Devel3

.github/workflows/ci.yaml

@@ -0,0 +1,24 @@
+name: C++ CI
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build-and-test:
+    name: C++ - ${{ github.event_name }}
+    runs-on: ubuntu-latest
+    permissions: 
+      actions: write
+      contents: read
+    steps:
+      # 1. Check out your code
+      - uses: actions/checkout@v4
+      # # 2. Install dependencies (if using vcpkg, Conan, etc.)
+      # - name: Install dependencies
+      #   run: sudo apt update && sudo apt install -y cmake g++ make
+      - run: cmake -S . -B build -DCMAKE_BUILD_TYPE=Release
+      - run: cmake --build build --parallel
+      - run: ctest --test-dir build --output-on-failure --verbose --no-compress-output

CMakeLists.txt

@@ -1,72 +1,91 @@
-cmake_minimum_required(VERSION 3.10)
+cmake_minimum_required(VERSION 3.16)
 project(YAMLWrapper)
 
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
-if(APPLE)
-    # Check for package managers
-    execute_process(COMMAND which brew OUTPUT_VARIABLE HOMEBREW_EXISTS OUTPUT_STRIP_TRAILING_WHITESPACE)
-    execute_process(COMMAND which port OUTPUT_VARIABLE MACPORTS_EXISTS OUTPUT_STRIP_TRAILING_WHITESPACE)
-    execute_process(COMMAND which conda OUTPUT_VARIABLE CONDA_EXISTS OUTPUT_STRIP_TRAILING_WHITESPACE)
+enable_testing()
+include(FetchContent)
+
+FetchContent_Declare(
+  yaml-cpp
+  GIT_REPOSITORY https://github.com/jbeder/yaml-cpp.git
+  GIT_TAG 0.8.0
+)
+FetchContent_Declare(
+  Catch2
+  GIT_REPOSITORY https://github.com/catchorg/Catch2.git
+  GIT_TAG v3.5.2
+)
+
+FetchContent_MakeAvailable(yaml-cpp)
+FetchContent_MakeAvailable(Catch2)
+add_subdirectory(tests)
+
+file(COPY ${CMAKE_SOURCE_DIR}/lattice_files/
+     DESTINATION ${CMAKE_BINARY_DIR}/lattice_files/)
+
+# if(APPLE)
+#     # Check for package managers
+#     execute_process(COMMAND which brew OUTPUT_VARIABLE HOMEBREW_EXISTS OUTPUT_STRIP_TRAILING_WHITESPACE)
+#     execute_process(COMMAND which port OUTPUT_VARIABLE MACPORTS_EXISTS OUTPUT_STRIP_TRAILING_WHITESPACE)
+#     execute_process(COMMAND which conda OUTPUT_VARIABLE CONDA_EXISTS OUTPUT_STRIP_TRAILING_WHITESPACE)
 
-    # Error if both Homebrew and MacPorts exist
-    if(HOMEBREW_EXISTS AND MACPORTS_EXISTS)
-        message(FATAL_ERROR 
-            "Both Homebrew and MacPorts detected. This can cause conflicts.\n"
-            "Please use only one package manager:\n"
-            "  - Homebrew found at: ${HOMEBREW_EXISTS}\n"
-            "  - MacPorts found at: ${MACPORTS_EXISTS}\n"
-            "Consider uninstalling one to avoid library conflicts."
-        )
-    endif()
+#     # Error if both Homebrew and MacPorts exist
+#     if(HOMEBREW_EXISTS AND MACPORTS_EXISTS)
+#         message(FATAL_ERROR 
+#             "Both Homebrew and MacPorts detected. This can cause conflicts.\n"
+#             "Please use only one package manager:\n"
+#             "  - Homebrew found at: ${HOMEBREW_EXISTS}\n"
+#             "  - MacPorts found at: ${MACPORTS_EXISTS}\n"
+#             "Consider uninstalling one to avoid library conflicts."
+#         )
+#     endif()
 
-    # Set RPATH based on which package manager is found
-    set(BASE_RPATH "@executable_path/../lib;@loader_path")
+#     # Set RPATH based on which package manager is found
+#     set(BASE_RPATH "@executable_path/../lib;@loader_path")
 
-    if(HOMEBREW_EXISTS)
-        message(STATUS "Using Homebrew package manager")
-        # Check if Apple Silicon or Intel
-        execute_process(
-            COMMAND uname -m
-            OUTPUT_VARIABLE ARCH
-            OUTPUT_STRIP_TRAILING_WHITESPACE
-        )
-        if(ARCH STREQUAL "arm64")
-            set(CMAKE_INSTALL_RPATH "${BASE_RPATH};/opt/homebrew/lib")
-            list(APPEND CMAKE_PREFIX_PATH "/opt/homebrew")
-        else()
-            set(CMAKE_INSTALL_RPATH "${BASE_RPATH};/usr/local/lib")
-            list(APPEND CMAKE_PREFIX_PATH "/usr/local")
-        endif()
-    elseif(MACPORTS_EXISTS)
-        message(STATUS "Using MacPorts package manager")
-        set(CMAKE_INSTALL_RPATH "${BASE_RPATH};/opt/local/lib")
-        list(APPEND CMAKE_PREFIX_PATH "/opt/local")
-    elseif(CONDA_EXISTS)
-        message(STATUS "Using Conda package manager")
-        # Get conda prefix
-        execute_process(
-            COMMAND conda info --base
-            OUTPUT_VARIABLE CONDA_PREFIX
-            OUTPUT_STRIP_TRAILING_WHITESPACE
-        )
-        set(CMAKE_INSTALL_RPATH "${BASE_RPATH};${CONDA_PREFIX}/lib")
-        list(APPEND CMAKE_PREFIX_PATH "${CONDA_PREFIX}")
-    else()
-        message(STATUS "No package manager detected, using default paths")
-        set(CMAKE_INSTALL_RPATH "${BASE_RPATH};/usr/local/lib")
-    endif()
+#     if(HOMEBREW_EXISTS)
+#         message(STATUS "Using Homebrew package manager")
+#         # Check if Apple Silicon or Intel
+#         execute_process(
+#             COMMAND uname -m
+#             OUTPUT_VARIABLE ARCH
+#             OUTPUT_STRIP_TRAILING_WHITESPACE
+#         )
+#         if(ARCH STREQUAL "arm64")
+#             set(CMAKE_INSTALL_RPATH "${BASE_RPATH};/opt/homebrew/lib")
+#             list(APPEND CMAKE_PREFIX_PATH "/opt/homebrew")
+#         else()
+#             set(CMAKE_INSTALL_RPATH "${BASE_RPATH};/usr/local/lib")
+#             list(APPEND CMAKE_PREFIX_PATH "/usr/local")
+#         endif()
+#     elseif(MACPORTS_EXISTS)
+#         message(STATUS "Using MacPorts package manager")
+#         set(CMAKE_INSTALL_RPATH "${BASE_RPATH};/opt/local/lib")
+#         list(APPEND CMAKE_PREFIX_PATH "/opt/local")
+#     elseif(CONDA_EXISTS)
+#         message(STATUS "Using Conda package manager")
+#         # Get conda prefix
+#         execute_process(
+#             COMMAND conda info --base
+#             OUTPUT_VARIABLE CONDA_PREFIX
+#             OUTPUT_STRIP_TRAILING_WHITESPACE
+#         )
+#         set(CMAKE_INSTALL_RPATH "${BASE_RPATH};${CONDA_PREFIX}/lib")
+#         list(APPEND CMAKE_PREFIX_PATH "${CONDA_PREFIX}")
+#     else()
+#         message(STATUS "No package manager detected, using default paths")
+#         set(CMAKE_INSTALL_RPATH "${BASE_RPATH};/usr/local/lib")
+#     endif()
 
-    set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
-    message(STATUS "RPATH set to: ${CMAKE_INSTALL_RPATH}")
-endif()
-
-find_package(yaml-cpp REQUIRED)
+#     set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
+#     message(STATUS "RPATH set to: ${CMAKE_INSTALL_RPATH}")
+# endif()
 
 add_library(yaml_c_wrapper SHARED src/yaml_c_wrapper.cpp)
 target_link_libraries(yaml_c_wrapper yaml-cpp)
 
-add_executable(yaml_reader src/yaml_reader.cpp)
-target_link_libraries(yaml_reader yaml_c_wrapper)
+add_executable(yaml_reader examples/yaml_reader.cpp)
+target_link_libraries(yaml_reader yaml_c_wrapper)

README.md

@@ -1,6 +1,6 @@
 ## Introduction
 yaml_c_wrapper.cpp wraps YAML::Node into C objects so they can be part of a shared object library to interface with other languages
-
+<!-- 
 First install yaml-cpp by running 
 
 macOS:  
@@ -20,16 +20,31 @@ cd yaml-cpp/src
 mkdir build && cd build  
 cmake ..  
 cmake --build .  
-cmake --install .  
+cmake --install .   -->
 
-Next, in pals-cpp, run  
+## Usage
+In pals-cpp, run  
 
-mkdir build && cd build  
-cmake .. -DYAML_BUILD_SHARED_LIBS=ON  
-make
-
-## Example
-See yaml_reader.cpp for an example of how to use the library to read a lattice file, 
-perform a basic manipulation, and write to another lattice file. 
-Navigate to the build directly and run  
-./yaml_reader
+cmake -DCMAKE_POLICY_VERSION_MINIMUM=3.5 -S . -B build 
+cmake --build build
+
+This builds libyaml_c_wrapper.dylib, a shared object library that can be used
+by other languages. 
+
+It also builds an executable using yaml_reader.cpp containing examples for how 
+to use the library to read lattice files, perform basic manipulations, and write
+to other lattice files. To see the output, navigate to the build directory and run  
+./yaml_reader
+
+It will also build the tests.
+
+## Testing
+In the root pals-cpp directory, run  
+ctest --test-dir build --output-on-failure  
+
+To run a specific test, run 
+ctest --test-dir build -R "Test Name"
+
+## Issue
+yaml-cpp's cmake only requires cmake version 3.4, which is deprecated. Warnings must
+be suppressed to run properly

examples/yaml_reader.cpp

@@ -0,0 +1,38 @@
+#include "../src/yaml_c_wrapper.h"
+#include <iostream>
+
+int main() {
+    // reading a lattice from a yaml file
+    YAMLNodeHandle handle = yaml_parse_file("../lattice_files/ex.yaml");
+    // printing to terminal
+    std::cout << yaml_to_string(handle) << std::endl << std::endl;
+
+    // type checking
+    std::cout << (yaml_is_sequence(handle)) << "\n";
+
+    // accessing sequence
+    YAMLNodeHandle node = yaml_get_index(handle, 0);
+    std::cout << "the first element is: \n" << yaml_to_string(node) << "\n";
+
+    // accessing map
+    std::cout << "\nthe value at key 'thingB' is: " << yaml_to_string(yaml_get_key(node, "thingB")) << "\n";
+
+    // creating a new node that's a map 
+    YAMLNodeHandle map = yaml_create_map();
+    yaml_set_int(map, "first", 1);
+
+    // creating a new node that's a sequence
+    YAMLNodeHandle sequence = yaml_create_sequence();
+    yaml_push_string(sequence, "magnet1");
+    yaml_push_string(sequence, "");
+    YAMLNodeHandle scalar = yaml_create_scalar();
+    yaml_set_scalar_string(scalar, "magnet2");
+    yaml_set_at_index(sequence, 1, scalar);
+
+    // adding new nodes to lattice
+    yaml_push_node(handle, map);
+    yaml_push_node(handle, sequence);
+
+    // writing modified lattice file to expand.yaml
+    yaml_write_file(handle, "../lattice_files/expand.yaml");
+}

lattice_files/ex.yaml

@@ -14,5 +14,4 @@
           length: 1.03
           direction: -1
       - a_subline:            # Item a_subline is repeated three times
-          repeat: 3
-          hi: 2
+          repeat: 3

src/yaml_c_wrapper.cpp

@@ -125,9 +125,6 @@ extern "C" {
         return static_cast<YAML::Node*>(handle)->size();
     }
 
-    // === ITERATION HELPERS ===
-
-    // For iterating over maps - get all keys
     char** yaml_get_keys(YAMLNodeHandle handle, int* out_count) {
         auto node = static_cast<YAML::Node*>(handle);
         if (!node->IsMap()) {
@@ -149,20 +146,6 @@ extern "C" {
         return result;
     }
 
