[v0.0.1] 2025-08-21

## Helios native C++
Fix helios-core submodule to point to correct remote commit
- Reset submodule to match actual remote state (228a3d389)
- Remove local divergent commits that don't exist on remote
- This fixes the git history display showing non-existent commits

## Context
- Add primitive data operations for all types (float, int, string, vec2/3/4, int2/3/4)
- Add primitive data query functions (exists, type, size)
- Add auto-detection getter and pseudo-color visualization support
- Extend Context.py with comprehensive primitive data methods
- Add robust error handling and cross-platform ctypes wrappers
- Include comprehensive test coverage for all primitive data operations
- Added Context::getPrimitiveDataArray() to return a numpy array of primitive data

Author: bnbailey-psl

README.md

@@ -3,7 +3,7 @@
 [![Test Linux](https://github.com/PlantSimulationLab/PyHelios/actions/workflows/pytest-linux.yml/badge.svg?branch=master)](https://github.com/PlantSimulationLab/PyHelios/actions/workflows/pytest-linux.yml) [![Test Windows](https://github.com/PlantSimulationLab/PyHelios/actions/workflows/pytest-windows.yml/badge.svg?branch=master)](https://github.com/PlantSimulationLab/PyHelios/actions/workflows/pytest-windows.yml) [![Test MacOS](https://github.com/PlantSimulationLab/PyHelios/actions/workflows/pytest-macos.yml/badge.svg?branch=master)](https://github.com/PlantSimulationLab/PyHelios/actions/workflows/pytest-macos.yml) [![Docs](https://github.com/PlantSimulationLab/PyHelios/actions/workflows/docs.yml/badge.svg?branch=master)](https://github.com/PlantSimulationLab/PyHelios/actions/workflows/docs.yml)
 
 <div align="center">
-  <img src="docs/images/PyHelios_logo_whiteborder.png"  alt="" width="300" />
+  <img src="https://raw.githubusercontent.com/PlantSimulationLab/PyHelios/master/docs/images/PyHelios_logo_whiteborder.png"  alt="" width="300" />
 </div>
 
 # PyHelios
@@ -123,24 +123,18 @@ from pyhelios.RadiationModel import RadiationModelError
 context = Context()
 # Add geometry (PLY files, patches, trees, etc.)
 
-try:
-    # RadiationModel automatically checks plugin availability
-    with RadiationModel(context) as radiation:
-        radiation.addRadiationBand("SW")
-        radiation.setDirectRayCount("SW", 100)
-        radiation.setDiffuseRayCount("SW", 300)
+with RadiationModel(context) as radiation:
+    radiation.addRadiationBand("SW")
+    radiation.setDirectRayCount("SW", 100)
+    radiation.setDiffuseRayCount("SW", 300)
 
-        # Run GPU simulation
-        radiation.runBand("SW")
-        results = radiation.getTotalAbsorbedFlux()
+    # Run GPU simulation
+    radiation.runBand("SW")
+    results = radiation.getTotalAbsorbedFlux()
 
-        # Apply native pseudocolor mapping for visualization
-        all_uuids = context.getAllUUIDs()
-        context.colorPrimitiveByDataPseudocolor(all_uuids, "radiation_flux_SW", "hot", 256)
-        
-except RadiationModelError as e:
-    print(f"Radiation modeling not available: {e}")
-    # Error includes specific instructions for enabling radiation plugin
+    # Apply native pseudocolor mapping for visualization
+    all_uuids = context.getAllUUIDs()
+    context.colorPrimitiveByDataPseudocolor(all_uuids, "radiation_flux_SW", "hot", 256)
 ```
 
 ### Command-Line Plugin Tools
@@ -179,39 +173,17 @@ pytest --cov=pyhelios
 
 PyHelios now supports **flexible plugin selection** for customized builds based on your hardware and requirements. Choose from **21 available plugins** using predefined profiles or explicit selection.
 
-### Quick Start with Profiles
-
-```bash
-# Minimal build (core functionality only)
-build_scripts/build_helios --profile minimal
-
-# Standard build (recommended for most users)
-build_scripts/build_helios --profile standard
-
-# GPU-accelerated build (requires CUDA for radiation modeling)
-build_scripts/build_helios --profile gpu-accelerated
-
-# Full research suite (comprehensive plugin set)
-build_scripts/build_helios --profile research
-```
-
 ### Advanced Plugin Selection
 
 ```bash
 # Custom plugin selection
-build_scripts/build_helios --plugins weberpenntree,canopygenerator,visualizer,energybalance
+build_scripts/build_helios --plugins weberpenntree,visualizer
 
