From 6c8e11ebefead266bfb18d25f941513a25418af2 Mon Sep 17 00:00:00 2001
From: nickbianco <nbianco@stanford.edu>
Date: Sat, 19 Oct 2024 13:58:01 -0700
Subject: [PATCH 01/15] Add Mac arm64 and Ubuntu 22 CI builds; reorganize
 continuous integration script

---
 .github/workflows/continuous_integration.yml | 492 +++++++++++--------
 1 file changed, 287 insertions(+), 205 deletions(-)

diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml
index fce0367436..1c3a7992b3 100644
--- a/.github/workflows/continuous_integration.yml
+++ b/.github/workflows/continuous_integration.yml
@@ -15,9 +15,8 @@ on:
       - '*'
 
 jobs:
-  windows:
-    name: Windows
-
+  windows2019:
+    name: Windows 2019
     runs-on: windows-2019
 
     steps:
@@ -115,53 +114,18 @@ jobs:
     - name: Upload opensim-core
       uses: actions/upload-artifact@v4
       with:
-        name: opensim-core-${{ steps.configure.outputs.version }}-win-2019
+        name: opensim-core-${{ steps.configure.outputs.version }}-win2019
         path: opensim-core-${{ steps.configure.outputs.version }}.zip
 
-    # TODO: Must be relative to the workspace?
-    # - name: Upload opensim-moco dependencies
-    #   uses: actions/upload-artifact@v1.0.0
-    #   with:
-    #     name: opensim-core-dependencies
-    #     path: opensim_dependencies_install.zip
-
-    # - name: Create release
-    #   id: create-release
-    #   uses: actions/create-release@v1.0.0
-    #   env:
-    #     GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-    #   with:
-    #     tag_name: ${{ github.ref }}
-    #     release_name: OpenSim Core ${{ github.ref }}
-    #     draft: true
-    #     prerelease: false
-
-    # - name: Zip opensim-core
-    #   run: |
-    #     7z a opensim-core-$VERSION.zip opensim-core-${VERSION}
-
-    # - name: Upload release asset
-    #   id: upload-release-asset
-    #   uses: actions/upload-release-asset@v1.0.1
-    #   env:
-    #     GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-    #   with:
-    #     upload_url: ${{ steps.create-release.outputs.upload_url }}
-    #     asset_path: ./opensim-core-${{ github.ref }}.zip
-    #     asset_name: opensim-core-${{ github.ref }}.zip
-    #     asset_content_type: application/zip
-
-  windows2022_target:
-    name: Windows2022 [target]
-
-    if: ${{ contains(github.event.pull_request.title, '[perf-win]') || contains(github.event.pull_request.body, '[perf-win]') }}
-
+  windows2022:
     runs-on: windows-2022
+    name: Windows 2022
+
+    outputs:
+      version: ${{ steps.configure.outputs.version }}
 
     steps:
     - uses: actions/checkout@v4
-      with:
-        ref: ${{ github.event.pull_request.base.ref }}
 
     - name: Install Doxygen
       # choco install doxygen.portable # <-- too unreliable.
@@ -174,7 +138,7 @@ jobs:
       uses: actions/setup-python@v4
       with:
         python-version: '3.10'
-        
+
     - name: Install numpy
       #Need numpy to use SWIG numpy typemaps.
       run: python3 -m pip install numpy==1.25
@@ -217,7 +181,7 @@ jobs:
         # TODO: Can remove /WX when we use that in CMakeLists.txt.
         # Set the CXXFLAGS environment variable to turn warnings into errors.
         # Skip timing test section included by default.
-        cmake -E env CXXFLAGS="/WX -DSKIP_TIMING" cmake $env:GITHUB_WORKSPACE -LAH -G"Visual Studio 17 2022" -A x64 -DCMAKE_INSTALL_PREFIX=~/opensim-core-install -DOPENSIM_DEPENDENCIES_DIR=~/opensim_dependencies_install -DOPENSIM_C3D_PARSER=ezc3d -DBUILD_PYTHON_WRAPPING=on -DBUILD_JAVA_WRAPPING=on -DPython3_ROOT_DIR=C:\hostedtoolcache\windows\Python\3.10.11\x64
+        cmake -E env CXXFLAGS="/WX -DSKIP_TIMING" cmake $env:GITHUB_WORKSPACE -LAH -G"Visual Studio 17 2022" -A x64 -DCMAKE_INSTALL_PREFIX=~/opensim-core-install -DOPENSIM_DEPENDENCIES_DIR=~/opensim_dependencies_install -DOPENSIM_C3D_PARSER=ezc3d -DOPENSIM_WITH_TROPTER=on -DOPENSIM_WITH_CASADI=on -DBUILD_PYTHON_WRAPPING=on -DBUILD_JAVA_WRAPPING=on -DPython3_ROOT_DIR=C:\hostedtoolcache\windows\Python\3.10.11\x64
         $env:match = cmake -L . | Select-String -Pattern OPENSIM_QUALIFIED_VERSION
         $version = $env:match.split('=')[1]
         echo $version
@@ -242,8 +206,8 @@ jobs:
       run: |
         chdir $env:GITHUB_WORKSPACE\\build
         chdir $env:GITHUB_WORKSPACE
-        Copy-Item -Path "~/opensim-core-install" -Destination "opensim-core-${{ github.event.pull_request.base.ref }}" -Recurse
-        7z a "opensim-core-${{ github.event.pull_request.base.ref }}.zip" "opensim-core-${{ github.event.pull_request.base.ref }}"
+        Copy-Item -Path "~/opensim-core-install" -Destination "opensim-core-${{ steps.configure.outputs.version }}" -Recurse
+        7z a "opensim-core-${{ steps.configure.outputs.version }}.zip" "opensim-core-${{ steps.configure.outputs.version }}"
 
     - name: Test Python bindings
       run: |
@@ -256,20 +220,19 @@ jobs:
     - name: Upload opensim-core
       uses: actions/upload-artifact@v4
       with:
-        name: opensim-core-${{ github.event.pull_request.base.ref }}-win
-        path: opensim-core-${{ github.event.pull_request.base.ref }}.zip
+        name: opensim-core-${{ steps.configure.outputs.version }}-win2022
+        path: opensim-core-${{ steps.configure.outputs.version }}.zip
 
-  windows2022_source:
-    
+  windows2022_perf:
     runs-on: windows-2022
-    
-    name: ${{ (contains(github.event.pull_request.title, '[perf-win]') || contains(github.event.pull_request.body, '[perf-win]')) && 'Windows2022 [source]' || 'Windows2022' }}
+    name: Windows 2022 [main]
 
-    outputs:
-      version: ${{ steps.configure.outputs.version }}
+    if: ${{ contains(github.event.pull_request.title, '[perf-win]') || contains(github.event.pull_request.body, '[perf-win]') }}
 
     steps:
     - uses: actions/checkout@v4
+      with:
+        ref: ${{ github.event.pull_request.base.ref }}
 
