Fix cmake install

.gitlab-ci.yml

@@ -272,6 +272,37 @@ tutorials-samples-no-gpu:
   only:
     - schedules
 
+installation:
+  <<: *global_job_definition
+  stage: build
+  image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-10.1
+  script:
+    - export myconfig=maxset with_coverage=false make_check=false
+    - export srcdir=${CI_PROJECT_DIR} test_timeout=1800
+    - bash maintainer/CI/build_cmake.sh
+    - cd build
+    # install ESPResSo (in CI, pypresso will run up to 5 times slower when
+    # located outside the build directory, hence the larger timeout value)
+    - make install
+    # get path of installed files
+    - CI_INSTALL_DIR="/tmp/espresso-unit-tests"
+    - CI_INSTALL_PYTHON_PATH=$(dirname $(find "${CI_INSTALL_DIR}/lib" -name espressomd))
+    # deploy object-in-fluid module
+    - cp -r "src/python/object_in_fluid" "${CI_INSTALL_PYTHON_PATH}/object_in_fluid"
+    # run all tests with the installed files
+    - sed -i "s|$(pwd)/pypresso|${CI_INSTALL_DIR}/bin/pypresso|" testsuite/{python,scripts/samples,scripts/tutorials}/CTestTestfile.cmake
+    # skip long tests
+    - sed -i "/tutorial_11-ferrofluid_3/d" testsuite/scripts/tutorials/CTestTestfile.cmake
+    - make -j2 check_python_skip_long
+    - make -j2 check_samples
+    - make -j2 check_tutorials
+  tags:
+    - docker
+    - linux
+    - cuda
+  timeout: 3h
+  when: manual
+
 empty:
   <<: *global_job_definition
   stage: build

CMakeLists.txt

@@ -29,14 +29,6 @@ endif()
 enable_language(CXX)
 
 set(PROJECT_VERSION "4.1.0")
-string(REGEX
-       REPLACE "^([1-9]+)\\.[0-9]+.*$"
-               "\\1"
-               SOVERSION
-               "${PROJECT_VERSION}")
-if(NOT ${SOVERSION} MATCHES "^[1-9]+$")
-  message(FATAL_ERROR "Could not determine SOVERSION from ${PROJECT_VERSION}")
-endif(NOT ${SOVERSION} MATCHES "^[1-9]+$")
 
 #
 # CMake internal vars

doc/sphinx/conf.py.in

@@ -67,9 +67,9 @@ author = 'C. Holm, F. Weik, R. Weeber'
 # built documents.
 #
 # The short X.Y version.
-version = '@PROJECT_VERSION@'
+version = '.'.join('@PROJECT_VERSION@'.split('.')[:2])
 # The full version, including alpha/beta/rc tags.
-release = '@SOVERSION@'
+release = '@PROJECT_VERSION@'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/sphinx/installation.rst

@@ -640,7 +640,7 @@ build directory and create a new one.
 .. _make\: Compiling, testing and installing:
 
 ``make``: Compiling, testing and installing
---------------------------------------------
+-------------------------------------------
 
 The command ``make`` is mainly used to compile the source code, but it
 can do a number of other things. The generic syntax of the ``make``
@@ -665,9 +665,12 @@ targets are available:
     Deletes all files that were created during the compilation.
 
 ``install``
-    Install |es|.
-    Use ``make DESTDIR=/home/john install`` to install to a
-    specific directory.
+    Install |es| in the path specified by the CMake variable
+    ``CMAKE_INSTALL_PREFIX``. The path can be changed by calling CMake
+    with ``cmake .. -DCMAKE_INSTALL_PREFIX=/path/to/espresso``. Do not use
+    ``make DESTDIR=/path/to/espresso install`` to install to a specific path,
+    this will cause issues with the runtime path (RPATH) and will conflict
+    with the CMake variable ``CMAKE_INSTALL_PREFIX`` if it has been set.
 
 ``doxygen``
     Creates the Doxygen code documentation in the :file:`doc/doxygen`

src/config/CMakeLists.txt

@@ -36,7 +36,6 @@ execute_process(COMMAND ${PYTHON_EXECUTABLE}
 add_library(EspressoConfig SHARED config-features.cpp)
 add_dependencies(EspressoConfig myconfig check_myconfig generate_config_features)
 install(TARGETS EspressoConfig LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)
-set_target_properties(EspressoConfig PROPERTIES SOVERSION ${SOVERSION})
 target_include_directories(EspressoConfig PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR})
 
 # Parse repository info from git if available

src/core/CMakeLists.txt

@@ -158,7 +158,6 @@ else(CUDA)
 endif(CUDA)
 
 install(TARGETS EspressoCore LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)
-set_target_properties(EspressoCore PROPERTIES SOVERSION ${SOVERSION})
 target_include_directories(EspressoCore PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 if(WITH_COVERAGE)
   target_compile_options(EspressoCore PUBLIC "$<$<CONFIG:Release>:-g>")

src/core/cluster_analysis/CMakeLists.txt

@@ -2,12 +2,11 @@ set(cluster_analysis_SRC
     Cluster.cpp
     ClusterStructure.cpp
 )
-add_library(cluster_analysis SHARED ${cluster_analysis_SRC})
-install(TARGETS cluster_analysis LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)
-set_target_properties(cluster_analysis PROPERTIES SOVERSION ${SOVERSION})
-set_target_properties(cluster_analysis PROPERTIES MACOSX_RPATH TRUE)
-target_link_libraries(cluster_analysis PUBLIC EspressoCore PRIVATE EspressoConfig)
+add_library(core_cluster_analysis SHARED ${cluster_analysis_SRC})
+install(TARGETS core_cluster_analysis LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)
+set_target_properties(core_cluster_analysis PROPERTIES MACOSX_RPATH TRUE)
+target_link_libraries(core_cluster_analysis PUBLIC EspressoCore PRIVATE EspressoConfig)
 
 if(GSL)
-target_link_libraries(cluster_analysis PRIVATE GSL::gsl GSL::gslcblas)
+target_link_libraries(core_cluster_analysis PRIVATE GSL::gsl GSL::gslcblas)
 endif()

src/core/io/mpiio/CMakeLists.txt

@@ -1,3 +1,4 @@
 add_library(mpiio SHARED mpiio.cpp)
 target_include_directories(mpiio PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 target_link_libraries(mpiio PRIVATE EspressoConfig EspressoCore MPI::MPI_CXX)
+install(TARGETS mpiio LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)

src/core/io/reader/CMakeLists.txt

@@ -1,3 +1,4 @@
 add_library(pdbreader SHARED readpdb.cpp)
 target_link_libraries(pdbreader PUBLIC EspressoConfig EspressoCore pdbparser)
 target_include_directories(pdbreader PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
+install(TARGETS pdbreader LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)

src/core/shapes/CMakeLists.txt

@@ -13,5 +13,4 @@ set(Shapes_SRC
 )
 add_library(Shapes SHARED ${Shapes_SRC})
 install(TARGETS Shapes LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)
-set_target_properties(Shapes PROPERTIES SOVERSION ${SOVERSION})
 target_link_libraries(Shapes PUBLIC EspressoConfig EspressoCore)

src/pdbparser/CMakeLists.txt

@@ -1,5 +1,6 @@
 add_library(pdbparser SHARED ${CMAKE_CURRENT_SOURCE_DIR}/src/PdbParser.cpp)
 target_include_directories(pdbparser PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/include)
+install(TARGETS pdbparser LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)
 if(WITH_UNIT_TESTS)
   add_subdirectory(unit_tests)
 endif(WITH_UNIT_TESTS)

src/python/espressomd/CMakeLists.txt

@@ -38,9 +38,9 @@ add_custom_command(OUTPUT code_info.pyx
         WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/myconfig.pxi
         )
 
-file(GLOB cython_SRC *.pyx)
 # Make the cython_SRC, cython_HEADER and cython_AUX a cached variable to
 # be able to extend it in the subdirectories.
+file(GLOB cython_SRC *.pyx)
 SET(cython_SRC  "${cython_SRC}" CACHE INTERNAL "cython_SRC")
 file(GLOB cython_HEADER *.pxd)
 SET(cython_HEADER  "${cython_HEADER}" CACHE INTERNAL "cython_HEADER")
@@ -53,6 +53,7 @@ add_subdirectory(io)
 list(APPEND cython_SRC ${CMAKE_CURRENT_BINARY_DIR}/code_info.pyx)
 list(REMOVE_DUPLICATES cython_SRC)
 
+# Configure, compile and install Cython files
 foreach(cython_file ${cython_SRC})
   get_filename_component(basename ${cython_file} NAME_WE)
   file(RELATIVE_PATH relpath ${CMAKE_CURRENT_SOURCE_DIR} ${cython_file})
@@ -107,11 +108,13 @@ foreach(cython_file ${cython_SRC})
       target_link_libraries(${target} PRIVATE EspressoConfig EspressoCore EspressoScriptInterface)
       target_include_directories(${target} SYSTEM PRIVATE ${PYTHON_INCLUDE_DIRS} ${NUMPY_INCLUDE_DIR})
       add_dependencies(espressomd ${target})
+      install(TARGETS ${target} LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)
   endif()
 endforeach()
 
 target_link_libraries(espressomd_profiler PRIVATE Profiler)
 
+# Configure Python files
 foreach(auxfile ${cython_AUX})
   get_filename_component(filename ${auxfile} NAME)
   file(RELATIVE_PATH relpath ${CMAKE_CURRENT_SOURCE_DIR} ${auxfile})
@@ -123,7 +126,6 @@ foreach(auxfile ${cython_AUX})
                     )
 endforeach(auxfile)
 
+# Install Python files
 install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} DESTINATION ${PYTHON_INSTDIR}
-	PATTERN "CMakeFiles" EXCLUDE PATTERN "*.cpp" EXCLUDE
-	PATTERN "*.cmake" EXCLUDE PATTERN "Makefile" EXCLUDE) 
-
+        FILES_MATCHING PATTERN "*.py")

src/script_interface/CMakeLists.txt

@@ -33,8 +33,7 @@ endif()
 
 add_library(EspressoScriptInterface SHARED ${EspressoScriptInterface_SRC})
 install(TARGETS EspressoScriptInterface LIBRARY DESTINATION ${PYTHON_INSTDIR}/espressomd)
-set_target_properties(EspressoScriptInterface PROPERTIES SOVERSION ${SOVERSION})
-target_link_libraries(EspressoScriptInterface PRIVATE EspressoConfig PUBLIC EspressoCore Shapes cluster_analysis mpiio pdbreader)
+target_link_libraries(EspressoScriptInterface PRIVATE EspressoConfig PUBLIC EspressoCore Shapes core_cluster_analysis mpiio pdbreader)
 if(HDF5_FOUND)
  target_link_libraries(EspressoScriptInterface PRIVATE H5mdCore)
 endif()

testsuite/cmake/BashUnitTests.sh

@@ -24,13 +24,14 @@
 ##      #define ELECTROSTATICS
 ##      #define EXTERNAL_FORCES
 ##    EOF
+##      cmake .. -DCMAKE_INSTALL_PREFIX=/tmp/espresso
 ##      make
-##      make install DESTDIR="install"
+##      make install
 ##    }
 ##
 ##    # cleanup
 ##    function tear_down() {
-##      rm -rf install
+##      rm -rf /tmp/espresso
 ##      make dist-clean
 ##    }
 ##

testsuite/cmake/CMakeLists.txt

@@ -12,29 +12,16 @@ function(CMAKE_TEST)
 endfunction(CMAKE_TEST)
 
 if(WITH_PYTHON AND PYTHONINTERP_FOUND)
-  set(TESTING_PYTHON TRUE)
   # obtain Python*_SITEARCH without find_package(Python*)
   execute_process(
     COMMAND "${PYTHON_EXECUTABLE}" -c "from distutils import sysconfig as sc;print(sc.get_python_lib(prefix='', plat_specific=True, standard_lib=False))"
     OUTPUT_VARIABLE Python_SITEARCH
     OUTPUT_STRIP_TRAILING_WHITESPACE)
-else()
-  set(TESTING_PYTHON FALSE)
-endif()
-set(DESTDIR "${CMAKE_CURRENT_BINARY_DIR}/install")
 
-add_custom_target(setup_install)
-add_custom_target(setup_install_destdir COMMAND make install DESTDIR="${DESTDIR}" WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
-add_dependencies(setup_install setup_install_destdir)
-cmake_test(FILE test_install_destdir.sh DEPENDENCIES BashUnitTests.sh test_install.sh)
-if(CMAKE_INSTALL_PREFIX STREQUAL "/tmp/espresso-unit-tests")
-  add_custom_target(setup_install_prefix COMMAND make install WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
-  add_dependencies(setup_install setup_install_prefix)
-  cmake_test(FILE test_install_prefix.sh DEPENDENCIES BashUnitTests.sh)
+  cmake_test(FILE test_install.sh DEPENDENCIES BashUnitTests.sh)
 endif()
 
-cmake_test(FILE test_python_bindings.sh DEPENDENCIES BashUnitTests.sh)
-
+add_custom_target(setup_install COMMAND make install WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
 add_custom_target(check_cmake_install COMMAND ${CMAKE_CTEST_COMMAND} --timeout ${TEST_TIMEOUT} -C serial --output-on-failure)
 add_dependencies(check_cmake_install setup_install)
 

testsuite/cmake/test_install.sh

@@ -16,21 +16,24 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-# test espresso installation
-function helper_test_install_common() {
-  local root=$1
-  local filepaths=("${root}/bin/pypresso" \
-                   "${root}/@Python_SITEARCH@/espressomd/EspressoCore.so" \
+# load bash unit testing library
+source BashUnitTests.sh
+
+# test installation and Python bindings
+function test_install() {
+  local filepaths=("@CMAKE_INSTALL_PREFIX@/bin/pypresso" \
+                   "@CMAKE_INSTALL_PREFIX@/@Python_SITEARCH@/espressomd/EspressoCore.so" \
+                   "@CMAKE_INSTALL_PREFIX@/@Python_SITEARCH@/espressomd/_init.so" \
+                   "@CMAKE_INSTALL_PREFIX@/@Python_SITEARCH@/espressomd/__init__.py"
                   )
-  if [ "@TESTING_PYTHON@" = "TRUE" ]
-  then
-    filepaths+=("${root}/@Python_SITEARCH@/espressomd/_init.so" \
-                "${root}/@Python_SITEARCH@/espressomd/__init__.py"
-               )
-  fi
-  for filepath in ${filepaths[@]}
-  do
+
+  for filepath in ${filepaths[@]}; do
     assert_file_exists "${filepath}"
   done
+
+  # check the espressomd module can be imported from pypresso
+  assert_return_code "@CMAKE_INSTALL_PREFIX@/bin/pypresso" -c "import espressomd"
 }
 
+# run tests
+run_test_suite