 # Interactive selection (guided setup)
 build_scripts/build_helios --interactive
 
 # Exclude problematic plugins
-build_scripts/build_helios --profile standard --exclude radiation
-
-# Discover optimal configuration for your system
-python -m pyhelios.plugins discover
-
-# Check plugin status and availability
-python -m pyhelios.plugins status
+build_scripts/build_helios --exclude radiation
 ```
 
 ### Configuration File Support
@@ -240,16 +212,6 @@ plugins:
 
 ## Troubleshooting
 
-### Native Library Requirements
-- **Problem**: Operations raise "mock mode" or "native library required" errors
-- **Solution**: Build and install native libraries using `build_scripts/build_helios`
-- **Note**: PyHelios requires native libraries for full functionality - mock mode is only for development/testing
-
-### Build Issues  
-- **Windows**: Ensure Visual Studio or Build Tools are installed
-- **macOS**: Install Xcode command line tools with `xcode-select --install`
-- **Linux**: Install build essentials with `sudo apt-get install build-essential cmake`
-
 ### Import Errors
 - Verify installation: `pip list | grep pyhelios`
 - Check Python version: Requires Python 3.7+

build_scripts/build_helios.py

@@ -1399,26 +1399,30 @@ def _patch_zlib_cmake_for_windows(self) -> None:
 
 def get_default_plugins() -> List[str]:
     """
-    Get the default set of plugins (all non-GPU-compute plugins, including visualization).
+    Get the default set of plugins (only the 3 currently integrated plugins).
     
-    Note: Visualization plugins like 'visualizer' only require OpenGL, not specialized
-    GPU compute APIs like CUDA/OptiX, so they should be included by default.
+    Currently only 3 plugins are integrated into PyHelios:
+    - visualizer: OpenGL-based 3D visualization
+    - weberpenntree: Procedural tree generation
+    - radiation: OptiX-accelerated ray tracing (GPU optional)
     
     Returns:
         List of default plugins
     """
+    # Only return the 3 plugins that are actually integrated into PyHelios
+    integrated_plugins = ["visualizer", "weberpenntree", "radiation"]
+    
+    # Filter by platform compatibility
     default_plugins = []
-    for name, metadata in PLUGIN_METADATA.items():
-        # Include if it's platform compatible and doesn't require specialized GPU compute
-        platform_name = platform.system().lower()
-        if platform_name == "darwin":
-            platform_name = "macos"
-        
-        if platform_name in metadata.platforms:
-            # Only exclude plugins that require specialized GPU compute (CUDA/OptiX)
-            # OpenGL-based visualization is not considered "GPU compute"
-            if not metadata.gpu_required:
-                default_plugins.append(name)
+    platform_name = platform.system().lower()
+    if platform_name == "darwin":
+        platform_name = "macos"
+    
+    for plugin in integrated_plugins:
+        if plugin in PLUGIN_METADATA:
+            metadata = PLUGIN_METADATA[plugin]
+            if platform_name in metadata.platforms:
+                default_plugins.append(plugin)
 
     return sorted(default_plugins)
 

docs/CHANGELOG.md

@@ -7,4 +7,21 @@
 ## Currently implemented plug-ins
 - `visualizer`
 - `radiation`
-- `weber-penn tree`
+- `weber-penn tree`
+
+# [v0.0.1] 2025-08-21
+
+## Helios native C++
+Fix helios-core submodule to point to correct remote commit  
+- Reset submodule to match actual remote state (228a3d389)  
+- Remove local divergent commits that don't exist on remote 
+- This fixes the git history display showing non-existent commits
+
+## Context
+- Add primitive data operations for all types (float, int, string, vec2/3/4, int2/3/4)
+- Add primitive data query functions (exists, type, size)
+- Add auto-detection getter and pseudo-color visualization support
+- Extend Context.py with comprehensive primitive data methods
+- Add robust error handling and cross-platform ctypes wrappers
+- Include comprehensive test coverage for all primitive data operations
+- Added Context::getPrimitiveDataArray() to return a numpy array of primitive data

docs/Doxyfile.python

@@ -6,7 +6,7 @@
 #---------------------------------------------------------------------------
 
 PROJECT_NAME           = "PyHelios"
-PROJECT_NUMBER         = 
+PROJECT_NUMBER         = 0.0.1
 PROJECT_BRIEF          = 
 PROJECT_LOGO           = docs/images/PyHelios_logo_whiteborder.png
 OUTPUT_DIRECTORY       = docs/generated

docs/api_guide.md

@@ -213,6 +213,93 @@ species = context.getPrimitiveDataString(uuid, "species")
 velocity_list = context.getPrimitiveDataVec3(uuid, "velocity")  # Returns [x, y, z]
 ```
 
