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_COMMON_ROUNDING_HPP
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#define XSIMD_COMMON_ROUNDING_HPP
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#include "./xsimd_common_details.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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// ceil
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template <class A, class T>
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XSIMD_INLINE batch<T, A> ceil(batch<T, A> const& self, requires_arch<common>) noexcept
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{
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batch<T, A> truncated_self = trunc(self);
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return select(truncated_self < self, truncated_self + 1, truncated_self);
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}
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// floor
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template <class A, class T>
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XSIMD_INLINE batch<T, A> floor(batch<T, A> const& self, requires_arch<common>) noexcept
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{
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batch<T, A> truncated_self = trunc(self);
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return select(truncated_self > self, truncated_self - 1, truncated_self);
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}
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// round
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template <class A, class T>
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XSIMD_INLINE batch<T, A> round(batch<T, A> const& self, requires_arch<common>) noexcept
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{
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auto v = abs(self);
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auto c = ceil(v);
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auto cp = select(c - 0.5 > v, c - 1, c);
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return select(v > constants::maxflint<batch<T, A>>(), self, copysign(cp, self));
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}
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// trunc
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template <class A, class T, class = typename std::enable_if<std::is_integral<T>::value, void>::type>
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XSIMD_INLINE batch<T, A> trunc(batch<T, A> const& self, requires_arch<common>) noexcept
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{
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return self;
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}
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template <class A>
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XSIMD_INLINE batch<float, A> trunc(batch<float, A> const& self, requires_arch<common>) noexcept
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{
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return select(abs(self) < constants::maxflint<batch<float, A>>(), to_float(to_int(self)), self);
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}
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template <class A>
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XSIMD_INLINE batch<double, A> trunc(batch<double, A> const& self, requires_arch<common>) noexcept
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{
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return select(abs(self) < constants::maxflint<batch<double, A>>(), to_float(to_int(self)), self);
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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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* Copyright (c) Marco Barbone *
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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_COMMON_SWIZZLE_HPP
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#define XSIMD_COMMON_SWIZZLE_HPP
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#include <cstddef>
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#include <cstdint>
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#include <type_traits>
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namespace xsimd
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{
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template <typename T, class A, T... Values>
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struct batch_constant;
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namespace kernel
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{
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namespace detail
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{
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// ────────────────────────────────────────────────────────────────────────
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// get_at<I,Values...> → the I-th element of the pack
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template <typename T, std::size_t I, T V0, T... Vs>
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struct get_at
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{
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static constexpr T value = get_at<T, I - 1, Vs...>::value;
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};
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template <typename T, T V0, T... Vs>
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struct get_at<T, 0, V0, Vs...>
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{
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static constexpr T value = V0;
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};
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// ────────────────────────────────────────────────────────────────────────
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// 1) identity_impl
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template <std::size_t /*I*/, typename T>
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XSIMD_INLINE constexpr bool identity_impl() noexcept { return true; }
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template <std::size_t I, typename T, T V0, T... Vs>
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XSIMD_INLINE constexpr bool identity_impl() noexcept
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{
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return V0 == static_cast<T>(I)
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&& identity_impl<I + 1, T, Vs...>();
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}
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// ────────────────────────────────────────────────────────────────────────
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// 2) bitmask_impl
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template <std::size_t /*I*/, std::size_t /*N*/, typename T>
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XSIMD_INLINE constexpr std::uint32_t bitmask_impl() noexcept { return 0u; }
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template <std::size_t I, std::size_t N, typename T, T V0, T... Vs>
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XSIMD_INLINE constexpr std::uint32_t bitmask_impl() noexcept
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{
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return (1u << (static_cast<std::uint32_t>(V0) & (N - 1)))
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| bitmask_impl<I + 1, N, T, Vs...>();
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}
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// ────────────────────────────────────────────────────────────────────────
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// 3) dup_lo_impl
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template <std::size_t I, std::size_t N, typename T,
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T... Vs, typename std::enable_if<I == N / 2, int>::type = 0>
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XSIMD_INLINE constexpr bool dup_lo_impl() noexcept { return true; }
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template <std::size_t I, std::size_t N, typename T,
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T... Vs, typename std::enable_if<(I < N / 2), int>::type = 0>
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XSIMD_INLINE constexpr bool dup_lo_impl() noexcept
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{
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return get_at<T, I, Vs...>::value < static_cast<T>(N / 2)
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&& get_at<T, I + N / 2, Vs...>::value == get_at<T, I, Vs...>::value
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&& dup_lo_impl<I + 1, N, T, Vs...>();
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}
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// ────────────────────────────────────────────────────────────────────────
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// 4) dup_hi_impl
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template <std::size_t I, std::size_t N, typename T,
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T... Vs, typename std::enable_if<I == N / 2, int>::type = 0>
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XSIMD_INLINE constexpr bool dup_hi_impl() noexcept { return true; }
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template <std::size_t I, std::size_t N, typename T,
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T... Vs, typename std::enable_if<(I < N / 2), int>::type = 0>
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XSIMD_INLINE constexpr bool dup_hi_impl() noexcept
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{
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return get_at<T, I, Vs...>::value >= static_cast<T>(N / 2)
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&& get_at<T, I, Vs...>::value < static_cast<T>(N)
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&& get_at<T, I + N / 2, Vs...>::value == get_at<T, I, Vs...>::value
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&& dup_hi_impl<I + 1, N, T, Vs...>();
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}
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// ────────────────────────────────────────────────────────────────────────
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// 1) helper to get the I-th value from the Vs pack
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template <std::size_t I, uint32_t Head, uint32_t... Tail>
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97
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struct get_nth_value
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{
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static constexpr uint32_t value = get_nth_value<I - 1, Tail...>::value;
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};
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template <uint32_t Head, uint32_t... Tail>
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struct get_nth_value<0, Head, Tail...>
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{
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104
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static constexpr uint32_t value = Head;
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105
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};
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107
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// ────────────────────────────────────────────────────────────────────────
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// 2) recursive cross‐lane test: true if any output‐lane i pulls from the opposite half
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109
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template <std::size_t I,
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110
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std::size_t N,
|
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111
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std::size_t H,
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112
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uint32_t... Vs>
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struct cross_impl
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{
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115
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// does element I cross? (i.e. i<H but V>=H) or (i>=H but V<H)
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116
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static constexpr uint32_t Vi = get_nth_value<I, Vs...>::value;
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117
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static constexpr bool curr = (I < H ? (Vi >= H) : (Vi < H));
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118
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static constexpr bool next = cross_impl<I + 1, N, H, Vs...>::value;
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119
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static constexpr bool value = curr || next;
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120
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};
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121
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template <std::size_t N, std::size_t H, uint32_t... Vs>
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122
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struct cross_impl<N, N, H, Vs...>
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123
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{
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static constexpr bool value = false;
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};
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126
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template <std::size_t I, std::size_t N, typename T,
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127
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T... Vs>
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128
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XSIMD_INLINE constexpr bool no_duplicates_impl() noexcept
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129
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{
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130
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// build the bitmask of (Vs & (N-1)) across all lanes
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131
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return detail::bitmask_impl<0, N, T, Vs...>() == ((1u << N) - 1u);
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132
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+
}
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133
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template <uint32_t... Vs>
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134
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XSIMD_INLINE constexpr bool no_duplicates_v() noexcept
|
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135
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{
|
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136
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// forward to your existing no_duplicates_impl
|
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137
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return no_duplicates_impl<0, sizeof...(Vs), uint32_t, Vs...>();
|
|
138
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+
}
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139
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template <uint32_t... Vs>
|
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140
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XSIMD_INLINE constexpr bool is_cross_lane() noexcept
|
|
141
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+
{
|
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142
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static_assert(sizeof...(Vs) >= 1, "Need at least one lane");
|
|
143
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return cross_impl<0, sizeof...(Vs), sizeof...(Vs) / 2, Vs...>::value;
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144
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}
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|
145
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+
template <typename T, T... Vs>
|
|
146
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+
XSIMD_INLINE constexpr bool is_identity() noexcept { return detail::identity_impl<0, T, Vs...>(); }
|
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147
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+
template <typename T, T... Vs>
|
|
148
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XSIMD_INLINE constexpr bool is_all_different() noexcept
|
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149
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{
|
|
150
|
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return detail::bitmask_impl<0, sizeof...(Vs), T, Vs...>() == ((1u << sizeof...(Vs)) - 1);
|
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151
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}
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152
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+
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153
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template <typename T, T... Vs>
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154
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XSIMD_INLINE constexpr bool is_dup_lo() noexcept { return detail::dup_lo_impl<0, sizeof...(Vs), T, Vs...>(); }
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155
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template <typename T, T... Vs>
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156
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XSIMD_INLINE constexpr bool is_dup_hi() noexcept { return detail::dup_hi_impl<0, sizeof...(Vs), T, Vs...>(); }
|
|
157
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+
template <typename T, class A, T... Vs>
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|
158
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+
XSIMD_INLINE constexpr bool is_identity(batch_constant<T, A, Vs...>) noexcept { return is_identity<T, Vs...>(); }
|
|
159
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+
template <typename T, class A, T... Vs>
|
|
160
|
+
XSIMD_INLINE constexpr bool is_all_different(batch_constant<T, A, Vs...>) noexcept { return is_all_different<T, Vs...>(); }
|
|
161
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+
template <typename T, class A, T... Vs>
|
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162
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XSIMD_INLINE constexpr bool is_dup_lo(batch_constant<T, A, Vs...>) noexcept { return is_dup_lo<T, Vs...>(); }
|
|
163
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+
template <typename T, class A, T... Vs>
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164
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XSIMD_INLINE constexpr bool is_dup_hi(batch_constant<T, A, Vs...>) noexcept { return is_dup_hi<T, Vs...>(); }
|
|
165
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+
template <typename T, class A, T... Vs>
|
|
166
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+
XSIMD_INLINE constexpr bool is_cross_lane(batch_constant<T, A, Vs...>) noexcept { return detail::is_cross_lane<Vs...>(); }
|
|
167
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+
template <typename T, class A, T... Vs>
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168
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+
XSIMD_INLINE constexpr bool no_duplicates(batch_constant<T, A, Vs...>) noexcept { return no_duplicates_impl<0, sizeof...(Vs), T, Vs...>(); }
|
|
169
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+
|
|
170
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+
} // namespace detail
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|
171
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} // namespace kernel
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|
172
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+
} // namespace xsimd
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|
173
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+
|
|
174
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+
#endif // XSIMD_COMMON_SWIZZLE_HPP
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