NeXus output on native HDF5, replacing the frozen napi (libNeXus)

.github/workflows/mcstas-basictest.yml

@@ -86,13 +86,13 @@ jobs:
       id: setup-linux
       if: matrix.method == 'source' && runner.os == 'Linux'
       run: |
-           sudo apt -y install libgsl-dev libnexus-dev
+           sudo apt -y install libgsl-dev libhdf5-dev
 
     - name: Setup (macOS, source build)
       id: setup-macos
       if: matrix.method == 'source' && runner.os == 'macOS'
       run: |
-           brew install bison flex gfortran gsl homebrew/science/nexusformat
+           brew install bison flex gfortran gsl hdf5
 
     - name: Setup (Windows, source build)
       id: setup-Windows
@@ -161,7 +161,6 @@ jobs:
            if [ "$RUNNER_OS" == "macOS" ] && [ -f "/opt/homebrew/opt/flex/bin/flex" ]; then export HOMEBRW="/opt/homebrew/opt"; export GSLFLAGS="-lgsl -lgslcblas -L/opt/homebrew/lib -I/opt/homebrew/include"; fi
            if [ "$RUNNER_OS" == "macOS" ] && [ -f "/usr/local/opt/flex/bin/flex" ]; then export HOMEBRW="/usr/local/opt"; export GSLFLAGS="-lgsl -lgslcblas -L/usr/local/lib -I/usr/local/include"; fi
            if [ "$RUNNER_OS" == "macOS" ]; then export EXTRA_ARGS_FOR_CMAKE="-DBISON_EXECUTABLE=${HOMEBRW}/bison/bin/bison -DFLEX_EXECUTABLE=${HOMEBRW}/flex/bin/flex -DCMAKE_Fortran_COMPILER=${HOMEBRW}/gfortran/bin/gfortran"; fi
-           if [ "$RUNNER_OS" == "Linux" ]; then export EXTRA_ARGS_FOR_CMAKE="-DNEXUSLIB=/usr/lib -DNEXUSINCLUDE=/usr/include/nexus"; fi
            if [ "$RUNNER_OS" == "Windows" ]; then export MPIINC=`cygpath -m -s  "${MSMPI_INC}"`; export MPILIB=`cygpath -m -s  "${MSMPI_LIB64}"`; export EXTRA_ARGS_FOR_CMAKE="-DMPILIBDIR=${MPILIB} -DMPIINCLUDEDIR=${MPIINC}"; fi
            cmake \
                -DCMAKE_INSTALL_PREFIX=../install_mcstas \

.github/workflows/mcxtrace-basictest.yml

@@ -86,7 +86,7 @@ jobs:
       id: setup-linux
       if: matrix.method == 'source' && runner.os == 'Linux'
       run: |
-           sudo apt -y install libgsl-dev libxrl-dev libnexus-dev
+           sudo apt -y install libgsl-dev libxrl-dev libhdf5-dev
 
     - name: Setup (macOS, source build)
       id: setup-macos
@@ -95,7 +95,7 @@ jobs:
       # cause build-issues. Will soon port basictest scripts to conda
       # for Windows/Linux
       run: |
-           brew install bison flex gfortran gsl
+           brew install bison flex gfortran gsl hdf5
            #if [ "${{ matrix.os }}" != "macos-15" ];
            #then
            #  brew tap tschoonj/tap
@@ -169,7 +169,6 @@ jobs:
            if [ "$RUNNER_OS" == "macOS" ] && [ -f "/opt/homebrew/opt/flex/bin/flex" ]; then export HOMEBRW="/opt/homebrew/opt"; export GSLFLAGS="-lgsl -lgslcblas -L/opt/homebrew/lib -I/opt/homebrew/include"; export XRLFLAGS="-lxrl -L/opt/homebrew/lib -I/opt/homebrew/include"; fi
            if [ "$RUNNER_OS" == "macOS" ] && [ -f "/usr/local/opt/flex/bin/flex" ]; then export HOMEBRW="/usr/local/opt"; export GSLFLAGS="-lgsl -lgslcblas -L/usr/local/lib -I/usr/local/include"; export XRLFLAGS="-lxrl -L/usr/local/lib -I/usr/local/include"; fi
            if [ "$RUNNER_OS" == "macOS" ]; then export EXTRA_ARGS_FOR_CMAKE="-DBISON_EXECUTABLE=${HOMEBRW}/bison/bin/bison -DFLEX_EXECUTABLE=${HOMEBRW}/flex/bin/flex -DCMAKE_Fortran_COMPILER=${HOMEBRW}/gfortran/bin/gfortran"; fi
-           if [ "$RUNNER_OS" == "Linux" ]; then export EXTRA_ARGS_FOR_CMAKE="-DNEXUSLIB=/usr/lib -DNEXUSINCLUDE=/usr/include/nexus"; fi
            if [ "$RUNNER_OS" == "Windows" ]; then export MPIINC=`cygpath -m -s  "${MSMPI_INC}"`; export MPILIB=`cygpath -m -s  "${MSMPI_LIB64}"`; export EXTRA_ARGS_FOR_CMAKE="-DMPILIBDIR=${MPILIB} -DMPIINCLUDEDIR=${MPIINC}"; fi
            cmake \
                -DCMAKE_INSTALL_PREFIX=../install_mcxtrace \

3rdparty/sync.sh

@@ -27,16 +27,6 @@ else
     git clone https://github.com/mctools/ncrystal.git
 fi
 
-if [ -d nexus-code ]; then
-    echo Updating existing NeXus clone
-    cd nexus-code
-    git pull
-    cd ..
-else
-    echo Cloning NeXus
-    git clone https://github.com/nexusformat/code nexus-code
-fi
-
 if [ -d xraylib ]; then
     echo Updating existing xraylib clone
     cd xraylib

buildscripts/build_pkg_ghostbsd

@@ -39,5 +39,4 @@ export MCINSTALL_PREFIX=/usr/local
 
 ./mkdist mcstas-ncrystal ${1} 3rdparty/ncrystal-package "" ghostbsd "" -- pkg
 ./mkdist mcstas-mcpl ${1} 3rdparty/mcpl-package "" ghostbsd "" -- pkg
-./mkdist mcstas-nexus ${1} 3rdparty/nexus-package "" ghostbsd "" -- pkg
 

cmake/Modules/InstallMCCODE.cmake

@@ -99,7 +99,7 @@ macro(installMCCODE)
 
   # update definitions to match choices
   if (USE_NEXUS)
-    AppendDef(HAVE_NEXUS="-DUSE_NEXUS -lNeXus")
+    AppendDef(HAVE_NEXUS="-DUSE_NEXUS -lhdf5")
     AppendDef(USE_NEXUS)
   endif()
 

cmake/Modules/MCUtil.cmake

@@ -61,12 +61,6 @@ macro(setupMCCODE FLAVOR)
     set(WINDOWS true)
   endif()
 
-  # Set Nexus linking flag
-  if(USE_NEXUS)
-    set(CMAKE_C_FLAGS  "${CMAKE_C_FLAGS}  -lNeXus")
-    set(CMAKE_C_LFLAGS "${CMAKE_C_LFLAGS} -lNeXus")
-  endif()
-
   # Set 32-bit flags
   if(ARCH EQUAL "i386")
     set(CMAKE_C_FLAGS  "-m32")

cmake/Modules/PlatformDefaults.cmake

@@ -223,17 +223,17 @@ function( detect_platform_variables resultvarname )
   provide_var( MPICC )
 
 
-  #NeXus-flags:
+  #NeXus-flags: NeXus output is written with HDF5 (NEXUSLIB/NEXUSINCLUDE: where libhdf5 and hdf5.h are)
   if ( NOT NEXUSFLAGS )
-    set(NEXUSFLAGS "-DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -lNeXus -lhdf5")#?? should probably have another value
+    set(NEXUSFLAGS "-DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -lhdf5")
     if ( MCCODE_BUILD_CONDA_PKG )
-      set( NEXUSFLAGS "-DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -I\$\{CONDA_PREFIX\}/include/nexus -I\$\{CONDA_PREFIX\}/include -Wl,-rpath,$\{CONDA_PREFIX\}/lib -L\$\{CONDA_PREFIX\}/lib -lNeXus -lhdf5" )
+      set( NEXUSFLAGS "-DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -I\$\{CONDA_PREFIX\}/include -Wl,-rpath,$\{CONDA_PREFIX\}/lib -L\$\{CONDA_PREFIX\}/lib -lhdf5" )
     endif()
     if ( WINDOWS )
       if ( "${CMAKE_C_COMPILER_ID}" STREQUAL "MSVC" )
-        set( NEXUSFLAGS " /DUSE_NEXUS /DNX_COMPRESSION=NX_COMP_LZW_LVL1 /DH5_BUILT_AS_DYNAMIC_LIB /I\$\{CONDA_PREFIX\}/Library/include/nexus /I\$\{CONDA_PREFIX\}/Library/include /link /LIBPATH:\$\{CONDA_PREFIX\}/Library/lib NeXus.lib hdf5.lib" )
+        set( NEXUSFLAGS " /DUSE_NEXUS /DNX_COMPRESSION=NX_COMP_LZW_LVL1 /DH5_BUILT_AS_DYNAMIC_LIB /I\$\{CONDA_PREFIX\}/Library/include /link /LIBPATH:\$\{CONDA_PREFIX\}/Library/lib hdf5.lib" )
       else()
-	set( NEXUSFLAGS "-DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -DH5_BUILT_AS_DYNAMIC_LIB -I\$\{CONDA_PREFIX\}/Library/include/nexus -I\$\{CONDA_PREFIX\}/Library/include -Wl,-rpath,$\{CONDA_PREFIX\}/Library/lib -L\$\{CONDA_PREFIX\}/Library/lib -lNeXus -lhdf5" )
+	set( NEXUSFLAGS "-DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -DH5_BUILT_AS_DYNAMIC_LIB -I\$\{CONDA_PREFIX\}/Library/include -Wl,-rpath,$\{CONDA_PREFIX\}/Library/lib -L\$\{CONDA_PREFIX\}/Library/lib -lhdf5" )
       endif()
     endif()
     if ( NEXUSLIB )

cmake/toolchains/deb32.cmake

@@ -10,10 +10,8 @@ set(MPICC "mpicc")
 set(MPILIB "mpi")
 set(OACCFLAGS "-fast -Minfo=accel -acc=gpu -gpu=managed -DOPENACC")
 set(MPIRUN "mpirun")
-set(NEXUSLIB "/usr/lib")
-set(NEXUSINCLUDE "/usr/include/nexus")
-# Packages are built before libnexus-dev/libhdf5-dev are installed: set the
+# Packages are built before libhdf5-dev is installed: set the
 # full flags. Debian's serial HDF5 is in /usr/include/hdf5/serial, linked as libhdf5_serial
-set(NEXUSFLAGS "-Wl,-rpath,/usr/lib -L/usr/lib -DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -lNeXus -lhdf5_serial -I/usr/include/nexus -I/usr/include/hdf5/serial")
+set(NEXUSFLAGS "-Wl,-rpath,/usr/lib -L/usr/lib -DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -lhdf5_serial -I/usr/include/hdf5/serial")
 set(MCCODE_CFLAGS "-fno-PIC -fPIE -flto -O3 -mtune=native -march=native -fno-math-errno -ftree-vectorize -g -DNDEBUG -D_POSIX_SOURCE -std=c99 -lm")
 set(EDITOR "gedit")