+#### Getting Multiple Primitive Data Values as Arrays
+
+PyHelios provides `getPrimitiveDataArray()` for efficiently retrieving primitive data from multiple primitives:
+
+```python
+import numpy as np
+
+# Create multiple primitives and set data
+patch_uuids = []
+for i in range(10):
+    uuid = context.addPatch(center=vec3(i, 0, 0))
+    context.setPrimitiveDataFloat(uuid, "temperature", 20.0 + i * 2.5)
+    context.setPrimitiveDataInt(uuid, "leaf_count", 50 + i * 10)
+    context.setPrimitiveDataString(uuid, "species", f"species_{i}")
+    patch_uuids.append(uuid)
+
+# Get data arrays - automatically determines appropriate NumPy dtype
+temperatures = context.getPrimitiveDataArray(patch_uuids, "temperature")
+# Returns: numpy.ndarray with dtype=float32, shape=(10,)
+# Values: [20.0, 22.5, 25.0, 27.5, 30.0, 32.5, 35.0, 37.5, 40.0, 42.5]
+
+leaf_counts = context.getPrimitiveDataArray(patch_uuids, "leaf_count")
+# Returns: numpy.ndarray with dtype=int32, shape=(10,)
+# Values: [50, 60, 70, 80, 90, 100, 110, 120, 130, 140]
+
+species_names = context.getPrimitiveDataArray(patch_uuids, "species")
+# Returns: numpy.ndarray with dtype=object, shape=(10,)
+# Values: ['species_0', 'species_1', ..., 'species_9']
+
+# Works with any primitive type and data type
+triangle_uuids = [
+    context.addTriangle(vec3(0,0,0), vec3(1,0,0), vec3(0.5,1,0)),
+    context.addTriangle(vec3(2,0,0), vec3(3,0,0), vec3(2.5,1,0))
+]
+for i, uuid in enumerate(triangle_uuids):
+    context.setPrimitiveDataFloat(uuid, "area", (i + 1) * 0.5)
+
+areas = context.getPrimitiveDataArray(triangle_uuids, "area")
+# Returns: numpy.ndarray with dtype=float32, shape=(2,)
+# Values: [0.5, 1.0]
+
+# Vector data returns 2D arrays
+for i, uuid in enumerate(patch_uuids[:3]):
+    context.setPrimitiveDataFloat(uuid, "velocity_x", float(i))
+    context.setPrimitiveDataFloat(uuid, "velocity_y", float(i + 10))
+    context.setPrimitiveDataFloat(uuid, "velocity_z", float(i + 20))
+
+velocities_x = context.getPrimitiveDataArray(patch_uuids[:3], "velocity_x")
+velocities_y = context.getPrimitiveDataArray(patch_uuids[:3], "velocity_y")
+velocities_z = context.getPrimitiveDataArray(patch_uuids[:3], "velocity_z")
+# Each returns: numpy.ndarray with dtype=float32, shape=(3,)
+
+# Combine into velocity vectors if needed
+velocities = np.column_stack([velocities_x, velocities_y, velocities_z])
+# Shape: (3, 3) - 3 primitives, each with 3D velocity
+```
+
+**Array Data Types:**
+- `int` data → `numpy.int32` array
+- `uint` data → `numpy.uint32` array  
+- `float` data → `numpy.float32` array
+- `double` data → `numpy.float64` array
+- `string` data → `numpy.object` array
+- `vec2/vec3/vec4` data → `numpy.float32` array with shape `(N, vector_size)`
+- `int2/int3/int4` data → `numpy.int32` array with shape `(N, vector_size)`
+
+**Error Handling:**
+```python
+# Empty UUID list
+try:
+    data = context.getPrimitiveDataArray([], "temperature")
+except ValueError as e:
+    print("Error:", e)  # "UUID list cannot be empty"
+
+# Invalid UUID
+try:
+    data = context.getPrimitiveDataArray([999999], "temperature")
+except ValueError as e:
+    print("Error:", e)  # "Primitive data 'temperature' does not exist for UUID 999999"
+
+# Non-existent data label
+try:
+    data = context.getPrimitiveDataArray(patch_uuids, "nonexistent_label")
+except ValueError as e:
+    print("Error:", e)  # "Primitive data 'nonexistent_label' does not exist for UUID <uuid>"
+```
+
 ### Actual File Operations
 
 These methods are verified from the wrapper implementation: