embodik 0.1.1__tar.gz

embodik-0.1.1/.gitattributes

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+# Auto detect text files and perform LF normalization
+* text=auto
+
+# Explicitly declare text files you want to always be normalized and converted
+# to native line endings on checkout.
+*.py text eol=lf
+*.cpp text eol=lf
+*.hpp text eol=lf
+*.h text eol=lf
+*.cmake text eol=lf
+*.yaml text eol=lf
+*.yml text eol=lf
+*.toml text eol=lf
+*.md text eol=lf
+*.txt text eol=lf
+*.json text eol=lf
+
+# Denote all files that are truly binary and should not be modified.
+*.png binary
+*.jpg binary
+*.jpeg binary
+*.gif binary
+*.ico binary
+*.pdf binary
+*.zip binary
+*.tar.gz binary
+*.so binary
+*.dylib binary
+*.dll binary
+*.a binary
+*.obj binary
+*.stl binary
+*.dae binary
+*.dae binary
+*.urdf binary
+*.xacro binary

embodik-0.1.1/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [ main, packaging-and-docs ]
+  pull_request:
+    branches: [ main, packaging-and-docs ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            build-essential \
+            cmake \
+            libeigen3-dev \
+            pkg-config
+
+      - name: Install Pinocchio
+        run: |
+          # Try to install via apt first, fallback to building from source if needed
+          sudo apt-get install -y robotpkg-pinocchio || echo "Pinocchio not available via apt, will need manual installation"
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install nanobind scikit-build-core[pyproject]
+          pip install pytest pytest-cov
+
+      - name: Install project dependencies
+        run: |
+          pip install numpy
+
+      - name: Build and install package
+        run: |
+          pip install -e .
+        env:
+          CMAKE_PREFIX_PATH: ${{ env.CMAKE_PREFIX_PATH }}
+
+      - name: Run tests
+        run: |
+          pytest test/ -v
+        continue-on-error: true
+
+      - name: Check code formatting
+        run: |
+          pip install black isort
+          black --check python/ test/ examples/ || true
+          isort --check python/ test/ examples/ || true
+        continue-on-error: true
+
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11"]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            build-essential \
+            cmake \
+            libeigen3-dev \
+            pkg-config
+
+      - name: Install Python build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build wheel
+
+      - name: Build wheel
+        run: |
+          python -m build --wheel
+        continue-on-error: true
+
+      - name: Verify wheel
+        run: |
+          pip install dist/*.whl
+        continue-on-error: true
+
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install documentation dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install mkdocs-material mkdocstrings[python]
+
+      - name: Build documentation
+        run: |
+          mkdocs build --strict
+        continue-on-error: true

embodik-0.1.1/.github/workflows/docs.yml

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+name: Documentation
+
+on:
+  push:
+    branches: [ main ]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Install Pixi
+        uses: prefix-dev/setup-pixi@v0
+
+      - name: Build and install package
+        run: |
+          pixi run install
+
+      - name: Build documentation
+        run: |
+          pixi run python -W ignore::DeprecationWarning:hppfcl -m mkdocs build --strict
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v4
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: ./site
+
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

embodik-0.1.1/.github/workflows/release.yml

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+name: Release
+
+on:
+  push:
+    tags:
+      - 'v*'
+
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      id-token: write
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            build-essential \
+            cmake \
+            libeigen3-dev \
+            pkg-config
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+
+      - name: Build source distribution and wheels
+        run: |
+          python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/
+
+      - name: Create GitHub Release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ github.ref }}
+          release_name: Release ${{ github.ref }}
+          draft: false
+          prerelease: false
+        continue-on-error: true

embodik-0.1.1/.gitignore

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+# Python build artifacts
+python_bindings/*.cmake
+python_bindings/CMakeFiles/
+python_bindings/build/
+python_bindings/*.a
+python_bindings/swift_ik_py/
+python_bindings/embodik_py/
+test/__pycache__/
+examples/__pycache__/
+examples/**/__pycache__/
+python_bindings/Makefile
+python_bindings/CMakeCache.txt
+python/embodik/__pycache__/
+*.pyc
+__pycache__/
+
+# Ignore generated type stubs and py.typed in build directories
+python_bindings/**/*.pyi
+python_bindings/**/py.typed
+build/**/*.pyi
+build/**/py.typed
+
+# CMake build artifacts (root directory)
+CMakeCache.txt
+CMakeFiles/
+CMakeInit.txt
+cmake_install.cmake
+build.ninja
+.cmake/
+cmake/
+
+# Ninja build system files
+.ninja_deps
+.ninja_log
+*.ninja
+
+# scikit-build-core artifacts
+.skbuild/
+.skbuild-info.json
+dist/
+*.egg-info/
+
+# Build directories
+build/
+install/
+
+# Compiled libraries and binaries
+*.so
+*.a
+*.dylib
+*.dll
+*.exe
+
+# Pixi lock file - COMMIT THIS for reproducibility (ensures consistent environments)
+# Both pixi.toml and pixi.lock should be version-controlled per Pixi documentation
+# Only ignore the .pixi/ directory (environment cache), not the lock file
+.pixi/
+
+# Data files
+*.h5
+*.npz
+*.pkl
+reachability_maps/
+robot_models_urdf/
+tmp_reach_test/
+
+# Documentation build artifacts
+docs/_build/
+docs/.doctrees/
+site/
+
+# Temporary files
+*.diff
+*.tmp
+*.swp
+*~
+
+# Ignore all Markdown files except README.md, docs, and important project files
+*.md
+!README.md
+!docs/**/*.md
+!plan_docs/**/*.md
+!CHANGELOG.md
+!CONTRIBUTING.md
+!LICENSE
+
+# Robot models
+examples/robot_models*/**

embodik-0.1.1/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.1.1] - 2025-01-09
+
+### Added
+- **PyPI Publishing**: Full wheel building and publishing workflow for TestPyPI and PyPI
+- **`embodik-sanitize-env` CLI**: Helper to sanitize `LD_LIBRARY_PATH` for clean pip installs
+- **`embodik-examples` CLI**: Tool to list and copy examples for pip-installed users
+- **Built-in robot presets**: `panda` and `iiwa` presets work without `robot_presets.yaml`
+- **sdist build support**: Source distribution builds now auto-detect PyPI `pin` wheel's Pinocchio
+
+### Changed
+- Simplified `_runtime_deps.py` - removed complex preloading logic, now just provides `import_pinocchio()` helper
+- Documentation updated to recommend `venv + pip + unset LD_LIBRARY_PATH` as primary user flow
+- ViserVisualizer now uses empty GeometryModel instead of None when collisions disabled
+
+### Fixed
+- Fixed `KeyError: 'pinocchio/frames/universe'` in ViserVisualizer when `load_collisions=False`
+- Fixed RPATH for `_embodik_impl.so` to correctly find `libembodik_core.so`
+- Fixed sdist builds failing to find Pinocchio by auto-detecting `pin` wheel's CMake config
+- Examples now work correctly for pip-installed users via `embodik-examples --copy`
+
+### Dependencies
+- Added `pin>=3.8.0` to build-system requirements for sdist builds
+- Added `pyyaml`, `robot_descriptions`, `viser`, `yourdfpy` to `[examples]` optional dependencies
+
+## [0.1.0] - 2025-12-12
+
+### Added
+- Initial release of embodiK
+- High-performance inverse kinematics solver with hierarchical task resolution
+- Python bindings using nanobind
+- Support for multiple task types (FrameTask, PostureTask, COMTask, JointTask, MultiJointTask)
+- Position and velocity IK solving
+- Optional visualization tools using Viser
+- Comprehensive test suite
+- Example scripts demonstrating various use cases
+
+### Technical Details
+- C++17 core library built on Pinocchio and Eigen3
+- Python 3.8+ support
+- Linux x86_64 support
+- CMake-based build system
+- scikit-build-core for Python packaging

