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Getting Started {#GettingStarted}

Cross-platform Python bindings for Helios 3D plant simulation library.

PyHelios provides a Python interface to the powerful Helios C++ library for 3D physical simulation of plant and environmental systems. It enables plant modeling, geometry manipulation, and biophysical simulations including GPU-accelerated radiation transfer, photosynthesis, and plant architecture modeling.

📖 Complete Documentation

⚠️Note that this is a work in progress. Not all Helios functionality has been implemented in PyHelios ⚠️

⚠️Help make PyHelios better by reporting issues: https://github.com/PlantSimulationLab/PyHelios/issues ⚠️

See the Helios C++ documentation for a more in-depth description of Helios: https://baileylab.ucdavis.edu/software/helios

Quick Start

Installation

Requirements: Python 3.10 or later (pre-built wheels available for Python 3.10–3.14)

Easy Install (Recommended):

pip install pyhelios3d

This installs pre-built PyHelios with platform-appropriate plugins:

  • macOS (Apple Silicon): All plugins including radiation via Vulkan backend
  • macOS (Intel): Pre-built wheels not available - please build from source
  • Windows/Linux: All plugins with GPU acceleration via OptiX backend (NVIDIA GPUs)

PyHelios automatically selects the best execution mode:

  • Plugins with GPU backends (radiation): Require GPU - Vulkan (all platforms) or OptiX (NVIDIA)
  • Plugins with CPU/GPU modes (energybalance): Work on all platforms, GPU acceleration optional
  • CPU-only plugins: Work on all platforms without special hardware

Note for Intel Mac Users: Due to GitHub Actions infrastructure limitations, pre-built wheels are only available for Apple Silicon Macs. Intel Mac users must build PyHelios from source following the macOS build instructions below.

Build from Source {#build-from-source}

If you need to customize plugins or build from source:

Windows {#windows}

Prerequisites:

  • Visual Studio 2019+ or Build Tools for Visual Studio
  • Python 3.10+
# Clone repository
git clone --recursive https://github.com/PlantSimulationLab/PyHelios.git
cd PyHelios/

# Build native libraries (optional - pre-built binaries included)
./build_scripts/build_helios

# Install PyHelios dependencies
pip install -e .

macOS {#macos}

Prerequisites:

  • Xcode command line tools
  • Python 3.10+
# Install Xcode command line tools
xcode-select --install

# Clone repository
git clone --recursive https://github.com/PlantSimulationLab/PyHelios.git
cd PyHelios/

# Install c++ dependencies and build native libraries
source helios-core/utilities/dependencies.sh
./build_scripts/build_helios

# Install PyHelios dependencies
pip install -e .

Linux (Ubuntu/Debian) {#linux}

Prerequisites:

  • Build essentials
  • CMake
  • Python 3.10+
# Clone repository
git clone --recursive https://github.com/PlantSimulationLab/PyHelios.git
cd PyHelios/

# Install c++ dependencies and build native libraries
source helios-core/utilities/dependencies.sh
./build_scripts/build_helios

# Install PyHelios dependencies
pip install -e .

GPU Features Setup (Optional)

PyHelios plugins have three types of GPU support:

GPU-Required Plugins:

  • Radiation Model: GPU-accelerated ray tracing via Vulkan (all GPUs) or OptiX (NVIDIA)
  • Aerial LiDAR: GPU-accelerated LiDAR simulation (CUDA)

GPU-Optional Plugins (work with or without GPU):

  • Energy Balance (v1.3.61+): Automatic mode selection - GPU (CUDA) → OpenMP (parallel CPU) → Serial CPU
    • CPU mode recommended for most workloads without GPU

CPU-Only Plugins (no GPU needed):

  • All other plugins (PlantArchitecture, Photosynthesis, SolarPosition, etc.)

For GPU Acceleration (optional), ensure you have at least one:

  • Vulkan loader library (macOS/Linux only; no extra packages on Windows)
  • OR for NVIDIA-optimized path: CUDA 12.0+ with driver >= 560 (OptiX 8.1) or CUDA 9.0+ with driver < 560 (OptiX 6.5)

The radiation plugin auto-detects the best available backend at runtime (OptiX 8 -> OptiX 6 -> Vulkan).

Verification:

vulkaninfo  # Should show Vulkan device information
# OR for NVIDIA:
nvidia-smi  # Should show GPU information

Testing GPU Features:

from pyhelios import Context, RadiationModel, EnergyBalanceModel

context = Context()

# Test GPU-required plugin (radiation)
try:
    radiation = RadiationModel(context)
    print("GPU radiation modeling available!")
except RuntimeError as e:
    print(f"Radiation requires GPU: {e}")

# Test GPU-optional plugin (energybalance)
with EnergyBalanceModel(context) as energy:
    if energy.isGPUAccelerationEnabled():
        print("EnergyBalance using GPU acceleration")
    else:
        print("EnergyBalance using CPU mode (OpenMP or serial)")

First Example

from pyhelios import Context
from pyhelios.types import *

# Create simulation context
context = Context()

# Add a patch primitive
center = vec3(2, 3, 4)
size = vec2(1, 1)
color = RGBcolor(0.25, 0.25, 0.25)
patch_uuid = context.addPatch(center=center, size=size, color=color)

print(f"Created patch: {patch_uuid}")

Documentation

Section Description
Getting Started Installation, setup, and first steps
User Guide Core concepts, API reference, and examples
Cross-Platform Platform-specific usage and deployment
Plugin System Available plugins and configuration

Key Features

  • Cross-platform: Windows, macOS, and Linux support
  • Plant modeling: 20+ plant species models in the plant architecture plug-in
  • GPU acceleration: Radiation simulation via Vulkan or OptiX backends
  • 3D visualization: OpenGL-based real-time rendering

Updating PyHelios

PyPI Installation

If you installed via pip, simply upgrade to the latest version:

pip install --upgrade pyhelios3d

Source Installation

If you built PyHelios from source, update with the latest changes:

# Update main repository and submodules recursively
git pull --recurse-submodules

# Alternative: Update main repo first, then submodules
git pull
git submodule update --init --recursive

# Rebuild native libraries after updates (recommended)
./build_scripts/build_helios --clean

# Reinstall PyHelios
pip install -e .

Important: Always use --recurse-submodules or manually update submodules when pulling updates, as PyHelios depends on the helios-core submodule for C++ functionality.

Quick Commands

# Test installation (uses subprocess isolation for robust testing)
pytest

# Check plugin status  
python -m pyhelios.plugins status

# Interactive plugin selection
./build_scripts/build_helios --interactive

Support

Note: This project is in active development. The API may change quickly - see docs/CHANGELOG.md for updates.

Project links

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Key dates

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  • Released:
Latest release

1 maintainer

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Credits

Author: Brian Bailey

GitHub Statistics

Data verified by PyPI on Aug 14, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

GNU General Public License v2 (GPLv2)

Requires

Python >=3.10

Provides Extra

dev test build

Tags

helios plant simulation 3d modeling ray tracing photosynthesis plant architecture

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The following attestation bundles were made for pyhelios3d-0.1.28-cp310-cp310-macosx_14_0_arm64.whl:

Publisher: build-wheels.yml on PlantSimulationLab/PyHelios

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

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This release

0.1.28 This release

15 files

0.1.27

15 files

0.1.26

15 files

0.1.25

15 files

0.1.24

15 files

0.1.23

15 files

0.1.22

15 files

0.1.21

15 files

0.1.20

15 files

0.1.19

15 files

0.1.18

15 files

0.1.17

15 files

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