     - name: Install Doxygen
       # choco install doxygen.portable # <-- too unreliable.
@@ -282,7 +245,7 @@ jobs:
       uses: actions/setup-python@v4
       with:
         python-version: '3.10'
-
+        
     - name: Install numpy
       #Need numpy to use SWIG numpy typemaps.
       run: python3 -m pip install numpy==1.25
@@ -325,7 +288,7 @@ jobs:
         # TODO: Can remove /WX when we use that in CMakeLists.txt.
         # Set the CXXFLAGS environment variable to turn warnings into errors.
         # Skip timing test section included by default.
-        cmake -E env CXXFLAGS="/WX -DSKIP_TIMING" cmake $env:GITHUB_WORKSPACE -LAH -G"Visual Studio 17 2022" -A x64 -DCMAKE_INSTALL_PREFIX=~/opensim-core-install -DOPENSIM_DEPENDENCIES_DIR=~/opensim_dependencies_install -DOPENSIM_C3D_PARSER=ezc3d -DOPENSIM_WITH_TROPTER=on -DOPENSIM_WITH_CASADI=on -DBUILD_PYTHON_WRAPPING=on -DBUILD_JAVA_WRAPPING=on -DPython3_ROOT_DIR=C:\hostedtoolcache\windows\Python\3.10.11\x64
+        cmake -E env CXXFLAGS="/WX -DSKIP_TIMING" cmake $env:GITHUB_WORKSPACE -LAH -G"Visual Studio 17 2022" -A x64 -DCMAKE_INSTALL_PREFIX=~/opensim-core-install -DOPENSIM_DEPENDENCIES_DIR=~/opensim_dependencies_install -DOPENSIM_C3D_PARSER=ezc3d -DBUILD_PYTHON_WRAPPING=on -DBUILD_JAVA_WRAPPING=on -DPython3_ROOT_DIR=C:\hostedtoolcache\windows\Python\3.10.11\x64
         $env:match = cmake -L . | Select-String -Pattern OPENSIM_QUALIFIED_VERSION
         $version = $env:match.split('=')[1]
         echo $version
@@ -350,8 +313,8 @@ jobs:
       run: |
         chdir $env:GITHUB_WORKSPACE\\build
         chdir $env:GITHUB_WORKSPACE
-        Copy-Item -Path "~/opensim-core-install" -Destination "opensim-core-${{ steps.configure.outputs.version }}" -Recurse
-        7z a "opensim-core-${{ steps.configure.outputs.version }}.zip" "opensim-core-${{ steps.configure.outputs.version }}"
+        Copy-Item -Path "~/opensim-core-install" -Destination "opensim-core-${{ github.event.pull_request.base.ref }}" -Recurse
+        7z a "opensim-core-${{ github.event.pull_request.base.ref }}.zip" "opensim-core-${{ github.event.pull_request.base.ref }}"
 
     - name: Test Python bindings
       run: |
@@ -364,26 +327,106 @@ jobs:
     - name: Upload opensim-core
       uses: actions/upload-artifact@v4
       with:
-        name: opensim-core-${{ steps.configure.outputs.version }}-win
-        path: opensim-core-${{ steps.configure.outputs.version }}.zip
+        name: opensim-core-${{ github.event.pull_request.base.ref }}-win2022
+        path: opensim-core-${{ github.event.pull_request.base.ref }}.zip
 
-  mac_target:
-    name: Mac [target]
+  performance_analysis_win:
+    runs-on: ubuntu-latest
+    name: Performance Analysis [Windows 2022]
 
-    runs-on: macos-14
+    env:
+      GH_TOKEN: ${{ github.token }}
 
-    if: ${{ contains(github.event.pull_request.title, '[perf-mac]') || contains(github.event.pull_request.body, '[perf-mac]') }}
+    needs:
+      - windows2022
+      - windows2022_perf
+
+    if: ${{ contains(github.event.pull_request.title, '[perf-win]') || contains(github.event.pull_request.body, '[perf-win]') }}
 
     steps:
-    - uses: actions/checkout@v4
+    - name: Trigger opensim-perf workflow
+      uses: Codex-/return-dispatch@v1.12.0
+      id: return_dispatch
       with:
-        ref: ${{ github.event.pull_request.base.ref }} 
+        token: ${{ secrets.PERF_DISPATCH_PAT }}
+        repo: opensim-perf
+        owner: opensim-org
+        ref: main
+        workflow: performance_analysis_win.yml
+        workflow_inputs: '{"commit_sha": "${{ github.event.pull_request.head.sha }}", "target_artifact_name": "opensim-core-${{ github.event.pull_request.base.ref }}-win2022", "source_artifact_name": "opensim-core-${{ needs.windows2022.outputs.version }}-win2022", "target_artifact_zip": "opensim-core-${{ github.event.pull_request.base.ref }}.zip", "source_artifact_zip": "opensim-core-${{ needs.windows2022.outputs.version }}.zip"}'
+
+    - name: Await opensim-perf workflow
+      uses: Codex-/await-remote-run@v1.11.0
+      with:
+        token: ${{ secrets.PERF_DISPATCH_PAT }}
+        repo: opensim-perf
+        owner: opensim-org
+        run_id: ${{ steps.return_dispatch.outputs.run_id }}
+        run_timeout_seconds: 10000
+
+    - name: Download performance analysis results
+      id: download-artifact
+      uses: dawidd6/action-download-artifact@v3.0.0
+      with:
+        github_token: ${{ secrets.PERF_DISPATCH_PAT }}
+        run_id: ${{ steps.return_dispatch.outputs.run_id }}
+        workflow: performance_analysis_win.yml
+        name: performance-results
+        path: results
+        repo: opensim-org/opensim-perf
+
+    - name: Post results to pull request description
+      run: |
+        PR_NUMBER=$(jq --raw-output .pull_request.number "$GITHUB_EVENT_PATH")
+        EXISTING_COMMENT_CONTENT=$(gh api /repos/opensim-org/opensim-core/pulls/${PR_NUMBER} | jq -r '.body')
+        CUSTOM_HEADER="### Performance analysis"
+
+        REVIEWABLE_TAG="<!-- Reviewable:start -->"
+        REVIEWABLE_CONTENT=""
+        if [[ $EXISTING_COMMENT_CONTENT == *"$REVIEWABLE_TAG"* ]]; then
+            REVIEWABLE_CONTENT=$(echo "$EXISTING_COMMENT_CONTENT" | awk "/$REVIEWABLE_TAG/,0")
+        fi
+
+        if [[ $EXISTING_COMMENT_CONTENT == *"$CUSTOM_HEADER"* ]]; then
+            CONTENT_TO_REPLACE=$(echo "$EXISTING_COMMENT_CONTENT" | awk "/$CUSTOM_HEADER/,0")
+        else
+            CONTENT_TO_REPLACE=${REVIEWABLE_CONTENT}
+        fi
+
+        NEW_CONTENT="${CUSTOM_HEADER}
+
+        Platform: Windows, self-hosted runner
+
+        $(cat results/performance_results.md)
 
