sequenzo 0.1.31__cp310-cp310-macosx_10_9_x86_64.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- _sequenzo_fastcluster.cpython-310-darwin.so +0 -0
- sequenzo/__init__.py +349 -0
- sequenzo/big_data/__init__.py +12 -0
- sequenzo/big_data/clara/__init__.py +26 -0
- sequenzo/big_data/clara/clara.py +476 -0
- sequenzo/big_data/clara/utils/__init__.py +27 -0
- sequenzo/big_data/clara/utils/aggregatecases.py +92 -0
- sequenzo/big_data/clara/utils/davies_bouldin.py +91 -0
- sequenzo/big_data/clara/utils/get_weighted_diss.cpython-310-darwin.so +0 -0
- sequenzo/big_data/clara/utils/wfcmdd.py +205 -0
- sequenzo/big_data/clara/visualization.py +88 -0
- sequenzo/clustering/KMedoids.py +178 -0
- sequenzo/clustering/__init__.py +30 -0
- sequenzo/clustering/clustering_c_code.cpython-310-darwin.so +0 -0
- sequenzo/clustering/hierarchical_clustering.py +1256 -0
- sequenzo/clustering/sequenzo_fastcluster/fastcluster.py +495 -0
- sequenzo/clustering/sequenzo_fastcluster/src/fastcluster.cpp +1877 -0
- sequenzo/clustering/sequenzo_fastcluster/src/fastcluster_python.cpp +1264 -0
- sequenzo/clustering/src/KMedoid.cpp +263 -0
- sequenzo/clustering/src/PAM.cpp +237 -0
- sequenzo/clustering/src/PAMonce.cpp +265 -0
- sequenzo/clustering/src/cluster_quality.cpp +496 -0
- sequenzo/clustering/src/cluster_quality.h +128 -0
- sequenzo/clustering/src/cluster_quality_backup.cpp +570 -0
- sequenzo/clustering/src/module.cpp +228 -0
- sequenzo/clustering/src/weightedinertia.cpp +111 -0
- sequenzo/clustering/utils/__init__.py +27 -0
- sequenzo/clustering/utils/disscenter.py +122 -0
- sequenzo/data_preprocessing/__init__.py +22 -0
- sequenzo/data_preprocessing/helpers.py +303 -0
- sequenzo/datasets/__init__.py +41 -0
- sequenzo/datasets/biofam.csv +2001 -0
- sequenzo/datasets/biofam_child_domain.csv +2001 -0
- sequenzo/datasets/biofam_left_domain.csv +2001 -0
- sequenzo/datasets/biofam_married_domain.csv +2001 -0
- sequenzo/datasets/chinese_colonial_territories.csv +12 -0
- sequenzo/datasets/country_co2_emissions.csv +194 -0
- sequenzo/datasets/country_co2_emissions_global_deciles.csv +195 -0
- sequenzo/datasets/country_co2_emissions_global_quintiles.csv +195 -0
- sequenzo/datasets/country_co2_emissions_local_deciles.csv +195 -0
- sequenzo/datasets/country_co2_emissions_local_quintiles.csv +195 -0
- sequenzo/datasets/country_gdp_per_capita.csv +194 -0
- sequenzo/datasets/dyadic_children.csv +61 -0
- sequenzo/datasets/dyadic_parents.csv +61 -0
- sequenzo/datasets/mvad.csv +713 -0
- sequenzo/datasets/pairfam_activity_by_month.csv +1028 -0
- sequenzo/datasets/pairfam_activity_by_year.csv +1028 -0
- sequenzo/datasets/pairfam_family_by_month.csv +1028 -0
- sequenzo/datasets/pairfam_family_by_year.csv +1028 -0
- sequenzo/datasets/political_science_aid_shock.csv +166 -0
- sequenzo/datasets/political_science_donor_fragmentation.csv +157 -0
- sequenzo/define_sequence_data.py +1400 -0
- sequenzo/dissimilarity_measures/__init__.py +31 -0
- sequenzo/dissimilarity_measures/c_code.cpython-310-darwin.so +0 -0
- sequenzo/dissimilarity_measures/get_distance_matrix.py +762 -0
- sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +246 -0
- sequenzo/dissimilarity_measures/src/DHDdistance.cpp +148 -0
- sequenzo/dissimilarity_measures/src/LCPdistance.cpp +114 -0
- sequenzo/dissimilarity_measures/src/LCPspellDistance.cpp +215 -0
- sequenzo/dissimilarity_measures/src/OMdistance.cpp +247 -0
- sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +281 -0
- sequenzo/dissimilarity_measures/src/__init__.py +0 -0
- sequenzo/dissimilarity_measures/src/dist2matrix.cpp +63 -0
- sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
- sequenzo/dissimilarity_measures/src/module.cpp +40 -0
- sequenzo/dissimilarity_measures/src/setup.py +30 -0
- sequenzo/dissimilarity_measures/src/utils.h +25 -0
- sequenzo/dissimilarity_measures/src/xsimd/.github/cmake-test/main.cpp +6 -0
- sequenzo/dissimilarity_measures/src/xsimd/benchmark/main.cpp +159 -0
- sequenzo/dissimilarity_measures/src/xsimd/benchmark/xsimd_benchmark.hpp +565 -0
- sequenzo/dissimilarity_measures/src/xsimd/docs/source/conf.py +37 -0
- sequenzo/dissimilarity_measures/src/xsimd/examples/mandelbrot.cpp +330 -0
- sequenzo/dissimilarity_measures/src/xsimd/examples/pico_bench.hpp +246 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +266 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +112 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +323 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +218 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +2583 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +880 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_rounding.hpp +72 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +978 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +1924 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +1144 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +656 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512cd.hpp +28 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +244 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512er.hpp +20 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +2650 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512ifma.hpp +20 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512pf.hpp +20 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +77 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +131 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vnni_avx512bw.hpp +20 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vnni_avx512vbmi2.hpp +20 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avxvnni.hpp +20 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +24 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +77 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +393 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +788 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +93 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx2.hpp +46 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +97 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +92 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_i8mm_neon64.hpp +17 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +142 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +3142 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +1543 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +1513 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +1260 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +2024 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +67 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse4_1.hpp +339 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse4_2.hpp +44 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +186 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +1155 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +1780 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +240 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +484 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +269 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +27 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/math/xsimd_rem_pio2.hpp +719 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/memory/xsimd_aligned_allocator.hpp +349 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/memory/xsimd_alignment.hpp +91 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +55 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +2765 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx2_register.hpp +44 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512bw_register.hpp +51 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512cd_register.hpp +51 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512dq_register.hpp +51 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512er_register.hpp +51 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512f_register.hpp +77 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512ifma_register.hpp +51 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512pf_register.hpp +51 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512vbmi2_register.hpp +51 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512vbmi_register.hpp +51 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512vnni_avx512bw_register.hpp +54 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx512vnni_avx512vbmi2_register.hpp +53 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avx_register.hpp +64 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_avxvnni_register.hpp +44 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +1524 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch_constant.hpp +300 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_common_arch.hpp +47 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_emulated_register.hpp +80 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_fma3_avx2_register.hpp +50 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_fma3_avx_register.hpp +50 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_fma3_sse_register.hpp +50 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_fma4_register.hpp +50 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_i8mm_neon64_register.hpp +55 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_neon64_register.hpp +55 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_neon_register.hpp +154 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_register.hpp +94 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +506 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_sse2_register.hpp +59 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_sse3_register.hpp +49 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_sse4_1_register.hpp +48 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_sse4_2_register.hpp +48 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_ssse3_register.hpp +48 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_sve_register.hpp +156 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +337 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_utils.hpp +536 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_wasm_register.hpp +59 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +75 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/architectures/dummy.cpp +7 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/doc/explicit_use_of_an_instruction_set.cpp +13 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/doc/explicit_use_of_an_instruction_set_mean.cpp +24 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/doc/explicit_use_of_an_instruction_set_mean_aligned.cpp +25 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/doc/explicit_use_of_an_instruction_set_mean_arch_independent.cpp +28 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/doc/explicit_use_of_an_instruction_set_mean_tag_dispatch.cpp +25 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/doc/manipulating_abstract_batches.cpp +7 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/doc/manipulating_parametric_batches.cpp +8 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/doc/sum.hpp +31 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/doc/sum_avx2.cpp +3 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/doc/sum_sse2.cpp +3 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/doc/writing_vectorized_code.cpp +11 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/main.cpp +31 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_api.cpp +230 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_arch.cpp +217 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_basic_math.cpp +183 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_batch.cpp +1049 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_bool.cpp +508 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_cast.cpp +409 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_complex.cpp +712 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_constant.cpp +286 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_float.cpp +141 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_int.cpp +365 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_manip.cpp +308 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_bitwise_cast.cpp +222 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_complex_exponential.cpp +226 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_complex_hyperbolic.cpp +183 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_complex_power.cpp +265 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_complex_trigonometric.cpp +236 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_conversion.cpp +248 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_custom_default_arch.cpp +28 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_error_gamma.cpp +170 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_explicit_batch_instantiation.cpp +32 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_exponential.cpp +202 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_extract_pair.cpp +92 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_fp_manipulation.cpp +77 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_gnu_source.cpp +30 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_hyperbolic.cpp +167 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_load_store.cpp +304 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_memory.cpp +61 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_poly_evaluation.cpp +64 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_power.cpp +184 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_rounding.cpp +199 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_select.cpp +101 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_shuffle.cpp +760 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_sum.cpp +4 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_sum.hpp +34 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_traits.cpp +172 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_trigonometric.cpp +208 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_utils.hpp +611 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_wasm/test_wasm_playwright.py +123 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_xsimd_api.cpp +1460 -0
- sequenzo/dissimilarity_measures/utils/__init__.py +16 -0
- sequenzo/dissimilarity_measures/utils/get_LCP_length_for_2_seq.py +44 -0
- sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-310-darwin.so +0 -0
- sequenzo/dissimilarity_measures/utils/seqconc.cpython-310-darwin.so +0 -0
- sequenzo/dissimilarity_measures/utils/seqdss.cpython-310-darwin.so +0 -0
- sequenzo/dissimilarity_measures/utils/seqdur.cpython-310-darwin.so +0 -0
- sequenzo/dissimilarity_measures/utils/seqlength.cpython-310-darwin.so +0 -0
- sequenzo/multidomain/__init__.py +23 -0
- sequenzo/multidomain/association_between_domains.py +311 -0
- sequenzo/multidomain/cat.py +597 -0
- sequenzo/multidomain/combt.py +519 -0
- sequenzo/multidomain/dat.py +81 -0
- sequenzo/multidomain/idcd.py +139 -0
- sequenzo/multidomain/linked_polyad.py +292 -0
- sequenzo/openmp_setup.py +233 -0
- sequenzo/prefix_tree/__init__.py +62 -0
- sequenzo/prefix_tree/hub.py +114 -0
- sequenzo/prefix_tree/individual_level_indicators.py +1321 -0
- sequenzo/prefix_tree/spell_individual_level_indicators.py +580 -0
- sequenzo/prefix_tree/spell_level_indicators.py +297 -0
- sequenzo/prefix_tree/system_level_indicators.py +544 -0
- sequenzo/prefix_tree/utils.py +54 -0
- sequenzo/seqhmm/__init__.py +95 -0
- sequenzo/seqhmm/advanced_optimization.py +305 -0
- sequenzo/seqhmm/bootstrap.py +411 -0
- sequenzo/seqhmm/build_hmm.py +142 -0
- sequenzo/seqhmm/build_mhmm.py +136 -0
- sequenzo/seqhmm/build_nhmm.py +121 -0
- sequenzo/seqhmm/fit_mhmm.py +62 -0
- sequenzo/seqhmm/fit_model.py +61 -0
- sequenzo/seqhmm/fit_nhmm.py +76 -0
- sequenzo/seqhmm/formulas.py +289 -0
- sequenzo/seqhmm/forward_backward_nhmm.py +276 -0
- sequenzo/seqhmm/gradients_nhmm.py +306 -0
- sequenzo/seqhmm/hmm.py +291 -0
- sequenzo/seqhmm/mhmm.py +314 -0
- sequenzo/seqhmm/model_comparison.py +238 -0
- sequenzo/seqhmm/multichannel_em.py +282 -0
- sequenzo/seqhmm/multichannel_utils.py +138 -0
- sequenzo/seqhmm/nhmm.py +270 -0
- sequenzo/seqhmm/nhmm_utils.py +191 -0
- sequenzo/seqhmm/predict.py +137 -0
- sequenzo/seqhmm/predict_mhmm.py +142 -0
- sequenzo/seqhmm/simulate.py +878 -0
- sequenzo/seqhmm/utils.py +218 -0
- sequenzo/seqhmm/visualization.py +910 -0
- sequenzo/sequence_characteristics/__init__.py +40 -0
- sequenzo/sequence_characteristics/complexity_index.py +49 -0
- sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +220 -0
- sequenzo/sequence_characteristics/plot_characteristics.py +593 -0
- sequenzo/sequence_characteristics/simple_characteristics.py +311 -0
- sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +39 -0
- sequenzo/sequence_characteristics/turbulence.py +155 -0
- sequenzo/sequence_characteristics/variance_of_spell_durations.py +86 -0
- sequenzo/sequence_characteristics/within_sequence_entropy.py +43 -0
- sequenzo/suffix_tree/__init__.py +66 -0
- sequenzo/suffix_tree/hub.py +114 -0
- sequenzo/suffix_tree/individual_level_indicators.py +1679 -0
- sequenzo/suffix_tree/spell_individual_level_indicators.py +493 -0
- sequenzo/suffix_tree/spell_level_indicators.py +248 -0
- sequenzo/suffix_tree/system_level_indicators.py +535 -0
- sequenzo/suffix_tree/utils.py +56 -0
- sequenzo/version_check.py +283 -0
- sequenzo/visualization/__init__.py +29 -0
- sequenzo/visualization/plot_mean_time.py +222 -0
- sequenzo/visualization/plot_modal_state.py +276 -0
- sequenzo/visualization/plot_most_frequent_sequences.py +147 -0
- sequenzo/visualization/plot_relative_frequency.py +405 -0
- sequenzo/visualization/plot_sequence_index.py +1175 -0
- sequenzo/visualization/plot_single_medoid.py +153 -0
- sequenzo/visualization/plot_state_distribution.py +651 -0
- sequenzo/visualization/plot_transition_matrix.py +190 -0
- sequenzo/visualization/utils/__init__.py +23 -0
- sequenzo/visualization/utils/utils.py +310 -0
- sequenzo/with_event_history_analysis/__init__.py +35 -0
- sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
- sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
- sequenzo-0.1.31.dist-info/METADATA +286 -0
- sequenzo-0.1.31.dist-info/RECORD +299 -0
- sequenzo-0.1.31.dist-info/WHEEL +5 -0
- sequenzo-0.1.31.dist-info/licenses/LICENSE +28 -0
- sequenzo-0.1.31.dist-info/top_level.txt +2 -0
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/***************************************************************************
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* Copyright (c) Johan Mabille, Sylvain Corlay, Wolf Vollprecht and *
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* Martin Renou *
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* Copyright (c) QuantStack *
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* Copyright (c) Serge Guelton *
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* *
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* Distributed under the terms of the BSD 3-Clause License. *
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* *
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* The full license is in the file LICENSE, distributed with this software. *
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****************************************************************************/
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#include "xsimd/xsimd.hpp"
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#ifndef XSIMD_NO_SUPPORTED_ARCHITECTURE
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#include "test_utils.hpp"
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template <class B>
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struct constant_batch_test
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{
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using batch_type = B;
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using value_type = typename B::value_type;
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using arch_type = typename B::arch_type;
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static constexpr size_t size = B::size;
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using array_type = std::array<value_type, size>;
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using bool_array_type = std::array<bool, size>;
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using batch_bool_type = typename batch_type::batch_bool_type;
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struct generator
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{
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static constexpr value_type get(size_t index, size_t /*size*/)
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{
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return index % 2 ? 0 : 1;
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}
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};
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void test_init_from_generator() const
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{
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array_type expected;
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size_t i = 0;
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std::generate(expected.begin(), expected.end(),
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[&i]()
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{ return generator::get(i++, size); });
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constexpr auto b = xsimd::make_batch_constant<value_type, generator, arch_type>();
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INFO("batch(value_type)");
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CHECK_BATCH_EQ((batch_type)b, expected);
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}
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void test_cast() const
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{
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constexpr auto cst_b = xsimd::make_batch_constant<value_type, generator, arch_type>();
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auto b0 = cst_b.as_batch();
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auto b1 = (batch_type)cst_b;
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CHECK_BATCH_EQ(b0, b1);
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// The actual values are already tested in test_init_from_generator
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}
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struct arange
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{
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static constexpr value_type get(size_t index, size_t /*size*/)
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{
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return static_cast<value_type>(index);
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}
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};
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void test_init_from_generator_arange() const
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{
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array_type expected;
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size_t i = 0;
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std::generate(expected.begin(), expected.end(),
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[&i]()
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{ return arange::get(i++, size); });
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constexpr auto b = xsimd::make_batch_constant<value_type, arange, arch_type>();
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INFO("batch(value_type)");
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CHECK_BATCH_EQ((batch_type)b, expected);
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}
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template <value_type V>
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struct constant
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{
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static constexpr value_type get(size_t /*index*/, size_t /*size*/)
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{
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return V;
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}
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};
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void test_init_from_constant() const
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{
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array_type expected;
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std::fill(expected.begin(), expected.end(), constant<3>::get(0, 0));
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constexpr auto b = xsimd::make_batch_constant<value_type, constant<3>, arch_type>();
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INFO("batch(value_type)");
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CHECK_BATCH_EQ((batch_type)b, expected);
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}
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void test_ops() const
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{
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constexpr auto n12 = xsimd::make_batch_constant<value_type, constant<12>, arch_type>();
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constexpr auto n3 = xsimd::make_batch_constant<value_type, constant<3>, arch_type>();
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constexpr auto n12_add_n3 = n12 + n3;
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constexpr auto n15 = xsimd::make_batch_constant<value_type, constant<15>, arch_type>();
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static_assert(std::is_same<decltype(n12_add_n3), decltype(n15)>::value, "n12 + n3 == n15");
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constexpr auto n12_sub_n3 = n12 - n3;
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constexpr auto n9 = xsimd::make_batch_constant<value_type, constant<9>, arch_type>();
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static_assert(std::is_same<decltype(n12_sub_n3), decltype(n9)>::value, "n12 - n3 == n9");
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constexpr auto n12_mul_n3 = n12 * n3;
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constexpr auto n36 = xsimd::make_batch_constant<value_type, constant<36>, arch_type>();
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static_assert(std::is_same<decltype(n12_mul_n3), decltype(n36)>::value, "n12 * n3 == n36");
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constexpr auto n12_div_n3 = n12 / n3;
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constexpr auto n4 = xsimd::make_batch_constant<value_type, constant<4>, arch_type>();
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static_assert(std::is_same<decltype(n12_div_n3), decltype(n4)>::value, "n12 / n3 == n4");
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constexpr auto n12_mod_n3 = n12 % n3;
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constexpr auto n0 = xsimd::make_batch_constant<value_type, constant<0>, arch_type>();
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static_assert(std::is_same<decltype(n12_mod_n3), decltype(n0)>::value, "n12 % n3 == n0");
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constexpr auto n12_land_n3 = n12 & n3;
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static_assert(std::is_same<decltype(n12_land_n3), decltype(n0)>::value, "n12 & n3 == n0");
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constexpr auto n12_lor_n3 = n12 | n3;
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static_assert(std::is_same<decltype(n12_lor_n3), decltype(n15)>::value, "n12 | n3 == n15");
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constexpr auto n12_lxor_n3 = n12 ^ n3;
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static_assert(std::is_same<decltype(n12_lxor_n3), decltype(n15)>::value, "n12 ^ n3 == n15");
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constexpr auto n12_uadd = +n12;
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static_assert(std::is_same<decltype(n12_uadd), decltype(n12)>::value, "+n12 == n12");
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constexpr auto n12_inv = ~n12;
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constexpr auto n12_inv_ = xsimd::make_batch_constant<value_type, constant<(value_type)~12>, arch_type>();
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static_assert(std::is_same<decltype(n12_inv), decltype(n12_inv_)>::value, "~n12 == n12_inv");
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constexpr auto n12_usub = -n12;
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constexpr auto n12_usub_ = xsimd::make_batch_constant<value_type, constant<(value_type)-12>, arch_type>();
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static_assert(std::is_same<decltype(n12_usub), decltype(n12_usub_)>::value, "-n12 == n12_usub");
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}
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};
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TEST_CASE_TEMPLATE("[constant batch]", B, BATCH_INT_TYPES)
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{
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constant_batch_test<B> Test;
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SUBCASE("init_from_generator") { Test.test_init_from_generator(); }
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SUBCASE("as_batch") { Test.test_cast(); }
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SUBCASE("init_from_generator_arange")
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{
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Test.test_init_from_generator_arange();
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}
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SUBCASE("init_from_constant") { Test.test_init_from_constant(); }
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SUBCASE("operators")
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{
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Test.test_ops();
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}
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}
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template <class B>
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struct constant_bool_batch_test
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{
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using batch_type = B;
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using value_type = typename B::value_type;
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using arch_type = typename B::arch_type;
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static constexpr size_t size = B::size;
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using array_type = std::array<value_type, size>;
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using bool_array_type = std::array<bool, size>;
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using batch_bool_type = typename batch_type::batch_bool_type;
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struct generator
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{
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static constexpr bool get(size_t index, size_t /*size*/)
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{
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return index % 2;
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}
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};
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void test_init_from_generator() const
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{
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bool_array_type expected;
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size_t i = 0;
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std::generate(expected.begin(), expected.end(),
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[&i]()
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{ return generator::get(i++, size); });
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constexpr auto b = xsimd::make_batch_bool_constant<value_type, generator, arch_type>();
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INFO("batch_bool_constant(value_type)");
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CHECK_BATCH_EQ((batch_bool_type)b, expected);
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}
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struct split
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{
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static constexpr bool get(size_t index, size_t size)
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{
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return index < size / 2;
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}
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};
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void test_init_from_generator_split() const
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{
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bool_array_type expected;
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size_t i = 0;
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std::generate(expected.begin(), expected.end(),
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[&i]()
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{ return split::get(i++, size); });
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constexpr auto b = xsimd::make_batch_bool_constant<value_type, split, arch_type>();
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INFO("batch_bool_constant(value_type)");
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CHECK_BATCH_EQ((batch_bool_type)b, expected);
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}
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struct inv_split
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{
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static constexpr bool get(size_t index, size_t size)
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{
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return !split().get(index, size);
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}
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};
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template <bool Val>
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struct constant
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{
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static constexpr bool get(size_t /*index*/, size_t /*size*/)
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{
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return Val;
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}
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};
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void test_cast() const
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{
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constexpr auto all_true = xsimd::make_batch_bool_constant<value_type, constant<true>, arch_type>();
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auto b0 = all_true.as_batch_bool();
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auto b1 = (batch_bool_type)all_true;
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CHECK_BATCH_EQ(b0, batch_bool_type(true));
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CHECK_BATCH_EQ(b1, batch_bool_type(true));
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}
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void test_ops() const
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{
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constexpr auto all_true = xsimd::make_batch_bool_constant<value_type, constant<true>, arch_type>();
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constexpr auto all_false = xsimd::make_batch_bool_constant<value_type, constant<false>, arch_type>();
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constexpr auto x = xsimd::make_batch_bool_constant<value_type, split, arch_type>();
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constexpr auto y = xsimd::make_batch_bool_constant<value_type, inv_split, arch_type>();
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constexpr auto x_or_y = x | y;
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static_assert(std::is_same<decltype(x_or_y), decltype(all_true)>::value, "x | y == true");
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constexpr auto x_lor_y = x || y;
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static_assert(std::is_same<decltype(x_lor_y), decltype(all_true)>::value, "x || y == true");
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constexpr auto x_and_y = x & y;
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static_assert(std::is_same<decltype(x_and_y), decltype(all_false)>::value, "x & y == false");
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constexpr auto x_land_y = x && y;
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static_assert(std::is_same<decltype(x_land_y), decltype(all_false)>::value, "x && y == false");
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constexpr auto x_xor_y = x ^ y;
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static_assert(std::is_same<decltype(x_xor_y), decltype(all_true)>::value, "x ^ y == true");
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constexpr auto not_x = !x;
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static_assert(std::is_same<decltype(not_x), decltype(y)>::value, "!x == y");
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constexpr auto inv_x = ~x;
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static_assert(std::is_same<decltype(inv_x), decltype(y)>::value, "~x == y");
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}
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};
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TEST_CASE_TEMPLATE("[constant bool batch]", B, BATCH_INT_TYPES)
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{
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constant_bool_batch_test<B> Test;
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SUBCASE("init_from_generator") { Test.test_init_from_generator(); }
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+
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SUBCASE("as_batch") { Test.test_cast(); }
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+
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SUBCASE("init_from_generator_split")
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{
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Test.test_init_from_generator_split();
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}
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+
SUBCASE("operators")
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282
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{
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283
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Test.test_ops();
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}
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}
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#endif
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@@ -0,0 +1,141 @@
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1
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+
/***************************************************************************
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2
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+
* Copyright (c) Johan Mabille, Sylvain Corlay, Wolf Vollprecht and *
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3
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+
* Martin Renou *
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4
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+
* Copyright (c) QuantStack *
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5
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+
* Copyright (c) Serge Guelton *
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+
* *
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7
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+
* Distributed under the terms of the BSD 3-Clause License. *
|
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+
* *
|
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+
* The full license is in the file LICENSE, distributed with this software. *
|
|
10
|
+
****************************************************************************/
|
|
11
|
+
|
|
12
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+
#include "xsimd/xsimd.hpp"
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|
13
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+
#ifndef XSIMD_NO_SUPPORTED_ARCHITECTURE
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+
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15
|
+
#include "test_utils.hpp"
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16
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+
|
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17
|
+
template <class B>
|
|
18
|
+
struct batch_float_test
|
|
19
|
+
{
|
|
20
|
+
using batch_type = B;
|
|
21
|
+
using value_type = typename B::value_type;
|
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22
|
+
static constexpr size_t size = B::size;
|
|
23
|
+
using array_type = std::array<value_type, size>;
|
|
24
|
+
using bool_array_type = std::array<bool, size>;
|
|
25
|
+
|
|
26
|
+
array_type lhs;
|
|
27
|
+
array_type rhs;
|
|
28
|
+
|
|
29
|
+
batch_float_test()
|
|
30
|
+
{
|
|
31
|
+
for (size_t i = 0; i < size; ++i)
|
|
32
|
+
{
|
|
33
|
+
lhs[i] = value_type(i) / 4 + value_type(1.2) * std::sqrt(value_type(i + 0.25));
|
|
34
|
+
if (lhs[i] == value_type(0))
|
|
35
|
+
{
|
|
36
|
+
lhs[i] += value_type(0.1);
|
|
37
|
+
}
|
|
38
|
+
rhs[i] = value_type(10.2) / (i + 2) + value_type(0.25);
|
|
39
|
+
}
|
|
40
|
+
}
|
|
41
|
+
|
|
42
|
+
void test_reciprocal() const
|
|
43
|
+
{
|
|
44
|
+
// reciprocal
|
|
45
|
+
{
|
|
46
|
+
array_type res, expected;
|
|
47
|
+
std::transform(lhs.cbegin(), lhs.cend(), expected.begin(),
|
|
48
|
+
[](const value_type& l)
|
|
49
|
+
{ return value_type(1) / l; });
|
|
50
|
+
batch_type res1 = reciprocal(batch_lhs());
|
|
51
|
+
res1.store_unaligned(res.data());
|
|
52
|
+
size_t diff = detail::get_nb_diff_near(res, expected, 1e-12f);
|
|
53
|
+
INFO("reciprocal");
|
|
54
|
+
CHECK_EQ(diff, 0);
|
|
55
|
+
}
|
|
56
|
+
}
|
|
57
|
+
|
|
58
|
+
void test_rsqrt() const
|
|
59
|
+
{
|
|
60
|
+
// rsqrt
|
|
61
|
+
{
|
|
62
|
+
array_type res, expected;
|
|
63
|
+
std::transform(lhs.cbegin(), lhs.cend(), expected.begin(),
|
|
64
|
+
[](const value_type& l)
|
|
65
|
+
{ return std::ceil((value_type(1) / std::sqrt(l)) * value_type(100)); });
|
|
66
|
+
batch_type res1 = ceil(rsqrt(batch_lhs()) * value_type(100));
|
|
67
|
+
res1.store_unaligned(res.data());
|
|
68
|
+
size_t diff = detail::get_nb_diff_near(res, expected, 1.5f * std::pow(2, 12));
|
|
69
|
+
INFO("rsqrt");
|
|
70
|
+
CHECK_EQ(diff, 0);
|
|
71
|
+
}
|
|
72
|
+
}
|
|
73
|
+
|
|
74
|
+
void test_sqrt() const
|
|
75
|
+
{
|
|
76
|
+
// sqrt
|
|
77
|
+
{
|
|
78
|
+
array_type expected;
|
|
79
|
+
std::transform(lhs.cbegin(), lhs.cend(), expected.begin(),
|
|
80
|
+
[](const value_type& l)
|
|
81
|
+
{ return std::sqrt(l); });
|
|
82
|
+
batch_type res = sqrt(batch_lhs());
|
|
83
|
+
INFO("sqrt");
|
|
84
|
+
CHECK_BATCH_EQ(res, expected);
|
|
85
|
+
}
|
|
86
|
+
}
|
|
87
|
+
|
|
88
|
+
void test_haddp() const
|
|
89
|
+
{
|
|
90
|
+
batch_type haddp_input[size];
|
|
91
|
+
for (size_t i = 0; i < size; i += 2)
|
|
92
|
+
{
|
|
93
|
+
haddp_input[i] = batch_lhs();
|
|
94
|
+
if (i + 1 < size)
|
|
95
|
+
{
|
|
96
|
+
haddp_input[i + 1] = batch_rhs();
|
|
97
|
+
}
|
|
98
|
+
}
|
|
99
|
+
array_type expected;
|
|
100
|
+
std::fill(expected.begin(), expected.end(), value_type(0));
|
|
101
|
+
for (size_t i = 0; i < size; ++i)
|
|
102
|
+
{
|
|
103
|
+
for (size_t j = 0; j < size; j += 2)
|
|
104
|
+
{
|
|
105
|
+
expected[j] += lhs[i];
|
|
106
|
+
if (j + 1 < size)
|
|
107
|
+
{
|
|
108
|
+
expected[j + 1] += rhs[i];
|
|
109
|
+
}
|
|
110
|
+
}
|
|
111
|
+
}
|
|
112
|
+
auto res = haddp(haddp_input);
|
|
113
|
+
INFO("haddp");
|
|
114
|
+
CHECK_BATCH_EQ(res, expected);
|
|
115
|
+
}
|
|
116
|
+
|
|
117
|
+
private:
|
|
118
|
+
batch_type batch_lhs() const
|
|
119
|
+
{
|
|
120
|
+
return batch_type::load_unaligned(lhs.data());
|
|
121
|
+
}
|
|
122
|
+
|
|
123
|
+
batch_type batch_rhs() const
|
|
124
|
+
{
|
|
125
|
+
return batch_type::load_unaligned(rhs.data());
|
|
126
|
+
}
|
|
127
|
+
};
|
|
128
|
+
|
|
129
|
+
TEST_CASE_TEMPLATE("[xsimd batch float]", B, BATCH_FLOAT_TYPES)
|
|
130
|
+
{
|
|
131
|
+
batch_float_test<B> Test;
|
|
132
|
+
|
|
133
|
+
SUBCASE("reciprocal") { Test.test_reciprocal(); }
|
|
134
|
+
|
|
135
|
+
SUBCASE("sqrt") { Test.test_sqrt(); }
|
|
136
|
+
|
|
137
|
+
SUBCASE("rsqrt") { Test.test_rsqrt(); }
|
|
138
|
+
|
|
139
|
+
SUBCASE("haddp") { Test.test_haddp(); }
|
|
140
|
+
}
|
|
141
|
+
#endif
|