[1.3.38] 2025-07-05

- Added `.gitattributes` file and modified build options for Windows to deal with potential file encoding issues on Windows.
- Edit to `utilities/run_samples.sh` to hopefully fix issues with log file outputting within GitHub Actions workflows.
- Moved `AGENTD.md` back to the base directory because it was not being applied globally when in `doc`.

- Added a check to `Context::addPolymeshObject()` to ensure that the UUIDs don't already belong to another object.
- Refactored `Primitive::setPrimitiveData()`, `Primitive::getPrimitiveData()`, `Context::setPrimitiveData()`, and `Context::getPrimitiveData()` to use templates to avoid a lot of redundant code.
- Refactored `Context::setGlobalData()` and `Context::getGlobalData()` to use templates to avoid a lot of redundant code.
- Re-wrote how templates are handled for `helios::resize_vector()`, `helios::flatten()` and `helios::powi()` to be more robust and explicitly correct.
- Removed overloaded version of `Context::setPrimitiveData( uint UUID, const char* label, HeliosDataType type, uint size, void* data )`, as it is not needed. The vector-based version of `Context::setPrimitiveData()` should be used instead.
- Re-wrote libjpeg error handling to me more robust.

- Some updates to object geometry updating.

- Added check for very small petiole length or radius so that it can be set by the user to be exactly 0.
- Fixed asset copy commands in CMakeLists.txt that could cause an error on some Windows systems.

- Re-wrote libjpeg error handling to me more robust.
- Fixed texture and shader copy commands in CMakeLists.txt that could cause an error on some Windows systems.
- Fixed an error in `Visualizer::displayImage()` where the arguments to `read_JPEG_file()` and `read_png_file()` were swapped.
- Fixed issues with `Visualizer::clearColor()` where the visualizer was not properly reverting to RGB coloring.
- Fixed where the colorbar range was not being automatically updated when switching between different primitive/object data visualizations.
- Fixed an error where tiled textures were showing ghost lines at the seams between adjacent tiles.
- Fixed 'haloing' around texture-masked primitives.
- Implemented a (temporary) fix to make sure that colors are updated if the user successively calls `Visualizer::colorContextPrimitivesByData()`, `Visualizer::colorContextObjectsByData()`, or `Visualizer::clearColor()`. A more efficient long-term fix is still needed.

- `plantID` can now be set as primitive or object data.
- Added an example to the documentation of manually grouping leaves into a plant ID
- Added self-test to check `plantID` assignment.

- CMake now uses consistent c++ standard for CUDA code based on the standard used for regular c++ code. It also now explicitly sets the c++ standard for Windows CUDA code.

Co-authored by: Sean Banks <smbanx@users.noreply.github.com>
Co-authored by: Kyle Rizzo <ktrizzo@users.noreply.github.com>

Author: bnbailey-psl

.clang-format

@@ -29,6 +29,7 @@ BreakBeforeBraces: Custom
 BreakConstructorInitializers: AfterColon
 BreakConstructorInitializersBeforeComma: false
 ColumnLimit: 250
+PenaltyBreakString: 1000
 ConstructorInitializerAllOnOneLineOrOnePerLine: false
 ContinuationIndentWidth: 8
 IncludeCategories: 

.gitattributes

@@ -0,0 +1,11 @@
+# Text files: always LF line-endings, UTF-8 working tree
+*.cpp  text eol=lf working-tree-encoding=UTF-8
+*.h    text eol=lf working-tree-encoding=UTF-8
+*.cu   text eol=lf working-tree-encoding=UTF-8
+*.cuh  text eol=lf working-tree-encoding=UTF-8
+
+# Everything else – let Git decide or treat as binary
+* text=auto
+*.png binary
+*.jpg binary
+*.jpeg binary

.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
+          if ! ./run_samples.sh --nogpu --visbuildonly --log-file ../linux_selftests.log; then
             echo "==== run_samples.sh failed; dumping linux_selftests.log ===="
-            cat 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
+          if ! ./run_samples.sh --nogpu --visbuildonly --log-file ../macos_selftests.log; then
             echo "==== run_samples.sh failed; dumping macos_selftests.log ===="
-            cat macos_selftests.log
+            cat ../macos_selftests.log
             exit 1
-          fi
+          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
+          if ! ./run_samples.sh --nogpu --visbuildonly --log-file ../windows_selftests.log; then
             echo "==== run_samples.sh failed; dumping windows_selftests.log ===="
-            cat windows_selftests.log
+            cat ../windows_selftests.log
             exit 1
           fi

doc/AGENTS.md AGENTS.mddoc/AGENTS.md renamed to AGENTS.md

@@ -55,6 +55,7 @@ if ( WIN32 )
         set( CMAKE_ARCHIVE_OUTPUT_DIRECTORY_${OUTPUTCONFIG} "${CMAKE_BINARY_DIR}/lib" )
     endforeach(OUTPUTCONFIG)
 endif()
+add_compile_options($<$<CXX_COMPILER_ID:MSVC>:/utf-8>)
 cmake_policy(SET CMP0079 NEW)
 set(CMAKE_WARN_DEPRECATED OFF CACHE BOOL "" FORCE)
 

core/CMake_project.cmake

@@ -57,6 +57,7 @@ constexpr float PI_F = 3.14159265358979323846f;
 #include <thread>
 #include <iomanip>
 #include <filesystem>
+#include <type_traits>
 
