move evolve code to core lib (#974)

molpopgen · Aug 31, 2022 · 5751b61 · 5751b61
1 parent 62afadb
commit 5751b61
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Showing 25 changed files with 19 additions and 26 deletions.
diff --git a/cpp_neutral_benchmark/CMakeLists.txt b/cpp_neutral_benchmark/CMakeLists.txt
@@ -1,15 +1,5 @@
 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)
+    cpp_neutral_benchmark.cc)                                       
 
 add_executable(cpp_neutral_benchmark ${CPP_NEUTRAL_BENCHMARK_SOURCES})
 add_dependencies(cpp_neutral_benchmark fwdpy11core header)

diff --git a/cpp_neutral_benchmark/cpp_neutral_benchmark.cc b/cpp_neutral_benchmark/cpp_neutral_benchmark.cc
@@ -12,7 +12,7 @@
 #include <fwdpy11/evolvets/SampleRecorder.hpp>
 #include <fwdpy11/evolvets/recorders.hpp>
 #include <fwdpy11/rng.hpp>
-#include "../fwdpy11/src/evolve_population/evolvets.hpp"
+#include <core/evolve_discrete_demes/evolvets.hpp>
 #include <boost/program_options.hpp>
 
 namespace po = boost::program_options;

diff --git a/fwdpy11/CMakeLists.txt b/fwdpy11/CMakeLists.txt
@@ -74,17 +74,7 @@ set(TS_SOURCES src/ts/init.cc src/ts/TreeIterator.cc src/ts/VariantIterator.cc
 
 set(EVOLVE_POPULATION_SOURCES src/evolve_population/init.cc
     src/evolve_population/_evolvets.cc
-    src/evolve_population/evolvets.cc
-    src/evolve_population/util.cc
-    src/evolve_population/cleanup_metadata.cc
-    src/evolve_population/diploid_pop_fitness.cc
-    src/evolve_population/index_and_count_mutations.cc
-    src/evolve_population/track_mutation_counts.cc
-    src/evolve_population/no_stopping.cc
-    src/evolve_population/remove_extinct_mutations.cc
-    src/evolve_population/track_ancestral_counts.cc
-    src/evolve_population/remove_extinct_genomes.cc
-    src/evolve_population/runtime_checks.cc)
+    src/evolve_population/no_stopping.cc)
 
 set(DISCRETE_DEMOGRAPHY_SOURCES src/discrete_demography/init.cc
     src/discrete_demography/MigrationMatrix.cc

diff --git a/fwdpy11/src/evolve_population/_evolvets.cc b/fwdpy11/src/evolve_population/_evolvets.cc
@@ -21,7 +21,7 @@
 
 #include <pybind11/pybind11.h>
 #include <pybind11/functional.h>
-#include "evolvets.hpp"
+#include <core/evolve_discrete_demes/evolvets.hpp>
 //#include <fwdpy11/discrete_demography/simulation/demographic_model_state.hpp>
 
 namespace py = pybind11;

diff --git a/lib/CMakeLists.txt b/lib/CMakeLists.txt
@@ -6,9 +6,22 @@ set(MUTATION_DOMINANCE_SOURCES mutation_dominance/dependency_injection.cc)
 set(DEMES_SOURCES
     demes/forward_graph.cc)
 
+set(EVOLVE_DISCRETE_DEMES_SOURCES
+    evolve_discrete_demes/cleanup_metadata.cc
+    evolve_discrete_demes/diploid_pop_fitness.cc
+    evolve_discrete_demes/evolvets.cc
+    evolve_discrete_demes/index_and_count_mutations.cc
+    evolve_discrete_demes/remove_extinct_genomes.cc
+    evolve_discrete_demes/remove_extinct_mutations.cc
+    evolve_discrete_demes/track_ancestral_counts.cc
+    evolve_discrete_demes/track_mutation_counts.cc
+    evolve_discrete_demes/runtime_checks.cc
+    evolve_discrete_demes/util.cc)
+
 set(ALL_SOURCES ${DISCRETE_DEMOGRAPHY_SOURCES}
     ${MUTATION_DOMINANCE_SOURCES}
-    ${DEMES_SOURCES})
+    ${DEMES_SOURCES}
+    ${EVOLVE_DISCRETE_DEMES_SOURCES})
 
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++14")
 add_library(fwdpy11core SHARED ${ALL_SOURCES})

diff --git a/fwdpy11/src/evolve_population/evolvets.hpp → lib/core/evolve_discrete_demes/evolvets.hpp b/fwdpy11/src/evolve_population/evolvets.hpp → lib/core/evolve_discrete_demes/evolvets.hpp
diff --git a/...src/evolve_population/cleanup_metadata.cc → ...evolve_discrete_demes/cleanup_metadata.cc b/...src/evolve_population/cleanup_metadata.cc → ...evolve_discrete_demes/cleanup_metadata.cc
diff --git a/...rc/evolve_population/cleanup_metadata.hpp → ...volve_discrete_demes/cleanup_metadata.hpp b/...rc/evolve_population/cleanup_metadata.hpp → ...volve_discrete_demes/cleanup_metadata.hpp
diff --git a/.../evolve_population/diploid_pop_fitness.cc → ...lve_discrete_demes/diploid_pop_fitness.cc b/.../evolve_population/diploid_pop_fitness.cc → ...lve_discrete_demes/diploid_pop_fitness.cc
diff --git a/...evolve_population/diploid_pop_fitness.hpp → ...ve_discrete_demes/diploid_pop_fitness.hpp b/...evolve_population/diploid_pop_fitness.hpp → ...ve_discrete_demes/diploid_pop_fitness.hpp
diff --git a/fwdpy11/src/evolve_population/evolvets.cc → lib/evolve_discrete_demes/evolvets.cc b/fwdpy11/src/evolve_population/evolvets.cc → lib/evolve_discrete_demes/evolvets.cc
@@ -18,7 +18,7 @@
 #include "remove_extinct_genomes.hpp"
 #include "runtime_checks.hpp"
 
-#include "evolvets.hpp"
+#include <core/evolve_discrete_demes/evolvets.hpp>
 
 namespace ddemog = fwdpy11::discrete_demography;
 

diff --git a/...e_population/index_and_count_mutations.cc → ...screte_demes/index_and_count_mutations.cc b/...e_population/index_and_count_mutations.cc → ...screte_demes/index_and_count_mutations.cc
diff --git a/..._population/index_and_count_mutations.hpp → ...crete_demes/index_and_count_mutations.hpp b/..._population/index_and_count_mutations.hpp → ...crete_demes/index_and_count_mutations.hpp
diff --git a/...olve_population/remove_extinct_genomes.cc → ..._discrete_demes/remove_extinct_genomes.cc b/...olve_population/remove_extinct_genomes.cc → ..._discrete_demes/remove_extinct_genomes.cc
diff --git a/...lve_population/remove_extinct_genomes.hpp → ...discrete_demes/remove_extinct_genomes.hpp b/...lve_population/remove_extinct_genomes.hpp → ...discrete_demes/remove_extinct_genomes.hpp
diff --git a/...ve_population/remove_extinct_mutations.cc → ...iscrete_demes/remove_extinct_mutations.cc b/...ve_population/remove_extinct_mutations.cc → ...iscrete_demes/remove_extinct_mutations.cc
diff --git a/...e_population/remove_extinct_mutations.hpp → ...screte_demes/remove_extinct_mutations.hpp b/...e_population/remove_extinct_mutations.hpp → ...screte_demes/remove_extinct_mutations.hpp
diff --git a/...1/src/evolve_population/runtime_checks.cc → lib/evolve_discrete_demes/runtime_checks.cc b/...1/src/evolve_population/runtime_checks.cc → lib/evolve_discrete_demes/runtime_checks.cc
diff --git a/.../src/evolve_population/runtime_checks.hpp → lib/evolve_discrete_demes/runtime_checks.hpp b/.../src/evolve_population/runtime_checks.hpp → lib/evolve_discrete_demes/runtime_checks.hpp
diff --git a/...olve_population/track_ancestral_counts.cc → ..._discrete_demes/track_ancestral_counts.cc b/...olve_population/track_ancestral_counts.cc → ..._discrete_demes/track_ancestral_counts.cc
diff --git a/...lve_population/track_ancestral_counts.hpp → ...discrete_demes/track_ancestral_counts.hpp b/...lve_population/track_ancestral_counts.hpp → ...discrete_demes/track_ancestral_counts.hpp
diff --git a/...volve_population/track_mutation_counts.cc → ...e_discrete_demes/track_mutation_counts.cc b/...volve_population/track_mutation_counts.cc → ...e_discrete_demes/track_mutation_counts.cc
diff --git a/...olve_population/track_mutation_counts.hpp → ..._discrete_demes/track_mutation_counts.hpp b/...olve_population/track_mutation_counts.hpp → ..._discrete_demes/track_mutation_counts.hpp
diff --git a/fwdpy11/src/evolve_population/util.cc → lib/evolve_discrete_demes/util.cc b/fwdpy11/src/evolve_population/util.cc → lib/evolve_discrete_demes/util.cc
diff --git a/fwdpy11/src/evolve_population/util.hpp → lib/evolve_discrete_demes/util.hpp b/fwdpy11/src/evolve_population/util.hpp → lib/evolve_discrete_demes/util.hpp