Feature/removing demographics (#107)

* I might've officially lost my mind

* updating the data types and cost effectiveness

* Working on some basic data structure stuff

* cleaning up respond to just have the model and the cost effectiveness

* I am confused about tests

* cost effectriveness testing

* adding tests for respond functions

* removing executable

* removing and updating the building tools

* addressing PR comments

* adding the clang-formatting workflow

* removing the branch name from the push on the formatting workflow

* removing release workflow

* quick update for the overdose thing to remove a needless vector and adding a size check

Author: MJC598

.github/workflows/clang-formatting.yml

@@ -0,0 +1,28 @@
+name: Clang Formatting
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+env:
+  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
+  BUILD_TYPE: Debug
+
+jobs:
+  cpp-linter:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: cpp-linter/cpp-linter-action@v2
+        id: linter
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          style: 'file'  # Use .clang-format config file. 
+          tidy-checks: '-*' # disable clang-tidy checks. 
+
+      - name: Fail fast?!
+        if: steps.linter.outputs.clang-format-checks-failed > 0
+        run: exit 1

.github/workflows/release.yml

@@ -58,13 +58,8 @@ endif()
 # Building the Library
 # ---------------------------------------------------------------------------------------
 set(RESPOND_SRCS 
-    src/data_ops/cost_loader.cpp
-    src/data_ops/data_formatter.cpp
-    src/data_ops/data_loader.cpp
-    src/data_ops/utility_loader.cpp
-    src/data_ops/writer.cpp
-    src/model/simulation.cpp
-    src/utils/logging.cpp
+    src/markov.cpp
+    src/logging.cpp
 )
 
 if(RESPOND_BUILD_SHARED_LIBS)
@@ -94,15 +89,14 @@ endif()
 
 target_compile_definitions(respond PUBLIC RESPOND_COMPILED_LIB)
 target_include_directories(respond ${RESPOND_INCLUDES_LEVEL} PUBLIC "$<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}/include>"
-                                                                  "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
-                                                                  PRIVATE "$<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}/src>")
+"$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>" PRIVATE 
+"$<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}/src>")
 
 include(MakeDependenciesAvailable)
 
 if (RESPOND_CALCULATE_COVERAGE)
     target_link_libraries(respond
     PUBLIC
-        datamanagement::datamanagement
         Eigen3::Eigen
     PRIVATE
         spdlog::spdlog
@@ -111,7 +105,6 @@ if (RESPOND_CALCULATE_COVERAGE)
 else()
     target_link_libraries(respond
     PUBLIC
-        datamanagement::datamanagement
         Eigen3::Eigen
     PRIVATE
         spdlog::spdlog

CMakeLists.txt

@@ -44,7 +44,6 @@
             "inherits": "configuration-common-linux",
             "cacheVariables": {
                 "CMAKE_BUILD_TYPE": "Debug",
-                "RESPOND_BUILD_EXECUTABLE": "ON",
                 "RESPOND_BUILD_TESTS": "ON",
                 "RESPOND_CALCULATE_COVERAGE": "ON",
                 "RESPOND_BUILD_BENCH": "OFF",
@@ -62,7 +61,6 @@
             "inherits": "configuration-common-linux",
             "cacheVariables": {
                 "CMAKE_BUILD_TYPE": "Release",
-                "RESPOND_BUILD_EXECUTABLE": "ON",
                 "RESPOND_BUILD_TESTS": "OFF",
                 "RESPOND_CALCULATE_COVERAGE": "OFF",
                 "RESPOND_BUILD_BENCH": "OFF",
@@ -79,17 +77,11 @@
         },
         {
             "name": "gcc-release-cluster",
-            "inherits": "gcc-release",
-            "cacheVariables": {
-                "CMAKE_PREFIX_PATH": "${fileDir}/lib/sqlitecpp"
-            }
+            "inherits": "gcc-release"
         },
         {
             "name": "gcc-debug-cluster",
-            "inherits": "gcc-debug",
-            "cacheVariables": {
-                "CMAKE_PREFIX_PATH": "${fileDir}/lib/sqlitecpp"
-            }
+            "inherits": "gcc-debug"
         }
     ],
     "buildPresets": [

CMakePresets.json

@@ -1,8 +1,3 @@
-if(RESPOND_BUILD_EXECUTABLE OR RESPOND_BUILD_ALL)
-    message(STATUS "Building Executable")
-    add_subdirectory(extras/executable)
-endif()
-
 if(RESPOND_BUILD_TESTS OR RESPOND_BUILD_ALL)
     message(STATUS "Generating tests")
     if(RESPOND_CALCULATE_COVERAGE)

cmake/BuildBinaries.cmake

@@ -2,12 +2,11 @@ include(FetchContent)
 
 include(LoadEigen)
 include(LoadSpdlog)
-include(LoadDataManagement)
 
 if(RESPOND_BUILD_TESTS STREQUAL "ON")
     include(LoadGtest)
-    FetchContent_MakeAvailable(Eigen3 spdlog datamanagement googletest)
+    FetchContent_MakeAvailable(Eigen3 spdlog googletest)
     include(GoogleTest)
 elseif(RESPOND_BUILD_TESTS STREQUAL "OFF")
-    FetchContent_MakeAvailable(Eigen3 spdlog datamanagement)
+    FetchContent_MakeAvailable(Eigen3 spdlog)
 endif()

cmake/LoadDataManagement.cmake

@@ -3,8 +3,6 @@ option(RESPOND_BUILD_ALL "Build all artifacts" OFF)
 # build position independent code
 option(RESPOND_BUILD_PIC "Build position independent code (-fPIC)" OFF)
 
-option(RESPOND_BUILD_EXECUTABLE "Build Executable for RESPOND" ON)
-
 # testing options
 option(RESPOND_BUILD_TESTS "Build tests" ON)
 

cmake/MakeDependenciesAvailable.cmake

@@ -8,5 +8,5 @@ Description: Syndemics Modeling Library
 URL: https://github.com/SyndemicsLab
 Version: @RESPOND_VERSION@
 CFlags: -I${includedir} @PKG_CONFIG_DEFINES@
-Libs: -L${libdir} -lspdlog -leigen -ldatamanagement
+Libs: -L${libdir} -lspdlog -leigen
 Requires: @PKG_CONFIG_REQUIRES@

cmake/options.cmake

@@ -3,7 +3,6 @@
 include(CMakeFindDependencyMacro)
 find_dependency(Eigen3)
 find_dependency(spdlog)
-find_dependency(datamanagement)
 
 include("${CMAKE_CURRENT_LIST_DIR}/respondConfigTargets.cmake")