 #ifdef USE_OPENMP
 #include <omp.h>
@@ -441,9 +442,19 @@ namespace helios {
      * \param[in] value Value to be clamped
      * \param[in] min Lower bound
      * \param[in] max Upper bound
-     * \ingroup functions */
+     * \ingroup functions
+     */
     template<typename anytype>
-    [[nodiscard]] anytype clamp(anytype value, anytype min, anytype max);
+    [[nodiscard]] anytype clamp(anytype value, anytype min, anytype max){
+        static_assert(std::is_same_v<anytype, int> || std::is_same_v<anytype, uint> || std::is_same_v<anytype, float> || std::is_same_v<anytype, double> || std::is_same_v<anytype, char> || std::is_same_v<anytype, unsigned char>,
+                          "helios::clamp() was called with an unsupported type.");
+        if (value < min) {
+            value = min;
+        } else if (value > max) {
+            value = max;
+        }
+        return value;
+    }
 
     //! Sum of a vector of floats
     /**
@@ -523,7 +534,10 @@ namespace helios {
      * \ingroup functions
     */
     template<typename anytype>
-    void resize_vector(std::vector<std::vector<anytype> > &vec, uint Nx, uint Ny);
+    typename std::enable_if<std::is_default_constructible<anytype>::value>::type
+    resize_vector(std::vector<std::vector<anytype>>& vec, size_t Nx, size_t Ny) {
+        vec.assign(Ny, std::vector<anytype>(Nx));
+    }
 
     //! Resize 3D C++ vector
     /**
@@ -534,7 +548,10 @@ namespace helios {
      * \ingroup functions
     */
     template<typename anytype>
-    void resize_vector(std::vector<std::vector<std::vector<anytype> > > &vec, uint Nx, uint Ny, uint Nz);
+    typename std::enable_if<std::is_default_constructible<anytype>::value>::type
+    resize_vector(std::vector<std::vector<std::vector<anytype> > > &vec, size_t Nx, size_t Ny, size_t Nz){
+        vec.assign(Nz, std::vector<std::vector<anytype>>(Ny, std::vector<anytype>(Nx)));
+    }
 
     //! Resize 4D C++ vector
     /**
@@ -546,7 +563,10 @@ namespace helios {
      * \ingroup functions
     */
     template<typename anytype>
-    void resize_vector(std::vector<std::vector<std::vector<std::vector<anytype> > > > &vec, uint Nx, uint Ny, uint Nz, uint Nw);
+    typename std::enable_if<std::is_default_constructible<anytype>::value>::type
+    resize_vector(std::vector<std::vector<std::vector<std::vector<anytype> > > > &vec, size_t Nx, size_t Ny, size_t Nz, size_t Nw){
+        vec.assign(Nw, std::vector<std::vector<std::vector<anytype>>>(Nz, std::vector<std::vector<anytype>>(Ny, std::vector<anytype>(Nx))));
+    }
 
     //! Blend two RGB colors together
     /**
@@ -657,7 +677,22 @@ namespace helios {
      * \param[in] exp Exponent to which the base is raised (must be a non-negative integer)
      */
     template<typename T>
-    T powi(T base, std::size_t exp);
+    T powi(T base, std::size_t exp){
+        static_assert(std::is_same_v<T, uint> || std::is_same_v<T, int> || std::is_same_v<T, float> || std::is_same_v<T, double> || std::is_same_v<T, char> || std::is_same_v<T, size_t>,
+                          "helios::powi() was called with an unsupported type.");
+        T result = static_cast<T>(1);
+        while (exp > 0) {
+            // If the low bit is set, multiply result by current base
+            if (exp & 1) {
+                result *= base;
+            }
+            // Square the base for the next bit
+            base *= base;
+            // Shift off the processed bit
+            exp >>= 1;
+        }
+        return result;
+    }
 
     //!Determine if two line segments intersect. The lines segments are defined by vertices (p1,q1) and (p2,q2)
     /**
@@ -805,24 +840,47 @@ namespace helios {
     * @tparam T Type of elements in the vector
     */
     template <typename T>
-    [[nodiscard]] std::vector<T> flatten(const std::vector<std::vector<T>>& vec);
+    [[nodiscard]] std::vector<T> flatten(const std::vector<std::vector<T>>& vec){
+        std::vector<T> result;
+        for (const auto &row: vec) {
+            result.insert(result.end(), row.begin(), row.end());
+        }
+        return result;
+    }
 
     //! Template function to flatten a 3D vector into a 1D vector
     /**
     * \ingroup functions
     * @tparam T Type of elements in the vector
     */
     template <typename T>
-    [[nodiscard]] std::vector<T> flatten(const std::vector<std::vector<std::vector<T>>>& vec);
+    [[nodiscard]] std::vector<T> flatten(const std::vector<std::vector<std::vector<T>>>& vec){
+        std::vector<T> result;
+        for (const auto &matrix: vec) {
+            for (const auto &row: matrix) {
+                result.insert(result.end(), row.begin(), row.end());
+            }
+        }
+        return result;
+    }
 
     //! Template function to flatten a 4D vector into a 1D vector
     /**
     * \ingroup functions
     * @tparam T Type of elements in the vector
     */
     template <typename T>
-    [[nodiscard]] std::vector<T> flatten(const std::vector<std::vector<std::vector<std::vector<T>>>>& vec);
-
+    [[nodiscard]] std::vector<T> flatten(const std::vector<std::vector<std::vector<std::vector<T>>>>& vec){
+        std::vector<T> result;
+        for (const auto &tensor: vec) {
+            for (const auto &matrix: tensor) {
+                for (const auto &row: matrix) {
+                    result.insert(result.end(), row.begin(), row.end());
+                }
+            }
+        }
+        return result;
+    }
 
     //! Function to perform cubic Hermite spline interpolation
     /**