From 046e717c0b0969265d7d2bd11ec0089adadb4147 Mon Sep 17 00:00:00 2001 From: Ryan Curtin Date: Wed, 14 Apr 2010 13:38:54 +0000 Subject: [PATCH] Set up cmake infrastructure for contrib, and by default compile those which already compile without me having to fight with it too much --- .../fastlib-cmake/contrib/CMakeLists.txt | 63 +++ .../contrib/archana/CMakeLists.txt | 28 ++ .../contrib/dongryel/CMakeLists.txt | 24 + .../dongryel/compression/CMakeLists.txt | 49 ++ .../fast_multipole_method/CMakeLists.txt | 84 ++++ .../contrib/dongryel/kde/CMakeLists.txt | 44 ++ .../dongryel/linear_algebra/CMakeLists.txt | 27 + .../dongryel/linear_regression/CMakeLists.txt | 35 ++ .../contrib/dongryel/lprcde/CMakeLists.txt | 27 + .../matrix_factorized_fmm/CMakeLists.txt | 36 ++ .../multitree_template/CMakeLists.txt | 18 + .../nested_summation_template/CMakeLists.txt | 21 + .../contrib/dongryel/pca/CMakeLists.txt | 27 + .../dongryel/proximity_project/CMakeLists.txt | 70 +++ .../dongryel/regression/CMakeLists.txt | 54 ++ .../contrib/dongryel/thor_kde/CMakeLists.txt | 27 + .../contrib/gmravi/CMakeLists.txt | 14 + .../gmravi/hyperkernel_kde/CMakeLists.txt | 95 ++++ .../local_kernel_machines/CMakeLists.txt | 64 +++ .../local_polynomial_density/CMakeLists.txt | 43 ++ .../contrib/houyang/CMakeLists.txt | 16 + .../houyang/allknn_balltree/CMakeLists.txt | 39 ++ .../houyang/allknn_kdtree/CMakeLists.txt | 36 ++ .../contrib/houyang/regmin/CMakeLists.txt | 33 ++ .../contrib/houyang/rvm/CMakeLists.txt | 29 ++ .../contrib/houyang/svm/CMakeLists.txt | 50 ++ .../contrib/huijing/CMakeLists.txt | 12 + .../contrib/huijing/centroids/CMakeLists.txt | 27 + .../fastlib-cmake/contrib/jim/CMakeLists.txt | 15 + .../contrib/jim/cart/CMakeLists.txt | 30 ++ .../jim/molecular_dynamics/CMakeLists.txt | 53 ++ .../contrib/jim/thor_md/CMakeLists.txt | 31 ++ .../contrib/jim/thor_npoint/CMakeLists.txt | 45 ++ .../contrib/march/CMakeLists.txt | 17 + .../contrib/march/emst_cover/CMakeLists.txt | 54 ++ .../contrib/march/error/CMakeLists.txt | 41 ++ .../contrib/march/fock_matrix/CMakeLists.txt | 60 +++ .../march/fock_matrix/cfmm/CMakeLists.txt | 34 ++ .../fock_matrix/chem_reader/CMakeLists.txt | 20 + .../fock_matrix/fock_impl/CMakeLists.txt | 37 ++ .../march/fock_matrix/link/CMakeLists.txt | 34 ++ .../fock_matrix/multi_tree/CMakeLists.txt | 63 +++ .../march/fock_matrix/naive/CMakeLists.txt | 31 ++ .../fock_matrix/prescreening/CMakeLists.txt | 31 ++ .../contrib/march/hf/CMakeLists.txt | 56 +++ .../contrib/march/npt/CMakeLists.txt | 40 ++ .../contrib/march/scf/CMakeLists.txt | 28 ++ .../contrib/niche/CMakeLists.txt | 27 + .../contrib/niche/dtw/CMakeLists.txt | 60 +++ .../contrib/niche/hshmm/CMakeLists.txt | 165 +++++++ .../niche/kernel_kmeans/CMakeLists.txt | 27 + .../contrib/niche/kernel_pca/CMakeLists.txt | 34 ++ .../niche/kernel_vector_mult/CMakeLists.txt | 35 ++ .../niche/kmeans_nonempty/CMakeLists.txt | 47 ++ .../contrib/niche/log_newhmm/CMakeLists.txt | 461 ++++++++++++++++++ .../contrib/niche/mmf/CMakeLists.txt | 100 ++++ .../contrib/niche/new_hmm/CMakeLists.txt | 437 +++++++++++++++++ .../niche/regularized_ISM/CMakeLists.txt | 11 + .../write_cvxmod_program/CMakeLists.txt | 36 ++ .../spike_train_dependence/CMakeLists.txt | 27 + .../contrib/niche/svm/CMakeLists.txt | 28 ++ .../contrib/nvasil/CMakeLists.txt | 23 + .../nvasil/all_centroid_knn/CMakeLists.txt | 27 + .../contrib/nvasil/convex_nmf/CMakeLists.txt | 38 ++ .../nvasil/dual_manifold/CMakeLists.txt | 40 ++ .../nvasil/multiscale_mvu/CMakeLists.txt | 27 + .../contrib/nvasil/mvu/CMakeLists.txt | 39 ++ .../contrib/nvasil/nmf_tree/CMakeLists.txt | 30 ++ .../nvasil/non_convex_mvu/CMakeLists.txt | 38 ++ .../nvasil/non_convex_nmf/CMakeLists.txt | 29 ++ .../fastlib-cmake/contrib/pram/CMakeLists.txt | 18 + .../contrib/pram/approx_nn/CMakeLists.txt | 39 ++ .../contrib/pram/covertrees/CMakeLists.txt | 36 ++ .../pram/covertrees/epxtl_gc/CMakeLists.txt | 33 ++ .../contrib/pram/density_tree/CMakeLists.txt | 27 + .../contrib/pram/lle/CMakeLists.txt | 37 ++ .../contrib/pram/mog_l2e/CMakeLists.txt | 39 ++ .../contrib/pram/opt/CMakeLists.txt | 29 ++ .../contrib/pram/sparsepca/CMakeLists.txt | 38 ++ .../contrib/rriegel/CMakeLists.txt | 12 + .../contrib/rriegel/nbc/CMakeLists.txt | 37 ++ .../contrib/soyeon/CMakeLists.txt | 23 + .../contrib/soyeon/ddcm_sim1/CMakeLists.txt | 35 ++ .../contrib/tqlong/2dfactor/CMakeLists.txt | 28 ++ .../contrib/tqlong/CMakeLists.txt | 21 + .../tqlong/PassiveAggressive/CMakeLists.txt | 32 ++ .../contrib/tqlong/gm/CMakeLists.txt | 30 ++ .../contrib/tqlong/graph/CMakeLists.txt | 28 ++ .../contrib/tqlong/hmm/CMakeLists.txt | 28 ++ .../contrib/tqlong/kfs/CMakeLists.txt | 28 ++ .../contrib/tqlong/optim/CMakeLists.txt | 29 ++ .../contrib/tqlong/quicsvd/CMakeLists.txt | 39 ++ .../contrib/tqlong/svm/CMakeLists.txt | 53 ++ .../fastlib-cmake/mlpack/CMakeLists.txt | 4 +- 94 files changed, 4319 insertions(+), 2 deletions(-) create mode 100644 fastlib/branches/fastlib-cmake/contrib/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/archana/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/dongryel/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/dongryel/compression/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/dongryel/fast_multipole_method/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/dongryel/kde/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/dongryel/linear_algebra/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/dongryel/linear_regression/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/dongryel/lprcde/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/dongryel/matrix_factorized_fmm/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/dongryel/multitree_template/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/dongryel/nested_summation_template/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/dongryel/pca/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/dongryel/proximity_project/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/dongryel/regression/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/dongryel/thor_kde/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/gmravi/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/gmravi/hyperkernel_kde/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/gmravi/local_kernel_machines/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/gmravi/local_polynomial_density/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/houyang/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/houyang/allknn_balltree/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/houyang/allknn_kdtree/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/houyang/regmin/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/houyang/rvm/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/houyang/svm/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/huijing/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/huijing/centroids/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/jim/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/jim/cart/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/jim/molecular_dynamics/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/jim/thor_md/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/jim/thor_npoint/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/march/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/march/emst_cover/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/march/error/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/cfmm/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/chem_reader/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/fock_impl/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/link/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/multi_tree/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/naive/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/prescreening/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/march/hf/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/march/npt/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/march/scf/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/niche/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/niche/dtw/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/niche/hshmm/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/niche/kernel_kmeans/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/niche/kernel_pca/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/niche/kernel_vector_mult/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/niche/kmeans_nonempty/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/niche/log_newhmm/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/niche/mmf/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/niche/new_hmm/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/niche/regularized_ISM/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/niche/regularized_ISM/write_cvxmod_program/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/niche/spike_train_dependence/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/niche/svm/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/nvasil/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/nvasil/all_centroid_knn/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/nvasil/convex_nmf/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/nvasil/dual_manifold/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/nvasil/multiscale_mvu/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/nvasil/mvu/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/nvasil/nmf_tree/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/nvasil/non_convex_mvu/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/nvasil/non_convex_nmf/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/pram/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/pram/approx_nn/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/pram/covertrees/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/pram/covertrees/epxtl_gc/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/pram/density_tree/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/pram/lle/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/pram/mog_l2e/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/pram/opt/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/pram/sparsepca/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/rriegel/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/rriegel/nbc/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/soyeon/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/soyeon/ddcm_sim1/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/tqlong/2dfactor/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/tqlong/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/tqlong/PassiveAggressive/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/tqlong/gm/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/tqlong/graph/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/tqlong/hmm/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/tqlong/kfs/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/tqlong/optim/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/tqlong/quicsvd/CMakeLists.txt create mode 100644 fastlib/branches/fastlib-cmake/contrib/tqlong/svm/CMakeLists.txt diff --git a/fastlib/branches/fastlib-cmake/contrib/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/CMakeLists.txt new file mode 100644 index 0000000000..92d649c8e2 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/CMakeLists.txt @@ -0,0 +1,63 @@ +cmake_minimum_required(VERSION 2.8) +project(MLPACK_CONTRIB C CXX Fortran) + +# compiler flags +set(CMAKE_CXX_FLAGS "-g -Wall") +add_definitions(-DDISABLE_DISK_MATRIX) + +# include directories +include_directories(..) +include_directories(../include) + +set(MLPACK_STD_LIBS fastlib lapack blas) +set(MLPACK_CONTRIB_SRCS) + +# now we need to recurse into each of the contrib methods +set(DIRS +# archana # <-- DCT.cc is not usable anywhere else, custom one-time code + dongryel + gmravi + houyang + huijing + jim + march + niche + nvasil + pram + rriegel + soyeon + tqlong +) + +foreach(dir ${DIRS}) + add_subdirectory(${dir}) +endforeach() + +# MLPACK_CONTRIB_SRCS is set in the subdirectories above +#message("output: ${MLPACK_CONTRIB_SRCS}") +add_library(mlpack_contrib ${MLPACK_CONTRIB_SRCS}) +add_dependencies(mlpack_contrib mlpack fastlib) + +# move header files to the right directory +file(GLOB_RECURSE INCLUDE_FILES RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.h) +add_custom_command(TARGET mlpack_contrib POST_BUILD + COMMENT "Moving header files to include/mlpack_contrib/" + COMMAND ${CMAKE_COMMAND} ARGS -E make_directory ${CMAKE_BINARY_DIR}/include/mlpack_contrib/) +foreach(incl_file ${INCLUDE_FILES}) + add_custom_command(TARGET mlpack_contrib POST_BUILD + COMMAND ${CMAKE_COMMAND} ARGS -E copy ${CMAKE_CURRENT_SOURCE_DIR}/${incl_file} ${CMAKE_BINARY_DIR}/include/mlpack_contrib/${incl_file}) +endforeach() + +# set installation rules for include files +#install(FILES ${CMAKE_BINARY_DIR}/include/mlpack_contrib/ +# DESTINATION include/mlpack_contrib) + +# set installation rules for mlpack_contrib programs +#install(PROGRAMS ${CMAKE_BINARY_DIR}/bin/ +# DESTINATION bin) + +install(TARGETS mlpack_contrib + RUNTIME DESTINATION bin + LIBRARY DESTINATION lib + ARCHIVE DESTINATION lib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/archana/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/archana/CMakeLists.txt new file mode 100644 index 0000000000..68be53ea5e --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/archana/CMakeLists.txt @@ -0,0 +1,28 @@ +cmake_minimum_required(VERSION 2.8) + +# This is not compiled into mlpack_contrib by default, since it appears to be custom one-time-use +# code that is not useful anywhere other than this one particular test + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + DCT.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# test executable +add_executable(dct + DCT.cc +) +# link dependencies of test executable +target_link_libraries(dct + fastlib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/dongryel/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/dongryel/CMakeLists.txt new file mode 100644 index 0000000000..c4530cfac0 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/dongryel/CMakeLists.txt @@ -0,0 +1,24 @@ +cmake_minimum_required(VERSION 2.8) + +# we just want to recurse into the child directories here +set(DIRS + compression +# fast_multipole_method ## awaiting resolution of #10 (libint dependency) +# kde ## requires memory manager (mmapmm) + linear_algebra + linear_regression ## requires memory manager (mmapmm) +# lprcde ## requires memory manager (mmapmm) +# matrix_factorized_fmm ## does not compile right +# multitree_template ## requires memory manager (mmapmm) + nested_summation_template + pca +# proximity_project ## requires memorymanager (mmapmm) +# regression +# thor_kde ## does not compile: linker error (investigate) +) + +foreach(dir ${DIRS}) + add_subdirectory(${dir}) +endforeach() + +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} PARENT_SCOPE) diff --git a/fastlib/branches/fastlib-cmake/contrib/dongryel/compression/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/dongryel/compression/CMakeLists.txt new file mode 100644 index 0000000000..4b67062ac4 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/dongryel/compression/CMakeLists.txt @@ -0,0 +1,49 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + adler32.c + compressed_matrix.h + compress.c + crc32.h + crc32.c + deflate.h + deflate.c + example.c + gzio.c + infback.c + inffast.h + inffast.c + inflate.h + inflate.c + inftrees.h + inftrees.c + minigzip.c + trees.h + trees.c + uncompr.c + zutil.h + zutil.c +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# test executable +add_executable(compression_test + compressed_matrix.h + compression_test.cc +) +# link dependencies of test executable +target_link_libraries(compression_test + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/dongryel/fast_multipole_method/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/dongryel/fast_multipole_method/CMakeLists.txt new file mode 100644 index 0000000000..46dbc0e463 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/dongryel/fast_multipole_method/CMakeLists.txt @@ -0,0 +1,84 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # continuous_fmm + continuous_fmm.h + fmm_stat.h + # fast_multipole_method + fast_multipole_method.h + fmm_stat.h + # chebyshev_fit + chebyshev_fit.h + # multibody_force + multibody_force_problem.h + multibody_kernel.h + # multibody_potential + at_potential_kernel.h + mbp_delta.h + mbp_global.h + mbp_kernel.h + mbp_query_postponed.h + mbp_query_result.h + mbp_query_summary.h + mbp_stat.h + multibody_potential_problem.h + three_body_gaussian_kernel.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# fast_multipole_method_bin executable +add_executable(fast_multipole_method + fast_multipole_method_main.cc +) +target_link_libraries(fast_multipole_method + fastlib + mlpack + mlpack_contrib +) + +add_executable(continuous_fmm + cfmm_main.cc +) +target_link_libraries(continuous_fmm + fastlib + mlpack + mlpack_contrib +) + +add_executable(multibody_force + multibody_force_main.cc +) +target_link_libraries(multibody_force + fastlib + mlpack + mlpack_contrib +) + +add_executable(multibody_potential + multibody_potential_main.cc +) +target_link_libraries(multibody_potential + fastlib + mlpack + mlpack_contrib +) + +# test executable +add_executable(chebyshev_fit_test + chebyshev_fit_test.cc +) +target_link_libraries(chebyshev_fit_test + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/dongryel/kde/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/dongryel/kde/CMakeLists.txt new file mode 100644 index 0000000000..1c201623c0 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/dongryel/kde/CMakeLists.txt @@ -0,0 +1,44 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + kde_cv.h + kde_delta.h + kde_error.h + kde_global.h + kde_problem.h + kde_query_postponed.h + kde_query_result.h + kde_query_summary.h + kde_stat.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable, renamed because MLPACK has a 'kde' program +add_executable(kde_dongryel + kde_main.cc +) +# link dependencies of test executable +target_link_libraries(kde_dongryel + fastlib + mlpack + mlpack_contrib +) + +add_executable(kde_cv_dongryel + kde_cv_main.cc +) +target_link_libraries(kde_cv_dongryel + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/dongryel/linear_algebra/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/dongryel/linear_algebra/CMakeLists.txt new file mode 100644 index 0000000000..0e0c8de5e2 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/dongryel/linear_algebra/CMakeLists.txt @@ -0,0 +1,27 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + kaczmarz_method.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# test executable +add_executable(linear_algebra_test + linear_algebra_test.cc +) +# link dependencies of test executable +target_link_libraries(linear_algebra_test + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/dongryel/linear_regression/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/dongryel/linear_regression/CMakeLists.txt new file mode 100644 index 0000000000..487a9acf20 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/dongryel/linear_regression/CMakeLists.txt @@ -0,0 +1,35 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # build.py did not include these in any library, but I have chosen to + linear_regression_model.h + linear_regression_model_dev.h + linear_regression_result.h + linear_regression_result_dev.h + qr_least_squares.h + qr_least_squares_dev.h + givens_rotate.h + givens_rotate_dev.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# test executable +add_executable(vif_test + vif_test.cc +) +# link dependencies of test executable +target_link_libraries(vif_test + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/dongryel/lprcde/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/dongryel/lprcde/CMakeLists.txt new file mode 100644 index 0000000000..d4bffc6fb2 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/dongryel/lprcde/CMakeLists.txt @@ -0,0 +1,27 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + nwrcde_problem.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(nwrcde + nwrcde_main.cc +) +# link dependencies of test executable +target_link_libraries(nwrcde + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/dongryel/matrix_factorized_fmm/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/dongryel/matrix_factorized_fmm/CMakeLists.txt new file mode 100644 index 0000000000..33749aec7a --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/dongryel/matrix_factorized_fmm/CMakeLists.txt @@ -0,0 +1,36 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + matrix_factorized_fmm.h + matrix_factorized_fmm_impl.h + matrix_factorized_fmm_stat.h +# naive_kde.h + matrix_factorized_local_expansion.h + matrix_factorized_local_expansion_impl.h + matrix_factorized_farfield_expansion.h + matrix_factorized_farfield_expansion_impl.h + cur_decomposition.h + matrix_factorized_kernel_aux.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(matrix_factorized_fmm + matrix_factorized_fmm_main.cc +) +# link dependencies of executable +target_link_libraries(matrix_factorized_fmm + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/dongryel/multitree_template/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/dongryel/multitree_template/CMakeLists.txt new file mode 100644 index 0000000000..7d892e0753 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/dongryel/multitree_template/CMakeLists.txt @@ -0,0 +1,18 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + multitree_dfs.h + multitree_dfs_impl.h + multitree_utility.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) diff --git a/fastlib/branches/fastlib-cmake/contrib/dongryel/nested_summation_template/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/dongryel/nested_summation_template/CMakeLists.txt new file mode 100644 index 0000000000..7b6e31addb --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/dongryel/nested_summation_template/CMakeLists.txt @@ -0,0 +1,21 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + function.h + nested_sum_utility.h + operator.h + ratio.h + strata.h + sum.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) diff --git a/fastlib/branches/fastlib-cmake/contrib/dongryel/pca/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/dongryel/pca/CMakeLists.txt new file mode 100644 index 0000000000..b616ba6256 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/dongryel/pca/CMakeLists.txt @@ -0,0 +1,27 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + pca.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(pca + main.cc +) +# link dependencies of executable +target_link_libraries(pca + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/dongryel/proximity_project/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/dongryel/proximity_project/CMakeLists.txt new file mode 100644 index 0000000000..f71feb7c29 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/dongryel/proximity_project/CMakeLists.txt @@ -0,0 +1,70 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + subspace_stat.h + cfmm_tree.h + cfmm_tree_impl.h + general_type_bounds.h + gen_hypercube_tree.h + gen_hypercube_tree_impl.h + gen_hypercube_tree_util.h + gen_range.h + gen_range.cc + gen_kdtree.h + gen_kdtree_impl.h + gen_kdtree_hyper.h + gen_kdtree_hyper_impl.h + gen_metric_tree.h + gen_metric_tree_impl.h + general_spacetree.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(cfmm_tree_test + cfmm_tree_test.cc +) +# link dependencies of executable +target_link_libraries(cfmm_tree_test + fastlib + mlpack + mlpack_contrib +) + +add_executable(gen_hypercube_tree_test + gen_hypercube_tree_test.cc +) +target_link_libraries(gen_hypercube_tree_test + fastlib + mlpack + mlpack_contrib +) + +add_executable(proximity_project + main.cc +) +target_link_libraries(proximity_project + fastlib + mlpack + mlpack_contrib +) + +add_executable(kfold_splitter + kfold_splitter.h + kfold_splitter.cc +) +target_link_libraries(kfold_splitter + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/dongryel/regression/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/dongryel/regression/CMakeLists.txt new file mode 100644 index 0000000000..1aa3d5fff5 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/dongryel/regression/CMakeLists.txt @@ -0,0 +1,54 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # dense_lpr + dense_lpr.h + dense_lpr_impl.h + epan_kernel_moment_info.h + lpr_util.h + matrix_util.h + multi_index_util.h + quick_prune_lpr.h + relative_prune_lpr.h + # krylov_lpr + # epan_kernel_moment_info.h # already included + krylov_lpr.h + krylov_lpr_setup_impl.h + krylov_lpr_solver_impl.h + krylov_lpr_test.h + # lpr_util.h # already included + multi_conjugate_gradient.h + multi_lanczos.h + naive_lpr.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(krylov_lpr + krylov_lpr_main.cc +) +# link dependencies of executable +target_link_libraries(krylov_lpr + fastlib + mlpack + mlpack_contrib +) + +add_executable(dense_lpr + dense_lpr_main.cc +) +target_link_libraries(dense_lpr + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/dongryel/thor_kde/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/dongryel/thor_kde/CMakeLists.txt new file mode 100644 index 0000000000..a278823efa --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/dongryel/thor_kde/CMakeLists.txt @@ -0,0 +1,27 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + thor_kde.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(thor_kde + thor_kde_main.cc +) +# link dependencies of executable +target_link_libraries(thor_kde + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/gmravi/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/gmravi/CMakeLists.txt new file mode 100644 index 0000000000..d49ebc0519 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/gmravi/CMakeLists.txt @@ -0,0 +1,14 @@ +cmake_minimum_required(VERSION 2.8) + +# we just want to recurse into the child directories here +set(DIRS +# hyperkernel_kde ## missing ichol.h +# local_kernel_machines ## does not compile, LocalKernelMachines::RunLocalKernelMachines_() fails to compile +# local_polynomial_density ## does not compile. +) + +foreach(dir ${DIRS}) + add_subdirectory(${dir}) +endforeach() + +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} PARENT_SCOPE) diff --git a/fastlib/branches/fastlib-cmake/contrib/gmravi/hyperkernel_kde/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/gmravi/hyperkernel_kde/CMakeLists.txt new file mode 100644 index 0000000000..a0e9424004 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/gmravi/hyperkernel_kde/CMakeLists.txt @@ -0,0 +1,95 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # hk_ippc_lib + hyperkernels.h + interior_point_pred_corr2.h + ichol_dynamic.h + dte.h + special_la.h + # test_ichol_lib ??? + ichol_dynamic.h + # adaptive_kde_lib + adaptive_kde.h + # variable_kde_lib + variable_nn_based_kde.h + # nn_kde_lib + nn_kde.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(hk_ippc + interior_point_pred_corr_main.cc +) +# link dependencies of executable +target_link_libraries(hk_ippc + fastlib + mlpack + mlpack_contrib +) + +#add_executable(varying_effects +# varying_effects.cc +#) +#target_link_libraries(varying_effects +# fastlib +# mlpack +# mlpack_contrib +#) + +add_executable(special_la_test # renamed from nonexplanatory "test" + special_la_main.cc +) +target_link_libraries(special_la_test + fastlib + mlpack + mlpack_contrib +) + +#add_executable(ichol_test +# test_ichol_main.cc +#) +#target_link_libraries(ichol_test +# fastlib +# mlpack +# mlpack_contrib +#) + +add_executable(adaptive_kde + adaptive_kde_main.cc +) +target_link_libraries(adaptive_kde + fastlib + mlpack + mlpack_contrib +) + +add_executable(variable_nn_based_kde + variable_nn_based_kde.h + variable_nn_based_kde_main.cc +) +target_link_libraries(variable_nn_based_kde + fastlib + mlpack + mlpack_contrib +) + +add_executable(nn_kde + nn_kde_main.cc +) +target_link_libraries(nn_kde + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/gmravi/local_kernel_machines/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/gmravi/local_kernel_machines/CMakeLists.txt new file mode 100644 index 0000000000..45cd7ac469 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/gmravi/local_kernel_machines/CMakeLists.txt @@ -0,0 +1,64 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # svm + opt_smo.h +# opt_sgd.h ## was in build.py but does not exist + svm.h + # svm_main.cc does not exist! + # utils + utils.h + utils.cc + # other things not properly documented or referenced in build.py + ocas.h + ocas.cc + ocas_line_search.h + ocas_line_search.cc + ocas_smo.h + ocas_smo.cc + range_search.h + my_crossvalidation.h + local_kernel_machines_def.h + local_kernel_machines_impl.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(local_kernel_machines + local_kernel_machines_main.cc +) +# link dependencies of executable +target_link_libraries(local_kernel_machines + fastlib + mlpack + mlpack_contrib +) + +# test executables (not documented in build.py) +add_executable(ocas_smo_test + ocas_smo_test.cc +) +target_link_libraries(ocas_smo_test + fastlib + mlpack + mlpack_contrib +) + +add_executable(range_search_test + range_search_test.cc +) +target_link_libraries(range_search_test + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/gmravi/local_polynomial_density/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/gmravi/local_polynomial_density/CMakeLists.txt new file mode 100644 index 0000000000..de07fdf4d4 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/gmravi/local_polynomial_density/CMakeLists.txt @@ -0,0 +1,43 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # naive_kde_local_polynomial + naive_kde_local_polynomial.h + vector_kernel.h + naive_local_likelihood.h + # density_crossvalidation + cross_validation.h + naive_kde.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(naive_kde_lp + naive_kde_local_polynomial_main.cc +) +# link dependencies of executable +target_link_libraries(naive_kde_lp + fastlib + mlpack + mlpack_contrib +) + +# test executables (not documented in build.py) +add_executable(crossvalidation + crossvalidation_density_estimates_main.cc +) +target_link_libraries(crossvalidation + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/houyang/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/houyang/CMakeLists.txt new file mode 100644 index 0000000000..74793aa14c --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/houyang/CMakeLists.txt @@ -0,0 +1,16 @@ +cmake_minimum_required(VERSION 2.8) + +# we just want to recurse into the child directories here +set(DIRS + allknn_balltree + allknn_kdtree + regmin + rvm +# svm ## requires mmanager +) + +foreach(dir ${DIRS}) + add_subdirectory(${dir}) +endforeach() + +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} PARENT_SCOPE) diff --git a/fastlib/branches/fastlib-cmake/contrib/houyang/allknn_balltree/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/houyang/allknn_balltree/CMakeLists.txt new file mode 100644 index 0000000000..27b653b6f4 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/houyang/allknn_balltree/CMakeLists.txt @@ -0,0 +1,39 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + gen_metric_tree.h + gen_metric_tree_impl.h + general_spacetree.h + allknn_balltree.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(bt_knn + allknn_balltree_test.cc +) +# link dependencies of executable +target_link_libraries(bt_knn + fastlib + mlpack + mlpack_contrib +) + +add_executable(allknn_balltree_graph + allknn_balltree_construct_graph.cc +) +target_link_libraries(allknn_balltree_graph + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/houyang/allknn_kdtree/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/houyang/allknn_kdtree/CMakeLists.txt new file mode 100644 index 0000000000..c028fdb97d --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/houyang/allknn_kdtree/CMakeLists.txt @@ -0,0 +1,36 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + allknn_kdtree.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(kdt_knn + allknn_kdtree_test.cc +) +# link dependencies of executable +target_link_libraries(kdt_knn + fastlib + mlpack + mlpack_contrib +) + +#add_executable(allknn_kdtree_graph +# allknn_kdtree_construct_graph.cc +#) +#target_link_libraries(allknn_kdtree_graph +# fastlib +# mlpack +# mlpack_contrib +#) diff --git a/fastlib/branches/fastlib-cmake/contrib/houyang/regmin/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/houyang/regmin/CMakeLists.txt new file mode 100644 index 0000000000..72e1028f31 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/houyang/regmin/CMakeLists.txt @@ -0,0 +1,33 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # svm + opt_smo.h + opt_sgd.h + opt_md.h + opt_tgd.h + regmin.h + regmin_data.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(regmin + regmin.cc +) +# link dependencies of executable +target_link_libraries(regmin + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/houyang/rvm/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/houyang/rvm/CMakeLists.txt new file mode 100644 index 0000000000..b82a4863c5 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/houyang/rvm/CMakeLists.txt @@ -0,0 +1,29 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + rvm.h + sbl_est.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(rvm + rvm_main.cc + rvm.h +) +# link dependencies of executable +target_link_libraries(rvm + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/houyang/svm/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/houyang/svm/CMakeLists.txt new file mode 100644 index 0000000000..fbccdb7f31 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/houyang/svm/CMakeLists.txt @@ -0,0 +1,50 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + general_spacetree.h + gen_kdtree.h + gen_metric_tree.h + gen_range.h + opt_fw.h + opt_lasvm.h + opt_par.h + opt_rivanov.h + opt_sgd.h + opt_smo.h + svm.h + general_type_bounds.h + gen_kdtree_impl.h + gen_metric_tree_impl.h + opt_cd.h + opt_hcy.h + opt_mfw.h + opt_pegasos.h + opt_sfw.h + opt_sgdwb.h + opt_sparsereg.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(svm_houyang + svm_main.cc + opt_smo.h + opt_sgd.h + svm.h +) +# link dependencies of executable +target_link_libraries(svm_houyang + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/huijing/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/huijing/CMakeLists.txt new file mode 100644 index 0000000000..b57e35c65a --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/huijing/CMakeLists.txt @@ -0,0 +1,12 @@ +cmake_minimum_required(VERSION 2.8) + +# we just want to recurse into the child directories here +set(DIRS +# centroids ## does not compile, likely needs some #includes +) + +foreach(dir ${DIRS}) + add_subdirectory(${dir}) +endforeach() + +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} PARENT_SCOPE) diff --git a/fastlib/branches/fastlib-cmake/contrib/huijing/centroids/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/huijing/centroids/CMakeLists.txt new file mode 100644 index 0000000000..1e22c62586 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/huijing/centroids/CMakeLists.txt @@ -0,0 +1,27 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # none! this should be changed +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(centroids + get_nodes.cc +) +# link dependencies of executable +target_link_libraries(centroids + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/jim/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/jim/CMakeLists.txt new file mode 100644 index 0000000000..bbd8f564d5 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/jim/CMakeLists.txt @@ -0,0 +1,15 @@ +cmake_minimum_required(VERSION 2.8) + +# we just want to recurse into the child directories here +set(DIRS + cart +# molecular_dynamics ## does not compile: DHrectBound<2> has no member named 'width' (does not make sense, it does) +# thor_md ## same error as above + thor_npoint +) + +foreach(dir ${DIRS}) + add_subdirectory(${dir}) +endforeach() + +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} PARENT_SCOPE) diff --git a/fastlib/branches/fastlib-cmake/contrib/jim/cart/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/jim/cart/CMakeLists.txt new file mode 100644 index 0000000000..ecf0844c3e --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/jim/cart/CMakeLists.txt @@ -0,0 +1,30 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # "cart_stuff" + cartree.h + split_tree.h + training_set.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(cart + cart_driver.cc +) +# link dependencies of executable +target_link_libraries(cart + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/jim/molecular_dynamics/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/jim/molecular_dynamics/CMakeLists.txt new file mode 100644 index 0000000000..ed6346e083 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/jim/molecular_dynamics/CMakeLists.txt @@ -0,0 +1,53 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # particle + particle_tree.h + two_body_stat.h + multi_physics_system.h + force_error.h + # particle2 + dual_physics_system.h + # test1 + test_particle_stat.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(particle_simulation + simulation_driver.cc +) +# link dependencies of executable +target_link_libraries(particle_simulation + fastlib + mlpack + mlpack_contrib +) + +add_executable(particle_stat_test + test_particle_stat.cc +) +target_link_libraries(particle_stat_test + fastlib + mlpack + mlpack_contrib +) + +add_executable(particle_dual_simulation + dual_simulation_driver.cc +) +target_link_libraries(particle_dual_simulation + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/jim/thor_md/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/jim/thor_md/CMakeLists.txt new file mode 100644 index 0000000000..b7b49eae8b --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/jim/thor_md/CMakeLists.txt @@ -0,0 +1,31 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + thor_md.h + dfs3.h + dfs3_impl.h + two_body.h + three_body.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(thor_md + thor_md_main.cc +) +# link dependencies of executable +target_link_libraries(thor_md + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/jim/thor_npoint/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/jim/thor_npoint/CMakeLists.txt new file mode 100644 index 0000000000..ac99a2aae1 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/jim/thor_npoint/CMakeLists.txt @@ -0,0 +1,45 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # thor_npc +# thor_npoint.h # was in build.py but does not exist + dfs3.h + dfs3_impl.h + two_point.h + three_point.h + thor_3point.h + # thor_2pc + thor_2point.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(thor_2pc + thor_2pt_main.cc +) +# link dependencies of executable +target_link_libraries(thor_2pc + fastlib + mlpack + mlpack_contrib +) + +# Does not compile correctly! +#add_executable(thor_3pc +# thor_3pt_main.cc +#) +#target_link_libraries(thor_3pc +# fastlib +# mlpack +# mlpack_contrib +#) diff --git a/fastlib/branches/fastlib-cmake/contrib/march/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/march/CMakeLists.txt new file mode 100644 index 0000000000..51b1b07ad0 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/march/CMakeLists.txt @@ -0,0 +1,17 @@ +cmake_minimum_required(VERSION 2.8) + +# we just want to recurse into the child directories here +set(DIRS + emst_cover + error +# fock_matrix ## awaiting resolution of #10 (requires libint) +# hf + npt +# scf ## awaiting resolution of #10 (requires libint) +) + +foreach(dir ${DIRS}) + add_subdirectory(${dir}) +endforeach() + +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} PARENT_SCOPE) diff --git a/fastlib/branches/fastlib-cmake/contrib/march/emst_cover/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/march/emst_cover/CMakeLists.txt new file mode 100644 index 0000000000..b93afbb96e --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/march/emst_cover/CMakeLists.txt @@ -0,0 +1,54 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # cover_tree + ctree.h + ctree_impl.h + cover_tree.h + # emst_cover + dtb_cover.h + emst_cover.h + # geomst2 + geomst2.h + # emst_cover.h # already included + # single_fragment + friedman_bentley.h + # emst_cover.h # already included + friedman_bentley.cc + # multi_fragment + multi_fragment.h + # emst_cover.h # already included + multi_fragment.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(emst_cover + emst_cover_main.cc +) +# link dependencies of executable +target_link_libraries(emst_cover + fastlib + mlpack + mlpack_contrib +) + +add_executable(mst_comparison + mst_comparison.h + comparison_main.cc +) +target_link_libraries(mst_comparison + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/march/error/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/march/error/CMakeLists.txt new file mode 100644 index 0000000000..c42a90e368 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/march/error/CMakeLists.txt @@ -0,0 +1,41 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # error_tester + naive_kernel_sum.h + hybrid_error_analysis.h + hybrid_error.h + hybrid_error_stat.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(error_tester + hybrid_error.cc +) +# link dependencies of executable +target_link_libraries(error_tester + fastlib + mlpack + mlpack_contrib +) + +#add_executable(naive_sum +# naive_kernel_sum.h +# naive_kernel_sum.cc +#) +#target_link_libraries(naive_sum +# fastlib +# mlpack +# mlpack_contrib +#) diff --git a/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/CMakeLists.txt new file mode 100644 index 0000000000..57bbfe3187 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/CMakeLists.txt @@ -0,0 +1,60 @@ +cmake_minimum_required(VERSION 2.8) + +# This project has subdirectories; we must recurse into them +add_subdirectory(cfmm) +add_subdirectory(chem_reader) +add_subdirectory(fock_impl) +add_subdirectory(link) +add_subdirectory(multi_tree) +add_subdirectory(naive) +add_subdirectory(prescreening) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # add_subdirectory commands have already added all of the subdir sources + + # fock_matrix_comparison + fock_matrix_comparison.h + fock_matrix_comparison.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(naive_fock_comparison +# naive_fock_matrix.h + naive_comparison.cc +) +# link dependencies of executable +target_link_libraries(naive_fock_comparison + fastlib + mlpack + mlpack_contrib +) + +add_executable(old_fock_matrix + cfmm/cfmm_coulomb.h + fock_matrix_main.cc +) +target_link_libraries(old_fock_matrix + fastlib + mlpack + mlpack_contrib +) + +add_executable(fock_matrix + fock_matrix_main.cc +) +target_link_libraries(fock_matrix + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/cfmm/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/cfmm/CMakeLists.txt new file mode 100644 index 0000000000..bd4d8a39aa --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/cfmm/CMakeLists.txt @@ -0,0 +1,34 @@ +cmake_minimum_required(VERSION 2.8) + +# This is not compiled into mlpack_contrib by default, since it appears to be custom one-time-use +# code that is not useful anywhere other than this one particular test + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # cfmm_coulomb + cfmm_coulomb.h + ../../../dongryel/fast_multipole_method/continuous_fmm.h + ../fock_impl/eri.h + cfmm_coulomb.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(cfmm_screening + cfmm_screening_main.cc +) +# link dependencies of executable +target_link_libraries(cfmm_screening + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/chem_reader/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/chem_reader/CMakeLists.txt new file mode 100644 index 0000000000..e7bcb07832 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/chem_reader/CMakeLists.txt @@ -0,0 +1,20 @@ +cmake_minimum_required(VERSION 2.8) + +# This is not compiled into mlpack_contrib by default, since it appears to be custom one-time-use +# code that is not useful anywhere other than this one particular test + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + chem_reader.h + chem_reader.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) diff --git a/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/fock_impl/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/fock_impl/CMakeLists.txt new file mode 100644 index 0000000000..7eab50315f --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/fock_impl/CMakeLists.txt @@ -0,0 +1,37 @@ +cmake_minimum_required(VERSION 2.8) + +# This is not compiled into mlpack_contrib by default, since it appears to be custom one-time-use +# code that is not useful anywhere other than this one particular test + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # eri + eri.h + eri.cc + shell_pair.h + shell_pair.cc + basis_shell.h + integral_tensor.h + integral_tensor.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(eri_test + eri_test.cc +) +# link dependencies of executable +target_link_libraries(eri_test + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/link/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/link/CMakeLists.txt new file mode 100644 index 0000000000..a585874e8c --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/link/CMakeLists.txt @@ -0,0 +1,34 @@ +cmake_minimum_required(VERSION 2.8) + +# This is not compiled into mlpack_contrib by default, since it appears to be custom one-time-use +# code that is not useful anywhere other than this one particular test + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # link_exchange + link.h + ../fock_impl/basis_shell.h + ../fock_impl/shell_pair.h + link.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(link_exchange + link_main.cc +) +# link dependencies of executable +target_link_libraries(link_exchange + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/multi_tree/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/multi_tree/CMakeLists.txt new file mode 100644 index 0000000000..44c5c0aa6d --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/multi_tree/CMakeLists.txt @@ -0,0 +1,63 @@ +cmake_minimum_required(VERSION 2.8) + +# This is not compiled into mlpack_contrib by default, since it appears to be custom one-time-use +# code that is not useful anywhere other than this one particular test + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # multi_tree_fock + multi_tree_fock.h + multi_tree_fock.cc + basis_shell_tree.h + basis_shell_tree.cc + shell_tree_impl.h + shell_tree_impl.cc + matrix_tree_impl.h + matrix_tree.cc + matrix_tree.h +# matrix_tree_bounds.cc # in build.py but does not exist + eri_bounds.h + eri_bounds.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(shell_tree_test + basis_shell_tree.h + basis_shell_tree.cc + shell_tree_impl.h + shell_tree_impl.cc + shell_tree_test.cc +) +# link dependencies of executable +target_link_libraries(shell_tree_test + fastlib + mlpack + mlpack_contrib +) + +add_executable(matrix_tree_test + basis_shell_tree.h + basis_shell_tree.cc + shell_tree_impl.h + shell_tree_impl.cc + matrix_tree.h + matrix_tree.cc + matrix_tree_impl.h + matrix_tree_impl.cc + matrix_tree_test.cc +) +target_link_libraries(matrix_tree_test + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/naive/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/naive/CMakeLists.txt new file mode 100644 index 0000000000..b0f9926af3 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/naive/CMakeLists.txt @@ -0,0 +1,31 @@ +cmake_minimum_required(VERSION 2.8) + +# This is not compiled into mlpack_contrib by default, since it appears to be custom one-time-use +# code that is not useful anywhere other than this one particular test + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + naive_fock_matrix.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(naive_fock + naive_fock_matrix.h + naive_fock_main.cc +) +# link dependencies of executable +target_link_libraries(naive_fock + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/prescreening/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/prescreening/CMakeLists.txt new file mode 100644 index 0000000000..ee87f11345 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/march/fock_matrix/prescreening/CMakeLists.txt @@ -0,0 +1,31 @@ +cmake_minimum_required(VERSION 2.8) + +# This is not compiled into mlpack_contrib by default, since it appears to be custom one-time-use +# code that is not useful anywhere other than this one particular test + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + schwartz_prescreening.h + schwartz_prescreening.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(schwartz_prescreening + schwartz_prescreening_main.cc +) +# link dependencies of executable +target_link_libraries(schwartz_prescreening + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/march/hf/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/march/hf/CMakeLists.txt new file mode 100644 index 0000000000..b498b13b1e --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/march/hf/CMakeLists.txt @@ -0,0 +1,56 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # dual_tree_integrals + dual_tree_integrals.h + dual_tree_integrals.cc + square_tree.h + # scf_solver + scf_solver.h + naive_fock_matrix.h + scf_solver.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(dual_tree_integrals + dual_tree_integrals.h + naive_fock_matrix.h + dual_tree_integrals_main.cc +) +# link dependencies of executable +target_link_libraries(dual_tree_integrals + fastlib + mlpack + mlpack_contrib +) + +add_executable(dualtree_fock_matrix_test + dual_tree_integrals.h + naive_fock_matrix.h + fock_matrix_test.cc +) +target_link_libraries(dualtree_fock_matrix_test + fastlib + mlpack + mlpack_contrib +) + +add_executable(hartree-fock + hf.cc +) +target_link_libraries(hartree-fock + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/march/npt/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/march/npt/CMakeLists.txt new file mode 100644 index 0000000000..991fbf4e2c --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/march/npt/CMakeLists.txt @@ -0,0 +1,40 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + matcher.h + matcher.cc + n_point.h + n_point.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(n_point_testing + n_point_testing.h + n_point_testing.cc +) +# link dependencies of executable +target_link_libraries(n_point_testing + fastlib + mlpack + mlpack_contrib +) + +add_executable(n_point + n_point_main.cc +) +target_link_libraries(n_point + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/march/scf/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/march/scf/CMakeLists.txt new file mode 100644 index 0000000000..0949f80d04 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/march/scf/CMakeLists.txt @@ -0,0 +1,28 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + scf_solver.h + scf_solver.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(scf_solver + scf_main.cc +) +# link dependencies of executable +target_link_libraries(scf_solver + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/niche/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/niche/CMakeLists.txt new file mode 100644 index 0000000000..ad5a77a284 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/niche/CMakeLists.txt @@ -0,0 +1,27 @@ +cmake_minimum_required(VERSION 2.8) + +# we just want to recurse into the child directories here +set(DIRS +# bayes_net_kde ## Huh? This is all MATLAB? +# dtw ## Does not compile right: ComputeDTWAlignmentScore() mismatch in calling syntax +# hmm ## Does not actually DO anything +# hshmm ## does not compile: invalid use of incomplete type 'struct stat' + kernel_kmeans + kernel_pca +# kernel_vector_mult ## Does not compile: mismatch in calling of KernelVectorMult::Init() +# kmeans_nonempty ## Too few arguments to do_mcf +# lds ## No actual usable code here +# log_newhmm ## apparent namespace conflicts? +# mmf ## apparent namespace conflicts? +# new_hmm ## apparent namespace conflicts? + regularized_ISM +# spike ## No actual code in here (except some LaTeX?) +# spike_train_dependence ## missing hsic.h +# svm ## does not compile, several mismatched function calls +) + +foreach(dir ${DIRS}) + add_subdirectory(${dir}) +endforeach() + +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} PARENT_SCOPE) diff --git a/fastlib/branches/fastlib-cmake/contrib/niche/dtw/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/niche/dtw/CMakeLists.txt new file mode 100644 index 0000000000..55b2f240a6 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/niche/dtw/CMakeLists.txt @@ -0,0 +1,60 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + dtw.h + dtw_impl.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(dtw + main.cc + dtw.h +) +# link dependencies of executable +target_link_libraries(dtw + fastlib + mlpack + mlpack_contrib +) + +add_executable(multidtw + dtw.h + dtw_impl.h + multivariate_main.cc +) +target_link_libraries(multidtw + fastlib + mlpack + mlpack_contrib +) + +add_executable(nearest_centroid + mean_ts_classifier.cc + dtw.h + dtw_impl.h +) +target_link_libraries(nearest_centroid + fastlib + mlpack + mlpack_contrib +) + +add_executable(arraylist_test + test_arraylist.cc +) +target_link_libraries(arraylist_test + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/niche/hshmm/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/niche/hshmm/CMakeLists.txt new file mode 100644 index 0000000000..b8d600576a --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/niche/hshmm/CMakeLists.txt @@ -0,0 +1,165 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + hmm.h + hmm_distance.h + gaussian.h + distribution.h + hshmm.h + lds.h + mmk.h + multinomial.h +# svm.h ## does not exist! +# svm.cc ## does not exist! +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(test_hmm_multinomial + load_profile.cc + test_hmm_multinomial.cc + +) +# link dependencies of executable +target_link_libraries(test_hmm_multinomial + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_hmm_gaussian + test_hmm_gaussian.cc +) +target_link_libraries(test_hmm_gaussian + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_lds + test_lds.cc +) +target_link_libraries(test_lds + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_gaussian + test_gaussian.cc +) +target_link_libraries(test_gaussian + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_distribution + test_distribution.cc +) +target_link_libraries(test_distribution + fastlib + mlpack + mlpack_contrib +) + +#add_executable(test_debug +# testdebug.cc +#) +#target_link_libraries(test_debug +# fastlib +# mlpack +# mlpack_contrib +#) + +add_executable(load_profile + load_profile.cc +) +target_link_libraries(load_profile + fastlib + mlpack + mlpack_contrib +) + +add_executable(hmm_testing + hmm_testing.cc + hmm_testing.h + test_hmm_multinomial.cc + ../mmf/mmf3.cc + ../svm/svm.h + ../svm/smo.h +) +target_link_libraries(hmm_testing + fastlib + mlpack + mlpack_contrib +) + +add_executable(hmm_generative_classifier + hmm_generative_classifier.cc + test_hmm_multinomial.cc + ../mmf/mmf3.cc + hmm_testing.h + ../svm/svm.h +) +target_link_libraries(hmm_generative_classifier + fastlib + mlpack + mlpack_contrib +) + +add_executable(read_variable_file + read_variable_file.cc + test_hmm_multinomial.cc + ../mmf/mmf3.cc + hmm_testing.h + ../svm/svm.h +) +target_link_libraries(read_variable_file + fastlib + mlpack + mlpack_contrib +) + +#add_executable(perm_dna +# perm_dna.cc +# test_hmm_multinomial.cc +# ../mmf/mmf3.cc +# hmm_testing.h +# ../svm/svm.h +#) +#target_link_libraries(perm_dna +# fastlib +# mlpack +# mlpack_contrib +#) + +#add_executable(test_serial +# test_serial.cc +#) +#target_link_libraries(test_serial +# fastlib +# mlpack +# mlpack_contrib +#) + +add_executable(test_obs_kernel + test_obs_kernel.cc + mmk.h +# ppk.h ## does not exist! +) +target_link_libraries(test_obs_kernel + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/niche/kernel_kmeans/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/niche/kernel_kmeans/CMakeLists.txt new file mode 100644 index 0000000000..eaa76820d0 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/niche/kernel_kmeans/CMakeLists.txt @@ -0,0 +1,27 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + kernel_kmeans.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(kernel_kmeans + main.cc +) +# link dependencies of executable +target_link_libraries(kernel_kmeans + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/niche/kernel_pca/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/niche/kernel_pca/CMakeLists.txt new file mode 100644 index 0000000000..02bc581c26 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/niche/kernel_pca/CMakeLists.txt @@ -0,0 +1,34 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + kernel_pca.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(kernel_pca_standalone + kernel_pca_main.cc +) +# link dependencies of executable +target_link_libraries(kernel_pca_standalone + fastlib +) + +add_executable(kernel_pca_from_lib + kernel_pca_main.cc +) +target_link_libraries(kernel_pca_from_lib + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/niche/kernel_vector_mult/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/niche/kernel_vector_mult/CMakeLists.txt new file mode 100644 index 0000000000..3bbd19c435 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/niche/kernel_vector_mult/CMakeLists.txt @@ -0,0 +1,35 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + kernel_vector_mult.h + solvelinsys.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(kernel_vector_mult + kernel_vector_mult_main.cc +) +# link dependencies of executable +target_link_libraries(kernel_vector_mult + fastlib +) + +add_executable(solvelinsys + solvelinsys_main.cc +) +target_link_libraries(solvelinsys + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/niche/kmeans_nonempty/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/niche/kmeans_nonempty/CMakeLists.txt new file mode 100644 index 0000000000..8a6c8bb588 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/niche/kmeans_nonempty/CMakeLists.txt @@ -0,0 +1,47 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + kmeans_nonempty.h + la_augment.h + do_mcf.h + mcf/readmin.c + mcf/mcfutil.c + mcf/pbeampp2.c + mcf/pstart.c + mcf/pbla.c + mcf/treeup.c + mcf/pflowup.c + mcf/psimplex.c + mcf/output.c +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(kmeans_nonempty_test + kmeans_nonempty.cc +) +# link dependencies of executable +target_link_libraries(kmeans_nonempty_test + fastlib + mlpack + mlpack_contrib +) + +add_executable(do_mcf + do_mcf.cc +) +target_link_libraries(do_mcf + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/niche/log_newhmm/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/niche/log_newhmm/CMakeLists.txt new file mode 100644 index 0000000000..cf3851bf6e --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/niche/log_newhmm/CMakeLists.txt @@ -0,0 +1,461 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + diag_gaussian.h + empirical_mmk.h + empirical_mmk_impl.h + fisher_kernel.h + fisher_kernel_impl.h + gaussian.h + generative_mmk.h + generative_mmk_impl.h + hmm.h + hmm_kernel_utils.h + isotropic_gaussian.h + kernel_pca.h + latent_mmk.h + latent_mmk_impl.h + la_utils.h + loghmm.h + logprob_matrixmult.h + mixture.h + multinomial.h + utils.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(test_emmk + test_emmk.cc + test_utils.h + test_engine.h + test_engine_impl.h +) +# link dependencies of executable +target_link_libraries(test_emmk + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_clique_mult + test_clique_mult.cc +) +target_link_libraries(test_clique_mult + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_fisher_kernel + test_fisher_kernel.cc + test_utils.h + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_fisher_kernel + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_gmmk_cont + test_gmmk.cc + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_gmmk_cont + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_bayes + test_bayes.cc + test_engine.h + test_engine_impl.h + test_utils.h +) +target_link_libraries(test_bayes + fastlib + mlpack + mlpack_contrib +) + +add_executable(save_one_hmm + save_one_hmm.cc + test_engine.h + test_engine_impl.h +) +target_link_libraries(save_one_hmm + fastlib + mlpack + mlpack_contrib +) + +add_executable(save_one_fmri_hmm + save_one_fmri_hmm.cc + test_engine.h + test_engine_impl.h +) +target_link_libraries(save_one_fmri_hmm + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_fmri_gmmk + test_fmri_gmmk.cc +# test_fmri_utils.cc + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_fmri_gmmk + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_fmri_bayes + test_fmri_bayes.cc + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_fmri_bayes + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_load + test_load.cc +) +target_link_libraries(test_load + fastlib + mlpack + mlpack_contrib +) + +#add_executable(test_k +# test_k.cc +#) +#target_link_libraries(test_k +# fastlib +# mlpack +# mlpack_contrib +#) + +add_executable(kernel_pca + kpca.cc + kernel_pca.h +) +target_link_libraries(kernel_pca + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_inbio_kpca + test_inbio_kpca.cc +) +target_link_libraries(test_inbio_kpca + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_kill_duplicate_points + test_kill_duplicate_points.cc +) +target_link_libraries(test_kill_duplicate_points + fastlib + mlpack + mlpack_contrib +) + +add_executable(save_one_dna_hmm + save_one_dna_hmm.cc +) +target_link_libraries(save_one_dna_hmm + fastlib + mlpack + mlpack_contrib +) + +add_executable(save_one_synth_hmm + save_one_synth_hmm.cc + test_engine.h + test_engine_impl.h +) +target_link_libraries(save_one_synth_hmm + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_dna_fisher_kernel + test_dna_fisher_kernel.cc + test_dna_utils.h + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_dna_fisher_kernel + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_synth_fisher_kernel + test_synth_fisher_kernel.cc + test_synth_utils.h + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_synth_fisher_kernel + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_dna_emmk + test_dna_emmk.cc + test_dna_utils.h + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_dna_emmk + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_synth_emmk + test_synth_emmk.cc + test_synth_utils.h + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_synth_emmk + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_dna_bayes + test_dna_bayes.cc + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_dna_bayes + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_synth_bayes + test_synth_bayes.cc + test_synth_utils.h + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_synth_bayes + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_dna_lmmk + test_dna_lmmk.cc + test_dna_utils.h + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_dna_lmmk + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_synth_lmmk + test_synth_lmmk.cc + test_synth_utils.h + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_synth_lmmk + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_dna_lmmk2 + test_dna_lmmk2.cc + test_dna_utils.h + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_dna_lmmk2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_synth_lmmk2 + test_synth_lmmk2.cc + test_synth_utils.h + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_synth_lmmk2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_dna_gmmk + test_dna_gmmk.cc + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_dna_gmmk + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_synth_gmmk + test_synth_gmmk.cc + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_synth_gmmk + fastlib + mlpack + mlpack_contrib +) + +add_executable(empirical_mmk + empirical_mmk.h + empirical_mmk_impl.h + empirical_mmk.cc +) +target_link_libraries(empirical_mmk + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_engine + test_engine.cc + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_engine + fastlib + mlpack + mlpack_contrib +) + +add_executable(get_optimal_kde_bandwidth + get_optimal_kde_bandwidth.cc +) +target_link_libraries(get_optimal_kde_bandwidth + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_isotropic_gaussian + test_isotropic_gaussian.cc + isotropic_gaussian.h +) +target_link_libraries(test_isotropic_gaussian + fastlib + mlpack + mlpack_contrib +) + +add_executable(generative_mmk + generative_mmk.cc +) +target_link_libraries(generative_mmk + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_latent_mmk + test_latent_mmk.cc +) +target_link_libraries(test_latent_mmk + fastlib + mlpack + mlpack_contrib +) + +add_executable(latent_mmk + latent_mmk.cc +) +target_link_libraries(latent_mmk + fastlib + mlpack + mlpack_contrib +) + +add_executable(loghmm + hmm.cc + loghmm.h +) +target_link_libraries(loghmm + fastlib + mlpack + mlpack_contrib +) + +add_executable(hmm_niche + hmm.cc + hmm.h +) +target_link_libraries(hmm_niche + fastlib + mlpack + mlpack_contrib +) + +#add_executable(test_template_classes +# test_template_classes.cc +# test_template_classes.h +#) +#target_link_libraries(test_template_classes +# fastlib +# mlpack +# mlpack_contrib +#) + +#add_executable(test_matrix +# testMatrix.cc +#) +#target_link_libraries(test_matrix +# fastlib +# mlpack +# mlpack_contrib +#) + +add_executable(otrav_mem_test + otrav_mem_test.cc +) +target_link_libraries(otrav_mem_test + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/niche/mmf/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/niche/mmf/CMakeLists.txt new file mode 100644 index 0000000000..5051d5a3c0 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/niche/mmf/CMakeLists.txt @@ -0,0 +1,100 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + support.h + support.cc + discreteHMM.h + discreteHMM.cc + gaussianHMM.h + gaussianHMM.cc + mixgaussHMM.h + mixgaussHMM.cc + mixtureDST.h + mixtureDST.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# all executables suffixed with _niche because I believe they already all exist in fastlib +# executable +add_executable(generate_niche + generate.cc +) +# link dependencies of executable +target_link_libraries(generate_niche + fastlib + mlpack + mlpack_contrib +) + +add_executable(loglik_niche + loglik.cc +) +target_link_libraries(loglik_niche + fastlib + mlpack + mlpack_contrib +) + +add_executable(viterbi_niche + viterbi.cc +) +target_link_libraries(viterbi_niche + fastlib + mlpack + mlpack_contrib +) + +add_executable(train_niche + train.cc +) +target_link_libraries(train_niche + fastlib + mlpack + mlpack_contrib +) + +add_executable(mmf_niche + mmf.cc +) +target_link_libraries(mmf_niche + fastlib + mlpack + mlpack_contrib +) + +add_executable(mmf1_niche + mmf1.cc +) +target_link_libraries(mmf1_niche + fastlib + mlpack + mlpack_contrib +) + +add_executable(mmf2_niche + mmf2.cc +) +target_link_libraries(mmf2_niche + fastlib + mlpack + mlpack_contrib +) + +add_executable(mmf3_niche + mmf3.cc +) +target_link_libraries(mmf3_niche + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/niche/new_hmm/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/niche/new_hmm/CMakeLists.txt new file mode 100644 index 0000000000..099df56fc6 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/niche/new_hmm/CMakeLists.txt @@ -0,0 +1,437 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + diag_gaussian.h + empirical_mmk.h + empirical_mmk_impl.h + fisher_kernel.h + fisher_kernel_impl.h + gaussian.h + generative_mmk.h + generative_mmk_impl.h + hmm.h + hmm_kernel_utils.h + isotropic_gaussian.h + kernel_pca.h + latent_mmk.h + latent_mmk_impl.h + la_utils.h + loghmm.h +# logprob_matrixmult.h + mixture.h + multinomial.h + utils.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +#add_executable(test_gmmk_cont_2 +# test_gmmk_cont.cc +# test_engine.h +# test_engine_impl.h +#) +#target_link_libraries(test_gmmk_cont_2 +# fastlib +# mlpack +# mlpack_contrib +#) + +#add_executable(test_gmmk_2 +# test_gmmk.cc +# test_engine.h +# test_engine_impl.h +#) +#target_link_libraries(test_gmmk_2 +# fastlib +# mlpack +# mlpack_contrib +#) + +add_executable(test_bayes_2 + test_bayes.cc + test_engine.h + test_engine_impl.h + test_utils.h +) +target_link_libraries(test_bayes_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(save_one_hmm_2 + save_one_hmm.cc + test_engine.h + test_engine_impl.h +) +target_link_libraries(save_one_hmm_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(save_one_fmri_hmm_2 + save_one_fmri_hmm.cc + test_engine.h + test_engine_impl.h +) +target_link_libraries(save_one_fmri_hmm_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_fmri_gmmk_2 + test_fmri_gmmk.cc +# test_fmri_utils.cc + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_fmri_gmmk_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_fmri_bayes_2 + test_fmri_bayes.cc + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_fmri_bayes_2 + fastlib + mlpack + mlpack_contrib +) + +#add_executable(test_load_2 +# test_load.cc +#) +#target_link_libraries(test_load_2 +# fastlib +# mlpack +# mlpack_contrib +#) + +#add_executable(test_k_2 +# test_k.cc +#) +#target_link_libraries(test_k_2 +# fastlib +# mlpack +# mlpack_contrib +#) + +add_executable(kernel_pca_2 + kpca.cc + kernel_pca.h +) +target_link_libraries(kernel_pca_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_inbio_kpca_2 + test_inbio_kpca.cc +) +target_link_libraries(test_inbio_kpca_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_kill_duplicate_points_2 + test_kill_duplicate_points.cc +) +target_link_libraries(test_kill_duplicate_points_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(save_one_dna_hmm_2 + save_one_dna_hmm.cc +) +target_link_libraries(save_one_dna_hmm_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(save_one_synth_hmm_2 + save_one_synth_hmm.cc + test_engine.h + test_engine_impl.h +) +target_link_libraries(save_one_synth_hmm_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_dna_fisher_kernel_2 + test_dna_fisher_kernel.cc + test_dna_utils.h + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_dna_fisher_kernel_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_synth_fisher_kernel_2 + test_synth_fisher_kernel.cc + test_synth_utils.h + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_synth_fisher_kernel_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_dna_emmk_2 + test_dna_emmk.cc + test_dna_utils.h + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_dna_emmk_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_synth_emmk_2 + test_synth_emmk.cc + test_synth_utils.h + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_synth_emmk_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_dna_bayes_2 + test_dna_bayes.cc + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_dna_bayes_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_synth_bayes_2 + test_synth_bayes.cc + test_synth_utils.h + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_synth_bayes_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_dna_lmmk_2 + test_dna_lmmk.cc + test_dna_utils.h + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_dna_lmmk_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_synth_lmmk_2 + test_synth_lmmk.cc + test_synth_utils.h + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_synth_lmmk_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_dna_lmmk2_2 + test_dna_lmmk2.cc + test_dna_utils.h + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_dna_lmmk2_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_synth_lmmk2_2 + test_synth_lmmk2.cc + test_synth_utils.h + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_synth_lmmk2_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_dna_gmmk_2 + test_dna_gmmk.cc + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_dna_gmmk_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_synth_gmmk_2 + test_synth_gmmk.cc + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_synth_gmmk_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(empirical_mmk_2 + empirical_mmk.h + empirical_mmk_impl.h + empirical_mmk.cc +) +target_link_libraries(empirical_mmk_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_engine_2 + test_engine.cc + test_engine.h + test_engine_impl.h +) +target_link_libraries(test_engine_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(get_optimal_kde_bandwidth_2 + get_optimal_kde_bandwidth.cc +) +target_link_libraries(get_optimal_kde_bandwidth_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_isotropic_gaussian_2 + test_isotropic_gaussian.cc + isotropic_gaussian.h +) +target_link_libraries(test_isotropic_gaussian_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(generative_mmk_2 + generative_mmk.cc +) +target_link_libraries(generative_mmk_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(test_latent_mmk_2 + test_latent_mmk.cc +) +target_link_libraries(test_latent_mmk_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(latent_mmk_2 + latent_mmk.cc +) +target_link_libraries(latent_mmk_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(loghmm_2 + hmm.cc + loghmm.h +) +target_link_libraries(loghmm_2 + fastlib + mlpack + mlpack_contrib +) + +add_executable(hmm_niche_2 + hmm.cc + hmm.h +) +target_link_libraries(hmm_niche_2 + fastlib + mlpack + mlpack_contrib +) + +#add_executable(test_template_classes_2 +# test_template_classes.cc +# test_template_classes.h +#) +#target_link_libraries(test_template_classes_2 +# fastlib +# mlpack +# mlpack_contrib +#) + +#add_executable(test_matrix_2 +# testMatrix.cc +#) +#target_link_libraries(test_matrix_2 +# fastlib +# mlpack +# mlpack_contrib +#) + +add_executable(otrav_mem_test_2 + otrav_mem_test.cc +) +target_link_libraries(otrav_mem_test_2 + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/niche/regularized_ISM/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/niche/regularized_ISM/CMakeLists.txt new file mode 100644 index 0000000000..57472ff309 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/niche/regularized_ISM/CMakeLists.txt @@ -0,0 +1,11 @@ +cmake_minimum_required(VERSION 2.8) + +# we just want to recurse into the child directories here +set(DIRS + # I don't know what the hell is in csdp_testing so I will ignore it + write_cvxmod_program +) + +foreach(dir ${DIRS}) + add_subdirectory(${dir}) +endforeach() diff --git a/fastlib/branches/fastlib-cmake/contrib/niche/regularized_ISM/write_cvxmod_program/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/niche/regularized_ISM/write_cvxmod_program/CMakeLists.txt new file mode 100644 index 0000000000..fbbda53d13 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/niche/regularized_ISM/write_cvxmod_program/CMakeLists.txt @@ -0,0 +1,36 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # no sources +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(write_cvxmod_prog + write_cvxmod_prog.cc +) +# link dependencies of executable +target_link_libraries(write_cvxmod_prog + fastlib + mlpack + mlpack_contrib +) + +add_executable(extract_dists + extract_dists.cc +) +target_link_libraries(extract_dists + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/niche/spike_train_dependence/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/niche/spike_train_dependence/CMakeLists.txt new file mode 100644 index 0000000000..730a4b3a99 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/niche/spike_train_dependence/CMakeLists.txt @@ -0,0 +1,27 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + hs_spike.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(hs_spike + hs_spike.cc +) +# link dependencies of executable +target_link_libraries(hs_spike + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/niche/svm/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/niche/svm/CMakeLists.txt new file mode 100644 index 0000000000..f16b0298a0 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/niche/svm/CMakeLists.txt @@ -0,0 +1,28 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + svm.h + smo.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(svm_niche + svm_main.cc +) +# link dependencies of executable +target_link_libraries(svm_niche + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/nvasil/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/nvasil/CMakeLists.txt new file mode 100644 index 0000000000..0479a8077c --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/nvasil/CMakeLists.txt @@ -0,0 +1,23 @@ +cmake_minimum_required(VERSION 2.8) + +# we just want to recurse into the child directories here +set(DIRS +# all_centroid_knn ## does not compile: fastlib::fx has changed +# allkfn ## this exists in MLPACK non-contrib already +# convex_nmf ## depends on l_bfgs code which does not exist +# dual_manifold ## depends on l_bfgs code which does not exist +# l_bfgs ## directory is empty +# manifold_plot ## MATLAB routines +# multiscale_mvu ## depends on l_bfgs code which does not exist +# mvu ## depends on l_bfgs code which does not exist + nmf_tree +# non_convex_mvu ## fastlib::fx syntax has changed, does not compile +# non_convex_nmf ## depends on l_bfgs code which does not exist +# test_svd ## directory is empty +) + +foreach(dir ${DIRS}) + add_subdirectory(${dir}) +endforeach() + +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} PARENT_SCOPE) diff --git a/fastlib/branches/fastlib-cmake/contrib/nvasil/all_centroid_knn/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/nvasil/all_centroid_knn/CMakeLists.txt new file mode 100644 index 0000000000..e1c43997d7 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/nvasil/all_centroid_knn/CMakeLists.txt @@ -0,0 +1,27 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + all_centroid_knn.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(all_centroid_knn_test + all_centroid_knn_test.cc +) +# link dependencies of executable +target_link_libraries(all_centroid_knn_test + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/nvasil/convex_nmf/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/nvasil/convex_nmf/CMakeLists.txt new file mode 100644 index 0000000000..f1c4b17aeb --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/nvasil/convex_nmf/CMakeLists.txt @@ -0,0 +1,38 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # nmflib + sdp_objectives.h + sdp_objectives_impl.h + sdp_nmf_engine.h + geometric_nmf.h + geometric_nmf_impl.h + geometric_nmf_engine.h + geometric_nmf_seq_engine.h + # gopnmflib + gop_nmf.h + gop_nmf_impl.h + splitter.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(nmf + main.cc +) +# link dependencies of executable +target_link_libraries(nmf + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/nvasil/dual_manifold/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/nvasil/dual_manifold/CMakeLists.txt new file mode 100644 index 0000000000..0267e6d164 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/nvasil/dual_manifold/CMakeLists.txt @@ -0,0 +1,40 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + dual_manifold_engine.h + dual_manifold_engine_impl.h + mvu_dot_prod_objective.h + mvu_dot_prod_objective_impl.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(dual_manifold + main.cc +) +# link dependencies of executable +target_link_libraries(dual_manifold + fastlib + mlpack + mlpack_contrib +) + +# test executable +add_executable(dual_manifold_test + dual_manifold_engine_test.cc +) +target_link_libraries(dual_manifold_test + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/nvasil/multiscale_mvu/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/nvasil/multiscale_mvu/CMakeLists.txt new file mode 100644 index 0000000000..758622b0d4 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/nvasil/multiscale_mvu/CMakeLists.txt @@ -0,0 +1,27 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + multiscale_mvu.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(multiscale_mvu_test + multiscale_mvu_test.cc +) +# link dependencies of executable +target_link_libraries(multiscale_mvu_test + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/nvasil/mvu/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/nvasil/mvu/CMakeLists.txt new file mode 100644 index 0000000000..6e092bcb76 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/nvasil/mvu/CMakeLists.txt @@ -0,0 +1,39 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + mvu_objectives.h + mvu_objectives_impl.h + mvu_classification.h + mvu_classification_impl.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(ncmvu + main.cc +) +# link dependencies of executable +target_link_libraries(ncmvu + fastlib + mlpack + mlpack_contrib +) + +add_executable(ncmvuc + main_classifier.cc +) +target_link_libraries(ncmvuc + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/nvasil/nmf_tree/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/nvasil/nmf_tree/CMakeLists.txt new file mode 100644 index 0000000000..65b68bb090 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/nvasil/nmf_tree/CMakeLists.txt @@ -0,0 +1,30 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + gop_tight_nmf_engine.h + gop_tight_nmf_engine_impl.h + relaxed_nmf_bound_tightener.h + relaxed_nmf_bound_tightener_impl.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +#add_executable(gop_tight_nmf_engine_test +# gop_tight_nmf_engine_test.cc +#) +# link dependencies of executable +#target_link_libraries(gop_tight_nmf_engine_test +# fastlib +# mlpack +# mlpack_contrib +#) diff --git a/fastlib/branches/fastlib-cmake/contrib/nvasil/non_convex_mvu/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/nvasil/non_convex_mvu/CMakeLists.txt new file mode 100644 index 0000000000..f2f3a0ecf1 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/nvasil/non_convex_mvu/CMakeLists.txt @@ -0,0 +1,38 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + non_convex_mvu.h + non_convex_mvu_impl.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(ncmvu_2 + main.cc +) +# link dependencies of executable +target_link_libraries(ncmvu_2 + fastlib + mlpack + mlpack_contrib +) + +# test executable +add_executable(ncmvu_test + non_convex_mvu_test.cc +) +target_link_libraries(ncmvu_test + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/nvasil/non_convex_nmf/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/nvasil/non_convex_nmf/CMakeLists.txt new file mode 100644 index 0000000000..84464b36a2 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/nvasil/non_convex_nmf/CMakeLists.txt @@ -0,0 +1,29 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + nmf_objectives.h + nmf_objectives_impl.h + nmf_engine.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(nonconvex_nmf + main.cc +) +# link dependencies of executable +target_link_libraries(nonconvex_nmf + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/pram/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/pram/CMakeLists.txt new file mode 100644 index 0000000000..12844b4388 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/pram/CMakeLists.txt @@ -0,0 +1,18 @@ +cmake_minimum_required(VERSION 2.8) + +# we just want to recurse into the child directories here +set(DIRS +# approx_nn ## requires errno, does not compile (simple #include) + covertrees + density_tree +# lle ## fastlib::fx syntax has changed, does not compile +# mog_l2e ## linker error against la:: components, does not link +# opt ## fastlib::fx syntax has changed, does not compile +# sparsepca ## fastlib::fx syntax has changed, does not compile +) + +foreach(dir ${DIRS}) + add_subdirectory(${dir}) +endforeach() + +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} PARENT_SCOPE) diff --git a/fastlib/branches/fastlib-cmake/contrib/pram/approx_nn/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/pram/approx_nn/CMakeLists.txt new file mode 100644 index 0000000000..5bffb16c26 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/pram/approx_nn/CMakeLists.txt @@ -0,0 +1,39 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # approxnn + approx_nn.h + # approxnn_dual + approx_nn_dual.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(approx_nn + main.cc +) +# link dependencies of executable +target_link_libraries(approx_nn + fastlib + mlpack + mlpack_contrib +) + +add_executable(approx_nn_dual + main_dual.cc +) +target_link_libraries(approx_nn_dual + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/pram/covertrees/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/pram/covertrees/CMakeLists.txt new file mode 100644 index 0000000000..13435e618b --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/pram/covertrees/CMakeLists.txt @@ -0,0 +1,36 @@ +cmake_minimum_required(VERSION 2.8) + +# We have subdirectories in this project +add_subdirectory(epxtl_gc) +#add_subdirectory(exptl) ## appears deprecated? + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + ctree.h + ctree_impl.h + cover_tree.h + allknn.h + allknn_impl.h + distances.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(cover_tree_test + cover_tree_test.cc +) +# link dependencies of executable +target_link_libraries(cover_tree_test + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/pram/covertrees/epxtl_gc/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/pram/covertrees/epxtl_gc/CMakeLists.txt new file mode 100644 index 0000000000..02e1f1efb6 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/pram/covertrees/epxtl_gc/CMakeLists.txt @@ -0,0 +1,33 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + ctree_gc.h + ctree_impl.h + cover_tree_gc.h + allknn_gc.h + allknn_impl.h + distances_gc.h + gonzalez_gc.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(cover_tree_test_gc + cover_tree_test_gc.cc +) +# link dependencies of executable +target_link_libraries(cover_tree_test_gc + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/pram/density_tree/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/pram/density_tree/CMakeLists.txt new file mode 100644 index 0000000000..10678545a3 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/pram/density_tree/CMakeLists.txt @@ -0,0 +1,27 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + dtree.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(dtree + main.cc +) +# link dependencies of executable +target_link_libraries(dtree + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/pram/lle/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/pram/lle/CMakeLists.txt new file mode 100644 index 0000000000..71c721ef5a --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/pram/lle/CMakeLists.txt @@ -0,0 +1,37 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + lle.h +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(lle + lle_main.cc +) +# link dependencies of executable +target_link_libraries(lle + fastlib + mlpack + mlpack_contrib +) + +# test executable +#add_executable(lle_tests +# lle_tests.cc +#) +#target_link_libraries(lle_tests +# fastlib +# mlpack +# mlpack_contrib +#) diff --git a/fastlib/branches/fastlib-cmake/contrib/pram/mog_l2e/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/pram/mog_l2e/CMakeLists.txt new file mode 100644 index 0000000000..1eb9bb441a --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/pram/mog_l2e/CMakeLists.txt @@ -0,0 +1,39 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + mog.h + phi.h + mog.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(mog_l2e_pram + mog_l2e_main.cc +) +# link dependencies of executable +target_link_libraries(mog_l2e_pram + fastlib + mlpack + mlpack_contrib +) + +# test executable +#add_executable(mog_l2e_tests +# mog_l2e_tests.cc +#) +#target_link_libraries(mog_l2e_tests +# fastlib +# mlpack +# mlpack_contrib +#) diff --git a/fastlib/branches/fastlib-cmake/contrib/pram/opt/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/pram/opt/CMakeLists.txt new file mode 100644 index 0000000000..a1449eedfc --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/pram/opt/CMakeLists.txt @@ -0,0 +1,29 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + optimizers_reloaded.h + optimizers_reloaded.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(optimizer_pram + phi.h + main.cc +) +# link dependencies of executable +target_link_libraries(optimizer_pram + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/pram/sparsepca/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/pram/sparsepca/CMakeLists.txt new file mode 100644 index 0000000000..d73c2a95cb --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/pram/sparsepca/CMakeLists.txt @@ -0,0 +1,38 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + sparsepca.h + sparsepca.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(sparse_pca + spca_main.cc +) +# link dependencies of executable +target_link_libraries(sparse_pca + fastlib + mlpack + mlpack_contrib +) + +# test executable +#add_executable(sparse_pca_tests +# sparsepca_tests.cc +#) +#target_link_libraries(sparse_pca_tests +# fastlib +# mlpack +# mlpack_contrib +#) diff --git a/fastlib/branches/fastlib-cmake/contrib/rriegel/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/rriegel/CMakeLists.txt new file mode 100644 index 0000000000..2a2d5a0bfd --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/rriegel/CMakeLists.txt @@ -0,0 +1,12 @@ +cmake_minimum_required(VERSION 2.8) + +# we just want to recurse into the child directories here +set(DIRS + nbc +) + +foreach(dir ${DIRS}) + add_subdirectory(${dir}) +endforeach() + +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} PARENT_SCOPE) diff --git a/fastlib/branches/fastlib-cmake/contrib/rriegel/nbc/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/rriegel/nbc/CMakeLists.txt new file mode 100644 index 0000000000..350004b289 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/rriegel/nbc/CMakeLists.txt @@ -0,0 +1,37 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # no sources to include in library! (this should be changed) +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(nbc_single + nbc-single.cc +) +# link dependencies of executable +target_link_libraries(nbc_single + fastlib + mlpack + mlpack_contrib +) + +# test executable +add_executable(nbc_multi + nbc-multi.cc +) +target_link_libraries(nbc_multi + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/soyeon/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/soyeon/CMakeLists.txt new file mode 100644 index 0000000000..bb3707b8b6 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/soyeon/CMakeLists.txt @@ -0,0 +1,23 @@ +cmake_minimum_required(VERSION 2.8) + +# we just want to recurse into the child directories here +set(DIRS +# DDCM ## unusable code +# ddcm_sim1 ## does not link; looking for nonexistent data::Load function +# ddcm_test ## apparent one-time use code +# ddcm_test2 ## apparent one-time use code +# ddcm_test3 ## apparent one-time use code +# obj ## apparently never finished +# objective ## newer code in objective2 +# objective2 ## used in ddcm_sim1? +# optimization ## used in ddcm_sim1? +# sampling ## used in ddcm_sim1? +# test ## apparently nothing useful (hello world? really?) +# test_trust ## appears to be a copy of other code +) + +foreach(dir ${DIRS}) + add_subdirectory(${dir}) +endforeach() + +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} PARENT_SCOPE) diff --git a/fastlib/branches/fastlib-cmake/contrib/soyeon/ddcm_sim1/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/soyeon/ddcm_sim1/CMakeLists.txt new file mode 100644 index 0000000000..0539e34bca --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/soyeon/ddcm_sim1/CMakeLists.txt @@ -0,0 +1,35 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + # sampling + sampling.h + sampling.cc + # objective2 + objective2.h + objective2.cc + # optimization + optimization.h + optimization.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(ddcm_test + ddcm_test.cc +) +# link dependencies of executable +target_link_libraries(ddcm_test + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/tqlong/2dfactor/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/tqlong/2dfactor/CMakeLists.txt new file mode 100644 index 0000000000..7a1b59651b --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/tqlong/2dfactor/CMakeLists.txt @@ -0,0 +1,28 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + 2dfactor.h +# 2dPCA.h ## in build.py but does not exist +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(2dfactor_test + 2dfactor_test.cc +) +# link dependencies of executable +target_link_libraries(2dfactor_test + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/tqlong/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/tqlong/CMakeLists.txt new file mode 100644 index 0000000000..f923baf644 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/tqlong/CMakeLists.txt @@ -0,0 +1,21 @@ +cmake_minimum_required(VERSION 2.8) + +# we just want to recurse into the child directories here +set(DIRS +# 2dfactor ## does not link; looking for nonexistent la:: functions + gm + graph +# hmm ## already exists elsewhere, appears to be a copy? + kfs +# mmf ## a copy already exists in contrib/niche?? + optim + PassiveAggressive +# quicsvd ## does not link; looking for nonexistent la:: functions + svm +) + +foreach(dir ${DIRS}) + add_subdirectory(${dir}) +endforeach() + +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} PARENT_SCOPE) diff --git a/fastlib/branches/fastlib-cmake/contrib/tqlong/PassiveAggressive/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/tqlong/PassiveAggressive/CMakeLists.txt new file mode 100644 index 0000000000..a1acaa62ed --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/tqlong/PassiveAggressive/CMakeLists.txt @@ -0,0 +1,32 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + pa.h + pa.cc + kernel.h + kernel.cc + dataGenerator.h + dataGenerator.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(passive_aggressive_test + pa_test.cc +) +# link dependencies of executable +target_link_libraries(passive_aggressive_test + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/tqlong/gm/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/tqlong/gm/CMakeLists.txt new file mode 100644 index 0000000000..ea12958d6d --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/tqlong/gm/CMakeLists.txt @@ -0,0 +1,30 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + gm.h + bipartie.h + factor_graph.h + gm.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(gm_test + gm_test.cc +) +# link dependencies of executable +target_link_libraries(gm_test + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/tqlong/graph/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/tqlong/graph/CMakeLists.txt new file mode 100644 index 0000000000..7c3b93daa7 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/tqlong/graph/CMakeLists.txt @@ -0,0 +1,28 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + graph.h + graph.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(maxflow + maxflow.cc +) +# link dependencies of executable +target_link_libraries(maxflow + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/tqlong/hmm/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/tqlong/hmm/CMakeLists.txt new file mode 100644 index 0000000000..7c3b93daa7 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/tqlong/hmm/CMakeLists.txt @@ -0,0 +1,28 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + graph.h + graph.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(maxflow + maxflow.cc +) +# link dependencies of executable +target_link_libraries(maxflow + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/tqlong/kfs/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/tqlong/kfs/CMakeLists.txt new file mode 100644 index 0000000000..117be474a0 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/tqlong/kfs/CMakeLists.txt @@ -0,0 +1,28 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + kfs.h + kfs.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(kfs + kfs_main.cc +) +# link dependencies of executable +target_link_libraries(kfs + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/tqlong/optim/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/tqlong/optim/CMakeLists.txt new file mode 100644 index 0000000000..5121e10785 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/tqlong/optim/CMakeLists.txt @@ -0,0 +1,29 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + optim.h + optim.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(optim_tqlong_test + optim_test.cc + myfun.h +) +# link dependencies of executable +target_link_libraries(optim_tqlong_test + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/tqlong/quicsvd/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/tqlong/quicsvd/CMakeLists.txt new file mode 100644 index 0000000000..43bc2d6de0 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/tqlong/quicsvd/CMakeLists.txt @@ -0,0 +1,39 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + cosine_tree.h + cosine_tree.cc + quicsvd.h + quicsvd.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(quicsvd_tqlong_test + quicsvd_test.cc +) +# link dependencies of executable +target_link_libraries(quicsvd_tqlong_test + fastlib + mlpack + mlpack_contrib +) + +add_executable(quicsvd_tqlong + quicsvd_main.cc +) +target_link_libraries(quicsvd_tqlong + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/contrib/tqlong/svm/CMakeLists.txt b/fastlib/branches/fastlib-cmake/contrib/tqlong/svm/CMakeLists.txt new file mode 100644 index 0000000000..dd45583678 --- /dev/null +++ b/fastlib/branches/fastlib-cmake/contrib/tqlong/svm/CMakeLists.txt @@ -0,0 +1,53 @@ +cmake_minimum_required(VERSION 2.8) + +# Define the files we need to compile +# Anything not in this list will not be compiled into the output library +# Do not include test programs here +set(SOURCES + svm_projection.h + project_simplex.cc + min_quad_on_simplex.cc + svm.h + seqminopt.cc + kernel_cache.cc + index_set.cc + kernel_function.cc + ptswarmopt.cc +) + +# add directory name to sources +set(DIR_SRCS) +foreach(file ${SOURCES}) + set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file}) +endforeach() +# append sources (with directory name) to list of all MLPACK sources (used at the parent scope) +set(MLPACK_CONTRIB_SRCS ${MLPACK_CONTRIB_SRCS} ${DIR_SRCS} PARENT_SCOPE) + +# executable +add_executable(smo_tqlong_test + smo_test.cc +) +# link dependencies of executable +target_link_libraries(smo_tqlong_test + fastlib + mlpack + mlpack_contrib +) + +#add_executable(pso_test +# pso_test.cc +#) +#target_link_libraries(pso_test +# fastlib +# mlpack +# mlpack_contrib +#) + +add_executable(svm_projection_test + svm_projection_test.cc +) +target_link_libraries(svm_projection_test + fastlib + mlpack + mlpack_contrib +) diff --git a/fastlib/branches/fastlib-cmake/mlpack/CMakeLists.txt b/fastlib/branches/fastlib-cmake/mlpack/CMakeLists.txt index 0f572594a2..2f5fdbc063 100644 --- a/fastlib/branches/fastlib-cmake/mlpack/CMakeLists.txt +++ b/fastlib/branches/fastlib-cmake/mlpack/CMakeLists.txt @@ -75,8 +75,8 @@ foreach(incl_file ${INCLUDE_FILES}) endforeach() # set installation rules for include files -install(FILES ${CMAKE_BINARY_DIR}/include/mlpack/ - DESTINATION include/mlpack) +#install(FILES ${CMAKE_BINARY_DIR}/include/mlpack/ +# DESTINATION include/mlpack) # set installation rules for mlpack programs #install(PROGRAMS ${CMAKE_BINARY_DIR}/bin