sequenzo 0.1.24__cp311-cp311-macosx_10_9_x86_64.whl
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- _sequenzo_fastcluster.cpython-311-darwin.so +0 -0
- sequenzo/__init__.py +240 -0
- sequenzo/big_data/__init__.py +12 -0
- sequenzo/big_data/clara/__init__.py +26 -0
- sequenzo/big_data/clara/clara.py +474 -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-311-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-311-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 +20 -0
- sequenzo/data_preprocessing/helpers.py +256 -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/mvad.csv +713 -0
- sequenzo/datasets/pairfam_family.csv +1867 -0
- sequenzo/datasets/polyadic_samplec1.csv +61 -0
- sequenzo/datasets/polyadic_samplep1.csv +61 -0
- sequenzo/datasets/polyadic_seqc1.csv +61 -0
- sequenzo/datasets/polyadic_seqp1.csv +61 -0
- sequenzo/define_sequence_data.py +609 -0
- sequenzo/dissimilarity_measures/__init__.py +31 -0
- sequenzo/dissimilarity_measures/c_code.cpython-311-darwin.so +0 -0
- sequenzo/dissimilarity_measures/get_distance_matrix.py +702 -0
- sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +241 -0
- sequenzo/dissimilarity_measures/src/DHDdistance.cpp +148 -0
- sequenzo/dissimilarity_measures/src/LCPdistance.cpp +114 -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 +34 -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-311-darwin.so +0 -0
- sequenzo/dissimilarity_measures/utils/seqconc.cpython-311-darwin.so +0 -0
- sequenzo/dissimilarity_measures/utils/seqdss.cpython-311-darwin.so +0 -0
- sequenzo/dissimilarity_measures/utils/seqdur.cpython-311-darwin.so +0 -0
- sequenzo/dissimilarity_measures/utils/seqlength.cpython-311-darwin.so +0 -0
- sequenzo/multidomain/__init__.py +23 -0
- sequenzo/multidomain/association_between_domains.py +311 -0
- sequenzo/multidomain/cat.py +431 -0
- sequenzo/multidomain/combt.py +519 -0
- sequenzo/multidomain/dat.py +89 -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 +43 -0
- sequenzo/prefix_tree/individual_level_indicators.py +1274 -0
- sequenzo/prefix_tree/system_level_indicators.py +465 -0
- sequenzo/prefix_tree/utils.py +54 -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 +48 -0
- sequenzo/suffix_tree/individual_level_indicators.py +1638 -0
- sequenzo/suffix_tree/system_level_indicators.py +456 -0
- sequenzo/suffix_tree/utils.py +56 -0
- sequenzo/visualization/__init__.py +29 -0
- sequenzo/visualization/plot_mean_time.py +194 -0
- sequenzo/visualization/plot_modal_state.py +276 -0
- sequenzo/visualization/plot_most_frequent_sequences.py +147 -0
- sequenzo/visualization/plot_relative_frequency.py +404 -0
- sequenzo/visualization/plot_sequence_index.py +951 -0
- sequenzo/visualization/plot_single_medoid.py +153 -0
- sequenzo/visualization/plot_state_distribution.py +627 -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-0.1.24.dist-info/METADATA +255 -0
- sequenzo-0.1.24.dist-info/RECORD +264 -0
- sequenzo-0.1.24.dist-info/WHEEL +5 -0
- sequenzo-0.1.24.dist-info/licenses/LICENSE +28 -0
- sequenzo-0.1.24.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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#ifndef XSIMD_FMA3_AVX_HPP
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#define XSIMD_FMA3_AVX_HPP
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#include "../types/xsimd_fma3_avx_register.hpp"
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namespace xsimd
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{
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namespace kernel
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{
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using namespace types;
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// fnma
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template <class A>
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XSIMD_INLINE batch<float, A> fnma(batch<float, A> const& x, batch<float, A> const& y, batch<float, A> const& z, requires_arch<fma3<avx>>) noexcept
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{
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return _mm256_fnmadd_ps(x, y, z);
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}
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template <class A>
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XSIMD_INLINE batch<double, A> fnma(batch<double, A> const& x, batch<double, A> const& y, batch<double, A> const& z, requires_arch<fma3<avx>>) noexcept
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{
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return _mm256_fnmadd_pd(x, y, z);
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}
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// fnms
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template <class A>
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XSIMD_INLINE batch<float, A> fnms(batch<float, A> const& x, batch<float, A> const& y, batch<float, A> const& z, requires_arch<fma3<avx>>) noexcept
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{
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return _mm256_fnmsub_ps(x, y, z);
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}
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template <class A>
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XSIMD_INLINE batch<double, A> fnms(batch<double, A> const& x, batch<double, A> const& y, batch<double, A> const& z, requires_arch<fma3<avx>>) noexcept
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{
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return _mm256_fnmsub_pd(x, y, z);
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}
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// fma
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template <class A>
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XSIMD_INLINE batch<float, A> fma(batch<float, A> const& x, batch<float, A> const& y, batch<float, A> const& z, requires_arch<fma3<avx>>) noexcept
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{
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return _mm256_fmadd_ps(x, y, z);
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}
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template <class A>
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XSIMD_INLINE batch<double, A> fma(batch<double, A> const& x, batch<double, A> const& y, batch<double, A> const& z, requires_arch<fma3<avx>>) noexcept
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{
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return _mm256_fmadd_pd(x, y, z);
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}
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// fms
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template <class A>
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XSIMD_INLINE batch<float, A> fms(batch<float, A> const& x, batch<float, A> const& y, batch<float, A> const& z, requires_arch<fma3<avx>>) noexcept
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{
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return _mm256_fmsub_ps(x, y, z);
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}
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template <class A>
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XSIMD_INLINE batch<double, A> fms(batch<double, A> const& x, batch<double, A> const& y, batch<double, A> const& z, requires_arch<fma3<avx>>) noexcept
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{
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return _mm256_fmsub_pd(x, y, z);
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}
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// fmas
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template <class A>
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XSIMD_INLINE batch<float, A> fmas(batch<float, A> const& x, batch<float, A> const& y, batch<float, A> const& z, requires_arch<fma3<avx>>) noexcept
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{
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return _mm256_fmaddsub_ps(x, y, z);
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}
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template <class A>
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XSIMD_INLINE batch<double, A> fmas(batch<double, A> const& x, batch<double, A> const& y, batch<double, A> const& z, requires_arch<fma3<avx>>) noexcept
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{
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return _mm256_fmaddsub_pd(x, y, z);
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}
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}
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}
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#endif
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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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#ifndef XSIMD_FMA3_AVX2_HPP
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#define XSIMD_FMA3_AVX2_HPP
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#include "../types/xsimd_fma3_avx2_register.hpp"
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// Allow inclusion of xsimd_fma3_avx.hpp
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#ifdef XSIMD_FMA3_AVX_HPP
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#undef XSIMD_FMA3_AVX_HPP
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#define XSIMD_FORCE_FMA3_AVX_HPP
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#endif
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// Disallow inclusion of ./xsimd_fma3_avx_register.hpp
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#ifndef XSIMD_FMA3_AVX_REGISTER_HPP
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#define XSIMD_FMA3_AVX_REGISTER_HPP
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#define XSIMD_FORCE_FMA3_AVX_REGISTER_HPP
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#endif
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// Include ./xsimd_fma3_avx.hpp but s/avx/avx2
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#define avx avx2
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#include "./xsimd_fma3_avx.hpp"
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#undef avx
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#undef XSIMD_FMA3_AVX_HPP
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// Carefully restore guards
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#ifdef XSIMD_FORCE_FMA3_AVX_HPP
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#define XSIMD_FMA3_AVX_HPP
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#undef XSIMD_FORCE_FMA3_AVX_HPP
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#endif
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#ifdef XSIMD_FORCE_FMA3_AVX_REGISTER_HPP
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#undef XSIMD_FMA3_AVX_REGISTER_HPP
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#undef XSIMD_FORCE_FMA3_AVX_REGISTER_HPP
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#endif
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#endif
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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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#ifndef XSIMD_FMA3_SSE_HPP
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#define XSIMD_FMA3_SSE_HPP
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#include "../types/xsimd_fma3_sse_register.hpp"
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namespace xsimd
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{
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namespace kernel
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{
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using namespace types;
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// fnma
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template <class A>
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XSIMD_INLINE batch<float, A> fnma(batch<float, A> const& x, batch<float, A> const& y, batch<float, A> const& z, requires_arch<fma3<sse4_2>>) noexcept
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{
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return _mm_fnmadd_ps(x, y, z);
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}
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template <class A>
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XSIMD_INLINE batch<double, A> fnma(batch<double, A> const& x, batch<double, A> const& y, batch<double, A> const& z, requires_arch<fma3<sse4_2>>) noexcept
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{
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return _mm_fnmadd_pd(x, y, z);
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}
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// fnms
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37
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template <class A>
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XSIMD_INLINE batch<float, A> fnms(batch<float, A> const& x, batch<float, A> const& y, batch<float, A> const& z, requires_arch<fma3<sse4_2>>) noexcept
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{
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return _mm_fnmsub_ps(x, y, z);
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}
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42
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|
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template <class A>
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XSIMD_INLINE batch<double, A> fnms(batch<double, A> const& x, batch<double, A> const& y, batch<double, A> const& z, requires_arch<fma3<sse4_2>>) noexcept
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{
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return _mm_fnmsub_pd(x, y, z);
|
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}
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48
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|
|
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// fma
|
|
50
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template <class A>
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|
51
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+
XSIMD_INLINE batch<float, A> fma(batch<float, A> const& x, batch<float, A> const& y, batch<float, A> const& z, requires_arch<fma3<sse4_2>>) noexcept
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{
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return _mm_fmadd_ps(x, y, z);
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}
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55
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|
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56
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+
template <class A>
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XSIMD_INLINE batch<double, A> fma(batch<double, A> const& x, batch<double, A> const& y, batch<double, A> const& z, requires_arch<fma3<sse4_2>>) noexcept
|
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{
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59
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return _mm_fmadd_pd(x, y, z);
|
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60
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+
}
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|
61
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+
|
|
62
|
+
// fms
|
|
63
|
+
template <class A>
|
|
64
|
+
XSIMD_INLINE batch<float, A> fms(batch<float, A> const& x, batch<float, A> const& y, batch<float, A> const& z, requires_arch<fma3<sse4_2>>) noexcept
|
|
65
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{
|
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66
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return _mm_fmsub_ps(x, y, z);
|
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67
|
+
}
|
|
68
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+
|
|
69
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+
template <class A>
|
|
70
|
+
XSIMD_INLINE batch<double, A> fms(batch<double, A> const& x, batch<double, A> const& y, batch<double, A> const& z, requires_arch<fma3<sse4_2>>) noexcept
|
|
71
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+
{
|
|
72
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return _mm_fmsub_pd(x, y, z);
|
|
73
|
+
}
|
|
74
|
+
// fms
|
|
75
|
+
template <class A>
|
|
76
|
+
XSIMD_INLINE batch<float, A> fmas(batch<float, A> const& x,
|
|
77
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+
batch<float, A> const& y,
|
|
78
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+
batch<float, A> const& z,
|
|
79
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+
requires_arch<fma3<sse4_2>>) noexcept
|
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80
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+
{
|
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81
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return _mm_fmaddsub_ps(x, y, z);
|
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82
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+
}
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83
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+
|
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84
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+
template <class A>
|
|
85
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XSIMD_INLINE batch<double, A> fmas(batch<double, A> const& x,
|
|
86
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+
batch<double, A> const& y,
|
|
87
|
+
batch<double, A> const& z,
|
|
88
|
+
requires_arch<fma3<sse4_2>>) noexcept
|
|
89
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+
{
|
|
90
|
+
return _mm_fmaddsub_pd(x, y, z);
|
|
91
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+
}
|
|
92
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+
|
|
93
|
+
}
|
|
94
|
+
|
|
95
|
+
}
|
|
96
|
+
|
|
97
|
+
#endif
|
|
@@ -0,0 +1,92 @@
|
|
|
1
|
+
/***************************************************************************
|
|
2
|
+
* Copyright (c) Johan Mabille, Sylvain Corlay, Wolf Vollprecht and *
|
|
3
|
+
* Martin Renou *
|
|
4
|
+
* Copyright (c) QuantStack *
|
|
5
|
+
* Copyright (c) Serge Guelton *
|
|
6
|
+
* *
|
|
7
|
+
* Distributed under the terms of the BSD 3-Clause License. *
|
|
8
|
+
* *
|
|
9
|
+
* The full license is in the file LICENSE, distributed with this software. *
|
|
10
|
+
****************************************************************************/
|
|
11
|
+
|
|
12
|
+
#ifndef XSIMD_FMA4_HPP
|
|
13
|
+
#define XSIMD_FMA4_HPP
|
|
14
|
+
|
|
15
|
+
#include "../types/xsimd_fma4_register.hpp"
|
|
16
|
+
|
|
17
|
+
namespace xsimd
|
|
18
|
+
{
|
|
19
|
+
|
|
20
|
+
namespace kernel
|
|
21
|
+
{
|
|
22
|
+
using namespace types;
|
|
23
|
+
|
|
24
|
+
// fnma
|
|
25
|
+
template <class A>
|
|
26
|
+
XSIMD_INLINE batch<float, A> fnma(batch<float, A> const& x, batch<float, A> const& y, batch<float, A> const& z, requires_arch<fma4>) noexcept
|
|
27
|
+
{
|
|
28
|
+
return _mm_nmacc_ps(x, y, z);
|
|
29
|
+
}
|
|
30
|
+
|
|
31
|
+
template <class A>
|
|
32
|
+
XSIMD_INLINE batch<double, A> fnma(batch<double, A> const& x, batch<double, A> const& y, batch<double, A> const& z, requires_arch<fma4>) noexcept
|
|
33
|
+
{
|
|
34
|
+
return _mm_nmacc_pd(x, y, z);
|
|
35
|
+
}
|
|
36
|
+
|
|
37
|
+
// fnms
|
|
38
|
+
template <class A>
|
|
39
|
+
XSIMD_INLINE batch<float, A> fnms(batch<float, A> const& x, batch<float, A> const& y, batch<float, A> const& z, requires_arch<fma4>) noexcept
|
|
40
|
+
{
|
|
41
|
+
return _mm_nmsub_ps(x, y, z);
|
|
42
|
+
}
|
|
43
|
+
|
|
44
|
+
template <class A>
|
|
45
|
+
XSIMD_INLINE batch<double, A> fnms(batch<double, A> const& x, batch<double, A> const& y, batch<double, A> const& z, requires_arch<fma4>) noexcept
|
|
46
|
+
{
|
|
47
|
+
return _mm_nmsub_pd(x, y, z);
|
|
48
|
+
}
|
|
49
|
+
|
|
50
|
+
// fma
|
|
51
|
+
template <class A>
|
|
52
|
+
XSIMD_INLINE batch<float, A> fma(batch<float, A> const& x, batch<float, A> const& y, batch<float, A> const& z, requires_arch<fma4>) noexcept
|
|
53
|
+
{
|
|
54
|
+
return _mm_macc_ps(x, y, z);
|
|
55
|
+
}
|
|
56
|
+
|
|
57
|
+
template <class A>
|
|
58
|
+
XSIMD_INLINE batch<double, A> fma(batch<double, A> const& x, batch<double, A> const& y, batch<double, A> const& z, requires_arch<fma4>) noexcept
|
|
59
|
+
{
|
|
60
|
+
return _mm_macc_pd(x, y, z);
|
|
61
|
+
}
|
|
62
|
+
|
|
63
|
+
// fms
|
|
64
|
+
template <class A>
|
|
65
|
+
XSIMD_INLINE batch<float, A> fms(batch<float, A> const& x, batch<float, A> const& y, batch<float, A> const& z, requires_arch<fma4>) noexcept
|
|
66
|
+
{
|
|
67
|
+
return _mm_msub_ps(x, y, z);
|
|
68
|
+
}
|
|
69
|
+
|
|
70
|
+
template <class A>
|
|
71
|
+
XSIMD_INLINE batch<double, A> fms(batch<double, A> const& x, batch<double, A> const& y, batch<double, A> const& z, requires_arch<fma4>) noexcept
|
|
72
|
+
{
|
|
73
|
+
return _mm_msub_pd(x, y, z);
|
|
74
|
+
}
|
|
75
|
+
|
|
76
|
+
// fmas
|
|
77
|
+
template <class A>
|
|
78
|
+
XSIMD_INLINE batch<float, A> fmas(batch<float, A> const& x, batch<float, A> const& y, batch<float, A> const& z, requires_arch<fma4>) noexcept
|
|
79
|
+
{
|
|
80
|
+
return _mm_maddsub_ps(x, y, z);
|
|
81
|
+
}
|
|
82
|
+
|
|
83
|
+
template <class A>
|
|
84
|
+
XSIMD_INLINE batch<double, A> fmas(batch<double, A> const& x, batch<double, A> const& y, batch<double, A> const& z, requires_arch<fma4>) noexcept
|
|
85
|
+
{
|
|
86
|
+
return _mm_maddsub_pd(x, y, z);
|
|
87
|
+
}
|
|
88
|
+
}
|
|
89
|
+
|
|
90
|
+
}
|
|
91
|
+
|
|
92
|
+
#endif
|
|
@@ -0,0 +1,17 @@
|
|
|
1
|
+
/***************************************************************************
|
|
2
|
+
* Copyright (c) Johan Mabille, Sylvain Corlay, Wolf Vollprecht and *
|
|
3
|
+
* Martin Renou *
|
|
4
|
+
* Copyright (c) QuantStack *
|
|
5
|
+
* Copyright (c) Serge Guelton *
|
|
6
|
+
* *
|
|
7
|
+
* Distributed under the terms of the BSD 3-Clause License. *
|
|
8
|
+
* *
|
|
9
|
+
* The full license is in the file LICENSE, distributed with this software. *
|
|
10
|
+
****************************************************************************/
|
|
11
|
+
|
|
12
|
+
#ifndef XSIMD_I8MM_NEON64_HPP
|
|
13
|
+
#define XSIMD_I8MM_NEON64_HPP
|
|
14
|
+
|
|
15
|
+
#include "../types/xsimd_i8mm_neon64_register.hpp"
|
|
16
|
+
|
|
17
|
+
#endif
|
|
@@ -0,0 +1,142 @@
|
|
|
1
|
+
/***************************************************************************
|
|
2
|
+
* Copyright (c) Johan Mabille, Sylvain Corlay, Wolf Vollprecht and *
|
|
3
|
+
* Martin Renou *
|
|
4
|
+
* Copyright (c) QuantStack *
|
|
5
|
+
* Copyright (c) Serge Guelton *
|
|
6
|
+
* *
|
|
7
|
+
* Distributed under the terms of the BSD 3-Clause License. *
|
|
8
|
+
* *
|
|
9
|
+
* The full license is in the file LICENSE, distributed with this software. *
|
|
10
|
+
****************************************************************************/
|
|
11
|
+
|
|
12
|
+
#ifndef XSIMD_ISA_HPP
|
|
13
|
+
#define XSIMD_ISA_HPP
|
|
14
|
+
|
|
15
|
+
#include "../config/xsimd_arch.hpp"
|
|
16
|
+
|
|
17
|
+
#include "./xsimd_common_fwd.hpp"
|
|
18
|
+
|
|
19
|
+
#if XSIMD_WITH_EMULATED
|
|
20
|
+
#include "./xsimd_emulated.hpp"
|
|
21
|
+
#endif
|
|
22
|
+
|
|
23
|
+
#if XSIMD_WITH_SSE2
|
|
24
|
+
#include "./xsimd_sse2.hpp"
|
|
25
|
+
#endif
|
|
26
|
+
|
|
27
|
+
#if XSIMD_WITH_SSE3
|
|
28
|
+
#include "./xsimd_sse3.hpp"
|
|
29
|
+
#endif
|
|
30
|
+
|
|
31
|
+
#if XSIMD_WITH_SSSE3
|
|
32
|
+
#include "./xsimd_ssse3.hpp"
|
|
33
|
+
#endif
|
|
34
|
+
|
|
35
|
+
#if XSIMD_WITH_SSE4_1
|
|
36
|
+
#include "./xsimd_sse4_1.hpp"
|
|
37
|
+
#endif
|
|
38
|
+
|
|
39
|
+
#if XSIMD_WITH_SSE4_2
|
|
40
|
+
#include "./xsimd_sse4_2.hpp"
|
|
41
|
+
#endif
|
|
42
|
+
|
|
43
|
+
#if XSIMD_WITH_FMA3_SSE
|
|
44
|
+
#include "./xsimd_fma3_sse.hpp"
|
|
45
|
+
#endif
|
|
46
|
+
|
|
47
|
+
#if XSIMD_WITH_FMA4
|
|
48
|
+
#include "./xsimd_fma4.hpp"
|
|
49
|
+
#endif
|
|
50
|
+
|
|
51
|
+
#if XSIMD_WITH_AVX
|
|
52
|
+
#include "./xsimd_avx.hpp"
|
|
53
|
+
#endif
|
|
54
|
+
|
|
55
|
+
#if XSIMD_WITH_FMA3_AVX
|
|
56
|
+
#include "./xsimd_fma3_avx.hpp"
|
|
57
|
+
#endif
|
|
58
|
+
|
|
59
|
+
#if XSIMD_WITH_AVXVNNI
|
|
60
|
+
#include "./xsimd_avxvnni.hpp"
|
|
61
|
+
#endif
|
|
62
|
+
|
|
63
|
+
#if XSIMD_WITH_AVX2
|
|
64
|
+
#include "./xsimd_avx2.hpp"
|
|
65
|
+
#endif
|
|
66
|
+
|
|
67
|
+
#if XSIMD_WITH_FMA3_AVX2
|
|
68
|
+
#include "./xsimd_fma3_avx2.hpp"
|
|
69
|
+
#endif
|
|
70
|
+
|
|
71
|
+
#if XSIMD_WITH_AVX512F
|
|
72
|
+
#include "./xsimd_avx512f.hpp"
|
|
73
|
+
#endif
|
|
74
|
+
|
|
75
|
+
#if XSIMD_WITH_AVX512DQ
|
|
76
|
+
#include "./xsimd_avx512dq.hpp"
|
|
77
|
+
#endif
|
|
78
|
+
|
|
79
|
+
#if XSIMD_WITH_AVX512BW
|
|
80
|
+
#include "./xsimd_avx512bw.hpp"
|
|
81
|
+
#endif
|
|
82
|
+
|
|
83
|
+
#if XSIMD_WITH_AVX512ER
|
|
84
|
+
#include "./xsimd_avx512er.hpp"
|
|
85
|
+
#endif
|
|
86
|
+
|
|
87
|
+
#if XSIMD_WITH_AVX512PF
|
|
88
|
+
#include "./xsimd_avx512pf.hpp"
|
|
89
|
+
#endif
|
|
90
|
+
|
|
91
|
+
#if XSIMD_WITH_AVX512IFMA
|
|
92
|
+
#include "./xsimd_avx512ifma.hpp"
|
|
93
|
+
#endif
|
|
94
|
+
|
|
95
|
+
#if XSIMD_WITH_AVX512VBMI
|
|
96
|
+
#include "./xsimd_avx512vbmi.hpp"
|
|
97
|
+
#endif
|
|
98
|
+
|
|
99
|
+
#if XSIMD_WITH_AVX512VBMI2
|
|
100
|
+
#include "./xsimd_avx512vbmi2.hpp"
|
|
101
|
+
#endif
|
|
102
|
+
|
|
103
|
+
#if XSIMD_WITH_AVX512VNNI_AVX512BW
|
|
104
|
+
#include "./xsimd_avx512vnni_avx512bw.hpp"
|
|
105
|
+
#endif
|
|
106
|
+
|
|
107
|
+
#if XSIMD_WITH_AVX512VNNI_AVX512VBMI2
|
|
108
|
+
#include "./xsimd_avx512vnni_avx512vbmi2.hpp"
|
|
109
|
+
#endif
|
|
110
|
+
|
|
111
|
+
#if XSIMD_WITH_NEON
|
|
112
|
+
#include "./xsimd_neon.hpp"
|
|
113
|
+
#endif
|
|
114
|
+
|
|
115
|
+
#if XSIMD_WITH_NEON64
|
|
116
|
+
#include "./xsimd_neon64.hpp"
|
|
117
|
+
#endif
|
|
118
|
+
|
|
119
|
+
#if XSIMD_WITH_I8MM_NEON64
|
|
120
|
+
#include "./xsimd_i8mm_neon64.hpp"
|
|
121
|
+
#endif
|
|
122
|
+
|
|
123
|
+
#if XSIMD_WITH_SVE
|
|
124
|
+
#include "./xsimd_sve.hpp"
|
|
125
|
+
#endif
|
|
126
|
+
|
|
127
|
+
#if XSIMD_WITH_RVV
|
|
128
|
+
#include "./xsimd_rvv.hpp"
|
|
129
|
+
#endif
|
|
130
|
+
|
|
131
|
+
#if XSIMD_WITH_WASM
|
|
132
|
+
#include "./xsimd_wasm.hpp"
|
|
133
|
+
#endif
|
|
134
|
+
|
|
135
|
+
#if XSIMD_WITH_VSX
|
|
136
|
+
#include "./xsimd_vsx.hpp"
|
|
137
|
+
#endif
|
|
138
|
+
|
|
139
|
+
// Must come last to have access to all conversion specializations.
|
|
140
|
+
#include "./xsimd_common.hpp"
|
|
141
|
+
|
|
142
|
+
#endif
|