+        ${REVIEWABLE_CONTENT}
+        "
+        NEW_COMMENT_BODY="${EXISTING_COMMENT_CONTENT/"${CONTENT_TO_REPLACE}"/${NEW_CONTENT}}"
+
+        # Update the existing description
+        gh api \
+            --method PATCH \
+            -H "Content-Type: application/json" \
+            -H "Accept: application/vnd.github.v3+json" \
+            -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \
+            repos/opensim-org/opensim-core/pulls/${PR_NUMBER} \
+            -f "body=${NEW_COMMENT_BODY}"
+
+  mac_x86_64:
+    runs-on: macos-14-large
+    name: Mac x86_64
+
+    outputs:
+      version: ${{ steps.configure.outputs.version }}
+
+    steps:
+    - uses: actions/checkout@v4
+    
     - name: Install Python packages
       uses: actions/setup-python@v4
       with:
         python-version: '3.10'
-        
+
     - name: Install Homebrew packages
       # Save the gfortran version to a file so we can use it in the cache key.
       run: |
@@ -478,9 +521,9 @@ jobs:
         make doxygen
         make install
         cd $GITHUB_WORKSPACE
-        mv $GITHUB_WORKSPACE/../opensim-core-install opensim-core-${{ github.event.pull_request.base.ref }}
-        zip --symlinks --recurse-paths --quiet opensim-core-${{ github.event.pull_request.base.ref }}.zip opensim-core-${{ github.event.pull_request.base.ref }}
-        mv opensim-core-${{ github.event.pull_request.base.ref }} $GITHUB_WORKSPACE/../opensim-core-install
+        mv $GITHUB_WORKSPACE/../opensim-core-install opensim-core-${{ steps.configure.outputs.version }}
+        zip --symlinks --recurse-paths --quiet opensim-core-${{ steps.configure.outputs.version }}.zip opensim-core-${{ steps.configure.outputs.version }}
+        mv opensim-core-${{ steps.configure.outputs.version }} $GITHUB_WORKSPACE/../opensim-core-install
 
     - name: Test Python bindings
       run: |
@@ -493,14 +536,14 @@ jobs:
       with:
         # The upload-artifact zipping does not preserve symlinks or executable
         # bits. So we zip ourselves, even though this causes a double-zip.
-        name: opensim-core-${{ github.event.pull_request.base.ref }}-mac
-        path: opensim-core-${{ github.event.pull_request.base.ref }}.zip
+        name: opensim-core-${{ steps.configure.outputs.version }}-mac_x86_64
+        path: opensim-core-${{ steps.configure.outputs.version }}.zip
 
-  mac_source:
+  mac_arm64:
 
     runs-on: macos-14
     
-    name: ${{ (contains(github.event.pull_request.title, '[perf-mac]') || contains(github.event.pull_request.body, '[perf-mac]')) && 'Mac [source]' || 'Mac' }}
+    name: 'Mac Arm64'
 
     outputs:
       version: ${{ steps.configure.outputs.version }}
@@ -622,107 +665,150 @@ jobs:
       with:
         # The upload-artifact zipping does not preserve symlinks or executable
         # bits. So we zip ourselves, even though this causes a double-zip.
-        name: opensim-core-${{ steps.configure.outputs.version }}-mac
+        name: opensim-core-${{ steps.configure.outputs.version }}-mac_arm64
         path: opensim-core-${{ steps.configure.outputs.version }}.zip
 
-  performance_analysis_win:
-    name: Performance Analysis (Windows)
-
-    env:
-      GH_TOKEN: ${{ github.token }}
-
-    needs:
-      - windows2022_target
-      - windows2022_source
-
-    runs-on: ubuntu-latest
+  mac_arm64_perf:
+    runs-on: macos-14
+    name: Mac Arm64 [main]
 
-    if: ${{ contains(github.event.pull_request.title, '[perf-win]') || contains(github.event.pull_request.body, '[perf-win]') }}
+    if: ${{ contains(github.event.pull_request.title, '[perf-mac]') || contains(github.event.pull_request.body, '[perf-mac]') }}
 
     steps:
-    - name: Trigger opensim-perf workflow
-      uses: Codex-/return-dispatch@v1.12.0
-      id: return_dispatch
+    - uses: actions/checkout@v4
       with:
-        token: ${{ secrets.PERF_DISPATCH_PAT }}
-        repo: opensim-perf
-        owner: opensim-org
-        ref: main
-        workflow: performance_analysis_win.yml
-        workflow_inputs: '{"commit_sha": "${{ github.event.pull_request.head.sha }}", "target_artifact_name": "opensim-core-${{ github.event.pull_request.base.ref }}-win", "source_artifact_name": "opensim-core-${{ needs.windows2022_source.outputs.version }}-win", "target_artifact_zip": "opensim-core-${{ github.event.pull_request.base.ref }}.zip", "source_artifact_zip": "opensim-core-${{ needs.windows2022_source.outputs.version }}.zip"}'
+        ref: ${{ github.event.pull_request.base.ref }} 
 
-    - name: Await opensim-perf workflow
-      uses: Codex-/await-remote-run@v1.11.0
+    - name: Install Python packages
+      uses: actions/setup-python@v4
       with:
-        token: ${{ secrets.PERF_DISPATCH_PAT }}
-        repo: opensim-perf
-        owner: opensim-org
-        run_id: ${{ steps.return_dispatch.outputs.run_id }}
-        run_timeout_seconds: 10000
+        python-version: '3.10'
+        
+    - name: Install Homebrew packages
+      # Save the gfortran version to a file so we can use it in the cache key.
+      run: |
+        brew install cmake pkgconfig autoconf libtool automake wget pcre doxygen llvm
+        brew reinstall gcc
+        pip3 install numpy==1.25
+        gfortran -v
+        mkdir gfortran_version
+        gfortran -v &> gfortran_version/gfortran_version.txt
 
-    - name: Download performance analysis results
-      id: download-artifact
-      uses: dawidd6/action-download-artifact@v3.0.0
+    - name: Cache SWIG
+      id: cache-swig
+      uses: actions/cache@v3
       with:
-        github_token: ${{ secrets.PERF_DISPATCH_PAT }}
-        run_id: ${{ steps.return_dispatch.outputs.run_id }}
-        workflow: performance_analysis_win.yml
-        name: performance-results
-        path: results
-        repo: opensim-org/opensim-perf
+        path: ~/swig
+        key: ${{ runner.os }}-swig
 
-    - name: Post results to pull request description
+    - name: Install SWIG
+      # if: steps.cache-swig.outputs.cache-hit != 'true'
       run: |
-        PR_NUMBER=$(jq --raw-output .pull_request.number "$GITHUB_EVENT_PATH")
-        EXISTING_COMMENT_CONTENT=$(gh api /repos/opensim-org/opensim-core/pulls/${PR_NUMBER} | jq -r '.body')
-        CUSTOM_HEADER="### Performance analysis"
+        mkdir ~/swig-source && cd ~/swig-source
+        wget https://github.com/swig/swig/archive/refs/tags/v4.1.1.tar.gz
+        tar xzf v4.1.1.tar.gz && cd swig-4.1.1
+        sh autogen.sh && ./configure --prefix=$HOME/swig --disable-ccache
+        make && make -j4 install
 
-        REVIEWABLE_TAG="<!-- Reviewable:start -->"
-        REVIEWABLE_CONTENT=""
-        if [[ $EXISTING_COMMENT_CONTENT == *"$REVIEWABLE_TAG"* ]]; then
-            REVIEWABLE_CONTENT=$(echo "$EXISTING_COMMENT_CONTENT" | awk "/$REVIEWABLE_TAG/,0")
-        fi
+    - name: Cache dependencies
+      id: cache-dependencies
+      uses: actions/cache@v3
+      with:
+        path: ~/opensim_dependencies_install
+        # If Homebrew updates the gcc package, then our cache of IPOPT is invalid.
+        # Specifically, the pkgcfg_lib_IPOPT_gfortran CMake variable becomes
+        # undefined.
+        key: ${{ runner.os }}-dependencies-${{ hashFiles('dependencies/*') }}-${{ hashFiles('gfortran_version/*') }}
 
-        if [[ $EXISTING_COMMENT_CONTENT == *"$CUSTOM_HEADER"* ]]; then
-            CONTENT_TO_REPLACE=$(echo "$EXISTING_COMMENT_CONTENT" | awk "/$CUSTOM_HEADER/,0")
-        else
-            CONTENT_TO_REPLACE=${REVIEWABLE_CONTENT}
-        fi
+    - name: Build dependencies
+      if: steps.cache-dependencies.outputs.cache-hit != 'true'
+      run: |
+        mkdir $GITHUB_WORKSPACE/../build_deps
+        cd $GITHUB_WORKSPACE/../build_deps
+        DEP_CMAKE_ARGS=($GITHUB_WORKSPACE/dependencies -LAH)
+        DEP_CMAKE_ARGS+=(-DCMAKE_INSTALL_PREFIX=~/opensim_dependencies_install)
+        DEP_CMAKE_ARGS+=(-DCMAKE_BUILD_TYPE=Release)
+        DEP_CMAKE_ARGS+=(-DSUPERBUILD_ezc3d=ON)
+        DEP_CMAKE_ARGS+=(-DOPENSIM_WITH_TROPTER=ON)
+        DEP_CMAKE_ARGS+=(-DOPENSIM_WITH_CASADI=ON)
+        DEP_CMAKE_ARGS+=(-DOPENSIM_DISABLE_LOG_FILE=ON)
+        DEP_CMAKE_ARGS+=(-DCMAKE_OSX_DEPLOYMENT_TARGET=11)
+        printf '%s\n' "${DEP_CMAKE_ARGS[@]}"
+        cmake "${DEP_CMAKE_ARGS[@]}"
+        make --jobs 4
 
-        NEW_CONTENT="${CUSTOM_HEADER}
+    - name: Configure opensim-core
+      id: configure
+      run: |
+        mkdir $GITHUB_WORKSPACE/../build
+        cd $GITHUB_WORKSPACE/../build
+        OSIM_CMAKE_ARGS=($GITHUB_WORKSPACE -LAH)
+        OSIM_CMAKE_ARGS+=(-DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/../opensim-core-install)
+        OSIM_CMAKE_ARGS+=(-DCMAKE_BUILD_TYPE=Release)
+        OSIM_CMAKE_ARGS+=(-DOPENSIM_DEPENDENCIES_DIR=~/opensim_dependencies_install)
+        OSIM_CMAKE_ARGS+=(-DCMAKE_OSX_DEPLOYMENT_TARGET=11)
+        OSIM_CMAKE_ARGS+=(-DOPENSIM_C3D_PARSER=ezc3d)
+        OSIM_CMAKE_ARGS+=(-DBUILD_PYTHON_WRAPPING=on -DBUILD_JAVA_WRAPPING=on)
+        OSIM_CMAKE_ARGS+=(-DSWIG_EXECUTABLE=$HOME/swig/bin/swig)
+        OSIM_CMAKE_ARGS+=(-DOPENSIM_INSTALL_UNIX_FHS=OFF)
+        OSIM_CMAKE_ARGS+=(-DOPENSIM_DOXYGEN_USE_MATHJAX=off)
+        # TODO: Update to simbody.github.io/latest
+        OSIM_CMAKE_ARGS+=(-DOPENSIM_SIMBODY_DOXYGEN_LOCATION="https://simbody.github.io/simtk.org/api_docs/simbody/latest/")
+        OSIM_CMAKE_ARGS+=(-DCMAKE_CXX_FLAGS="-Werror, -Wdeprecated-copy")
+        printf '%s\n' "${OSIM_CMAKE_ARGS[@]}"
+        cmake "${OSIM_CMAKE_ARGS[@]}"
+        VERSION=`cmake -L . | grep OPENSIM_QUALIFIED_VERSION | cut -d "=" -f2`
+        echo $VERSION
+        echo "VERSION=$VERSION" >> $GITHUB_ENV
+        echo "version=$VERSION" >> $GITHUB_OUTPUT
 
-        Platform: Windows, self-hosted runner
+    - name: Build opensim-core
+      run: |
+        cd $GITHUB_WORKSPACE/../build
+        make --jobs 4
 
-        $(cat results/performance_results.md)
+    - name: Test opensim-core
+      run: |
+        cd $GITHUB_WORKSPACE/../build
+        ctest --parallel 4 --output-on-failure
 
-        ${REVIEWABLE_CONTENT}
-        "
-        NEW_COMMENT_BODY="${EXISTING_COMMENT_CONTENT/"${CONTENT_TO_REPLACE}"/${NEW_CONTENT}}"
+    - name: Install opensim-core
+      run: |
+        cd $GITHUB_WORKSPACE/../build
+        make doxygen
+        make install
+        cd $GITHUB_WORKSPACE
+        mv $GITHUB_WORKSPACE/../opensim-core-install opensim-core-${{ github.event.pull_request.base.ref }}
+        zip --symlinks --recurse-paths --quiet opensim-core-${{ github.event.pull_request.base.ref }}.zip opensim-core-${{ github.event.pull_request.base.ref }}
+        mv opensim-core-${{ github.event.pull_request.base.ref }} $GITHUB_WORKSPACE/../opensim-core-install
 
-        # Update the existing description
-        gh api \
-            --method PATCH \
-            -H "Content-Type: application/json" \
-            -H "Accept: application/vnd.github.v3+json" \
-            -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \
-            repos/opensim-org/opensim-core/pulls/${PR_NUMBER} \
-            -f "body=${NEW_COMMENT_BODY}"
+    - name: Test Python bindings
+      run: |
+        cd $GITHUB_WORKSPACE/../opensim-core-install/sdk/Python
+        # Run the python tests, verbosely.
+        python3 -m unittest discover --start-directory opensim/tests --verbose
 
-  performance_analysis_mac:
+    - name: Upload opensim-core
+      uses: actions/upload-artifact@v4
+      with:
+        # The upload-artifact zipping does not preserve symlinks or executable
+        # bits. So we zip ourselves, even though this causes a double-zip.
+        name: opensim-core-${{ github.event.pull_request.base.ref }}-mac_arm64
+        path: opensim-core-${{ github.event.pull_request.base.ref }}.zip
 
-    name: Performance Analysis (Mac)
+  performance_analysis_mac:
+    runs-on: ubuntu-latest
+    name: Performance Analysis [Mac Arm64]
 
     env:
       GH_TOKEN: ${{ github.token }}
 
-    needs:
-      - mac_target
-      - mac_source
-
-    runs-on: ubuntu-latest
-
     if: ${{ contains(github.event.pull_request.title, '[perf-mac]') || contains(github.event.pull_request.body, '[perf-mac]') }}
 
+    needs:
+        - mac_arm64
+        - mac_arm64_perf
+
     steps:
     - name: Trigger opensim-perf workflow
       uses: Codex-/return-dispatch@v1.12.0
@@ -733,7 +819,7 @@ jobs:
         owner: opensim-org
         ref: main
         workflow: performance_analysis_mac.yml
-        workflow_inputs: '{"commit_sha": "${{ github.event.pull_request.head.sha }}", "target_artifact_name": "opensim-core-${{ github.event.pull_request.base.ref }}-mac", "source_artifact_name": "opensim-core-${{ needs.mac_source.outputs.version }}-mac", "target_artifact_zip": "opensim-core-${{ github.event.pull_request.base.ref }}.zip", "source_artifact_zip": "opensim-core-${{ needs.mac_source.outputs.version }}.zip"}'
+        workflow_inputs: '{"commit_sha": "${{ github.event.pull_request.head.sha }}", "target_artifact_name": "opensim-core-${{ github.event.pull_request.base.ref }}-mac", "source_artifact_name": "opensim-core-${{ needs.mac_arm64.outputs.version }}-mac", "target_artifact_zip": "opensim-core-${{ github.event.pull_request.base.ref }}.zip", "source_artifact_zip": "opensim-core-${{ needs.mac_arm64.outputs.version }}.zip"}'
 
     - name: Await opensim-perf workflow
       uses: Codex-/await-remote-run@v1.11.0
@@ -793,8 +879,7 @@ jobs:
           -f "body=${NEW_COMMENT_BODY}"
 
   ubuntu20:
-    name: Ubuntu2004
-
+    name: Ubuntu 20.04
     runs-on: ubuntu-20.04
 
     steps:
@@ -888,7 +973,7 @@ jobs:
         make --jobs 4 install
         cd $GITHUB_WORKSPACE
         mv $GITHUB_WORKSPACE/../opensim-core-install opensim-core-${{ steps.configure.outputs.version }}
-        zip --symlinks --recurse-paths --quiet opensim-core-${{ steps.configure.outputs.version }}-ub20.zip opensim-core-${{ steps.configure.outputs.version }}
+        zip --symlinks --recurse-paths --quiet opensim-core-${{ steps.configure.outputs.version }}-ubuntu20.zip opensim-core-${{ steps.configure.outputs.version }}
         mv opensim-core-${{ steps.configure.outputs.version }} $GITHUB_WORKSPACE/../opensim-core-install
 
     # - name: Test Python bindings
@@ -903,13 +988,12 @@ jobs:
       with:
         # The upload-artifact zipping does not preserve symlinks or executable
         # bits. So we zip ourselves, even though this causes a double-zip.
-        name: opensim-core-${{ steps.configure.outputs.version }}-ub20-linux
-        path: opensim-core-${{ steps.configure.outputs.version }}-ub20.zip
+        name: opensim-core-${{ steps.configure.outputs.version }}-ubuntu20-linux
+        path: opensim-core-${{ steps.configure.outputs.version }}-ubuntu20.zip
 
-  ubuntu20-nomoco:
-    name: Ubuntu2004-nomoco
-
-    runs-on: ubuntu-20.04
+  ubuntu22:
+    name: Ubuntu 22.04
+    runs-on: ubuntu-22.04
 
     steps:
     - uses: actions/checkout@v4
@@ -935,6 +1019,7 @@ jobs:
         tar xzf v4.1.1.tar.gz && cd swig-4.1.1
         sh autogen.sh && ./configure --prefix=$HOME/swig --disable-ccache
         make && make -j4 install
+
     - name: Cache dependencies
       id: cache-dependencies
       uses: actions/cache@v3
@@ -943,7 +1028,7 @@ jobs:
         key: ${{ runner.os }}-dependencies-${{ hashFiles('dependencies/*') }}
 
     - name: Build dependencies
-      if: steps.cache-dependencies.outputs.cache-hit != 'true'
+      # if: steps.cache-dependencies.outputs.cache-hit != 'true'
       run: |
         mkdir $GITHUB_WORKSPACE/../build_deps
         cd $GITHUB_WORKSPACE/../build_deps
@@ -951,8 +1036,8 @@ jobs:
         DEP_CMAKE_ARGS+=(-DCMAKE_INSTALL_PREFIX=~/opensim_dependencies_install)
         DEP_CMAKE_ARGS+=(-DCMAKE_BUILD_TYPE=Release)
         DEP_CMAKE_ARGS+=(-DSUPERBUILD_ezc3d=ON)
-        DEP_CMAKE_ARGS+=(-DOPENSIM_WITH_TROPTER=OFF)
-        DEP_CMAKE_ARGS+=(-DOPENSIM_WITH_CASADI=OFF)
+        DEP_CMAKE_ARGS+=(-DOPENSIM_WITH_TROPTER=ON)
+        DEP_CMAKE_ARGS+=(-DOPENSIM_WITH_CASADI=ON)
         printf '%s\n' "${DEP_CMAKE_ARGS[@]}"
         cmake "${DEP_CMAKE_ARGS[@]}"
         make --jobs 4
@@ -972,8 +1057,6 @@ jobs:
         OSIM_CMAKE_ARGS+=(-DSWIG_EXECUTABLE=~/swig/bin/swig)
         OSIM_CMAKE_ARGS+=(-DOPENSIM_INSTALL_UNIX_FHS=OFF)
         OSIM_CMAKE_ARGS+=(-DOPENSIM_DOXYGEN_USE_MATHJAX=off)
-        OSIM_CMAKE_ARGS+=(-DOPENSIM_WITH_TROPTER=off)
-        OSIM_CMAKE_ARGS+=(-DOPENSIM_WITH_CASADI=off)
         # TODO: Update to simbody.github.io/latest
         OSIM_CMAKE_ARGS+=(-DOPENSIM_SIMBODY_DOXYGEN_LOCATION="https://simbody.github.io/simtk.org/api_docs/simbody/latest/")
         OSIM_CMAKE_ARGS+=(-DCMAKE_CXX_FLAGS="-Werror")
@@ -994,7 +1077,7 @@ jobs:
         cd $GITHUB_WORKSPACE/../build
         # TODO: Temporary for python to find Simbody libraries.
         export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/opensim_dependencies_install/simbody/lib
-        # ctest --parallel 4 --output-on-failure
+        ctest --parallel 4 --output-on-failure
 
     - name: Install opensim-core
       run: |
@@ -1003,61 +1086,60 @@ jobs:
         make --jobs 4 install
         cd $GITHUB_WORKSPACE
         mv $GITHUB_WORKSPACE/../opensim-core-install opensim-core-${{ steps.configure.outputs.version }}
-        zip --symlinks --recurse-paths --quiet opensim-core-${{ steps.configure.outputs.version }}-ub20.zip opensim-core-${{ steps.configure.outputs.version }}
+        zip --symlinks --recurse-paths --quiet opensim-core-${{ steps.configure.outputs.version }}-ubuntu22.zip opensim-core-${{ steps.configure.outputs.version }}
         mv opensim-core-${{ steps.configure.outputs.version }} $GITHUB_WORKSPACE/../opensim-core-install
 
-    # - name: Test Python bindings
-    #   run: |
-    #     echo "TODO: Skipping Python tests."
-    #     # cd $GITHUB_WORKSPACE/../opensim-core-install/sdk/Python
-    #     # Run the python tests, verbosely.
-    #     # python3 -m unittest discover --start-directory opensim/tests --verbose
+    - name: Test Python bindings
+      run: |
+        cd $GITHUB_WORKSPACE/../opensim-core-install/sdk/Python
+        Run the python tests, verbosely.
+        python3 -m unittest discover --start-directory opensim/tests --verbose
 
     - name: Upload opensim-core
       uses: actions/upload-artifact@v4
       with:
         # The upload-artifact zipping does not preserve symlinks or executable
         # bits. So we zip ourselves, even though this causes a double-zip.
-        name: opensim-core-${{ steps.configure.outputs.version }}-ub20-nomoco-linux
-        path: opensim-core-${{ steps.configure.outputs.version }}-ub20.zip
-  
-  windows2022-gui:
-      name: Windows2022-gui
+        name: opensim-core-${{ steps.configure.outputs.version }}-ubuntu22-linux
+        path: opensim-core-${{ steps.configure.outputs.version }}-ubuntu22.zip
+
+  build_gui:
+    name: Build GUI [win2022]
   
-      runs-on: windows-2022
+    runs-on: windows-2022
 
-      env:
-        GH_TOKEN: ${{ github.token }}
+    env:
+      GH_TOKEN: ${{ github.token }}
   
-      if: ${{ contains(github.event.pull_request.title, '[build-gui]') || contains(github.event.pull_request.body, '[build-gui]') }}
+    if: ${{ contains(github.event.pull_request.title, '[build-gui]') || contains(github.event.pull_request.body, '[build-gui]') }}
   
-      steps:
-      - name: Dispatch opensim-gui workflow and get the run ID
-        uses: codex-/return-dispatch@v1
-        id: return_dispatch
-        with:
-          token: ${{ secrets.ACTION_SECRET }}
-          ref: refs/heads/main 
-          repo: opensim-gui
-          owner: opensim-org
-          workflow: build-on-core-pr.yml
-
-      - name: Use the output run ID
-        run: echo ${{steps.return_dispatch.outputs.run_id}}
-        
-      - name: Await opensim-gui workflow
-        uses: Codex-/await-remote-run@v1.11.0
-        with:
-           token: ${{ secrets.ACTION_SECRET }}
-           repo: opensim-gui
-           owner: opensim-org
-           run_id: ${{ steps.return_dispatch.outputs.run_id }}
-           run_timeout_seconds: 10000
+    steps:
+    - name: Dispatch opensim-gui workflow and get the run ID
+      uses: codex-/return-dispatch@v1
+      id: return_dispatch
+      with:
+        token: ${{ secrets.ACTION_SECRET }}
+        ref: refs/heads/main 
+        repo: opensim-gui
+        owner: opensim-org
+        workflow: build-on-core-pr.yml
 
+    - name: Use the output run ID
+      run: echo ${{steps.return_dispatch.outputs.run_id}}
+    
+    - name: Await opensim-gui workflow
+      uses: Codex-/await-remote-run@v1.11.0
+      with:
+        token: ${{ secrets.ACTION_SECRET }}
+        repo: opensim-gui
+        owner: opensim-org
+        run_id: ${{ steps.return_dispatch.outputs.run_id }}
+        run_timeout_seconds: 10000
+        
   style:
     name: Style
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v4

From 006181e661a6cec382e7620825d5ae61c8e48d0b Mon Sep 17 00:00:00 2001
From: nickbianco <nbianco@stanford.edu>
Date: Sat, 19 Oct 2024 14:06:04 -0700
Subject: [PATCH 02/15] Use `macos-13` runner for x86_64 builds

---
 .github/workflows/continuous_integration.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml
index 1c3a7992b3..09a2356040 100644
--- a/.github/workflows/continuous_integration.yml
+++ b/.github/workflows/continuous_integration.yml
@@ -413,7 +413,7 @@ jobs:
             -f "body=${NEW_COMMENT_BODY}"
 
   mac_x86_64:
-    runs-on: macos-14-large
+    runs-on: macos-13
     name: Mac x86_64
 
     outputs:

From 2fd95564114ccec7428d7e532c45eb957b49df70 Mon Sep 17 00:00:00 2001
From: nickbianco <nbianco@stanford.edu>
Date: Sun, 20 Oct 2024 12:55:00 -0700
Subject: [PATCH 03/15] Re-enable Python tests on Ubuntu 20

---
 .github/workflows/continuous_integration.yml | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml
index 09a2356040..83beb1446d 100644
--- a/.github/workflows/continuous_integration.yml
+++ b/.github/workflows/continuous_integration.yml
@@ -976,12 +976,11 @@ jobs:
         zip --symlinks --recurse-paths --quiet opensim-core-${{ steps.configure.outputs.version }}-ubuntu20.zip opensim-core-${{ steps.configure.outputs.version }}
         mv opensim-core-${{ steps.configure.outputs.version }} $GITHUB_WORKSPACE/../opensim-core-install
 
-    # - name: Test Python bindings
-    #   run: |
-    #     echo "TODO: Skipping Python tests."
-    #     # cd $GITHUB_WORKSPACE/../opensim-core-install/sdk/Python
-    #     # Run the python tests, verbosely.
-    #     # python3 -m unittest discover --start-directory opensim/tests --verbose
+    - name: Test Python bindings
+      run: |
+        cd $GITHUB_WORKSPACE/../opensim-core-install/sdk/Python
+        Run the python tests, verbosely.
+        python3 -m unittest discover --start-directory opensim/tests --verbose
 
     - name: Upload opensim-core
       uses: actions/upload-artifact@v4

From df3861060ce52e883e72e6ff57298f1fe8f6a699 Mon Sep 17 00:00:00 2001
From: nickbianco <nbianco@stanford.edu>
Date: Sun, 20 Oct 2024 13:24:24 -0700
Subject: [PATCH 04/15] Try to avoid Mat44 compiler error on Ubuntu 22

---
 OpenSim/Simulation/Wrap/WrapEllipsoid.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/OpenSim/Simulation/Wrap/WrapEllipsoid.cpp b/OpenSim/Simulation/Wrap/WrapEllipsoid.cpp
index 4dcaf4a697..9a5d98e34d 100644
--- a/OpenSim/Simulation/Wrap/WrapEllipsoid.cpp
+++ b/OpenSim/Simulation/Wrap/WrapEllipsoid.cpp
@@ -696,7 +696,7 @@ int WrapEllipsoid::calcTangentPoint(double p1e, SimTK::Vec3& r1, SimTK::Vec3& p1
             }
 
             for (i = 0; i < 4; i++)
-                diag[i] = dedth2[i][i];
+                diag[i] = dedth2(i, i);
 
             nit2 = 0;
 

From 8aac050a2abea8c7828301dc75075369e0180ee0 Mon Sep 17 00:00:00 2001
From: nickbianco <nbianco@stanford.edu>
Date: Mon, 21 Oct 2024 14:02:28 -0700
Subject: [PATCH 05/15] Fix typo

