trying to install opensim from sources (without moco)

.github/workflows/configure_opensim_env.sh

@@ -0,0 +1,94 @@
+#!/bin/bash
+#
+# Point a conda environment at a locally built OpenSim, so that
+# `import opensim` works without manually exporting PYTHONPATH/LD_LIBRARY_PATH
+# every time.
+#
+# It writes conda "activate.d"/"deactivate.d" hooks into the CURRENTLY ACTIVE
+# conda environment. Those hooks export PYTHONPATH/LD_LIBRARY_PATH
+# automatically every time you `conda activate <env>`, and unset them again
+# on `conda deactivate` -- no manual exporting needed after this.
+#
+# --- Usage ---
+#
+# 1. Build OpenSim first (only needs to be done once, or again after pulling
+#    changes to install_opensim.sh), e.g.:
+#
+#      conda activate biobuddy
+#      bash .github/workflows/install_opensim.sh "$CONDA_PREFIX"
+#
+#    This creates ./opensim/opensim_core_install relative to wherever you ran
+#    the build command from.
+#
+# 2. With that SAME conda env still active, run this script from the same
+#    directory, pointing it at the install directory if it isn't the default:
+#
+#      bash .github/workflows/configure_opensim_env.sh [path/to/opensim_core_install]
+#
+#    (defaults to ./opensim/opensim_core_install if no argument is given)
+#
+# 3. Re-activate the env so the hook actually runs, then test:
+#
+#      conda deactivate
+#      conda activate biobuddy
+#      python -c "import opensim; print(opensim.GetVersion())"
+#
+# Re-run this script any time OpenSim gets rebuilt or moved to a new path.
+
+set -e
+
+OPENSIM_INSTALL="${1:-$(pwd)/opensim/opensim_core_install}"
+
+if [ -z "$CONDA_PREFIX" ]; then
+    echo "Error: no conda environment is active. Run 'conda activate <env>' first." >&2
+    exit 1
+fi
+
+if [ ! -d "$OPENSIM_INSTALL" ]; then
+    echo "Error: OpenSim install directory not found: $OPENSIM_INSTALL" >&2
+    echo "Pass the path explicitly, e.g.: bash $0 /path/to/opensim_core_install" >&2
+    exit 1
+fi
+
+# Find the "opensim" python package directory (the folder containing
+# __init__.py) so we can put its PARENT on PYTHONPATH.
+OPENSIM_PY_INIT=$(find "$OPENSIM_INSTALL" -path "*/opensim/__init__.py" | head -n1)
+if [ -z "$OPENSIM_PY_INIT" ]; then
+    echo "Error: could not find an 'opensim/__init__.py' under $OPENSIM_INSTALL" >&2
+    echo "Did the build finish and install successfully (with BUILD_PYTHON_WRAPPING=on)?" >&2
+    exit 1
+fi
+OPENSIM_PY_PKG_PARENT=$(dirname "$(dirname "$OPENSIM_PY_INIT")")
+
+# Collect every directory containing a compiled shared library (OpenSim's own
+# libs plus the bundled Simbody ones), so the compiled extension modules can
+# resolve them at runtime.
+LIB_DIRS=$(find "$OPENSIM_INSTALL" -name "*.so*" -exec dirname {} \; | sort -u | paste -sd:)
+
+ACTIVATE_DIR="$CONDA_PREFIX/etc/conda/activate.d"
+DEACTIVATE_DIR="$CONDA_PREFIX/etc/conda/deactivate.d"
+mkdir -p "$ACTIVATE_DIR" "$DEACTIVATE_DIR"
+
+cat > "$ACTIVATE_DIR/opensim.sh" <<EOF
+# Auto-generated by configure_opensim_env.sh -- do not edit by hand,
+# re-run the script instead if OpenSim gets rebuilt or moved.
+export _OLD_PYTHONPATH="\$PYTHONPATH"
+export _OLD_LD_LIBRARY_PATH="\$LD_LIBRARY_PATH"
+export PYTHONPATH="$OPENSIM_PY_PKG_PARENT:\$PYTHONPATH"
+export LD_LIBRARY_PATH="$LIB_DIRS:\$CONDA_PREFIX/lib:\$LD_LIBRARY_PATH"
+EOF
+
+cat > "$DEACTIVATE_DIR/opensim.sh" <<'EOF'
+# Auto-generated by configure_opensim_env.sh
+export PYTHONPATH="$_OLD_PYTHONPATH"
+export LD_LIBRARY_PATH="$_OLD_LD_LIBRARY_PATH"
+unset _OLD_PYTHONPATH _OLD_LD_LIBRARY_PATH
+EOF
+
+echo "Done."
+echo "  OpenSim python package dir: $OPENSIM_PY_PKG_PARENT"
+echo "  Library dirs:               $LIB_DIRS"
+echo ""
+echo "Now run this to make it take effect:"
+echo "  conda deactivate && conda activate $(basename "$CONDA_PREFIX")"
+echo '  python -c "import opensim; print(opensim.GetVersion())"'

.github/workflows/install_opensim.sh

@@ -0,0 +1,77 @@
+#!/bin/bash
+
+# Exit when an error happens instead of continue.
+set -e
+
+# Default values for flags.
+DEBUG_TYPE="Release"
+NUM_JOBS=${OPENSIM_BUILD_JOBS:-24}
+MOCO="off"
+ORG="nickbianco"
+BRANCH="dc7e1f0a18905fcd17cbbee9f923a70b4cb9de99"
+GENERATOR="Ninja"
+PYTHON_ROOT_DIR=$1
+WORKING_DIR="$(pwd)/opensim"
+if [ -d "$WORKING_DIR" ]; then
+    rm -rf "$WORKING_DIR"
+fi
+mkdir -p "$WORKING_DIR"
+
+# Get opensim-core. Fetch the pinned commit directly instead of cloning the
+# whole repo and checking it out afterwards: if that commit is later dropped
+# from whatever branch it was on (rebase/branch deletion upstream), a normal
+# clone stops including it and `git checkout $BRANCH` fails with "unable to
+# read tree", even though the commit object itself still exists and remains
+# directly fetchable by SHA.
+mkdir -p "$WORKING_DIR/opensim-core"
+cd "$WORKING_DIR/opensim-core"
+git init -q
+git remote add origin https://github.com/$ORG/opensim-core.git
+git fetch --depth 1 origin $BRANCH
+git checkout -q FETCH_HEAD
+
+# Build opensim-core dependencies.
+mkdir -p "$WORKING_DIR/opensim-core/dependencies/build"
+cd "$WORKING_DIR/opensim-core/dependencies/build"
+cmake "$WORKING_DIR/opensim-core/dependencies" -G"$GENERATOR" -DCMAKE_BUILD_TYPE=$DEBUG_TYPE -DCMAKE_INSTALL_PREFIX="$WORKING_DIR/opensim_dependencies_install/" -DSUPERBUILD_ezc3d=off -DOPENSIM_WITH_CASADI=$MOCO -DBUILD_PYTHON_WRAPPING=on -DPython3_ROOT_DIR="$PYTHON_ROOT_DIR"
+cmake . -LAH
+
+# opensim-core's own dependencies/CMakeLists.txt pins Simbody to a raw commit
+# on nickbianco's fork. That commit can become orphaned (unreachable from any
+# branch) if the fork gets rebased/cleaned up upstream, which makes
+# ExternalProject_Add's normal git clone fail with "reference is not a tree" /
+# "unable to read tree", even though the commit object itself still exists
+# and remains directly fetchable by SHA (same class of issue as the
+# opensim-core checkout above). Work around it the same way: fetch Simbody by
+# SHA ourselves into the exact source dir ExternalProject expects, then mark
+# its git-clone step as already done via the stamp file it checks, so the
+# build skips straight to configuring/building the pre-fetched source.
+SIMBODY_GIT_URL="https://github.com/nickbianco/simbody.git"
+SIMBODY_GIT_TAG="6cd18d8b8466b3e574377a6b5acd942af78c7a88"
+SIMBODY_SOURCE_DIR="$WORKING_DIR/opensim-core/dependencies/simbody"
+SIMBODY_STAMP_DIR="$WORKING_DIR/opensim-core/dependencies/build/simbody/stamp"
+
+rm -rf "$SIMBODY_SOURCE_DIR"
+mkdir -p "$SIMBODY_SOURCE_DIR"
+(
+    cd "$SIMBODY_SOURCE_DIR"
+    git init -q
+    git remote add origin "$SIMBODY_GIT_URL"
+    git fetch --depth 1 origin "$SIMBODY_GIT_TAG"
+    git checkout -q FETCH_HEAD
+    if [ -f .gitmodules ]; then
+        git submodule update --init --recursive
+    fi
+)
+cp "$SIMBODY_STAMP_DIR/simbody-gitinfo.txt" "$SIMBODY_STAMP_DIR/simbody-gitclone-lastrun.txt"
+touch "$SIMBODY_STAMP_DIR/simbody-gitclone-lastrun.txt"
+
+cmake --build . --config $DEBUG_TYPE -j$NUM_JOBS
+
+
+# Build and install opensim-core.
+mkdir -p "$WORKING_DIR/opensim-core/build"
+cd "$WORKING_DIR/opensim-core/build"
+cmake "$WORKING_DIR/opensim-core" -G"$GENERATOR" -DCMAKE_BUILD_TYPE=$DEBUG_TYPE -DOPENSIM_DEPENDENCIES_DIR="$WORKING_DIR/opensim_dependencies_install/" -DOPENSIM_C3D_PARSER=None -DBUILD_TESTING=off -DCMAKE_INSTALL_PREFIX="$WORKING_DIR/opensim_core_install" -DOPENSIM_INSTALL_UNIX_FHS=off -DOPENSIM_WITH_CASADI=$MOCO -DBUILD_PYTHON_WRAPPING=on -DPython3_ROOT_DIR="$PYTHON_ROOT_DIR"
+cmake --build . --config $DEBUG_TYPE -j$NUM_JOBS
+cmake --install .

.github/workflows/run_tests.yml

@@ -47,26 +47,63 @@ jobs:
           submodules: recursive
           fetch-depth: 0
 
+      - name: Free disk space
+        run: |
+          # Building OpenSim from source (Simbody + the full OpenSim/Moco
+          # tree) plus conda/biorbd needs more disk than the ~14GB free by
+          # default on GitHub runners. Remove large preinstalled toolchains
+          # we don't use to make room, otherwise the build (or even the
+          # earlier `git clone` of opensim-core) can silently run out of
+          # space and fail with an unrelated-looking error.
+          sudo rm -rf /usr/share/dotnet /opt/ghc /usr/local/lib/android /opt/hostedtoolcache/CodeQL
+          sudo docker image prune --all --force || true
+          df -h /
+
       - name: Setup conda
         uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-version: latest
 
       - name: Set up Python
         run: |
-          conda install -cconda-forge python=3.11.11 pip 
+          conda install -cconda-forge python=3.11.11 pip
+
+      - name: Install system dependencies for building OpenSim
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y --no-install-recommends \
+            build-essential cmake ninja-build \
+            libblas-dev liblapack-dev \
+            freeglut3-dev libxi-dev libxmu-dev \
+            pkg-config
+          pip install swig
 
       - name: Install dependencies
         run: | 
           pip install . && pip uninstall -y biobuddy
           pip install scipy==1.17.0 numpy==2.4.1 lxml ezc3d matplotlib plotly
-          conda install biorbd=1.11.2=py311h9439bbc_1 graphviz -cconda-forge
+          conda install biorbd graphviz -cconda-forge
 
       - name: Install test dependencies
         run: |
           pip install pytest pytest-cov codecov
           conda install -c conda-forge deepdiff pinocchio pandas
-          conda install -c opensim-org opensim=4.5.1
+
+      - name: Build and install OpenSim from source
+        run: |
+          # Cap parallel compile jobs to the runner's core count: the script
+          # defaults to 24 jobs, which OOM-kills the compiler on standard
+          # (4-core) GitHub runners partway through the build.
+          export OPENSIM_BUILD_JOBS=$(nproc)
+          bash .github/workflows/install_opensim.sh "$CONDA_PREFIX"
+
+          OPENSIM_INSTALL="$(pwd)/opensim/opensim_core_install"
+          OPENSIM_PY_INIT=$(find "$OPENSIM_INSTALL" -path "*/opensim/__init__.py" | head -n1)
+          OPENSIM_PY_PKG_PARENT=$(dirname "$(dirname "$OPENSIM_PY_INIT")")
+          LIB_DIRS=$(find "$OPENSIM_INSTALL" -name "*.so*" -exec dirname {} \; | sort -u | paste -sd:)
+
+          echo "PYTHONPATH=$OPENSIM_PY_PKG_PARENT:$PYTHONPATH" >> "$GITHUB_ENV"
+          echo "LD_LIBRARY_PATH=$LIB_DIRS:$LD_LIBRARY_PATH" >> "$GITHUB_ENV"
 
       - name: List conda packages
         run: conda list
@@ -102,4 +139,5 @@ jobs:
           pip install .
           cd
           python -c "import biobuddy"
-          cd $BASE_FOLDER
+          cd $BASE_FOLDER
+

.gitignore

@@ -190,3 +190,5 @@ examples/data/hide_and_seek/
 examples/models/hide_and_seek/
 
 examples/data/arm26_allbiceps_1dof.png
+
+opensim/

biobuddy/components/functions.py

@@ -114,24 +114,27 @@ def _calculate_coefficients(self):
 
         # Handle the case with only 2 points (linear interpolation)
         if self.nb_nodes == 2:
-            t = self.safe_max(self.x_points[1] - self.x_points[0])
-            self.b[0] = self.b[1] = (self.y_points[1] - self.y_points[0]) / t
-            self.c[0] = self.c[1] = 0.0
-            self.d[0] = self.d[1] = 0.0
+            t = (self.safe_max(self.x_points[1] - self.x_points[0])).reshape(-1)[0]
+            self.b[0] = ((self.y_points[1] - self.y_points[0]) / t).reshape(-1)[0]
+            self.b[1] = self.b[0]
+            self.c[0] = 0.0
+            self.c[1] = 0.0
+            self.d[0] = 0.0
+            self.d[1] = 0.0
             return
 
         nm1 = self.nb_nodes - 1
         nm2 = self.nb_nodes - 2
 
         # Set up tridiagonal system:
         # b = diagonal, d = offdiagonal, c = right-hand side
-        self.d[0] = self.safe_max(self.x_points[1] - self.x_points[0])
-        self.c[1] = (self.y_points[1] - self.y_points[0]) / self.d[0]
+        self.d[0] = (self.safe_max(self.x_points[1] - self.x_points[0])).reshape(-1)[0]
+        self.c[1] = ((self.y_points[1] - self.y_points[0]) / self.d[0]).reshape(-1)[0]
 
         for i in range(1, nm1):
-            self.d[i] = self.safe_max(self.x_points[i + 1] - self.x_points[i])
+            self.d[i] = (self.safe_max(self.x_points[i + 1] - self.x_points[i])).reshape(-1)[0]
             self.b[i] = 2.0 * (self.d[i - 1] + self.d[i])
-            self.c[i + 1] = (self.y_points[i + 1] - self.y_points[i]) / self.d[i]
+            self.c[i + 1] = ((self.y_points[i + 1] - self.y_points[i]) / self.d[i]).reshape(-1)[0]
             self.c[i] = self.c[i + 1] - self.c[i]
 
         # End conditions. Third derivatives at x[0] and x[self.nb_nodes-1]
@@ -142,12 +145,12 @@ def _calculate_coefficients(self):
         self.c[nm1] = 0.0
 
         if self.nb_nodes > 3:
-            d31 = self.safe_max(self.x_points[3] - self.x_points[1])
-            d20 = self.safe_max(self.x_points[2] - self.x_points[0])
-            d1 = self.safe_max(self.x_points[nm1] - self.x_points[self.nb_nodes - 3])
-            d2 = self.safe_max(self.x_points[nm2] - self.x_points[self.nb_nodes - 4])
-            d30 = self.safe_max(self.x_points[3] - self.x_points[0])
-            d3 = self.safe_max(self.x_points[nm1] - self.x_points[self.nb_nodes - 4])
+            d31 = (self.safe_max(self.x_points[3] - self.x_points[1])).reshape(-1)[0]
+            d20 = (self.safe_max(self.x_points[2] - self.x_points[0])).reshape(-1)[0]
+            d1 = (self.safe_max(self.x_points[nm1] - self.x_points[self.nb_nodes - 3])).reshape(-1)[0]
+            d2 = (self.safe_max(self.x_points[nm2] - self.x_points[self.nb_nodes - 4])).reshape(-1)[0]
+            d30 = (self.safe_max(self.x_points[3] - self.x_points[0])).reshape(-1)[0]
+            d3 = (self.safe_max(self.x_points[nm1] - self.x_points[self.nb_nodes - 4])).reshape(-1)[0]
 
             self.c[0] = self.c[2] / d31 - self.c[1] / d20
             self.c[nm1] = self.c[nm2] / d1 - self.c[self.nb_nodes - 3] / d2
@@ -167,14 +170,14 @@ def _calculate_coefficients(self):
             self.c[i] = (self.c[i] - self.d[i] * self.c[i + 1]) / self.b[i]
 
         # Compute polynomial coefficients
-        self.b[nm1] = (self.y_points[nm1] - self.y_points[nm2]) / self.d[nm2] + self.d[nm2] * (
-            self.c[nm2] + 2.0 * self.c[nm1]
-        )
+        self.b[nm1] = (
+            (self.y_points[nm1] - self.y_points[nm2]) / self.d[nm2] + self.d[nm2] * (self.c[nm2] + 2.0 * self.c[nm1])
+        ).reshape(-1)[0]
 
         for i in range(nm1):
-            self.b[i] = (self.y_points[i + 1] - self.y_points[i]) / self.d[i] - self.d[i] * (
-                self.c[i + 1] + 2.0 * self.c[i]
-            )
+            self.b[i] = (
+                (self.y_points[i + 1] - self.y_points[i]) / self.d[i] - self.d[i] * (self.c[i + 1] + 2.0 * self.c[i])
+            ).reshape(-1)[0]
             self.d[i] = (self.c[i + 1] - self.c[i]) / self.d[i]
             self.c[i] *= 3.0