cmake/toolchains/deb64.cmake

@@ -10,10 +10,8 @@ set(MPICC "mpicc")
 set(OACCFLAGS "-fast -Minfo=accel -acc=gpu -gpu=managed -DOPENACC")
 set(MPILIB "mpi")
 set(MPIRUN "mpirun")
-set(NEXUSLIB "/usr/lib")
-set(NEXUSINCLUDE "/usr/include/nexus")
-# Packages are built before libnexus-dev/libhdf5-dev are installed: set the
+# Packages are built before libhdf5-dev is installed: set the
 # full flags. Debian's serial HDF5 is in /usr/include/hdf5/serial, linked as libhdf5_serial
-set(NEXUSFLAGS "-Wl,-rpath,/usr/lib -L/usr/lib -DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -lNeXus -lhdf5_serial -I/usr/include/nexus -I/usr/include/hdf5/serial")
+set(NEXUSFLAGS "-Wl,-rpath,/usr/lib -L/usr/lib -DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -lhdf5_serial -I/usr/include/hdf5/serial")
 set(MCCODE_CFLAGS "-fno-PIC -fPIE -flto -O3 -mtune=native -march=native -fno-math-errno -ftree-vectorize -g -DNDEBUG -D_POSIX_SOURCE -std=c99 -lm")
 set(EDITOR "gedit")

cmake/toolchains/deb64arm.cmake

@@ -10,10 +10,8 @@ set(MPICC "mpicc")
 set(MPILIB "mpi")
 set(OACCFLAGS "-fast -Minfo=accel -acc=gpu -gpu=managed -DOPENACC")
 set(MPIRUN "mpirun")
-set(NEXUSLIB "/usr/lib")
-set(NEXUSINCLUDE "/usr/include/nexus")
-# Packages are built before libnexus-dev/libhdf5-dev are installed: set the
+# Packages are built before libhdf5-dev is installed: set the
 # full flags. Debian's serial HDF5 is in /usr/include/hdf5/serial, linked as libhdf5_serial
-set(NEXUSFLAGS "-Wl,-rpath,/usr/lib -L/usr/lib -DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -lNeXus -lhdf5_serial -I/usr/include/nexus -I/usr/include/hdf5/serial")
+set(NEXUSFLAGS "-Wl,-rpath,/usr/lib -L/usr/lib -DUSE_NEXUS -DNX_COMPRESSION=NX_COMP_LZW_LVL1 -lhdf5_serial -I/usr/include/hdf5/serial")
 set(MCCODE_CFLAGS "-fno-PIC -fPIE -flto -O3 -mtune=native -march=native -fno-math-errno -ftree-vectorize -g -DNDEBUG -D_POSIX_SOURCE -std=c99 -lm")
 set(EDITOR "gedit")

cmake/toolchains/mac-silicon.cmake

@@ -16,6 +16,6 @@ set(XRLFLAGS "-IGETPATH(miniconda3/include) -Wl,-rpath,GETPATH(miniconda3/lib) -
 set(MPIRUN "mpirun")
 set(MPILIB "mpi")
 set(NEXUSLIB "GETPATH(miniconda3/lib)")
-set(NEXUSINCLUDE "GETPATH(miniconda3/include/nexus)")
+set(NEXUSINCLUDE "GETPATH(miniconda3/include)")
 set(MCCODE_CFLAGS "-g -O2 -DNDEBUG -lm -std=c99")
 set(EDITOR "open")

cmake/toolchains/mac.cmake

@@ -16,6 +16,6 @@ set(XRLFLAGS "-IGETPATH(miniconda3/include) -Wl,-rpath,GETPATH(miniconda3/lib) -
 set(MPIRUN "mpirun")
 set(MPILIB "mpi")
 set(NEXUSLIB "GETPATH(miniconda3/lib)")
-set(NEXUSINCLUDE "GETPATH(miniconda3/include/nexus)")
+set(NEXUSINCLUDE "GETPATH(miniconda3/include)")
 set(MCCODE_CFLAGS "-g -O2 -DNDEBUG -lm -std=c99")
 set(EDITOR "open")

cmake/toolchains/mingw64.cmake

@@ -41,8 +41,8 @@ set(MPILIB "msmpi")
 set(MCCODE_CFLAGS "-flto -O3 -mtune=native -fno-math-errno -ftree-vectorize -g -DNDEBUG -D_POSIX_SOURCE -std=c99 -lm")
 set(EDITOR "start")
 
-# NeXus location defaults
-set(NEXUSINCLUDE "GETPATH(../miniconda3/Library/include/nexus)")
+# HDF5 location for NeXus output
+set(NEXUSINCLUDE "GETPATH(../miniconda3/Library/include)")
 set(NEXUSLIB "GETPATH(../miniconda3/Library/lib)")
 
 # HDFviewer