Merge pull request #26 from rk-lindsey/develop

Update main from develop: Sync BB/GH; Add CI; Conda compatibility
rk-lindsey · Jan 14, 2022 · 7ca7d39 · 7ca7d39
2 parents 5ff5668 + 03f5688
commit 7ca7d39
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -17,36 +17,53 @@ jobs:
     - name: Set up environment (Linux)
       if: contains(matrix.os, 'ubuntu')
       run: |
-        echo "ROOTFOLDER=${PWD}" >> $GITHUB_ENV
+        echo "SOURCEDIR=${PWD}" >> $GITHUB_ENV
+        echo "WORKDIR=${PWD}" >> $GITHUB_ENV
         echo "FC=gfortran" >> $GITHUB_ENV
         echo "CC=gcc" >> $GITHUB_ENV
+        echo "CXX=g++" >> $GITHUB_ENV
         sudo apt-get update
         sudo apt-get install cmake ninja-build
 
     - name: Set up environment (OSX)
       if: contains(matrix.os, 'macos')
       run: |
-        echo "ROOTFOLDER=${PWD}" >> $GITHUB_ENV
+        echo "SOURCEDIR=${PWD}" >> $GITHUB_ENV
+        echo "WORKDIR=${PWD}" >> $GITHUB_ENV
         echo "FC=gfortran-9" >> $GITHUB_ENV
         echo "CC=gcc-9" >> $GITHUB_ENV
+        echo "CXX=g++-9" >> $GITHUB_ENV
         brew install ninja
 
     - name: Configure build
-      run: >-
-        cmake -B _build -G Ninja
-        -DCMAKE_INSTALL_PREFIX=${ROOTFOLDER}/_install
-        -DWITH_FORTRAN08_API=1
+      run: |
+        mkdir ${WORKDIR}/_build
+        cd ${WORKDIR}/_build
+        cmake -G Ninja -DCMAKE_INSTALL_PREFIX=${WORKDIR}/_install -DWITH_FORTRAN08_API=1 -DTEST_LABELS="minimal" ${SOURCEDIR}
+        cd -
 
     - name: Build project
       run: |
-        cmake --build _build
+        cd ${WORKDIR}/_build
+        ninja all
+        cd -
+
+    - name: Test project
+      run: |
+        cd ${WORKDIR}/_build
+        ctest
+        cd -
 
     - name: Install project
       run: |
-        cmake --install _build
+        cd ${WORKDIR}/_build
+        ninja install
+        cd -
 
     - name: Run integration test
       run: |
-        CMAKE_PREFIX_PATH=${ROOTFOLDER}/_install cmake -B _build_integtest -G Ninja ${ROOTFOLDER}/serial_interface/examples/fortran08
-        cmake --build _build_integtest
-        LD_LIBRARY_PATH=${ROOTFOLDER}/_install/lib ./_build_integtest/test_chimescalc ${ROOTFOLDER}/serial_interface/tests/force_fields/test_params.CHON.txt serial_interface/tests/configurations/CHON.testfile.000.xyz | grep "Energy (kcal/mol) -7.83714"
+        mkdir ${WORKDIR}/_build_integtest
+        cd ${WORKDIR}/_build_integtest
+        CMAKE_PREFIX_PATH=${WORKDIR}/_install cmake -G Ninja ${SOURCEDIR}/serial_interface/examples/fortran08
+        ninja all
+        LD_LIBRARY_PATH=${WORKDIR}/_install/lib ./test_chimescalc ${SOURCEDIR}/serial_interface/tests/force_fields/test_params.CHON.txt ${SOURCEDIR}/serial_interface/tests/configurations/CHON.testfile.000.xyz | grep "Energy (kcal/mol): -7.83714"
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,8 +1,8 @@
 cmake_minimum_required(VERSION 3.13)
 
-############################################################
+####################################################################################################
 # General settings
-############################################################
+####################################################################################################
 
 project(ChimesCalc
     VERSION 1.0
@@ -29,9 +29,9 @@ if(NEEDS_LIB_M)
 endif()
 
 
-###############################################################################
-# C++/C library
-###############################################################################
+####################################################################################################
+# Static/shared library
+####################################################################################################
 
 set(c-sources
     "chimesFF/src/chimesFF.cpp"
@@ -65,102 +65,62 @@ target_compile_features(ChimesCalc PRIVATE cxx_std_11)
 install(TARGETS ChimesCalc
     EXPORT ${PROJECT_NAME_LOWER}-targets
     LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}"
-    PUBLIC_HEADER DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/${INSTALL_INCLUDEDIR}")
+    PUBLIC_HEADER DESTINATION "${INSTALL_INCLUDEDIR}")
 
 
-############################################################
+####################################################################################################
 # Executables for C/C++
-############################################################
+####################################################################################################
 
-add_executable(CPP-interface serial_interface/examples/cpp/main.cpp)
-target_link_libraries(CPP-interface ChimesCalc)
-target_compile_features   (CPP-interface PUBLIC cxx_std_11)
-target_compile_definitions(CPP-interface PRIVATE "DEBUG=${DEBUG}")
+# Main executable installed as chimescalc
+add_executable(ChimesCalcExe serial_interface/examples/cpp/main.cpp)
+set_target_properties(ChimesCalcExe PROPERTIES OUTPUT_NAME "chimescalc")
+target_link_libraries(ChimesCalcExe ChimesCalc)
+target_compile_features   (ChimesCalcExe PUBLIC cxx_std_11)
+target_compile_definitions(ChimesCalcExe PRIVATE "DEBUG=${DEBUG}")
 
+install(TARGETS ChimesCalcExe DESTINATION ${CMAKE_INSTALL_BINDIR})
 
-if(NOT CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
-	  install(TARGETS CPP-interface
-        DESTINATION ${CMAKE_INSTALL_PREFIX}/serial_interface/examples/cpp/ OPTIONAL)
-endif()
-
-add_executable(C_wrapper-direct_interface chimesFF/examples/c/main.c)
-target_link_libraries     (C_wrapper-direct_interface ChimesCalc ${LIB_M})
-target_compile_features   (C_wrapper-direct_interface PRIVATE cxx_std_11)
-target_compile_definitions(C_wrapper-direct_interface PRIVATE "DEBUG=${DEBUG}")
-
-
-if(NOT CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
-	  install(TARGETS C_wrapper-direct_interface
-        DESTINATION ${CMAKE_INSTALL_PREFIX}/chimesFF/examples/c/ OPTIONAL)
-endif()
-
-
-add_executable(C_wrapper-serial_interface serial_interface/examples/c/main.c)
-target_link_libraries     (C_wrapper-serial_interface ChimesCalc)
-target_compile_features   (C_wrapper-serial_interface PRIVATE cxx_std_11)
-target_compile_definitions(C_wrapper-serial_interface PRIVATE "DEBUG=${DEBUG}")
-
-if(NOT CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
-	  install(TARGETS C_wrapper-serial_interface
-        DESTINATION ${CMAKE_INSTALL_PREFIX}/serial_interface/examples/c/ OPTIONAL)
-endif()
+# Test executables
+add_executable(chimescalc-test_direct-C chimesFF/examples/c/main.c)
+target_link_libraries     (chimescalc-test_direct-C ChimesCalc ${LIB_M})
+target_compile_features   (chimescalc-test_direct-C PRIVATE cxx_std_11)
+target_compile_definitions(chimescalc-test_direct-C PRIVATE "DEBUG=${DEBUG}")
 
+add_executable(chimescalc-test_serial-C serial_interface/examples/c/main.c)
+target_link_libraries     (chimescalc-test_serial-C ChimesCalc)
+target_compile_features   (chimescalc-test_serial-C PRIVATE cxx_std_11)
+target_compile_definitions(chimescalc-test_serial-C PRIVATE "DEBUG=${DEBUG}")
 
-############################################################
-# Executables/libraries for Python
-############################################################
 
+####################################################################################################
+# Dynamically loadable library (e.g for Python)
+####################################################################################################
 
-# Shared: .dylib
-# Static: .a
-# Module: .so
+add_library(ChimesCalc_dynamic MODULE "${c-sources}")
 
-add_library(lib-C_wrapper-direct_interface MODULE
-    ${CMAKE_CURRENT_SOURCE_DIR}/chimesFF/api/chimescalc_C.cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/chimesFF/src/chimesFF.cpp)
+set_target_properties(ChimesCalc_dynamic
+    PROPERTIES OUTPUT_NAME "chimescalc_dl")
 
-# Prevent CMake from prepending "lib" to libwrapper-C.so
-set_target_properties     (lib-C_wrapper-direct_interface PROPERTIES PREFIX "")
-# Tell it which language to use
-set_target_properties     (lib-C_wrapper-direct_interface PROPERTIES LINKER_LANGUAGE CXX)
-target_include_directories(lib-C_wrapper-direct_interface
-    PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/chimesFF/src/)
-target_include_directories(lib-C_wrapper-direct_interface
-    PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/chimesFF/api/)
-target_compile_features   (lib-C_wrapper-direct_interface PUBLIC cxx_std_11)
-
-if(NOT CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
-	  install(TARGETS lib-C_wrapper-direct_interface
-        DESTINATION ${CMAKE_INSTALL_PREFIX}/chimesFF/examples/python/ OPTIONAL)
-endif()
+target_include_directories(ChimesCalc_dynamic PUBLIC
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/chimesFF/src>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/chimesFF/api>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/serial_interface/src>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/serial_interface/api>
+    $<INSTALL_INTERFACE:${INSTALL_INCLUDEDIR}>)
 
+target_compile_definitions(ChimesCalc_dynamic PRIVATE "DEBUG=${DEBUG}")
+target_compile_features(ChimesCalc_dynamic PRIVATE cxx_std_11)
 
-add_library(lib-C_wrapper-serial_interface MODULE
-    ${CMAKE_CURRENT_SOURCE_DIR}/serial_interface/api/chimescalc_serial_C.cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/serial_interface/src/serial_chimes_interface.cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/chimesFF/src/chimesFF.cpp)
-
-# Prevent CMake from prepending "lib" to libwrapper-C.so
-set_target_properties     (lib-C_wrapper-serial_interface PROPERTIES PREFIX "")
-# Tell it which language to use
-set_target_properties     (lib-C_wrapper-serial_interface PROPERTIES LINKER_LANGUAGE CXX)
-target_include_directories(lib-C_wrapper-serial_interface
-    PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/serial_interface/api/)
-target_include_directories(lib-C_wrapper-serial_interface
-    PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/serial_interface/src/)
-target_include_directories(lib-C_wrapper-serial_interface
-    PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/chimesFF/src/)
-target_compile_features   (lib-C_wrapper-serial_interface PUBLIC cxx_std_11)
-
-if(NOT CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
-	  install(TARGETS lib-C_wrapper-serial_interface
-        DESTINATION ${CMAKE_INSTALL_PREFIX}/serial_interface/examples/python/ OPTIONAL)
-endif()
+install(TARGETS ChimesCalc_dynamic
+    EXPORT ${PROJECT_NAME_LOWER}-targets
+    LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}"
+    PUBLIC_HEADER DESTINATION "${INSTALL_INCLUDEDIR}")
 
 
-###############################################################################
-# Fortran library (separate library as it needs Fortran runtime to be linked)
-###############################################################################
+####################################################################################################
+# Fortran wrappers (not contained in base library as it requires Fortran runtime library)
+####################################################################################################
 
 if(WITH_FORTRAN_API OR WITH_FORTRAN08_API)
 
@@ -196,47 +156,26 @@ if(WITH_FORTRAN_API OR WITH_FORTRAN08_API)
     install(DIRECTORY "${moddir}/" DESTINATION "${INSTALL_MODULEDIR}")
 
 
-    ############################################################
+    ################################################################################################
     # Executables for Fortran (90/08)
-    ############################################################
-
-    add_executable(fortran_wrapper-direct_interface chimesFF/examples/fortran/main.F90)
-    target_link_libraries     (fortran_wrapper-direct_interface ChimesCalc_Fortran)
-    target_compile_definitions(fortran_wrapper-direct_interface PRIVATE "DEBUG=${DEBUG}")
-
-    if(NOT CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
-        install(TARGETS fortran_wrapper-direct_interface
-            DESTINATION ${CMAKE_INSTALL_PREFIX}/chimesFF/examples/fortran/ OPTIONAL)
-    endif()
-
+    ################################################################################################
 
-    add_executable(fortran_wrapper-serial_interface serial_interface/examples/fortran/main.F90)
-    target_link_libraries     (fortran_wrapper-serial_interface ChimesCalc_Fortran)
-    target_compile_definitions(fortran_wrapper-serial_interface PRIVATE "DEBUG=${DEBUG}")
-
-    if(NOT CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
-    	    install(TARGETS fortran_wrapper-direct_interface
-              DESTINATION ${CMAKE_INSTALL_PREFIX}/serial_interface/examples/fortran/ OPTIONAL)
-    endif()
+    add_executable(chimescalc-test_serial-F serial_interface/examples/fortran/main.F90)
+    target_link_libraries(chimescalc-test_serial-F ChimesCalc_Fortran)
+    target_compile_definitions(chimescalc-test_serial-F PRIVATE "DEBUG=${DEBUG}")
 
     # Optional, as ancient Fortran compilers may have difficulties with it
     if(WITH_FORTRAN08_API)
-        add_executable(fortran08_wrapper-serial_interface
-            serial_interface/examples/fortran08/main.F90)
-        target_link_libraries	  (fortran08_wrapper-serial_interface ChimesCalc_Fortran)
-	      target_compile_definitions(fortran08_wrapper-serial_interface PRIVATE "DEBUG=${DEBUG}")
-
-	      if(NOT CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
-	          install(TARGETS fortran08_wrapper-serial_interface
-                DESTINATION ${CMAKE_INSTALL_PREFIX}/serial_interface/examples/fortran08/ OPTIONAL)
-	      endif()
+        add_executable(chimescalc-test_serial-F08 serial_interface/examples/fortran08/main.F90)
+        target_link_libraries(chimescalc-test_serial-F08 ChimesCalc_Fortran)
+	      target_compile_definitions(chimescalc-test_serial-F08 PRIVATE "DEBUG=${DEBUG}")
     endif()
 
 endif()
 
-###############################################################################
+####################################################################################################
 # Create CMake export file
-###############################################################################
+####################################################################################################
 
 include(CMakePackageConfigHelpers)
 
@@ -260,3 +199,68 @@ install(
     FILES "${CMAKE_CURRENT_BINARY_DIR}/cmake/${PROJECT_NAME_LOWER}-config.cmake"
     "${CMAKE_CURRENT_BINARY_DIR}/cmake/${PROJECT_NAME_LOWER}-config-version.cmake"
     DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME_LOWER}")
+
+
+####################################################################################################
+# Add regression tests for the various APIs
+####################################################################################################
+
+enable_testing()
+
+set(apis
+    "cpp;${CMAKE_CURRENT_BINARY_DIR}/chimescalc"
+    "c;${CMAKE_CURRENT_BINARY_DIR}/chimescalc-test_serial-C"
+    "fortran;${CMAKE_CURRENT_BINARY_DIR}/chimescalc-test_serial-F"
+    "fortran08;${CMAKE_CURRENT_BINARY_DIR}/chimescalc-test_serial-F08")
+
+set(_testdir "${CMAKE_CURRENT_SOURCE_DIR}/serial_interface/tests")
+file(STRINGS ${_testdir}/test_list.dat _testcases)
+foreach(_testcase IN LISTS _testcases)
+    if("${_testcase}" STREQUAL "")
+        continue()
+    endif()
+    list(GET _testcase 0 _paramfile)
+    string(STRIP "${_paramfile}" _paramfile)
+    list(GET _testcase 1 _geometry)
+    string(STRIP "${_geometry}" _geometry)
+    string(REPLACE "#" "" _geometry_escaped "${_geometry}")
+    list(GET _testcase 2 _configopt)
+    string(STRIP "${_configopt}" _configopt)
+    list(GET _testcase 3 _testlabels)
+    string(STRIP "${_testlabels}" _testlabels)
+
+    set(_add_test False)
+    foreach(_label IN LISTS TEST_LABELS)
+        if("${_testlabels}" MATCHES "${_label}")
+            set(_add_test True)
+            break()
+        endif()
+    endforeach()
+    if(NOT _add_test)
+        continue()
+    endif()
+
+    set(_apis "${apis}")
+    list(LENGTH _apis _apis_length )
+    while(_apis_length GREATER 0)
+        list(POP_FRONT _apis _api_abbrev)
+        list(POP_FRONT _apis _api_executable)
+        #message(STATUS "Test added: ${_api_abbrev}:${_paramfile}:${_geometry_escaped}")
+        list(LENGTH _apis _apis_length)
+
+        add_test(
+            NAME "${_api_abbrev}/${_paramfile}:${_geometry_escaped}"
+            COMMAND
+                ${_testdir}/run_single_test.sh
+                ${_api_executable}
+                ${_paramfile}
+                ${_geometry}
+                ${_configopt}
+                ${CMAKE_CURRENT_BINARY_DIR}/_test/${_api_abbrev}/${_paramfile}:${_geometry_escaped})
+        if("${_api_abbrev}" STREQUAL "py")
+            set_tests_properties("${_api_abbrev}/${_paramfile}:${_geometry_escaped}"
+                PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                ENVIRONMENT "LD_LIBRARY_PATH=${CMAKE_CURRENT_BINARY_DIR}")
+        endif()
+    endwhile()
+endforeach()
diff --git a/chimesFF/api/chimescalc_py.py b/chimesFF/api/chimescalc_py.py
@@ -2,13 +2,10 @@
 
 	A simple python interface for chimesFF access.
 
-	Expects "libwrapper-C.so" in the same directory as this script
-
-
 	The following must be included in any python script calling this wrapper:
 
 		import chimescalc_py
-		chimescalc_py.chimes_wrapper = chimescalc_py.init_chimes_wrapper("/path/to/lib-C_wrapper-direct_interface.so")
+		chimescalc_py.chimes_wrapper = chimescalc_py.init_chimes_wrapper("libchimescalc-direct_dl.so")
 		chimescalc_py.set_chimes()
 		chimescalc_py.init_chimes()
 		chimescalc_py.read_params("some_parameter_file.txt")

diff --git a/chimesFF/examples/c/Makefile b/chimesFF/examples/c/Makefile
@@ -22,14 +22,14 @@ test_wrapper-C.o : main.c $(WRAPPER_SRC) $(WRAPPER_HDR)
 LINKS = chimesFF.o test_wrapper-C.o chimescalc_C.o
 
 test_wrapper-C : $(LINKS)
-	$(CXX)  $(LINKS) -o C_wrapper-direct_interface
+	$(CXX)  $(LINKS) -o chimescalc-test_direct-C
 
 clean:
 	rm -f *.o
 
 clean-all:
 	rm -f *.o
-	rm -f C_wrapper-direct_interface
+	rm -f chimescalc-test_direct-C
 
 all:
 	make chimesFF.o

diff --git a/chimesFF/examples/cpp/Makefile b/chimesFF/examples/cpp/Makefile
@@ -6,6 +6,6 @@ CXX_SRC = main.cpp $(CXX_LOC)/../../../serial_interface/src/serial_chimes_interf
 CXX_HDR = $(CXX_LOC)/../../../serial_interface/src/serial_chimes_interface.h $(CXX_LOC)/../../src/chimesFF.h
 
 all: $(CXX_SRC) $(CXX_HDR)
-	$(CXX) $(CXX_SRC)  -o CPP-interface -I $(CXX_LOC)/../../src -I $(CXX_LOC)/../../../serial_interface/src/
+	$(CXX) $(CXX_SRC)  -o chimescalc -I $(CXX_LOC)/../../src -I $(CXX_LOC)/../../../serial_interface/src/
 clean:
-	rm -f CPP-interface
+	rm -f chimescalc