[v0.1.11] 2025-12-05

- Updated helios-core to v1.3.59

## Core
- Added `magnitude()` and `normalize()` methods to vec2 and vec3
- Added `scale()` method to RGBcolor and RGBAcolor for color intensity adjustment
- Added `JulianDay()`, `incrementDay()`, and `isLeapYear()` methods to Date
- Added `scaleConeObjectLength()` and `scaleConeObjectGirth()` methods for cone object manipulation

## Solar Position
- Added modern state-based API with `setAtmosphericConditions()`, `getAtmosphericConditions()`, and parameter-free flux methods
- Added `getAmbientLongwaveFlux()` for ambient longwave radiation calculation
- Added Prague Sky Model support with `enablePragueSkyModel()`, `updatePragueSkyModel()`, `isPragueSkyModelEnabled()`, and `pragueSkyModelNeedsUpdate()`

## Leaf Optics
- Added `optionalOutputPrimitiveData()` for selective biochemical property output (chlorophyll, carotenoid, water, etc.)
- CRITICAL BUG: leaf optics was not being built with default build

## WeberPennTree
- Added `loadXML()` method for loading custom tree species from XML files
- Extended `buildTree()` to accept custom species names (strings) in addition to `WPTType` enum

Author: bnbailey-psl

README.md

@@ -57,7 +57,7 @@ cd PyHelios/
 # Build native libraries (optional - pre-built binaries included)
 ./build_scripts/build_helios
 
-# Install PyHelios
+# Install PyHelios dependencies
 pip install -e .
 ```
 
@@ -75,11 +75,11 @@ xcode-select --install
 git clone --recursive https://github.com/PlantSimulationLab/PyHelios.git
 cd PyHelios/
 
-# Install dependencies and build native libraries
+# Install c++ dependencies and build native libraries
 source helios-core/utilities/dependencies.sh
 ./build_scripts/build_helios
 
-# Install PyHelios
+# Install PyHelios dependencies
 pip install -e .
 ```
 
@@ -95,11 +95,11 @@ pip install -e .
 git clone --recursive https://github.com/PlantSimulationLab/PyHelios.git
 cd PyHelios/
 
-# Install dependencies and build native libraries
+# Install c++ dependencies and build native libraries
 source helios-core/utilities/dependencies.sh
 ./build_scripts/build_helios
 