embodik-0.1.1/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.16)
+project(embodik VERSION 0.1.1)
+
+# Python is used to auto-discover Pinocchio (PyPI `pin`) CMake config during sdist builds.
+find_package(Python REQUIRED COMPONENTS Interpreter)
+
+# C++ standard
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+# Options
+option(BUILD_PYTHON_BINDINGS "Build Python bindings" ON)
+option(BUILD_TESTS "Build unit tests" ON)
+option(BUILD_EXAMPLES "Build examples" ON)
+
+# Find dependencies
+find_package(Eigen3 3.3 REQUIRED NO_MODULE)
+
+# If the user doesn't have a system Pinocchio install, try to locate the CMake config
+# shipped with the PyPI `pin` wheel (import name: `pinocchio`).
+#
+# This helps `pip install` from sdist (when a wheel isn't available) in a plain venv.
+if(NOT DEFINED pinocchio_DIR AND NOT DEFINED ENV{pinocchio_DIR})
+    execute_process(
+        COMMAND "${Python_EXECUTABLE}" -c
+            "import pathlib, sys\n"
+            "try:\n"
+            "  import pinocchio\n"
+            "except Exception:\n"
+            "  sys.exit(1)\n"
+            "p = pathlib.Path(pinocchio.__file__).resolve()\n"
+            "# .../cmeel.prefix/lib/pythonX/site-packages/pinocchio/__init__.py\n"
+            "prefix = p.parents[4]\n"
+            "print(str(prefix))\n"
+        RESULT_VARIABLE _pin_prefix_rc
+        OUTPUT_VARIABLE _pin_prefix
+        OUTPUT_STRIP_TRAILING_WHITESPACE
+    )
+    if(_pin_prefix_rc EQUAL 0 AND _pin_prefix)
+        message(STATUS "Detected PyPI `pin` prefix: ${_pin_prefix}")
+        # Prefer the `pin` wheel's CMake packages over any local Pinocchio installs.
+        list(PREPEND CMAKE_PREFIX_PATH "${_pin_prefix}")
+        # Force pinocchio_DIR to the wheel-provided config to avoid accidentally
+        # picking up a locally-built Pinocchio (which can bake in incompatible Boost SONAMEs).
+        set(pinocchio_DIR "${_pin_prefix}/lib/cmake/pinocchio" CACHE PATH "Pinocchio CMake package directory" FORCE)
+        message(STATUS "Forcing pinocchio_DIR=${pinocchio_DIR}")
+    endif()
+endif()
+
+find_package(pinocchio REQUIRED)
+
+# Add compile options
+if(CMAKE_COMPILER_IS_GNUCXX OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+    add_compile_options(-Wall -Wextra -Wpedantic)
+endif()
+
+# Create main library
+add_library(embodik_core SHARED
+    cpp_core/src/robot_model.cpp
+    cpp_core/src/tasks.cpp
+    cpp_core/src/kinematics_solver.cpp
+)
+
+target_include_directories(embodik_core PUBLIC
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/cpp_core/include>
+    $<INSTALL_INTERFACE:include>
+)
+
+# For inplace editable installs, copy core library to python/embodik directory
+# Always copy for editable installs (editable.mode = "inplace" in pyproject.toml)
+add_custom_command(TARGET embodik_core POST_BUILD
+    COMMAND ${CMAKE_COMMAND} -E copy_if_different
+        $<TARGET_FILE:embodik_core>
+        "${CMAKE_CURRENT_SOURCE_DIR}/python/embodik/"
+    COMMENT "Copying core library to python/embodik for editable install"
+)
+
+target_link_libraries(embodik_core PUBLIC
+    Eigen3::Eigen
+    pinocchio::pinocchio
+)
+
+# Python bindings
+if(BUILD_PYTHON_BINDINGS)
+    add_subdirectory(python_bindings)
+endif()
+
+# Tests
+if(BUILD_TESTS)
+    enable_testing()
+    if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/test/CMakeLists.txt")
+        add_subdirectory(test)
+    endif()
+endif()
+
+# Examples
+if(BUILD_EXAMPLES)
+    if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/examples/CMakeLists.txt")
+        add_subdirectory(examples)
+    endif()
+endif()
+
+# Installation
+install(TARGETS embodik_core
+    EXPORT embodik_targets
+    LIBRARY DESTINATION lib
+    ARCHIVE DESTINATION lib
+    RUNTIME DESTINATION bin
+)
+
+install(DIRECTORY cpp_core/include/
+    DESTINATION include
+)
+
+install(EXPORT embodik_targets
+    FILE embodik_targets.cmake
+    NAMESPACE embodik::
+    DESTINATION lib/cmake/embodik
+)
+
+# Python package installation
+# Note: scikit-build-core handles Python package installation via wheel.packages
+# The extension module is installed by python_bindings/CMakeLists.txt
+# Python source files are included via wheel.packages in pyproject.toml
+
+# Install examples directory for pip-installed users
+install(DIRECTORY examples/
+    DESTINATION share/embodik/examples
+    FILES_MATCHING
+        PATTERN "*.py"
+        PATTERN "*.yaml"
+        PATTERN "*.md"
+    PATTERN "__pycache__" EXCLUDE
+    PATTERN "*.pyc" EXCLUDE
+)

embodik-0.1.1/CONTRIBUTING.md

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+# Contributing to embodiK
+
+Thank you for your interest in contributing to embodiK! This document provides guidelines and instructions for contributing.
+
+## Code of Conduct
+
+By participating in this project, you agree to maintain a respectful and inclusive environment for all contributors.
+
+## How to Contribute
+
+### Reporting Issues
+
+Before creating an issue, please:
+1. Check if the issue already exists
+2. Use a clear, descriptive title
+3. Provide a minimal example that reproduces the issue
+4. Include your environment details (OS, Python version, etc.)
+
+### Submitting Pull Requests
+
+1. **Fork the repository** and create a branch from `main`
+2. **Make your changes** following our coding standards
+3. **Add tests** for new functionality
+4. **Update documentation** if needed
+5. **Run tests** locally before submitting
+6. **Submit a pull request** with a clear description
+
+### Development Setup
+
+#### Option 1: Using Pixi (Recommended)
+
+Pixi provides a reproducible development environment with all dependencies managed automatically.
+
+1. Install Pixi:
+   ```bash
+   curl -fsSL https://pixi.sh/install.sh | bash
+   ```
+
+2. Clone your fork:
+   ```bash
+   git clone https://github.com/YOUR_USERNAME/embodik.git
+   cd embodik
+   ```
+
+3. Install the package in development mode:
+   ```bash
+   pixi run install
+   # Or with auto-rebuild on import:
+   pixi run install-rebuild
+   ```
+
+4. Activate the pixi environment:
+   ```bash
+   pixi shell
+   ```
+
+All system dependencies (CMake, Eigen, Pinocchio, etc.) are automatically managed by pixi.
+
+#### Option 2: Manual Setup
+
+1. Clone your fork:
+   ```bash
+   git clone https://github.com/YOUR_USERNAME/embodik.git
+   cd embodik
+   ```
+
+2. Install system dependencies:
+   - CMake 3.16+
+   - C++17 compiler (GCC 7+, Clang 5+)
+   - Eigen3 development headers (`libeigen3-dev` on Ubuntu)
+   - Pinocchio library
+
+3. Install in development mode:
+   ```bash
+   pip install -e ".[dev]"
+   ```
+
+### Coding Standards
+
+- **Python**: Follow PEP 8 style guide
+- **C++**: Follow the existing code style (C++17 standard)
+- **Documentation**: Use docstrings for all public functions/classes
+- **Tests**: Write tests for new features and bug fixes
+
+### Running Tests
+
+**With Pixi:**
+```bash
+pixi run test
+pixi run test-verbose
+pixi run test-cov  # With coverage (requires dev feature)
+```
+
+**Without Pixi:**
+```bash
+# Run Python tests
+pytest
+
+# Run with coverage
+pytest --cov=embodik --cov-report=html
+
+# Run C++ tests
+cd build && ctest
+```
+
+### Code Formatting
+
+We use `black` and `isort` for Python code formatting:
+
+**With Pixi:**
+```bash
+pixi run format      # Format code
+pixi run lint        # Check formatting
+```
+
+**Without Pixi:**
+```bash
+# Format code
+black python/ test/ examples/
+isort python/ test/ examples/
+
+# Check formatting
+black --check python/ test/ examples/
+isort --check python/ test/ examples/
+```
+
+### Documentation
+
+- Update docstrings for any new public APIs
+- Update relevant documentation files in `docs/`
+- Build docs locally to verify:
+  ```bash
+  # With Pixi
+  pixi run docs-serve
+
+  # Without Pixi
+  mkdocs serve
+  ```
+
+### Commit Messages
+
+Use clear, descriptive commit messages:
+- Start with a verb in imperative mood (e.g., "Add", "Fix", "Update")
+- Keep the first line under 72 characters
+- Add more details in the body if needed
+
+Example:
+```
+Add support for joint limit constraints
+
+- Implement joint limit checking in kinematics solver
+- Add tests for limit enforcement
+- Update documentation with examples
+```
+
+## Questions?
+
+Feel free to open an issue for questions or reach out to the maintainers.
+
+Thank you for contributing to embodiK!