---
 .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 83beb1446d..020cde298e 100644
--- a/.github/workflows/continuous_integration.yml
+++ b/.github/workflows/continuous_integration.yml
@@ -979,7 +979,7 @@ jobs:
     - name: Test Python bindings
       run: |
         cd $GITHUB_WORKSPACE/../opensim-core-install/sdk/Python
-        Run the python tests, verbosely.
+        # Run the python tests, verbosely.
         python3 -m unittest discover --start-directory opensim/tests --verbose
 
     - name: Upload opensim-core
@@ -1091,7 +1091,7 @@ jobs:
     - name: Test Python bindings
       run: |
         cd $GITHUB_WORKSPACE/../opensim-core-install/sdk/Python
-        Run the python tests, verbosely.
+        # Run the python tests, verbosely.
         python3 -m unittest discover --start-directory opensim/tests --verbose
 
     - name: Upload opensim-core

From 8aeea5dd9726c0237a2170548c79f849a3035e27 Mon Sep 17 00:00:00 2001
From: nickbianco <nbianco@stanford.edu>
Date: Mon, 21 Oct 2024 16:00:45 -0700
Subject: [PATCH 06/15] Try Python 3.11 on Ubuntu 22

---
 .github/workflows/continuous_integration.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml
index 020cde298e..e59f9e0e44 100644
--- a/.github/workflows/continuous_integration.yml
+++ b/.github/workflows/continuous_integration.yml
@@ -1000,7 +1000,7 @@ jobs:
     - name: Install Python packages
       uses: actions/setup-python@v4
       with:
-        python-version: '3.10'
+        python-version: '3.11'
 
     - name: Install Numpy
       run: |

From 91cf2b585f0a703726aa3953fc47c7160e729d26 Mon Sep 17 00:00:00 2001
From: Ayman Habib <ahabib@stanford.edu>
Date: Tue, 22 Oct 2024 13:15:54 -0700
Subject: [PATCH 07/15] Update continuous_integration.yml

Add debugging line
---
 .github/workflows/continuous_integration.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml
index e59f9e0e44..1c6fbc0380 100644
--- a/.github/workflows/continuous_integration.yml
+++ b/.github/workflows/continuous_integration.yml
@@ -964,6 +964,7 @@ jobs:
         cd $GITHUB_WORKSPACE/../build
         # TODO: Temporary for python to find Simbody libraries.
         export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/opensim_dependencies_install/simbody/lib
+        echo $LD_LIBRARY_PATH
         ctest --parallel 4 --output-on-failure
 
     - name: Install opensim-core

From ea77475f9cba06a3afcedc3084c1b22bb4fcdd5d Mon Sep 17 00:00:00 2001
From: nickbianco <nbianco@stanford.edu>
Date: Tue, 22 Oct 2024 14:50:21 -0700
Subject: [PATCH 08/15] Disable python tests on Ubuntu

---
 .github/workflows/continuous_integration.yml | 23 ++++++++++----------
 1 file changed, 11 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml
index 1c6fbc0380..a1ebbeb15b 100644
--- a/.github/workflows/continuous_integration.yml
+++ b/.github/workflows/continuous_integration.yml
@@ -959,13 +959,12 @@ jobs:
         cd $GITHUB_WORKSPACE/../build
         make --jobs 4
 
-    - name: Test opensim-core
-      run: |
-        cd $GITHUB_WORKSPACE/../build
-        # TODO: Temporary for python to find Simbody libraries.
-        export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/opensim_dependencies_install/simbody/lib
-        echo $LD_LIBRARY_PATH
-        ctest --parallel 4 --output-on-failure
+    # - name: Test opensim-core
+    #   run: |
+    #     cd $GITHUB_WORKSPACE/../build
+    #     # TODO: Temporary for python to find Simbody libraries.
+    #     export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/opensim_dependencies_install/simbody/lib
+    #     ctest --parallel 4 --output-on-failure
 
     - name: Install opensim-core
       run: |
@@ -1089,11 +1088,11 @@ jobs:
         zip --symlinks --recurse-paths --quiet opensim-core-${{ steps.configure.outputs.version }}-ubuntu22.zip opensim-core-${{ steps.configure.outputs.version }}
         mv opensim-core-${{ steps.configure.outputs.version }} $GITHUB_WORKSPACE/../opensim-core-install
 
-    - name: Test Python bindings
-      run: |
-        cd $GITHUB_WORKSPACE/../opensim-core-install/sdk/Python
-        # Run the python tests, verbosely.
-        python3 -m unittest discover --start-directory opensim/tests --verbose
+    # - name: Test Python bindings
+    #   run: |
+    #     cd $GITHUB_WORKSPACE/../opensim-core-install/sdk/Python
+    #     # Run the python tests, verbosely.
+    #     python3 -m unittest discover --start-directory opensim/tests --verbose
 
     - name: Upload opensim-core
       uses: actions/upload-artifact@v4

From 6ccb4aacb43fdc474c665713697e254f1c46fe84 Mon Sep 17 00:00:00 2001
From: nickbianco <nbianco@stanford.edu>
Date: Wed, 23 Oct 2024 09:49:32 -0700
Subject: [PATCH 09/15] Comment out Python tests on Ubuntu 20

---
 .github/workflows/continuous_integration.yml | 22 ++++++++++----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml
index a1ebbeb15b..d65ce610d0 100644
--- a/.github/workflows/continuous_integration.yml
+++ b/.github/workflows/continuous_integration.yml
@@ -959,12 +959,12 @@ jobs:
         cd $GITHUB_WORKSPACE/../build
         make --jobs 4
 
-    # - name: Test opensim-core
-    #   run: |
-    #     cd $GITHUB_WORKSPACE/../build
-    #     # TODO: Temporary for python to find Simbody libraries.
-    #     export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/opensim_dependencies_install/simbody/lib
-    #     ctest --parallel 4 --output-on-failure
+    - name: Test opensim-core
+      run: |
+        cd $GITHUB_WORKSPACE/../build
+        # TODO: Temporary for python to find Simbody libraries.
+        export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/opensim_dependencies_install/simbody/lib
+        ctest --parallel 4 --output-on-failure
 
     - name: Install opensim-core
       run: |
@@ -976,11 +976,11 @@ jobs:
         zip --symlinks --recurse-paths --quiet opensim-core-${{ steps.configure.outputs.version }}-ubuntu20.zip opensim-core-${{ steps.configure.outputs.version }}
         mv opensim-core-${{ steps.configure.outputs.version }} $GITHUB_WORKSPACE/../opensim-core-install
 
-    - name: Test Python bindings
-      run: |
-        cd $GITHUB_WORKSPACE/../opensim-core-install/sdk/Python
-        # Run the python tests, verbosely.
-        python3 -m unittest discover --start-directory opensim/tests --verbose
+    # - name: Test Python bindings
+    #   run: |
+    #     cd $GITHUB_WORKSPACE/../opensim-core-install/sdk/Python
+    #     # Run the python tests, verbosely.
+    #     python3 -m unittest discover --start-directory opensim/tests --verbose
 
     - name: Upload opensim-core
       uses: actions/upload-artifact@v4

From fdbc503dfa6e76d30d12276861f6f995bcedb172 Mon Sep 17 00:00:00 2001
From: nickbianco <nbianco@stanford.edu>
Date: Wed, 23 Oct 2024 10:49:43 -0700
Subject: [PATCH 10/15] Set Ubuntu22 back to Python 3.10

---
 .github/workflows/continuous_integration.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml
index d65ce610d0..7b70801e24 100644
--- a/.github/workflows/continuous_integration.yml
+++ b/.github/workflows/continuous_integration.yml
@@ -1000,7 +1000,7 @@ jobs:
     - name: Install Python packages
       uses: actions/setup-python@v4
       with:
-        python-version: '3.11'
+        python-version: '3.10'
 
     - name: Install Numpy
       run: |

From f0e47468bd07b84a7e81c8903e6d1a05081a45a1 Mon Sep 17 00:00:00 2001
From: nickbianco <nbianco@stanford.edu>
Date: Wed, 23 Oct 2024 13:26:22 -0700
Subject: [PATCH 11/15] Dummy commit to trigger Mac perf workflow

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

diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml
index 7b70801e24..523c99c653 100644
--- a/.github/workflows/continuous_integration.yml
+++ b/.github/workflows/continuous_integration.yml
@@ -540,9 +540,7 @@ jobs:
         path: opensim-core-${{ steps.configure.outputs.version }}.zip
 
   mac_arm64:
-
     runs-on: macos-14
-    
     name: 'Mac Arm64'
 
     outputs:
@@ -1104,7 +1102,6 @@ jobs:
 
   build_gui:
     name: Build GUI [win2022]
-  
     runs-on: windows-2022
 
     env:

From 514f39a44af419786f5411204f05b09a91692083 Mon Sep 17 00:00:00 2001
From: nickbianco <nbianco@stanford.edu>
Date: Wed, 23 Oct 2024 14:24:17 -0700
Subject: [PATCH 12/15] Use correct Mac Arm64 artifact names for perf analysis

---
 .github/workflows/continuous_integration.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml
index 523c99c653..60c95ee43b 100644
--- a/.github/workflows/continuous_integration.yml
+++ b/.github/workflows/continuous_integration.yml
@@ -536,12 +536,12 @@ jobs:
       with:
         # The upload-artifact zipping does not preserve symlinks or executable
         # bits. So we zip ourselves, even though this causes a double-zip.
-        name: opensim-core-${{ steps.configure.outputs.version }}-mac_x86_64
+        name: opensim-core-${{ steps.configure.outputs.version }}-mac-x86_64
         path: opensim-core-${{ steps.configure.outputs.version }}.zip
 
   mac_arm64:
     runs-on: macos-14
-    name: 'Mac Arm64'
+    name: Mac Arm64
 
     outputs:
       version: ${{ steps.configure.outputs.version }}
@@ -663,7 +663,7 @@ jobs:
       with:
         # The upload-artifact zipping does not preserve symlinks or executable
         # bits. So we zip ourselves, even though this causes a double-zip.
-        name: opensim-core-${{ steps.configure.outputs.version }}-mac_arm64
+        name: opensim-core-${{ steps.configure.outputs.version }}-mac-arm64
         path: opensim-core-${{ steps.configure.outputs.version }}.zip
 
   mac_arm64_perf:
@@ -791,7 +791,7 @@ jobs:
       with:
         # The upload-artifact zipping does not preserve symlinks or executable
         # bits. So we zip ourselves, even though this causes a double-zip.
-        name: opensim-core-${{ github.event.pull_request.base.ref }}-mac_arm64
+        name: opensim-core-${{ github.event.pull_request.base.ref }}-mac-arm64
         path: opensim-core-${{ github.event.pull_request.base.ref }}.zip
 
   performance_analysis_mac:
@@ -817,7 +817,7 @@ jobs:
         owner: opensim-org
         ref: main
         workflow: performance_analysis_mac.yml
-        workflow_inputs: '{"commit_sha": "${{ github.event.pull_request.head.sha }}", "target_artifact_name": "opensim-core-${{ github.event.pull_request.base.ref }}-mac", "source_artifact_name": "opensim-core-${{ needs.mac_arm64.outputs.version }}-mac", "target_artifact_zip": "opensim-core-${{ github.event.pull_request.base.ref }}.zip", "source_artifact_zip": "opensim-core-${{ needs.mac_arm64.outputs.version }}.zip"}'
+        workflow_inputs: '{"commit_sha": "${{ github.event.pull_request.head.sha }}", "target_artifact_name": "opensim-core-${{ github.event.pull_request.base.ref }}-mac-arm64", "source_artifact_name": "opensim-core-${{ needs.mac_arm64.outputs.version }}-mac-arm64", "target_artifact_zip": "opensim-core-${{ github.event.pull_request.base.ref }}.zip", "source_artifact_zip": "opensim-core-${{ needs.mac_arm64.outputs.version }}.zip"}'
 
     - name: Await opensim-perf workflow
       uses: Codex-/await-remote-run@v1.11.0

From 568804661ced15b179f31d529594a3287aa73861 Mon Sep 17 00:00:00 2001
From: nickbianco <nbianco@stanford.edu>
Date: Thu, 24 Oct 2024 10:47:26 -0700
Subject: [PATCH 13/15] Test [build-gui] workflow

---
 .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 60c95ee43b..cf15fce96a 100644
--- a/.github/workflows/continuous_integration.yml
+++ b/.github/workflows/continuous_integration.yml
@@ -1101,8 +1101,8 @@ jobs:
         path: opensim-core-${{ steps.configure.outputs.version }}-ubuntu22.zip
 
   build_gui:
-    name: Build GUI [win2022]
-    runs-on: windows-2022
+    name: Build GUI
+    runs-on: ubuntu-latest
 
     env:
       GH_TOKEN: ${{ github.token }}

From 55b9a1415a0b350aae6fab59d0bf880fff8239a8 Mon Sep 17 00:00:00 2001
From: nickbianco <nbianco@stanford.edu>
Date: Thu, 24 Oct 2024 10:51:29 -0700
Subject: [PATCH 14/15] Revert to windows-2022 runner for GUI build

---
 .github/workflows/continuous_integration.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml
index cf15fce96a..e3a3101fa1 100644
--- a/.github/workflows/continuous_integration.yml
+++ b/.github/workflows/continuous_integration.yml
@@ -1102,7 +1102,7 @@ jobs:
 
   build_gui:
     name: Build GUI
-    runs-on: ubuntu-latest
+    runs-on: windows-2022
 
     env:
       GH_TOKEN: ${{ github.token }}

From 2711a12d6ed558533db1681c3657ba6706eeeb6c Mon Sep 17 00:00:00 2001
From: nickbianco <nbianco@stanford.edu>
Date: Thu, 24 Oct 2024 11:14:10 -0700
Subject: [PATCH 15/15] Use ubuntu-latest for GUI job

---
 .github/workflows/continuous_integration.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml
index e3a3101fa1..cf15fce96a 100644
--- a/.github/workflows/continuous_integration.yml
+++ b/.github/workflows/continuous_integration.yml
@@ -1102,7 +1102,7 @@ jobs:
 
   build_gui:
     name: Build GUI
-    runs-on: windows-2022
+    runs-on: ubuntu-latest
 
     env:
       GH_TOKEN: ${{ github.token }}