[1.3.44] 2025-08-10

* Added `BUILD_TESTS` CMake option to conditionally build test executables instead of building them by default
* Test file renamed to `run_tests.sh`, and now runs tests without needing any of the sample projects (`samples/`)
* Deleted most of the `samples/[*]_selftest` directories, as they are no longer needed for testing. `context_selftest`, `energybalance_selftest`, and `radiation_selftest` were left because they are referenced in YouTube tutorials
* Added compiler warning suppression for third-party libraries (zlib, libpng, libjpeg) to reduce build noise
* Helios now builds with OpenMP parallelization enabled by default if available

## Context
- Added automatic filtering of zero-area primitives in addSphere(), addTube(), addDisk(), addCone(), and other geometric construction methods
- Improved tube generation robustness by handling degenerate cross products when axis vectors are parallel or near-vertical
- Added minimum size validation (1e-6) for patch primitives to prevent numerical precision issues
- Added debug warnings for malformed triangles with near-zero area
- Deprecated `Context::getPrimitiveDataType(uint, const char*)` and `Context::getObjectDataType(uint, const char*)` in favor of `Context::getPrimitiveDataType(const char*)` and `Context::getObjectDataType(const char*)`
- Added new `fzero()` function overload that returns convergence status
- Implemented linspace utility functions in `global.h`/`global.cpp` for float, vec2, vec3, and vec4 types

## Plant Architecture
- Fixed leaf prototype scale validation to ensure minimum positive values
- Updated petiole handling to preserve intended leaf generation

## Radiation
- Enhanced camera image processing pipeline with spectral correction and improved white balance workflow
- Added Gray Edge white balance algorithm implementation for color constancy
- Fixed gamma compression application in image processing pipeline
- Improved gain adjustment and histogram equalization for better image quality
- Substantially refactored `RadiationModel::updateGeometry()` and `RadiationModel::updateRadiativeProperties()` methods for improved efficiency:
  - Replaced O(n) std::find operations with O(1) unordered_set lookups in geometry updates
  - Added spectral integration caching to avoid redundant computations
  - Implemented OpenMP parallelization for radiative property calculations
  - Optimized map access patterns and reduced memory allocations

## Photosynthesis
- Improved temporal continuity in Farquhar model by initializing Ci with previous timestep values
- Enhanced convergence behavior with better initial guesses for intercellular CO2 concentration

## Stomatal Conductance
- Enhanced Ball-Woodrow-Berry model convergence with improved initial surface vapor pressure estimates
- Increased numerical solver tolerance and iteration limits for better stability in vapor pressure calculations

## Project Builder
- Removed `linspace` function from `ProjectBuilder.cpp` since it is now available in the Helios core
- `CMakeLists.txt` was missing the conditional include guards for the canopy generator plug-in, which would cause a linker error if the plug-in was not built

Author: bnbailey-psl

.github/workflows/linux_GPU_selftests.yaml

@@ -36,8 +36,8 @@ jobs:
       - name: Bash script
         run: |
           cd utilities
-          if ! ./run_samples.sh --visbuildonly --log-file linux_GPU_selftests.log; then
-            echo "==== run_samples.sh failed; dumping linux_GPU_selftests.log ===="
+          if ! ./run_tests.sh --visbuildonly --log-file linux_GPU_selftests.log; then
+            echo "==== run_tests.sh failed; dumping linux_GPU_selftests.log ===="
             cat linux_GPU_selftests.log
             exit 1
           fi

.github/workflows/linux_selftests.yaml

@@ -42,8 +42,8 @@ jobs:
       - name: Bash script
         run: |
           cd utilities
-          if ! ./run_samples.sh --nogpu --visbuildonly --log-file ../linux_selftests.log; then
-            echo "==== run_samples.sh failed; dumping linux_selftests.log ===="
+          if ! ./run_tests.sh --nogpu --visbuildonly --log-file ../linux_selftests.log; then
+            echo "==== run_tests.sh failed; dumping linux_selftests.log ===="
             cat ../linux_selftests.log
             exit 1
           fi

.github/workflows/mac_selftests.yaml

@@ -28,8 +28,8 @@ jobs:
       - name: Bash script
         run: |
           cd utilities
-          if ! ./run_samples.sh --nogpu --visbuildonly --log-file ../macos_selftests.log; then
-            echo "==== run_samples.sh failed; dumping macos_selftests.log ===="
+          if ! ./run_tests.sh --nogpu --visbuildonly --log-file ../macos_selftests.log; then
+            echo "==== run_tests.sh failed; dumping macos_selftests.log ===="
             cat ../macos_selftests.log
             exit 1
           fi

.github/workflows/windows_selftests.yaml

@@ -26,8 +26,8 @@ jobs:
         shell: bash
         run: |
           cd utilities
-          if ! ./run_samples.sh --nogpu --visbuildonly --log-file ../windows_selftests.log; then
-            echo "==== run_samples.sh failed; dumping windows_selftests.log ===="
+          if ! ./run_tests.sh --nogpu --visbuildonly --log-file ../windows_selftests.log; then
+            echo "==== run_tests.sh failed; dumping windows_selftests.log ===="
             cat ../windows_selftests.log
             exit 1
           fi

core/CMakeLists.txt

@@ -47,12 +47,25 @@ add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/lib/libjpeg-9a" "${CMAKE_BINARY_DI
 
 target_link_libraries( helios PRIVATE png_static  jpeg ) #note that zlib is already linked by libpng
 
+# Suppress warnings for third-party libraries
+if(TARGET zlibstatic)
+    target_compile_options(zlibstatic PRIVATE $<$<C_COMPILER_ID:Clang,AppleClang,GNU>:-w>)
+endif()
+if(TARGET png_static)
+    target_compile_options(png_static PRIVATE $<$<C_COMPILER_ID:Clang,AppleClang,GNU>:-w>)
+endif()
+if(TARGET jpeg)
+    target_compile_options(jpeg PRIVATE $<$<C_COMPILER_ID:Clang,AppleClang,GNU>:-w>)
+endif()
+
 set(CMAKE_MESSAGE_LOG_LEVEL ${SAVED_LOG_LEVEL})
 
 file( COPY "${CMAKE_CURRENT_SOURCE_DIR}/lib/images" DESTINATION "${CMAKE_BINARY_DIR}/lib/" )
 file( COPY "${CMAKE_CURRENT_SOURCE_DIR}/lib/models" DESTINATION "${CMAKE_BINARY_DIR}/lib/" )
 file( COPY "${CMAKE_CURRENT_SOURCE_DIR}/lib/testdata" DESTINATION "${CMAKE_BINARY_DIR}/lib/" )
 
-add_executable( context_tests tests/TestMain.cpp )
-target_link_libraries( context_tests PRIVATE helios )
-add_test( NAME context_tests COMMAND context_tests )
+if(BUILD_TESTS)
+    add_executable( context_tests tests/TestMain.cpp )
+    target_link_libraries( context_tests PRIVATE helios )
+    add_test( NAME context_tests COMMAND context_tests )
+endif()

core/CMake_project.cmake

@@ -1,4 +1,5 @@
-option(ENABLE_OPENMP "Enable building with OpenMP" OFF)
+option(ENABLE_OPENMP "Enable building with OpenMP" ON)
+option(BUILD_TESTS "Build test executables" OFF)
 
 # Set CMake policies to avoid warnings on newer CMake versions
 if(POLICY CMP0074)

core/include/Context.h

@@ -3166,7 +3166,7 @@ namespace helios {
          * \return Helios data type of primitive data
          * \sa HeliosDataType
          */
-        HeliosDataType getPrimitiveDataType(uint UUID, const char *label) const;
+        DEPRECATED( HeliosDataType getPrimitiveDataType(uint UUID, const char *label) const );
 
         //! Get the expected data type for a primitive data label (cached lookup)
         /**
@@ -4115,7 +4115,7 @@ namespace helios {
          * \return Helios data type of primitive data
          * \sa HeliosDataType
          */
-        HeliosDataType getObjectDataType(uint objID, const char *label) const;
+        DEPRECATED( HeliosDataType getObjectDataType(uint objID, const char *label) const );
 
         //! Get the expected data type for an object data label (cached lookup)
         /**

core/include/global.h

@@ -16,16 +16,37 @@
 #ifndef HELIOS_GLOBAL
 #define HELIOS_GLOBAL
 
-//! Macro for marking functions as deprecated.
-#ifdef __GNUC__
-#define DEPRECATED(func) func __attribute__((deprecated))
+//! Macro for marking functions as deprecated with optional custom message.
+// MSVC requires __declspec to come BEFORE the function declaration
+#if __cplusplus >= 201402L && defined(__has_cpp_attribute) && __has_cpp_attribute(deprecated)
+    #define DEPRECATED_MSG(msg, func) [[deprecated(msg)]] func
+    #define DEPRECATED_NOMSG(func) [[deprecated]] func
+#elif defined(__GNUC__) || defined(__clang__)
+    #define DEPRECATED_MSG(msg, func) func __attribute__((deprecated(msg)))
+    #define DEPRECATED_NOMSG(func) func __attribute__((deprecated))
 #elif defined(_MSC_VER)
-#define DEPRECATED(func) __declspec(deprecated) func
+    // MSVC has issues with custom deprecation messages, use simple deprecation
+    #define DEPRECATED_MSG(msg, func) __declspec(deprecated) func
+    #define DEPRECATED_NOMSG(func) __declspec(deprecated) func
 #else
-#pragma message("WARNING: You need to implement DEPRECATED for this compiler")
-#define DEPRECATED(func) func
+    #pragma message("WARNING: You need to implement DEPRECATED for this compiler")
+    #define DEPRECATED_MSG(msg, func) func
+    #define DEPRECATED_NOMSG(func) func
 #endif
 
+// Helper macro to count arguments
+#define GET_ARG_COUNT(...) GET_ARG_COUNT_IMPL(__VA_ARGS__, 2, 1)
+#define GET_ARG_COUNT_IMPL(_1, _2, N, ...) N
+
+// Main DEPRECATED macro that dispatches based on argument count with corrected parameter order
+#define DEPRECATED(...) GET_DEPRECATED_MACRO(__VA_ARGS__)(__VA_ARGS__)
+#define GET_DEPRECATED_MACRO(...) GET_DEPRECATED_MACRO_IMPL(GET_ARG_COUNT(__VA_ARGS__))
+#define GET_DEPRECATED_MACRO_IMPL(count) GET_DEPRECATED_MACRO_IMPL2(count)
+#define GET_DEPRECATED_MACRO_IMPL2(count) DEPRECATED_##count##_ARGS
+
+#define DEPRECATED_1_ARGS(func) DEPRECATED_NOMSG(func)
+#define DEPRECATED_2_ARGS(func, msg) DEPRECATED_MSG(msg, func)
+
 //! Pi constant.
 #ifndef M_PI
 #define M_PI 3.14159265358979323846
@@ -980,6 +1001,19 @@ namespace helios {
      */
     [[nodiscard]] float fzero(float (*function)(float value, std::vector<float> &variables, const void *parameters), std::vector<float> &variables, const void *parameters, float init_guess, float err_tol = 0.0001f, int max_iterations = 100);
 
+    //! Use Newton-Raphson method to find the zero of a function with convergence status
+    /**
+     * \param[in] function Function to be evaluated. The function should take as its first argument the value at which the function should be evaluated, as second argument any function arguments.
+     * \param[in] variables Vector of function arguments
+     * \param[in] parameters Pointer to any additional parameters needed by the function
+     * \param[in] init_guess Initial guess for the zero of the function.
+     * \param[out] converged Boolean indicating whether the solver converged successfully.
+     * \param[in] err_tol [optional] Maximum allowable relative error in solution.
+     * \param[in] max_iterations [optional] Maximum number of iterations to allow before exiting solver.
+     * \return Value of function zero (best estimate even if not converged).
+     */
+    [[nodiscard]] float fzero(float (*function)(float value, std::vector<float> &variables, const void *parameters), std::vector<float> &variables, const void *parameters, float init_guess, bool &converged, float err_tol = 0.0001f, int max_iterations = 100);
+
     //! Function to perform linear interpolation based on a vector of discrete (x,y) values
     /**
      * \param[in] points Vector of (x,y) pairs. x values must be monotonically increasing and not duplicated.
@@ -996,6 +1030,46 @@ namespace helios {
      */
     [[nodiscard]] float point_distance(const helios::vec3 &p1, const helios::vec3 &p2);
 
+    //! Generate linearly spaced values between two endpoints
+    /**
+     * \param[in] start Starting value
+     * \param[in] end Ending value
+     * \param[in] num Number of uniformly spaced points to generate
+     * \return Vector of linearly spaced float values
+     * \ingroup functions
+     */
+    [[nodiscard]] std::vector<float> linspace(float start, float end, int num);
+
+    //! Generate linearly spaced vec2 values between two endpoints
+    /**
+     * \param[in] start Starting vec2 value
+     * \param[in] end Ending vec2 value
+     * \param[in] num Number of uniformly spaced points to generate
+     * \return Vector of linearly spaced vec2 values
+     * \ingroup functions
+     */
+    [[nodiscard]] std::vector<vec2> linspace(const vec2 &start, const vec2 &end, int num);
+
+    //! Generate linearly spaced vec3 values between two endpoints
+    /**
+     * \param[in] start Starting vec3 value
+     * \param[in] end Ending vec3 value
+     * \param[in] num Number of uniformly spaced points to generate
+     * \return Vector of linearly spaced vec3 values
+     * \ingroup functions
+     */
+    [[nodiscard]] std::vector<vec3> linspace(const vec3 &start, const vec3 &end, int num);
+
+    //! Generate linearly spaced vec4 values between two endpoints
+    /**
+     * \param[in] start Starting vec4 value
+     * \param[in] end Ending vec4 value
+     * \param[in] num Number of uniformly spaced points to generate
+     * \return Vector of linearly spaced vec4 values
+     * \ingroup functions
+     */
+    [[nodiscard]] std::vector<vec4> linspace(const vec4 &start, const vec4 &end, int num);
+
     //! Parse a file string to get the extension
     /**
      * Example: /path/to/file/filename.ext -> extension=".ext"