Include json via CMake

.github/workflows/build_and_test_mac.yaml

@@ -31,7 +31,7 @@ jobs:
           brew install gnu-time gcc@15
           brew install open-mpi --build-from-source --cc=gcc-15
           brew install hdf5-mpi --build-from-source --cc=gcc-15
-          brew install fftw eigen
+          brew install fftw eigen nlohmann-json
 
       - name: Set up pixi
         uses: prefix-dev/[email protected]

.pre-commit-config.yaml

@@ -20,5 +20,4 @@ repos:
     hooks:
     -   id: clang-format
         args: ['--style=file']
-        exclude: "include/json.hpp"
         types_or: [c++]

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## latest
 
+- Include nlohmann-json via cmake [#87](https://github.com/DataAnalyticsEngineering/FANS/pull/87)
 - Relaxed versions in Pixi build workflow [#86](https://github.com/DataAnalyticsEngineering/FANS/pull/86)
 - Bump version in MacOS CI [#85](https://github.com/DataAnalyticsEngineering/FANS/pull/85)
 - Pixi build workflow for MacOS and Linux [#82](https://github.com/DataAnalyticsEngineering/FANS/pull/82) [#84](https://github.com/DataAnalyticsEngineering/FANS/pull/84)

CMakeLists.txt

@@ -98,7 +98,7 @@ if (FANS_LIBRARY_FOR_MICRO_MANAGER)
     )
     FetchContent_MakeAvailable(pybind11)
 endif()
-
+find_package(nlohmann_json REQUIRED)
 # ##############################################################################
 # TARGETS
 # ##############################################################################
@@ -141,7 +141,6 @@ target_include_directories(FANS_FANS PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_SO
 # FANS.h header that consuming projects can use
 set_property(TARGET FANS_FANS PROPERTY PUBLIC_HEADER
         include/general.h
-        include/json.hpp
         include/matmodel.h
         include/reader.h
         include/solverCG.h
@@ -200,6 +199,7 @@ target_link_libraries(FANS_FANS PUBLIC ${FFTW3_LIBRARIES})
 target_compile_definitions(FANS_FANS PUBLIC ${FFTW3_DEFINITIONS})
 
 target_link_libraries(FANS_FANS PUBLIC Eigen3::Eigen)
+target_link_libraries(FANS_FANS PUBLIC nlohmann_json::nlohmann_json)
 
 target_link_libraries(FANS_main PRIVATE FANS::FANS)
 

README.md

@@ -24,6 +24,7 @@ FANS has the following dependencies:
 - HDF5 with MPI support
 - Eigen3
 - FFTW3 with MPI support
+- nlohmann-json (for JSON input parsing)
 
 ### Installing dependencies
 
@@ -35,7 +36,8 @@ FANS has the following dependencies:
       libopenmpi-dev \
       libeigen3-dev \
       libfftw3-dev \
-      libfftw3-mpi-dev
+      libfftw3-mpi-dev \
+      nlohmann-json3-dev
   ```
 
 - On macOS, you can obtain the dependencies using `brew` and set the environment variables:
@@ -44,7 +46,7 @@ FANS has the following dependencies:
   brew install gnu-time cmake gcc@15
   brew install open-mpi --build-from-source --cc=gcc-15
   brew install hdf5-mpi --build-from-source --cc=gcc-15
-  brew install fftw eigen
+  brew install fftw eigen nlohmann-json
 
   export CC=gcc-15 CXX=g++-15 MPICC=mpicc MPICXX=mpicxx
   ```
@@ -77,14 +79,15 @@ Spack is a package manager designed for high-performance computing environments.
     spack install hdf5 +cxx +mpi
     spack install eigen
     spack install fftw +mpi
+    spack install nlohmann-json
     ```
 
     Additionally, optimized FFTW implementations can be used depending on your system's architecture, for example `amdfftw` (For AMD systems) or `cray-fftw` (For Cray systems), or `fujitsu-fftw` (For Fujitsu systems).
 
 3. **Load Dependencies** Once dependencies are installed, load them before building:
 
     ```bash
-    spack load cmake mpi hdf5 eigen fftw
+    spack load cmake mpi hdf5 eigen fftw nlohmann-json
     ```
 
 ## Building

docker/Dockerfile

@@ -40,6 +40,7 @@ RUN apt-get update -qq && apt-get install -y --no-install-recommends \
     libeigen3-dev \
     libfftw3-dev \
     libfftw3-mpi-dev \
+    nlohmann-json3-dev \
 # Required for preCICE Micro Manager Python bindings
     python3-dev \
 # Clean up

include/general.h

@@ -17,7 +17,7 @@
 using namespace std;
 
 // JSON
-#include <json.hpp>
+#include <nlohmann/json.hpp>
 using nlohmann::json;
 using namespace nlohmann;