-# Install PyHelios
+# Install PyHelios dependencies
 pip install -e .
 ```
 

build_scripts/build_helios.py

@@ -1638,6 +1638,7 @@ def get_default_plugins() -> List[str]:
     - solarposition: Solar position calculations and sun angle modeling
     - photosynthesis: Photosynthesis modeling and carbon assimilation
     - plantarchitecture: Advanced plant structure and architecture modeling with procedural plant library
+    - leafoptics: Implementation of PROSPECT-PRO leaf optical model
 
     Returns:
         List of default plugins

docs/CHANGELOG.md

@@ -1,5 +1,28 @@
 # Changelog
 
+# [v0.1.11] 2025-12-05
+
+- Updated helios-core to v1.3.59
+
+## Core
+- Added `magnitude()` and `normalize()` methods to vec2 and vec3
+- Added `scale()` method to RGBcolor and RGBAcolor for color intensity adjustment
+- Added `JulianDay()`, `incrementDay()`, and `isLeapYear()` methods to Date
+- Added `scaleConeObjectLength()` and `scaleConeObjectGirth()` methods for cone object manipulation
+
+## Solar Position
+- Added modern state-based API with `setAtmosphericConditions()`, `getAtmosphericConditions()`, and parameter-free flux methods
+- Added `getAmbientLongwaveFlux()` for ambient longwave radiation calculation
+- Added Prague Sky Model support with `enablePragueSkyModel()`, `updatePragueSkyModel()`, `isPragueSkyModelEnabled()`, and `pragueSkyModelNeedsUpdate()`
+
+## Leaf Optics
+- Added `optionalOutputPrimitiveData()` for selective biochemical property output (chlorophyll, carotenoid, water, etc.)
+- CRITICAL BUG: leaf optics was not being built with default build
+
+## WeberPennTree
+- Added `loadXML()` method for loading custom tree species from XML files
+- Extended `buildTree()` to accept custom species names (strings) in addition to `WPTType` enum
+
 # [v0.1.10] 2025-12-02
 
 🚨++ New Plug-in Integrated ++ 🚨

docs/Doxyfile.python

@@ -40,8 +40,7 @@ PYTHON_DOCSTRING       = YES
 INHERIT_DOCS           = YES
 SEPARATE_MEMBER_PAGES  = NO
 TAB_SIZE               = 4
-ALIASES                = 
-TCL_SUBST              = 
+ALIASES                =
 OPTIMIZE_OUTPUT_FOR_C  = NO
 OPTIMIZE_OUTPUT_JAVA   = YES
 OPTIMIZE_FOR_FORTRAN   = NO
@@ -129,6 +128,7 @@ INPUT                  = pyhelios \
                          docs/file_io.md \
                          docs/cross_platform.md \
                          docs/plugin_system.md \
+                         docs/cuda_setup.md \
                          docs/plugin_integration_guide.md \
                          docs/plugin_boundarylayerconductance.md \
                          docs/plugin_energybalance.md \
@@ -150,6 +150,8 @@ FILE_PATTERNS          = *.py \
 RECURSIVE              = YES
 EXCLUDE                = pyhelios/plugins/__pycache__ \
                          pyhelios/__pycache__ \
+                         docs/plugin_integration_guide.md \
+                         docs/cpp_plugin_integration_guide.md \
                          pyhelios/wrappers/UBoundaryLayerConductanceWrapper.py \
                          pyhelios/wrappers/UContextWrapper.py \
                          pyhelios/wrappers/UGlobalWrapper.py \
@@ -175,13 +177,13 @@ EXCLUDE                = pyhelios/plugins/__pycache__ \
 EXCLUDE_SYMLINKS       = NO
 EXCLUDE_PATTERNS       = */__pycache__/* \
                          */.*
-EXCLUDE_SYMBOLS        = 
+EXCLUDE_SYMBOLS        = *::int *::float *::str *::bool *::list *::tuple *::dict
 EXAMPLE_PATH           = docs/examples
 EXAMPLE_PATTERNS       = *.py
 EXAMPLE_RECURSIVE      = YES
 IMAGE_PATH             = docs/images
 INPUT_FILTER           = 
-FILTER_PATTERNS        = *.py="doxypypy --autobrief --autocode"
+FILTER_PATTERNS        = *.py="doxypypy --autobrief"
 FILTER_SOURCE_FILES    = NO
 FILTER_SOURCE_PATTERNS = 
 USE_MDFILE_AS_MAINPAGE = README.md
@@ -199,10 +201,6 @@ REFERENCES_LINK_SOURCE = YES
 SOURCE_TOOLTIPS        = YES
 USE_HTAGS              = NO
 VERBATIM_HEADERS       = YES
-CLANG_ASSISTED_PARSING = NO
-CLANG_ADD_INC_PATHS    = YES
-CLANG_OPTIONS          = 
-CLANG_DATABASE_PATH    = 
 
 #---------------------------------------------------------------------------
 # Configuration options related to the alphabetical class index
@@ -218,7 +216,7 @@ IGNORE_PREFIX          =
 GENERATE_HTML          = YES
 HTML_OUTPUT            = html
 HTML_FILE_EXTENSION    = .html
-HTML_HEADER            = docs/header.html
+# HTML_HEADER            = docs/header.html
 HTML_FOOTER            = 
 HTML_STYLESHEET        = 
 HTML_EXTRA_STYLESHEET  = docs/assets/doxygen-awesome.css \
@@ -235,7 +233,6 @@ HTML_EXTRA_FILES       = docs/assets/doxygen-awesome-darkmode-toggle.js \
 HTML_COLORSTYLE_HUE    = 220
 HTML_COLORSTYLE_SAT    = 100
 HTML_COLORSTYLE_GAMMA  = 80
-HTML_TIMESTAMP         = NO
 HTML_DYNAMIC_MENUS     = YES
 HTML_DYNAMIC_SECTIONS  = YES
 HTML_INDEX_NUM_ENTRIES = 100
@@ -268,12 +265,12 @@ TREEVIEW_WIDTH         = 250
 EXT_LINKS_IN_WINDOW    = NO
 HTML_FORMULA_FORMAT    = png
 FORMULA_FONTSIZE       = 10
-FORMULA_TRANSPARENT    = YES
 FORMULA_MACROFILE      = 
-USE_MATHJAX            = NO
+USE_MATHJAX            = YES
+MATHJAX_VERSION        = MathJax_3
 MATHJAX_FORMAT         = HTML-CSS
-MATHJAX_RELPATH        = http://cdn.mathjax.org/mathjax/latest
-MATHJAX_EXTENSIONS     = 
+MATHJAX_RELPATH        = https://cdn.jsdelivr.net/npm/mathjax@3
+MATHJAX_EXTENSIONS     =
 MATHJAX_CODEFILE       = 
 SEARCHENGINE           = YES
 SERVER_BASED_SEARCH    = NO
@@ -353,13 +350,10 @@ EXTERNAL_PAGES         = YES
 # Configuration options related to the dot tool
 #---------------------------------------------------------------------------
 
-CLASS_DIAGRAMS         = YES
 DIA_PATH               = 
 HIDE_UNDOC_RELATIONS   = YES
 HAVE_DOT               = YES
 DOT_NUM_THREADS        = 0
-DOT_FONTNAME           = Helvetica
-DOT_FONTSIZE           = 10
 DOT_FONTPATH           = 
 CLASS_GRAPH            = YES
 COLLABORATION_GRAPH    = YES
@@ -384,7 +378,6 @@ PLANTUML_CFG_FILE      =
 PLANTUML_INCLUDE_PATH  = 
 DOT_GRAPH_MAX_NODES    = 50
 MAX_DOT_GRAPH_DEPTH    = 0
-DOT_TRANSPARENT        = NO
 DOT_MULTI_TARGETS      = NO
 GENERATE_LEGEND        = YES
 DOT_CLEANUP            = YES

docs/DoxygenLayout.xml

@@ -18,6 +18,7 @@
       <!-- Currently Implemented Plugins (Alphabetized) -->
       <tab type="user" visible="yes" url="@ref BoundaryLayerConductanceDoc" title="Boundary Layer Conductance"/>
       <tab type="user" visible="yes" url="@ref EnergyBalanceDoc" title="Energy Balance Model"/>
+      <tab type="user" visible="yes" url="@ref LeafOpticsDoc" title="Leaf Optics Model"/>
       <tab type="user" visible="yes" url="@ref PhotosynthesisDoc" title="Photosynthesis Model"/>
       <tab type="user" visible="yes" url="@ref PlantArchitectureDoc" title="Plant Architecture"/>
       <tab type="user" visible="yes" url="@ref RadiationDoc" title="Radiation Model"/>