-    runs-on: macos-14
+    runs-on: ubuntu-latest
 
     if: ${{ contains(github.event.pull_request.title, '[perf-mac]') || contains(github.event.pull_request.body, '[perf-mac]') }}
 

From 678a86e633ede6244cb484c5343a8f4e9803ae6f Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Tue, 1 Oct 2024 10:09:07 -0700
Subject: [PATCH 03/24] Fix Mac build failures

---
 .../Test/testDeGrooteFregly2016Muscle.cpp       | 17 ++++++++++-------
 Vendors/tropter/tests/test_derivatives.cpp      |  5 +++--
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
index 07d6951a1c..2565ef232f 100644
--- a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
+++ b/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::WithinRel(0.0, 1e-10));
 
             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::WithinRel(0.0, 1e-10));
+            CHECK_THAT(muscle.getActiveFiberForceAlongTendon(state),
+                    Catch::Matchers::WithinRel(0.0, 1e-10));
             CHECK(muscle.getPassiveFiberForce(state) == Approx(Fmax * fpass));
             CHECK(muscle.getPassiveFiberForceAlongTendon(state) ==
                     Approx(Fmax * fpass));
@@ -635,10 +638,10 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
 
             SimTK::Real tendonStiffness = SimTK::Infinity;
             CHECK(muscle.getTendonStiffness(state) == SimTK::Infinity);
-            CHECK(muscle.getMuscleStiffness(state) ==
-                    Approx(muscle.calcMuscleStiffness(
-                            tendonStiffness, fiberStiffnessAlongTendon)));
-
+            SimTK::Real muscleStiffness = muscle.calcMuscleStiffness(
+                    tendonStiffness, fiberStiffnessAlongTendon);
+            CHECK_THAT(muscle.getMuscleStiffness(state),
+                    Catch::Matchers::WithinRel(muscleStiffness, 1e-10));
             CHECK(muscle.getFiberActivePower(state) == Approx(0.0));
             CHECK(muscle.getFiberPassivePower(state) ==
                     Approx(Vmax * Fmax * fpass));
diff --git a/Vendors/tropter/tests/test_derivatives.cpp b/Vendors/tropter/tests/test_derivatives.cpp
index b20979ab38..187574fd0f 100644
--- a/Vendors/tropter/tests/test_derivatives.cpp
+++ b/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::WithinRel(
+                                actual_hessian_values[inz], 1e-5));
             }
         }
         {

From 25be1b38a346ac6253e17d341506bad6a8cb4811 Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Tue, 1 Oct 2024 11:17:40 -0700
Subject: [PATCH 04/24] Reduce tolerances on failing tests

---
 .../Actuators/Test/testDeGrooteFregly2016Muscle.cpp   | 11 ++++++-----
 Vendors/tropter/tests/test_derivatives.cpp            |  2 +-
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
index 2565ef232f..f556a09ee0 100644
--- a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
+++ b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
@@ -598,15 +598,15 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
             CHECK(muscle.getPennationAngularVelocity(state) == 0);
             CHECK(muscle.getTendonVelocity(state) == 0);
             CHECK_THAT(muscle.getForceVelocityMultiplier(state),
-                    Catch::Matchers::WithinRel(0.0, 1e-10));
+                    Catch::Matchers::WithinRel(0.0, 1e-8));
 
             model.realizeDynamics(state);
             const auto Fmax = muscle.getMaxIsometricForce();
             const auto fpass = muscle.calcPassiveForceMultiplier(1.0);
             CHECK_THAT(muscle.getActiveFiberForce(state),
-                    Catch::Matchers::WithinRel(0.0, 1e-10));
+                    Catch::Matchers::WithinRel(0.0, 1e-8));
             CHECK_THAT(muscle.getActiveFiberForceAlongTendon(state),
-                    Catch::Matchers::WithinRel(0.0, 1e-10));
+                    Catch::Matchers::WithinRel(0.0, 1e-8));
             CHECK(muscle.getPassiveFiberForce(state) == Approx(Fmax * fpass));
             CHECK(muscle.getPassiveFiberForceAlongTendon(state) ==
                     Approx(Fmax * fpass));
@@ -641,8 +641,9 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
             SimTK::Real muscleStiffness = muscle.calcMuscleStiffness(
                     tendonStiffness, fiberStiffnessAlongTendon);
             CHECK_THAT(muscle.getMuscleStiffness(state),
-                    Catch::Matchers::WithinRel(muscleStiffness, 1e-10));
-            CHECK(muscle.getFiberActivePower(state) == Approx(0.0));
+                    Catch::Matchers::WithinRel(muscleStiffness, 1e-8));
+            CHECK_THAT(muscle.getFiberActivePower(state),
+                    Catch::Matchers::WithinRel(0.0, 1e-8));
             CHECK(muscle.getFiberPassivePower(state) ==
                     Approx(Vmax * Fmax * fpass));
             CHECK(muscle.getTendonPower(state) == Approx(0.0));
diff --git a/Vendors/tropter/tests/test_derivatives.cpp b/Vendors/tropter/tests/test_derivatives.cpp
index 187574fd0f..e85d31c73d 100644
--- a/Vendors/tropter/tests/test_derivatives.cpp
+++ b/Vendors/tropter/tests/test_derivatives.cpp
@@ -658,7 +658,7 @@ TEST_CASE("User-supplied sparsity of Hessian of Lagrangian")
                 INFO(inz << " (" << i << " " << j << ")");
                 REQUIRE_THAT(analytical_hessian(i, j), 
                         Catch::Matchers::WithinRel(
-                                actual_hessian_values[inz], 1e-5));
+                                actual_hessian_values[inz], 1e-4));
             }
         }
         {

From a8f706162a3028acbc4968c23fda9f1745e4620f Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Tue, 1 Oct 2024 18:01:18 -0700
Subject: [PATCH 05/24] Use WithinAbs over WithinRel

---
 .../Actuators/Test/testDeGrooteFregly2016Muscle.cpp    | 10 +++++-----
 Vendors/tropter/tests/test_derivatives.cpp             |  4 ++--
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
index f556a09ee0..c55a4c34e9 100644
--- a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
+++ b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
@@ -598,15 +598,15 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
             CHECK(muscle.getPennationAngularVelocity(state) == 0);
             CHECK(muscle.getTendonVelocity(state) == 0);
             CHECK_THAT(muscle.getForceVelocityMultiplier(state),
-                    Catch::Matchers::WithinRel(0.0, 1e-8));
+                    Catch::Matchers::WithinAbs(0.0));
 
             model.realizeDynamics(state);
             const auto Fmax = muscle.getMaxIsometricForce();
             const auto fpass = muscle.calcPassiveForceMultiplier(1.0);
             CHECK_THAT(muscle.getActiveFiberForce(state),
-                    Catch::Matchers::WithinRel(0.0, 1e-8));
+                    Catch::Matchers::WithinAbs(0.0));
             CHECK_THAT(muscle.getActiveFiberForceAlongTendon(state),
-                    Catch::Matchers::WithinRel(0.0, 1e-8));
+                    Catch::Matchers::WithinAbs(0.0));
             CHECK(muscle.getPassiveFiberForce(state) == Approx(Fmax * fpass));
             CHECK(muscle.getPassiveFiberForceAlongTendon(state) ==
                     Approx(Fmax * fpass));
@@ -641,9 +641,9 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
             SimTK::Real muscleStiffness = muscle.calcMuscleStiffness(
                     tendonStiffness, fiberStiffnessAlongTendon);
             CHECK_THAT(muscle.getMuscleStiffness(state),
-                    Catch::Matchers::WithinRel(muscleStiffness, 1e-8));
+                    Catch::Matchers::WithinAbs(muscleStiffness));
             CHECK_THAT(muscle.getFiberActivePower(state),
-                    Catch::Matchers::WithinRel(0.0, 1e-8));
+                    Catch::Matchers::WithinAbs(0.0));
             CHECK(muscle.getFiberPassivePower(state) ==
                     Approx(Vmax * Fmax * fpass));
             CHECK(muscle.getTendonPower(state) == Approx(0.0));
diff --git a/Vendors/tropter/tests/test_derivatives.cpp b/Vendors/tropter/tests/test_derivatives.cpp
index e85d31c73d..2dfa55c4cd 100644
--- a/Vendors/tropter/tests/test_derivatives.cpp
+++ b/Vendors/tropter/tests/test_derivatives.cpp
@@ -657,8 +657,8 @@ TEST_CASE("User-supplied sparsity of Hessian of Lagrangian")
                 const auto& j = hes_sparsity.col[inz];
                 INFO(inz << " (" << i << " " << j << ")");
                 REQUIRE_THAT(analytical_hessian(i, j), 
-                        Catch::Matchers::WithinRel(
-                                actual_hessian_values[inz], 1e-4));
+                        Catch::Matchers::WithinAbs(
+                                actual_hessian_values[inz], 1e-5));
             }
         }
         {

From fc851e1eaafebdb89750dcf14d9ded46c8498707 Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Tue, 1 Oct 2024 18:38:26 -0700
Subject: [PATCH 06/24] Add tolerances for WithinAbs usages

---
 .github/workflows/continuous_integration.yml  | 21 ++++++++-----------
 .../Test/testDeGrooteFregly2016Muscle.cpp     | 10 ++++-----
 2 files changed, 14 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml
index c47540f39e..6b22fca9e2 100644
--- a/.github/workflows/continuous_integration.yml
+++ b/.github/workflows/continuous_integration.yml
@@ -26,10 +26,9 @@ jobs:
     - name: Install Doxygen
       # choco install doxygen.portable # <-- too unreliable.
       run: |
-        choco install doxygen.portable
-        # (New-Object System.Net.WebClient).DownloadFile("https://sourceforge.net/projects/myosin/files/doxygen-1.8.14.windows.x64.bin.zip/download", "doxygen.zip")
-        # 7z x $env:GITHUB_WORKSPACE/doxygen.zip -odoxygen
-        # echo "$env:GITHUB_WORKSPACE\\doxygen" >> $GITHUB_PATH
+        (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/download", "doxygen.zip")
+        7z x $env:GITHUB_WORKSPACE/doxygen.zip -odoxygen
+        echo "$env:GITHUB_WORKSPACE\\doxygen" >> $GITHUB_PATH
 
     - name: Install Python packages
       uses: actions/setup-python@v4
@@ -167,10 +166,9 @@ jobs:
     - name: Install Doxygen
       # choco install doxygen.portable # <-- too unreliable.
       run: |
-        choco install doxygen.portable
-        # (New-Object System.Net.WebClient).DownloadFile("https://sourceforge.net/projects/myosin/files/doxygen-1.8.14.windows.x64.bin.zip/download", "doxygen.zip")
-        # 7z x $env:GITHUB_WORKSPACE/doxygen.zip -odoxygen
-        # echo "$env:GITHUB_WORKSPACE\\doxygen" >> $GITHUB_PATH
+        (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/download", "doxygen.zip")
+        7z x $env:GITHUB_WORKSPACE/doxygen.zip -odoxygen
+        echo "$env:GITHUB_WORKSPACE\\doxygen" >> $GITHUB_PATH
 
     - name: Install Python packages
       uses: actions/setup-python@v4
@@ -276,10 +274,9 @@ jobs:
     - name: Install Doxygen
       # choco install doxygen.portable # <-- too unreliable.
       run: |
-        choco install doxygen.portable
-        # (New-Object System.Net.WebClient).DownloadFile("https://sourceforge.net/projects/myosin/files/doxygen-1.8.14.windows.x64.bin.zip/download", "doxygen.zip")
-        # 7z x $env:GITHUB_WORKSPACE/doxygen.zip -odoxygen
-        # echo "$env:GITHUB_WORKSPACE\\doxygen" >> $GITHUB_PATH
+        (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/download", "doxygen.zip")
+        7z x $env:GITHUB_WORKSPACE/doxygen.zip -odoxygen
+        echo "$env:GITHUB_WORKSPACE\\doxygen" >> $GITHUB_PATH
 
     - name: Install Python packages
       uses: actions/setup-python@v4
diff --git a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
index c55a4c34e9..ca7cb0049f 100644
--- a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
+++ b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
@@ -598,15 +598,15 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
             CHECK(muscle.getPennationAngularVelocity(state) == 0);
             CHECK(muscle.getTendonVelocity(state) == 0);
             CHECK_THAT(muscle.getForceVelocityMultiplier(state),
-                    Catch::Matchers::WithinAbs(0.0));
+                    Catch::Matchers::WithinAbs(0.0, 1e-10));
 
             model.realizeDynamics(state);
             const auto Fmax = muscle.getMaxIsometricForce();
             const auto fpass = muscle.calcPassiveForceMultiplier(1.0);
             CHECK_THAT(muscle.getActiveFiberForce(state),
-                    Catch::Matchers::WithinAbs(0.0));
+                    Catch::Matchers::WithinAbs(0.0, 1e-10));
             CHECK_THAT(muscle.getActiveFiberForceAlongTendon(state),
-                    Catch::Matchers::WithinAbs(0.0));
+                    Catch::Matchers::WithinAbs(0.0, 1e-10));
             CHECK(muscle.getPassiveFiberForce(state) == Approx(Fmax * fpass));
             CHECK(muscle.getPassiveFiberForceAlongTendon(state) ==
                     Approx(Fmax * fpass));
@@ -641,9 +641,9 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
             SimTK::Real muscleStiffness = muscle.calcMuscleStiffness(
                     tendonStiffness, fiberStiffnessAlongTendon);
             CHECK_THAT(muscle.getMuscleStiffness(state),
-                    Catch::Matchers::WithinAbs(muscleStiffness));
+                    Catch::Matchers::WithinAbs(muscleStiffness, 1e-10));
             CHECK_THAT(muscle.getFiberActivePower(state),
-                    Catch::Matchers::WithinAbs(0.0));
+                    Catch::Matchers::WithinAbs(0.0, 1e-10));
             CHECK(muscle.getFiberPassivePower(state) ==
                     Approx(Vmax * Fmax * fpass));
             CHECK(muscle.getTendonPower(state) == Approx(0.0));

From 0ea8583cf6229e965b70ec586d86442a5f38e959 Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Tue, 1 Oct 2024 19:27:10 -0700
Subject: [PATCH 07/24] Try using checkout@v4 to avoid temp HOME directory
 issue

---
 .github/workflows/continuous_integration.yml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml
index 6b22fca9e2..108aa79b69 100644
--- a/.github/workflows/continuous_integration.yml
+++ b/.github/workflows/continuous_integration.yml
@@ -21,7 +21,7 @@ jobs:
     runs-on: windows-2019
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install Doxygen
       # choco install doxygen.portable # <-- too unreliable.
@@ -159,7 +159,7 @@ jobs:
     runs-on: windows-2022
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         ref: ${{ github.event.pull_request.base.ref }}
 
@@ -269,7 +269,7 @@ jobs:
       version: ${{ steps.configure.outputs.version }}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install Doxygen
       # choco install doxygen.portable # <-- too unreliable.
@@ -375,7 +375,7 @@ jobs:
     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 }} 
 
@@ -506,7 +506,7 @@ jobs:
       version: ${{ steps.configure.outputs.version }}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     
     - name: Install Python packages
       uses: actions/setup-python@v4
@@ -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.

From 4c1e2beaa64324042dda464110c4331299ad714f Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Tue, 1 Oct 2024 19:32:45 -0700
Subject: [PATCH 08/24] Use correct URL for doxygen download

---
 .github/workflows/continuous_integration.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml
index 108aa79b69..fce0367436 100644
--- a/.github/workflows/continuous_integration.yml
+++ b/.github/workflows/continuous_integration.yml
@@ -26,7 +26,7 @@ jobs:
     - name: Install Doxygen
       # choco install doxygen.portable # <-- too unreliable.
       run: |
-        (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/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
 
@@ -166,7 +166,7 @@ jobs:
     - name: Install Doxygen
       # choco install doxygen.portable # <-- too unreliable.
       run: |
-        (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/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
 
@@ -274,7 +274,7 @@ jobs:
     - name: Install Doxygen
       # choco install doxygen.portable # <-- too unreliable.
       run: |
-        (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/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
 

From 38ede67dff0b401e2ed58b39ed8b63dd27c3b66f Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Tue, 1 Oct 2024 20:15:44 -0700
Subject: [PATCH 09/24] Add some debugging print out statements

---
 OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
index ca7cb0049f..a58fe7f20f 100644
--- a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
+++ b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
@@ -640,6 +640,12 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
             CHECK(muscle.getTendonStiffness(state) == SimTK::Infinity);
             SimTK::Real muscleStiffness = muscle.calcMuscleStiffness(
                     tendonStiffness, fiberStiffnessAlongTendon);
+            CAPTURE(muscleStiffness);
+            CAPTURE(tendonStiffness);
+            CAPTURE(fiberStiffnessAlongTendon);
+            const MuscleDynamicsInfo& mdi = getMuscleDynamicsInfo(s)
+            CAPTURE(mdi.tendonStiffness);
+            CAPTURE(mdi.fiberStiffnessAlongTendon);
             CHECK_THAT(muscle.getMuscleStiffness(state),
                     Catch::Matchers::WithinAbs(muscleStiffness, 1e-10));
             CHECK_THAT(muscle.getFiberActivePower(state),

From 93c571f50504a05b025622ca7e69ef1782470f2d Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Tue, 1 Oct 2024 20:36:04 -0700
Subject: [PATCH 10/24] Add missing semicolon

---
 OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
index a58fe7f20f..f05d6b733a 100644
--- a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
+++ b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
@@ -643,7 +643,7 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
             CAPTURE(muscleStiffness);
             CAPTURE(tendonStiffness);
             CAPTURE(fiberStiffnessAlongTendon);
-            const MuscleDynamicsInfo& mdi = getMuscleDynamicsInfo(s)
+            const MuscleDynamicsInfo& mdi = getMuscleDynamicsInfo(s);
             CAPTURE(mdi.tendonStiffness);
             CAPTURE(mdi.fiberStiffnessAlongTendon);
             CHECK_THAT(muscle.getMuscleStiffness(state),

From e6c3e8e2f1024bab1dd01a8d4e7601f41883b202 Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Tue, 1 Oct 2024 22:25:41 -0700
Subject: [PATCH 11/24] Fix typo

---
 OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
index f05d6b733a..d5df9adfde 100644
--- a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
+++ b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
@@ -643,7 +643,7 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
             CAPTURE(muscleStiffness);
             CAPTURE(tendonStiffness);
             CAPTURE(fiberStiffnessAlongTendon);
-            const MuscleDynamicsInfo& mdi = getMuscleDynamicsInfo(s);
+            const MuscleDynamicsInfo& mdi = muscle.getMuscleDynamicsInfo(s);
             CAPTURE(mdi.tendonStiffness);
             CAPTURE(mdi.fiberStiffnessAlongTendon);
             CHECK_THAT(muscle.getMuscleStiffness(state),

From 8d67de218ca483e441270bc090cc8009bf2acd27 Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Wed, 2 Oct 2024 08:25:27 -0700
Subject: [PATCH 12/24] Fix debugging outputs

---
 OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
index d5df9adfde..d69788f140 100644
--- a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
+++ b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
@@ -26,6 +26,7 @@
 #include <OpenSim/Common/STOFileAdapter.h>
 #include <OpenSim/Moco/osimMoco.h>
 #include <OpenSim/Simulation/Model/Model.h>
+#include <OpenSim/Simulation/Model/Muscle.h>
 #include <OpenSim/Simulation/SimbodyEngine/SliderJoint.h>
 #include <OpenSim/Tools/CMCTool.h>
 #include <OpenSim/Actuators/CoordinateActuator.h>
@@ -643,9 +644,8 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
             CAPTURE(muscleStiffness);
             CAPTURE(tendonStiffness);
             CAPTURE(fiberStiffnessAlongTendon);
-            const MuscleDynamicsInfo& mdi = muscle.getMuscleDynamicsInfo(s);
-            CAPTURE(mdi.tendonStiffness);
-            CAPTURE(mdi.fiberStiffnessAlongTendon);
+            CAPTURE(muscle.getTendonStiffness(state));
+            CAPTURE(muscle.getFiberStiffnessAlongTendon(state));
             CHECK_THAT(muscle.getMuscleStiffness(state),
                     Catch::Matchers::WithinAbs(muscleStiffness, 1e-10));
             CHECK_THAT(muscle.getFiberActivePower(state),

From 3587789cce52fe54c05aebb0683f732106203623 Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Wed, 2 Oct 2024 08:28:27 -0700
Subject: [PATCH 13/24] Remove unused timing code from testOutputReporter

---
 OpenSim/Analyses/Test/testOutputReporter.cpp | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/OpenSim/Analyses/Test/testOutputReporter.cpp b/OpenSim/Analyses/Test/testOutputReporter.cpp
index 13eb7791e5..47bb36c027 100644
--- a/OpenSim/Analyses/Test/testOutputReporter.cpp
+++ b/OpenSim/Analyses/Test/testOutputReporter.cpp
@@ -27,6 +27,7 @@
 #include <OpenSim/Auxiliary/auxiliaryTestFunctions.h>
 #include <OpenSim/Analyses/OutputReporter.h>
 
+#include "OpenSim/Common/Logger.h"
 #include <catch2/catch_all.hpp>
 
 using namespace OpenSim;
@@ -197,16 +198,11 @@ void simulateMuscle(
     state.setTime(initialTime);
     manager.initialize(state);
 
-    cout << "\nIntegrating from " << initialTime << " to " << finalTime << endl;
+    log_info("Integrating from {} to {}", initialTime, finalTime);
 
-    // 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
     //==========================================================================

From 5f3a5e76ead444dff96bc6430e6378f5429435d2 Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Wed, 2 Oct 2024 09:29:24 -0700
Subject: [PATCH 14/24] Use WithinRel comparison for fiber stiffness since were
 using a finite-differenced estimate

---
 .../Actuators/Test/testDeGrooteFregly2016Muscle.cpp    | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
index d69788f140..79f35cd9d1 100644
--- a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
+++ b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
@@ -634,8 +634,10 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
             SimTK::Real fiberStiffnessAlongTendon =
                     diffFiberStiffnessAlongTendon.calcDerivative(
                             muscle.get_optimal_fiber_length());
-            CHECK(muscle.getFiberStiffnessAlongTendon(state) ==
-                    Approx(fiberStiffnessAlongTendon));
+            CAPTURE(muscle.getFiberStiffnessAlongTendon(state));
+            CAPTURE(fiberStiffnessAlongTendon);
+            CHECK_THAT(muscle.getFiberStiffnessAlongTendon(state),
+                    Catch::Matchers::WithinRel(fiberStiffnessAlongTendon, 1e-6));
 
             SimTK::Real tendonStiffness = SimTK::Infinity;
             CHECK(muscle.getTendonStiffness(state) == SimTK::Infinity);
@@ -643,11 +645,9 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
                     tendonStiffness, fiberStiffnessAlongTendon);
             CAPTURE(muscleStiffness);
             CAPTURE(tendonStiffness);
-            CAPTURE(fiberStiffnessAlongTendon);
             CAPTURE(muscle.getTendonStiffness(state));
-            CAPTURE(muscle.getFiberStiffnessAlongTendon(state));
             CHECK_THAT(muscle.getMuscleStiffness(state),
-                    Catch::Matchers::WithinAbs(muscleStiffness, 1e-10));
+                    Catch::Matchers::WithinRel(muscleStiffness, 1e-6));
             CHECK_THAT(muscle.getFiberActivePower(state),
                     Catch::Matchers::WithinAbs(0.0, 1e-10));
             CHECK(muscle.getFiberPassivePower(state) ==

From bc3545f26cbe697e4142a5162609eeab2c0ed74e Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Wed, 2 Oct 2024 09:39:40 -0700
Subject: [PATCH 15/24] Add some debug print outs

---
 OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp | 5 -----
 OpenSim/Analyses/OutputReporter.cpp                     | 4 ++++
 OpenSim/Simulation/Model/AnalysisSet.cpp                | 8 ++++----
 3 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
index 79f35cd9d1..5e947ccc06 100644
--- a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
+++ b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
@@ -634,8 +634,6 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
             SimTK::Real fiberStiffnessAlongTendon =
                     diffFiberStiffnessAlongTendon.calcDerivative(
                             muscle.get_optimal_fiber_length());
-            CAPTURE(muscle.getFiberStiffnessAlongTendon(state));
-            CAPTURE(fiberStiffnessAlongTendon);
             CHECK_THAT(muscle.getFiberStiffnessAlongTendon(state),
                     Catch::Matchers::WithinRel(fiberStiffnessAlongTendon, 1e-6));
 
@@ -643,9 +641,6 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
             CHECK(muscle.getTendonStiffness(state) == SimTK::Infinity);
             SimTK::Real muscleStiffness = muscle.calcMuscleStiffness(
                     tendonStiffness, fiberStiffnessAlongTendon);
-            CAPTURE(muscleStiffness);
-            CAPTURE(tendonStiffness);
-            CAPTURE(muscle.getTendonStiffness(state));
             CHECK_THAT(muscle.getMuscleStiffness(state),
                     Catch::Matchers::WithinRel(muscleStiffness, 1e-6));
             CHECK_THAT(muscle.getFiberActivePower(state),
diff --git a/OpenSim/Analyses/OutputReporter.cpp b/OpenSim/Analyses/OutputReporter.cpp
index 772dcfc4dd..585e52507e 100644
--- a/OpenSim/Analyses/OutputReporter.cpp
+++ b/OpenSim/Analyses/OutputReporter.cpp
@@ -130,23 +130,27 @@ int OutputReporter::printResults(const std::string& baseName,
         return 0;
     }
 
+    log_info("OutputReporter checking extension is .sto: {}", extension);
     OPENSIM_THROW_IF_FRMOBJ(IO::Lowercase(extension) != ".sto",
         Exception, "Only writing results to '.sto' format is supported.");
 
     std::string prefix = dir.empty() ? "" : dir + "/";
 
+    log_info("OutputReporter.printResults: Writing double results to {}.", prefix);
     auto& tableD = _tableReporterDouble->getTable();
     if (tableD.getNumColumns()) {
         STOFileAdapter_<double>::write(tableD,
             prefix + baseName + "_Outputs" + extension);
     }
 
+    log_info("OutputReporter.printResults: Writing Vec3 results to {}.", prefix);
     auto& tableV3 = _tableReporterVec3->getTable();
     if (tableV3.getNumColumns()) {
         STOFileAdapter_<SimTK::Vec3>::write(tableV3,
             prefix + baseName + "_OutputsVec3" + extension);
     }
 
+    log_info("OutputReporter.printResults: Writing SpatialVec results to {}.", prefix);
     auto& tableSV = _tableReporterSpatialVec->getTable();
     if (tableSV.getNumColumns()) {
         STOFileAdapter_<SimTK::SpatialVec>::write(tableSV,
diff --git a/OpenSim/Simulation/Model/AnalysisSet.cpp b/OpenSim/Simulation/Model/AnalysisSet.cpp
index 094593d232..59fb4f6bc9 100644
--- a/OpenSim/Simulation/Model/AnalysisSet.cpp
+++ b/OpenSim/Simulation/Model/AnalysisSet.cpp
@@ -254,11 +254,11 @@ void AnalysisSet::
 printResults(const string &aBaseName,const string &aDir,double aDT,
                  const string &aExtension)
 {
-    int i;
-    int size = getSize();
-    for(i=0;i<size;i++) {
+    for(int i = 0; i < getSize(); i++) {
         Analysis& analysis = get(i);
-        if(analysis.getOn() && analysis.getPrintResultFiles()) analysis.printResults(aBaseName,aDir,aDT,aExtension);
+        if(analysis.getOn() && analysis.getPrintResultFiles()) {
+            analysis.printResults(aBaseName, aDir, aDT, aExtension);
+        }
     }
 }
 //=============================================================================

From 1e13a8b9b0f86909804ca3260d003df8c0d7710d Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Wed, 2 Oct 2024 10:27:18 -0700
Subject: [PATCH 16/24] Fix indexing typo and add more debug statements

---
 OpenSim/Analyses/Test/testOutputReporter.cpp | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/OpenSim/Analyses/Test/testOutputReporter.cpp b/OpenSim/Analyses/Test/testOutputReporter.cpp
index 47bb36c027..e4118cca3e 100644
--- a/OpenSim/Analyses/Test/testOutputReporter.cpp
+++ b/OpenSim/Analyses/Test/testOutputReporter.cpp
@@ -211,20 +211,24 @@ void simulateMuscle(
     //==========================================================================
     // 5. Verify files were written with correct values
     //==========================================================================
+    log_info("Loading the results from file");
     TimeSeriesTable tableD("testOutputReporter_Outputs.sto");
     TimeSeriesTable_<SimTK::Vec3> tableV3("testOutputReporter_OutputsVec3.sto");
     TimeSeriesTable_<SimTK::SpatialVec> tableSV("testOutputReporter_OutputsSpatialVec.sto");
 
+    log_info("Indexing initial values");
     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];
 
+    log_info("Checking initial values");
     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);
 
+    log_info("Indexing final values");
     double val_tf = tableD.getIndependentColumn()[tableD.getNumRows() - 1];
     const SimTK::Real& val_ke = tableD.getRowAtIndex(tableD.getNumRows() - 1)[0];
     const Vec3& val_omega = tableV3.getRowAtIndex(tableV3.getNumRows() - 1)[1];
@@ -236,6 +240,7 @@ void simulateMuscle(
     auto ang_acc = ball->getAngularAccelerationInGround(state);
     auto reaction = slider->calcReactionOnChildExpressedInGround(state);
 
+    log_info("Checking final values");
     ASSERT_EQUAL(state.getTime(), val_tf, SimTK::Eps);
     ASSERT_EQUAL(ke, val_ke, SimTK::Eps);
     ASSERT_EQUAL(ang_acc, val_omega, SimTK::Eps);

From 94db2012895d9725baa4eace9be1906542d4f192 Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Wed, 2 Oct 2024 11:04:28 -0700
Subject: [PATCH 17/24] Even more debug statements

---
 OpenSim/Analyses/Test/testOutputReporter.cpp | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/OpenSim/Analyses/Test/testOutputReporter.cpp b/OpenSim/Analyses/Test/testOutputReporter.cpp
index e4118cca3e..d7b77d8e8b 100644
--- a/OpenSim/Analyses/Test/testOutputReporter.cpp
+++ b/OpenSim/Analyses/Test/testOutputReporter.cpp
@@ -245,6 +245,8 @@ void simulateMuscle(
     ASSERT_EQUAL(ke, val_ke, SimTK::Eps);
     ASSERT_EQUAL(ang_acc, val_omega, SimTK::Eps);
     ASSERT_EQUAL(reaction, val_jrf, SimTK::Eps);
+
+    log_info("Exiting simulateMuscle");
 }
 
 TEST_CASE("Output Reporter")
@@ -261,4 +263,6 @@ TEST_CASE("Output Reporter")
     simulateMuscle( muscle,
         IntegrationAccuracy,
         true);
+
+    log_info("Exiting testOutputReporter");
 }

From bfc635b62d29cd771aa0fb59de0dca817f702f96 Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Wed, 2 Oct 2024 12:07:18 -0700
Subject: [PATCH 18/24] Try using Catch2 comparisons

---
 OpenSim/Analyses/Test/testOutputReporter.cpp | 40 ++++++++++++++++----
 1 file changed, 32 insertions(+), 8 deletions(-)

diff --git a/OpenSim/Analyses/Test/testOutputReporter.cpp b/OpenSim/Analyses/Test/testOutputReporter.cpp
index d7b77d8e8b..eaad9474d9 100644
--- a/OpenSim/Analyses/Test/testOutputReporter.cpp
+++ b/OpenSim/Analyses/Test/testOutputReporter.cpp
@@ -223,10 +223,21 @@ void simulateMuscle(
     const SimTK::SpatialVec& val_jrf0 = tableSV.getRowAtIndex(0)[1];
 
     log_info("Checking initial values");
-    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);
+    // 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));
+        }
+    }
 
     log_info("Indexing final values");
     double val_tf = tableD.getIndependentColumn()[tableD.getNumRows() - 1];
@@ -240,11 +251,24 @@ void simulateMuscle(
     auto ang_acc = ball->getAngularAccelerationInGround(state);
     auto reaction = slider->calcReactionOnChildExpressedInGround(state);
 
+    log_info("Checking final time {}: ", state.getTime());
+
     log_info("Checking final values");
-    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);
+    // 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, SimTK::Eps));
+    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));
+        }
+    }
 
     log_info("Exiting simulateMuscle");
 }

From 5398b4600c861b09d8e1231dae50b86a8a6cd4c9 Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Wed, 2 Oct 2024 12:57:04 -0700
Subject: [PATCH 19/24] Loosen tolerance on kinetic energy check

---
 OpenSim/Analyses/Test/testOutputReporter.cpp | 23 +-------------------
 OpenSim/Simulation/Model/AnalysisSet.cpp     |  8 +++----
 2 files changed, 5 insertions(+), 26 deletions(-)

diff --git a/OpenSim/Analyses/Test/testOutputReporter.cpp b/OpenSim/Analyses/Test/testOutputReporter.cpp
index eaad9474d9..dec5f1eb10 100644
--- a/OpenSim/Analyses/Test/testOutputReporter.cpp
+++ b/OpenSim/Analyses/Test/testOutputReporter.cpp
@@ -211,23 +211,15 @@ void simulateMuscle(
     //==========================================================================
     // 5. Verify files were written with correct values
     //==========================================================================
-    log_info("Loading the results from file");
     TimeSeriesTable tableD("testOutputReporter_Outputs.sto");
     TimeSeriesTable_<SimTK::Vec3> tableV3("testOutputReporter_OutputsVec3.sto");
     TimeSeriesTable_<SimTK::SpatialVec> tableSV("testOutputReporter_OutputsSpatialVec.sto");
 
-    log_info("Indexing initial values");
     double val_t0 = tableD.getIndependentColumn()[0];
     const SimTK::Real& val_ke0 = tableD.getRowAtIndex(0)[0];
     const Vec3& val_omega0 = tableV3.getRowAtIndex(0)[1];
     const SimTK::SpatialVec& val_jrf0 = tableSV.getRowAtIndex(0)[1];
 
-    log_info("Checking initial values");
-    // 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) {
@@ -239,7 +231,6 @@ void simulateMuscle(
         }
     }
 
-    log_info("Indexing final values");
     double val_tf = tableD.getIndependentColumn()[tableD.getNumRows() - 1];
     const SimTK::Real& val_ke = tableD.getRowAtIndex(tableD.getNumRows() - 1)[0];
     const Vec3& val_omega = tableV3.getRowAtIndex(tableV3.getNumRows() - 1)[1];
@@ -251,16 +242,8 @@ void simulateMuscle(
     auto ang_acc = ball->getAngularAccelerationInGround(state);
     auto reaction = slider->calcReactionOnChildExpressedInGround(state);
 
-    log_info("Checking final time {}: ", state.getTime());
-
-    log_info("Checking final values");
-    // 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, 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));
@@ -269,8 +252,6 @@ void simulateMuscle(
                     Catch::Matchers::WithinAbs(val_jrf[j][i], SimTK::Eps));
         }
     }
-
-    log_info("Exiting simulateMuscle");
 }
 
 TEST_CASE("Output Reporter")
@@ -287,6 +268,4 @@ TEST_CASE("Output Reporter")
     simulateMuscle( muscle,
         IntegrationAccuracy,
         true);
-
-    log_info("Exiting testOutputReporter");
 }
diff --git a/OpenSim/Simulation/Model/AnalysisSet.cpp b/OpenSim/Simulation/Model/AnalysisSet.cpp
index 59fb4f6bc9..e8d0f4e54f 100644
--- a/OpenSim/Simulation/Model/AnalysisSet.cpp
+++ b/OpenSim/Simulation/Model/AnalysisSet.cpp
@@ -254,11 +254,11 @@ void AnalysisSet::
 printResults(const string &aBaseName,const string &aDir,double aDT,
                  const string &aExtension)
 {
-    for(int i = 0; i < getSize(); i++) {
+    int i;
+    int size = getSize();
+    for(i=0;i<getSize();i++) {
         Analysis& analysis = get(i);
-        if(analysis.getOn() && analysis.getPrintResultFiles()) {
-            analysis.printResults(aBaseName, aDir, aDT, aExtension);
-        }
+        if(analysis.getOn() && analysis.getPrintResultFiles()) analysis.printResults(aBaseName, aDir, aDT, aExtension);
     }
 }
 //=============================================================================

From 9b5a1a5990e4fa7e6b672535257ef929951ed7f5 Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Wed, 2 Oct 2024 12:57:56 -0700
Subject: [PATCH 20/24] Revert AnalysisSet changes

---
 OpenSim/Simulation/Model/AnalysisSet.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/OpenSim/Simulation/Model/AnalysisSet.cpp b/OpenSim/Simulation/Model/AnalysisSet.cpp
index e8d0f4e54f..094593d232 100644
--- a/OpenSim/Simulation/Model/AnalysisSet.cpp
+++ b/OpenSim/Simulation/Model/AnalysisSet.cpp
@@ -256,9 +256,9 @@ printResults(const string &aBaseName,const string &aDir,double aDT,
 {
     int i;
     int size = getSize();
-    for(i=0;i<getSize();i++) {
+    for(i=0;i<size;i++) {
         Analysis& analysis = get(i);
-        if(analysis.getOn() && analysis.getPrintResultFiles()) analysis.printResults(aBaseName, aDir, aDT, aExtension);
+        if(analysis.getOn() && analysis.getPrintResultFiles()) analysis.printResults(aBaseName,aDir,aDT,aExtension);
     }
 }
 //=============================================================================

From 6a19e3ccced8a5373ef143af8109a386caee324a Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Wed, 2 Oct 2024 12:58:41 -0700
Subject: [PATCH 21/24] Revert OutputReporter.cpp changes

---
 OpenSim/Analyses/OutputReporter.cpp | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/OpenSim/Analyses/OutputReporter.cpp b/OpenSim/Analyses/OutputReporter.cpp
index 585e52507e..772dcfc4dd 100644
--- a/OpenSim/Analyses/OutputReporter.cpp
+++ b/OpenSim/Analyses/OutputReporter.cpp
@@ -130,27 +130,23 @@ int OutputReporter::printResults(const std::string& baseName,
         return 0;
     }
 
-    log_info("OutputReporter checking extension is .sto: {}", extension);
     OPENSIM_THROW_IF_FRMOBJ(IO::Lowercase(extension) != ".sto",
         Exception, "Only writing results to '.sto' format is supported.");
 
     std::string prefix = dir.empty() ? "" : dir + "/";
 
-    log_info("OutputReporter.printResults: Writing double results to {}.", prefix);
     auto& tableD = _tableReporterDouble->getTable();
     if (tableD.getNumColumns()) {
         STOFileAdapter_<double>::write(tableD,
             prefix + baseName + "_Outputs" + extension);
     }
 
-    log_info("OutputReporter.printResults: Writing Vec3 results to {}.", prefix);
     auto& tableV3 = _tableReporterVec3->getTable();
     if (tableV3.getNumColumns()) {
         STOFileAdapter_<SimTK::Vec3>::write(tableV3,
             prefix + baseName + "_OutputsVec3" + extension);
     }
 
-    log_info("OutputReporter.printResults: Writing SpatialVec results to {}.", prefix);
     auto& tableSV = _tableReporterSpatialVec->getTable();
     if (tableSV.getNumColumns()) {
         STOFileAdapter_<SimTK::SpatialVec>::write(tableSV,

From a08f3bae6677b7b7efa5a400947a46a695bd16f3 Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Wed, 2 Oct 2024 17:14:16 -0700
Subject: [PATCH 22/24] Remove unused header includes

---
 OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp | 1 -
 OpenSim/Analyses/Test/testOutputReporter.cpp            | 3 ---
 2 files changed, 4 deletions(-)

diff --git a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
index 5e947ccc06..bd0c3533f0 100644
--- a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
+++ b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
@@ -26,7 +26,6 @@
 #include <OpenSim/Common/STOFileAdapter.h>
 #include <OpenSim/Moco/osimMoco.h>
 #include <OpenSim/Simulation/Model/Model.h>
-#include <OpenSim/Simulation/Model/Muscle.h>
 #include <OpenSim/Simulation/SimbodyEngine/SliderJoint.h>
 #include <OpenSim/Tools/CMCTool.h>
 #include <OpenSim/Actuators/CoordinateActuator.h>
diff --git a/OpenSim/Analyses/Test/testOutputReporter.cpp b/OpenSim/Analyses/Test/testOutputReporter.cpp
index dec5f1eb10..c1451df6a4 100644
--- a/OpenSim/Analyses/Test/testOutputReporter.cpp
+++ b/OpenSim/Analyses/Test/testOutputReporter.cpp
@@ -27,7 +27,6 @@
 #include <OpenSim/Auxiliary/auxiliaryTestFunctions.h>
 #include <OpenSim/Analyses/OutputReporter.h>
 
-#include "OpenSim/Common/Logger.h"
 #include <catch2/catch_all.hpp>
 
 using namespace OpenSim;
@@ -198,8 +197,6 @@ void simulateMuscle(
     state.setTime(initialTime);
     manager.initialize(state);
 
-    log_info("Integrating from {} to {}", initialTime, finalTime);
-
     // simulate
     state = manager.integrate(finalTime);
 

From d0852c157eade382cb15dfe5d3bd3b5ec47ec1a0 Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Thu, 3 Oct 2024 09:31:16 -0700
Subject: [PATCH 23/24] Use SimTK::Eps over custom tolerances; add TODO about
 failing testOutputReporter test

---
 OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
index bd0c3533f0..c266322837 100644
--- a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
+++ b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
@@ -598,15 +598,15 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
             CHECK(muscle.getPennationAngularVelocity(state) == 0);
             CHECK(muscle.getTendonVelocity(state) == 0);
             CHECK_THAT(muscle.getForceVelocityMultiplier(state),
-                    Catch::Matchers::WithinAbs(0.0, 1e-10));
+                    Catch::Matchers::WithinAbs(0.0, SimTK::Eps));
 
             model.realizeDynamics(state);
             const auto Fmax = muscle.getMaxIsometricForce();
             const auto fpass = muscle.calcPassiveForceMultiplier(1.0);
             CHECK_THAT(muscle.getActiveFiberForce(state),
-                    Catch::Matchers::WithinAbs(0.0, 1e-10));
+                    Catch::Matchers::WithinAbs(0.0, SimTK::Eps));
             CHECK_THAT(muscle.getActiveFiberForceAlongTendon(state),
-                    Catch::Matchers::WithinAbs(0.0, 1e-10));
+                    Catch::Matchers::WithinAbs(0.0, SimTK::Eps));
             CHECK(muscle.getPassiveFiberForce(state) == Approx(Fmax * fpass));
             CHECK(muscle.getPassiveFiberForceAlongTendon(state) ==
                     Approx(Fmax * fpass));
@@ -643,7 +643,7 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
             CHECK_THAT(muscle.getMuscleStiffness(state),
                     Catch::Matchers::WithinRel(muscleStiffness, 1e-6));
             CHECK_THAT(muscle.getFiberActivePower(state),
-                    Catch::Matchers::WithinAbs(0.0, 1e-10));
+                    Catch::Matchers::WithinAbs(0.0, SimTK::Eps));
             CHECK(muscle.getFiberPassivePower(state) ==
                     Approx(Vmax * Fmax * fpass));
             CHECK(muscle.getTendonPower(state) == Approx(0.0));

From a05e4dbd660843889dfb293e08e5f3acb0039e1f Mon Sep 17 00:00:00 2001
From: Nicholas Bianco <nbianco@stanford.edu>
Date: Thu, 3 Oct 2024 16:34:04 -0700
Subject: [PATCH 24/24] Revert usages of SimTK::Eps

---
 OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
index c266322837..bd0c3533f0 100644
--- a/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
+++ b/OpenSim/Actuators/Test/testDeGrooteFregly2016Muscle.cpp
@@ -598,15 +598,15 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
             CHECK(muscle.getPennationAngularVelocity(state) == 0);
             CHECK(muscle.getTendonVelocity(state) == 0);
             CHECK_THAT(muscle.getForceVelocityMultiplier(state),
-                    Catch::Matchers::WithinAbs(0.0, SimTK::Eps));
+                    Catch::Matchers::WithinAbs(0.0, 1e-10));
 
             model.realizeDynamics(state);
             const auto Fmax = muscle.getMaxIsometricForce();
             const auto fpass = muscle.calcPassiveForceMultiplier(1.0);
             CHECK_THAT(muscle.getActiveFiberForce(state),
-                    Catch::Matchers::WithinAbs(0.0, SimTK::Eps));
+                    Catch::Matchers::WithinAbs(0.0, 1e-10));
             CHECK_THAT(muscle.getActiveFiberForceAlongTendon(state),
-                    Catch::Matchers::WithinAbs(0.0, SimTK::Eps));
+                    Catch::Matchers::WithinAbs(0.0, 1e-10));
             CHECK(muscle.getPassiveFiberForce(state) == Approx(Fmax * fpass));
             CHECK(muscle.getPassiveFiberForceAlongTendon(state) ==
                     Approx(Fmax * fpass));
@@ -643,7 +643,7 @@ TEST_CASE("DeGrooteFregly2016Muscle basics") {
             CHECK_THAT(muscle.getMuscleStiffness(state),
                     Catch::Matchers::WithinRel(muscleStiffness, 1e-6));
             CHECK_THAT(muscle.getFiberActivePower(state),
-                    Catch::Matchers::WithinAbs(0.0, SimTK::Eps));
+                    Catch::Matchers::WithinAbs(0.0, 1e-10));
             CHECK(muscle.getFiberPassivePower(state) ==
                     Approx(Vmax * Fmax * fpass));
             CHECK(muscle.getTendonPower(state) == Approx(0.0));