-    void yaml_free_keys(char** keys, int count) {
-        for (int i = 0; i < count; i++) {
-            delete[] keys[i];
-        }
-        delete[] keys;
-    }
-
-    // Set node at index for sequences
-    void yaml_set_at_index(YAMLNodeHandle handle, int index, YAMLNodeHandle value) {
-        auto node = static_cast<YAML::Node*>(handle);
-        auto val_node = static_cast<YAML::Node*>(value);
-        (*node)[index] = *val_node;
-    }
-
     // === CONVERT TO C TYPES (caller must free returned strings) ===
     char* yaml_as_string(YAMLNodeHandle handle) {
         try {
@@ -225,6 +208,37 @@ extern "C" {
         auto val_node = static_cast<YAML::Node*>(value);
         (*node)[key] = *val_node;
     }
+
+    void yaml_set_scalar_string(YAMLNodeHandle handle, const char* value) {
+        if (handle == nullptr || value == nullptr) return;
+        auto node = static_cast<YAML::Node*>(handle);
+        *node = value;
+    }
+
+    void yaml_set_scalar_int(YAMLNodeHandle handle, int value) {
+        if (handle == nullptr) return;
+        auto node = static_cast<YAML::Node*>(handle);
+        *node = value;
+    }
+
+    void yaml_set_scalar_float(YAMLNodeHandle handle, double value) {
+        if (handle == nullptr) return;
+        auto node = static_cast<YAML::Node*>(handle);
+        *node = value;
+    }
+
+    void yaml_set_scalar_bool(YAMLNodeHandle handle, bool value) {
+        if (handle == nullptr) return;
+        auto node = static_cast<YAML::Node*>(handle);
+        *node = value;
+    }
+
+    // Set node at index for sequences
+    void yaml_set_at_index(YAMLNodeHandle handle, int index, YAMLNodeHandle value) {
+        auto node = static_cast<YAML::Node*>(handle);
+        auto val_node = static_cast<YAML::Node*>(value);
+        (*node)[index] = *val_node;
+    }
 
     void yaml_push_string(YAMLNodeHandle handle, const char* value) {
         auto node = static_cast<YAML::Node*>(handle);
@@ -395,6 +409,14 @@ extern "C" {
     void yaml_free_string(char* str) {
         delete[] str;
     }
+
+    void yaml_free_keys(char** keys, int count) {
+        for (int i = 0; i < count; i++) {
+            delete[] keys[i];
+        }
+        delete[] keys;
+    }
+
 
     YAMLNodeHandle yaml_clone(YAMLNodeHandle handle) {
         return new YAML::Node(YAML::Clone(*static_cast<YAML::Node*>(handle)));

src/yaml_c_wrapper.h

@@ -13,6 +13,7 @@ typedef void* YAMLNodeHandle;
 YAMLNodeHandle yaml_create_node(void);
 YAMLNodeHandle yaml_create_map(void);
 YAMLNodeHandle yaml_create_sequence(void);
+YAMLNodeHandle yaml_create_scalar();
 void yaml_delete_node(YAMLNodeHandle handle);
 
 // === PARSING ===
@@ -24,7 +25,6 @@ bool yaml_is_scalar(YAMLNodeHandle handle);
 bool yaml_is_sequence(YAMLNodeHandle handle);
 bool yaml_is_map(YAMLNodeHandle handle);
 bool yaml_is_null(YAMLNodeHandle handle);
-bool yaml_is_defined(YAMLNodeHandle handle);
 
 // === ACCESS ===
 YAMLNodeHandle yaml_get_key(YAMLNodeHandle handle, const char* key);
@@ -46,6 +46,12 @@ void yaml_set_float(YAMLNodeHandle handle, const char* key, double value);
 void yaml_set_bool(YAMLNodeHandle handle, const char* key, bool value);
 void yaml_set_node(YAMLNodeHandle handle, const char* key, YAMLNodeHandle value);
 
+void yaml_set_scalar_string(YAMLNodeHandle handle, const char* value);
+void yaml_set_scalar_int(YAMLNodeHandle handle, int value);
+void yaml_set_scalar_float(YAMLNodeHandle handle, double value);
+void yaml_set_scalar_bool(YAMLNodeHandle handle, bool value);
+
+void yaml_set_at_index(YAMLNodeHandle handle, int index, YAMLNodeHandle value) ;
 void yaml_push_string(YAMLNodeHandle handle, const char* value);
 void yaml_push_int(YAMLNodeHandle handle, int value);
 void yaml_push_float(YAMLNodeHandle handle, double value);