Use cmake for all target builds (#971)

* removes all use of autoconf/automake

.github/workflows/tests.yml

@@ -94,8 +94,9 @@ jobs:
         run: |
           source ~/.bashrc
           conda activate anaconda-client-env
-          cd cpptests && autoreconf --install && ./configure && cd ..
-          make check -C cpptests
+          cmake -S. -Bbuild_cpp_tests -DBUILD_CPP_UNIT_TESTS=ON
+          cmake --build build_cpp_tests -t fwdpy11_cpp_tests -j 4
+          cmake --build build_cpp_tests -t test
 
       - name: Run Python tests
         # shell: bash -l {0}

.github/workflows/ubuntu.yml

@@ -105,26 +105,21 @@ jobs:
             CXX=$CXX CC=$CC python -m pip install -e .
 
       - name: Build C++ tests
-        working-directory: cpptests
         run: |
-          autoreconf --install
-          CPPFLAGS=$CPPFLAGS CC=$CC CXX=$CXX ./configure
-          make -j 3
+          cmake -E env CPPFLAGS="$CPPFLAGS" \
+            cmake -E env CC="$CC" \
+            cmake -E env CXX="$CXX" cmake -S. -Bbuild_cpp_tests -DBUILD_CPP_UNIT_TESTS=ON
+          cmake --build build_cpp_tests -t fwdpy11_cpp_tests -j 4
 
       - name: Run C++ tests
-        working-directory: cpptests
         run: |
-          make check
-          # Clean up so that the next step can work...
-          make clean
+          cmake --build build_cpp_tests -t test
 
       - name: Build and run standalone C++ program
-        working-directory: cpp_neutral_benchmark
         run: |
-          autoreconf --install
-          CXXFLAGS="-O3 -g" CC=$CC CXX=$CXX ./configure
-          make -j 3
-          ./cpp_neutral_benchmark
+          cmake -E env CC=$CC cmake -E env CXX=$CXX cmake -S. -Bbuild_cpp -DBUILD_CPP_BENCHMARK=ON
+          cmake --build build_cpp -t cpp_neutral_benchmark -j 4
+          ./build_cpp/cpp_neutral_benchmark/cpp_neutral_benchmark
 
       - name: Run Python tests
         run: |

CMakeLists.txt

@@ -25,6 +25,7 @@ option(USE_WEFFCPP "Use -Weffc++ during compilation" OFF)
 option(ENABLE_PROFILING "Compile to enable code profiling" OFF)
 option(BUILD_PYTHON_UNIT_TESTS "Build C++ modules for unit tests" ON)
 option(BUILD_CPP_UNIT_TESTS "Build C++ unit test suite" OFF)
+option(BUILD_CPP_BENCHMARK "Build C++ benchmark program" OFF)
 option(DISABLE_LTO "Disable link-time optimization (LTO)" OFF)
 option(CMAKE_BUILD "Set to ON when building with cmake. Set to off from, e.g., setup.py." ON)
 include_directories(BEFORE
@@ -62,3 +63,6 @@ if(BUILD_CPP_UNIT_TESTS)
     enable_testing()
     add_subdirectory(cpptests)
 endif(BUILD_CPP_UNIT_TESTS)
+if(BUILD_CPP_BENCHMARK)
+    add_subdirectory(cpp_neutral_benchmark)
+endif(BUILD_CPP_BENCHMARK)

cpp_neutral_benchmark/CMakeLists.txt

@@ -0,0 +1,23 @@
+SET(CPP_NEUTRAL_BENCHMARK_SOURCES 
+    cpp_neutral_benchmark.cc                                       
+    ../fwdpy11/src/evolve_population/remove_extinct_genomes.cc
+    ../fwdpy11/src/evolve_population/remove_extinct_mutations.cc
+    ../fwdpy11/src/evolve_population/diploid_pop_fitness.cc
+    ../fwdpy11/src/evolve_population/runtime_checks.cc
+    ../fwdpy11/src/evolve_population/track_mutation_counts.cc
+    ../fwdpy11/src/evolve_population/track_ancestral_counts.cc
+    ../fwdpy11/src/evolve_population/index_and_count_mutations.cc
+    ../fwdpy11/src/evolve_population/util.cc
+    ../fwdpy11/src/evolve_population/evolvets.cc
+    ../fwdpy11/src/evolve_population/cleanup_metadata.cc)
+
+add_executable(cpp_neutral_benchmark ${CPP_NEUTRAL_BENCHMARK_SOURCES})
+add_dependencies(cpp_neutral_benchmark fwdpy11core header)
+target_link_directories(cpp_neutral_benchmark PRIVATE ${CMAKE_SOURCE_DIR}/fwdpy11)
+target_link_libraries(cpp_neutral_benchmark PRIVATE fwdpy11core boost_program_options GSL::gsl GSL::gslcblas) 
+if (NOT APPLE)
+    target_link_options(cpp_neutral_benchmark BEFORE PUBLIC LINKER:--no-as-needed -ldl)
+endif()
+
+target_include_directories(cpp_neutral_benchmark BEFORE PUBLIC ${CMAKE_SOURCE_DIR}/fwdpy11/headers ${CMAKE_SOURCE_DIR}/fwdpy11/headers/fwdpp ${CMAKE_SOURCE_DIR}/fwdpy11/src/evolve_population)
+

cpptests/CMakeLists.txt

@@ -12,6 +12,9 @@ add_executable(fwdpy11_cpp_tests ${CPPTEST_SOURCES})
 add_dependencies(fwdpy11_cpp_tests fwdpy11core header)
 target_link_directories(fwdpy11_cpp_tests PRIVATE ${CMAKE_SOURCE_DIR}/fwdpy11)
 target_link_libraries(fwdpy11_cpp_tests PRIVATE boost_unit_test_framework fwdpy11core GSL::gsl GSL::gslcblas) 
+if (NOT APPLE)
+    target_link_options(fwdpy11_cpp_tests BEFORE PUBLIC LINKER:--no-as-needed -ldl)
+endif()
 set_target_properties(fwdpy11_cpp_tests PROPERTIES COMPILE_FLAGS "${CMAKE_CXX_FLAGS} -DBOOST_TEST_DYN_LINK")
 
 add_test(NAME fwdpy11_cpp_tests

doc/misc/changelog.md

@@ -3,6 +3,13 @@
 Major changes are listed below.  Each release likely contains fiddling with back-end code,
 updates to latest `fwdpp` version, etc.
 
+## Next release
+
+Build system and CI
+
+* Remove all use of automake/autoconf.
+  PR {pr}`971`.
+
 ## 0.18.3
 
 Bug fixes:

requirements/conda_minimal_deps.txt

@@ -8,8 +8,6 @@ tskit
 msprime
 gsl
 boost
-autoconf
-automake
 pytest
 pytest-xdist
 demes==0.2.0