Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes

cmake/Modules/GenerateBinaryHeader.cmake

@@ -1,3 +1,3 @@
 # utility script to call GenerateBinaryHeader function
 include(${SOURCE_DIR}/Modules/LAMMPSUtils.cmake)
-GenerateBinaryHeader(${VARNAME} ${HEADER_FILE} ${SOURCE_FILES})
+GenerateBinaryHeader(${VARNAME} ${HEADER_FILE} ${SOURCE_FILE})

cmake/Modules/LAMMPSUtils.cmake

@@ -71,19 +71,15 @@ macro(pkg_depends PKG1 PKG2)
 endmacro()
 
 # CMake-only replacement for bin2c and xxd
-function(GenerateBinaryHeader varname outfile files)
+function(GenerateBinaryHeader varname outfile infile)
     message("Creating ${outfile}...")
     file(WRITE ${outfile} "// CMake generated file\n")
-    math(EXPR ARG_END   "${ARGC}-1")
 
-    foreach(IDX RANGE 2 ${ARG_END})
+    file(READ ${infile} content HEX)
-        list(GET ARGV ${IDX} filename)
-        file(READ ${filename} content HEX)
     string(REGEX REPLACE "([0-9a-f][0-9a-f])" "0x\\1," content "${content}")
     string(REGEX REPLACE ",$" "" content "${content}")
     file(APPEND ${outfile} "const unsigned char ${varname}[] = { ${content} };\n")
     file(APPEND ${outfile} "const unsigned int ${varname}_size = sizeof(${varname});\n")
-    endforeach()
 endfunction(GenerateBinaryHeader)
 
 # fetch missing potential files

cmake/Modules/Packages/GPU.cmake

@@ -309,7 +309,7 @@ elseif(GPU_API STREQUAL "HIP")
     endif()
 
     add_custom_command(OUTPUT ${CUBIN_H_FILE}
-      COMMAND ${CMAKE_COMMAND} -D SOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR} -D VARNAME=${CU_NAME} -D HEADER_FILE=${CUBIN_H_FILE} -D SOURCE_FILES=${CUBIN_FILE} -P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/GenerateBinaryHeader.cmake
+      COMMAND ${CMAKE_COMMAND} -D SOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR} -D VARNAME=${CU_NAME} -D HEADER_FILE=${CUBIN_H_FILE} -D SOURCE_FILE=${CUBIN_FILE} -P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/GenerateBinaryHeader.cmake
       DEPENDS ${CUBIN_FILE}
       COMMENT "Generating ${CU_NAME}_cubin.h")
 

tools/singularity/fedora32_mingw.def

@@ -30,12 +30,12 @@ From: fedora:32
                mingw32-expat mingw64-expat \
                mingw64-expat-static mingw32-expat-static \
                mingw32-sqlite-static mingw64-sqlite-static \
-               enchant python3-virtualenv doxygen \
+               enchant python3-virtualenv doxygen latexmk \
                texlive-latex-fonts texlive-pslatex texlive-collection-latexrecommended \
                texlive-latex texlive-latexconfig doxygen-latex texlive-collection-latex \
                texlive-latex-bin texlive-lualatex-math texlive-fncychap texlive-tabulary \
                texlive-framed texlive-wrapfig texlive-upquote texlive-capt-of \
-               texlive-needspace texlive-titlesec texlive-anysize texlive-dvipng \
+               texlive-needspace texlive-titlesec texlive-anysize texlive-dvipng texlive-xindy \
                blas-devel lapack-devel libyaml-devel openkim-models kim-api-devel \
                zstd libzstd-devel
         dnf clean all

tools/singularity/ubuntu18.04.def

@@ -64,6 +64,8 @@ From: ubuntu:18.04
         texlive-publishers \
         texlive-science \
         dvipng \
+        latexmk \
+        xindy \
         vim-nox \
         virtualenv \
         voro++-dev \

unittest/python/CMakeLists.txt

@@ -37,7 +37,7 @@ if (Python_EXECUTABLE)
         set(PYTHON_TEST_RUNNER ${Python_EXECUTABLE} -u)
     endif()
   else()
-    set(PYTHON_TEST_RUNNER ${Python_EXECUTABLE})
+    set(PYTHON_TEST_RUNNER ${Python_EXECUTABLE} -u)
   endif()
 
   add_test(NAME PythonOpen

unittest/python/python-open.py

@@ -12,7 +12,11 @@ except:
     pass
 
 try:
-    lmp = lammps()
+    if 'LAMMPS_MACHINE_NAME' in os.environ:
+        machine = os.environ['LAMMPS_MACHINE_NAME']
+    else:
+        machine = ""
+    lmp = lammps(name=machine)
     has_mpi = lmp.has_mpi_support
     lmp.close()
 except: