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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#ifndef XSIMD_NUMERICAL_CONSTANT_HPP
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#define XSIMD_NUMERICAL_CONSTANT_HPP
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#include <limits>
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#include "../types/xsimd_utils.hpp"
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namespace xsimd
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{
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namespace constants
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{
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#define XSIMD_DEFINE_CONSTANT(NAME, SINGLE, DOUBLE) \
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template <class T> \
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XSIMD_INLINE T NAME() noexcept \
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{ \
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return T(NAME<typename T::value_type>()); \
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} \
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template <> \
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XSIMD_INLINE float NAME<float>() noexcept \
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{ \
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return SINGLE; \
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} \
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template <> \
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XSIMD_INLINE double NAME<double>() noexcept \
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{ \
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return DOUBLE; \
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}
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#define XSIMD_DEFINE_CONSTANT_HEX(NAME, SINGLE, DOUBLE) \
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template <class T> \
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XSIMD_INLINE T NAME() noexcept \
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{ \
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return T(NAME<typename T::value_type>()); \
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} \
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template <> \
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XSIMD_INLINE float NAME<float>() noexcept \
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{ \
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return bit_cast<float>((uint32_t)SINGLE); \
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} \
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template <> \
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XSIMD_INLINE double NAME<double>() noexcept \
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{ \
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return bit_cast<double>((uint64_t)DOUBLE); \
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}
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// Under fast-math, GCC might replace signmask (minus zero) by zero
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#if defined(__FAST_MATH__) && defined(__GNUC__) && !defined(__clang__)
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#pragma GCC push_options
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#pragma GCC optimize("signed-zeros")
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#endif
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#ifndef __FAST_MATH__
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XSIMD_DEFINE_CONSTANT(infinity, (std::numeric_limits<float>::infinity()), (std::numeric_limits<double>::infinity()))
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XSIMD_DEFINE_CONSTANT(minusinfinity, (-infinity<float>()), (-infinity<double>()))
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#endif
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XSIMD_DEFINE_CONSTANT(invlog_2, 1.442695040888963407359924681001892137426645954152986f, 1.442695040888963407359924681001892137426645954152986)
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XSIMD_DEFINE_CONSTANT_HEX(invlog_2hi, 0x3fb8b000, 0x3ff7154765200000)
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XSIMD_DEFINE_CONSTANT_HEX(invlog_2lo, 0xb9389ad4, 0x3de705fc2eefa200)
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XSIMD_DEFINE_CONSTANT(invlog10_2, 3.32192809488736234787031942949f, 3.32192809488736234787031942949)
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XSIMD_DEFINE_CONSTANT_HEX(invpi, 0x3ea2f983, 0x3fd45f306dc9c883)
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XSIMD_DEFINE_CONSTANT(log_2, 0.6931471805599453094172321214581765680755001343602553f, 0.6931471805599453094172321214581765680755001343602553)
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XSIMD_DEFINE_CONSTANT_HEX(log_2hi, 0x3f318000, 0x3fe62e42fee00000)
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XSIMD_DEFINE_CONSTANT_HEX(log_2lo, 0xb95e8083, 0x3dea39ef35793c76)
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XSIMD_DEFINE_CONSTANT_HEX(log10_2hi, 0x3e9a0000, 0x3fd3440000000000)
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XSIMD_DEFINE_CONSTANT_HEX(log10_2lo, 0x39826a14, 0x3ed3509f79fef312)
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XSIMD_DEFINE_CONSTANT_HEX(logeps, 0xc17f1402, 0xc04205966f2b4f12)
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XSIMD_DEFINE_CONSTANT_HEX(logpi, 0x3f928682, 0x3ff250d048e7a1bd)
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XSIMD_DEFINE_CONSTANT_HEX(logsqrt2pi, 0x3f6b3f8e, 0x3fed67f1c864beb5)
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XSIMD_DEFINE_CONSTANT(maxflint, 16777216.0f, 9007199254740992.0)
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XSIMD_DEFINE_CONSTANT(maxlog, 88.3762626647949f, 709.78271289338400)
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XSIMD_DEFINE_CONSTANT(maxlog2, 127.0f, 1023.)
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XSIMD_DEFINE_CONSTANT(maxlog10, 38.23080825805664f, 308.2547155599167)
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XSIMD_DEFINE_CONSTANT_HEX(mediumpi, 0x43490fdb, 0x412921fb54442d18)
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XSIMD_DEFINE_CONSTANT(minlog, -88.3762626647949f, -708.3964185322641)
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XSIMD_DEFINE_CONSTANT(minlog2, -127.0f, -1023.)
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XSIMD_DEFINE_CONSTANT(minlog10, -37.89999771118164f, -308.2547155599167)
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XSIMD_DEFINE_CONSTANT_HEX(nan, 0xffffffff, 0xffffffffffffffff)
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XSIMD_DEFINE_CONSTANT_HEX(oneosqrteps, 0x453504f3, 0x4190000000000000)
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XSIMD_DEFINE_CONSTANT_HEX(oneotwoeps, 0x4a800000, 0x4320000000000000)
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XSIMD_DEFINE_CONSTANT_HEX(pi, 0x40490fdb, 0x400921fb54442d18)
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XSIMD_DEFINE_CONSTANT_HEX(pio_2lo, 0xb33bbd2e, 0x3c91a62633145c07)
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XSIMD_DEFINE_CONSTANT_HEX(pio_4lo, 0xb2bbbd2e, 0x3c81a62633145c07)
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XSIMD_DEFINE_CONSTANT_HEX(pio2, 0x3fc90fdb, 0x3ff921fb54442d18)
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XSIMD_DEFINE_CONSTANT_HEX(pio2_1, 0x3fc90f80, 0x3ff921fb54400000)
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XSIMD_DEFINE_CONSTANT_HEX(pio2_1t, 0x37354443, 0x3dd0b4611a626331)
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XSIMD_DEFINE_CONSTANT_HEX(pio2_2, 0x37354400, 0x3dd0b4611a600000)
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XSIMD_DEFINE_CONSTANT_HEX(pio2_2t, 0x2e85a308, 0x3ba3198a2e037073)
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XSIMD_DEFINE_CONSTANT_HEX(pio2_3, 0x2e85a300, 0x3ba3198a2e000000)
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XSIMD_DEFINE_CONSTANT_HEX(pio2_3t, 0x248d3132, 0x397b839a252049c1)
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XSIMD_DEFINE_CONSTANT_HEX(pio4, 0x3f490fdb, 0x3fe921fb54442d18)
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XSIMD_DEFINE_CONSTANT_HEX(signmask, 0x80000000, 0x8000000000000000)
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XSIMD_DEFINE_CONSTANT(smallestposval, std::numeric_limits<float>::min(), std::numeric_limits<double>::min())
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XSIMD_DEFINE_CONSTANT_HEX(sqrt_2pi, 0x40206c99, 0x40040d931ff62704)
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XSIMD_DEFINE_CONSTANT_HEX(sqrteps, 0x39b504f3, 0x3e50000000000000)
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XSIMD_DEFINE_CONSTANT_HEX(tanpio8, 0x3ed413cd, 0x3fda827999fcef31)
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XSIMD_DEFINE_CONSTANT_HEX(tan3pio8, 0x401a827a, 0x4003504f333f9de6)
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XSIMD_DEFINE_CONSTANT_HEX(twentypi, 0x427b53d1, 0x404f6a7a2955385e)
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XSIMD_DEFINE_CONSTANT_HEX(twoopi, 0x3f22f983, 0x3fe45f306dc9c883)
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XSIMD_DEFINE_CONSTANT(twotonmb, 8388608.0f, 4503599627370496.0)
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XSIMD_DEFINE_CONSTANT_HEX(twotonmbo3, 0x3ba14518, 0x3ed428a2f98d7286)
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#if defined(__FAST_MATH__) && defined(__GNUC__) && !defined(__clang__)
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#pragma GCC pop_options
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#endif
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#undef XSIMD_DEFINE_CONSTANT
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#undef XSIMD_DEFINE_CONSTANT_HEX
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template <class T>
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constexpr T allbits() noexcept;
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template <class T>
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constexpr as_integer_t<T> mask1frexp() noexcept;
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template <class T>
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constexpr as_integer_t<T> mask2frexp() noexcept;
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template <class T>
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constexpr as_integer_t<T> maxexponent() noexcept;
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template <class T>
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constexpr as_integer_t<T> maxexponentm1() noexcept;
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template <class T>
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constexpr int32_t nmb() noexcept;
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template <class T>
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constexpr T zero() noexcept;
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template <class T>
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constexpr T minvalue() noexcept;
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template <class T>
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constexpr T maxvalue() noexcept;
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/**************************
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* allbits implementation *
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**************************/
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namespace detail
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{
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template <class T, bool = std::is_integral<T>::value>
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struct allbits_impl
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{
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static constexpr T get_value() noexcept
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{
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return T(~0);
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}
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};
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template <class T>
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struct allbits_impl<T, false>
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{
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static constexpr T get_value() noexcept
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{
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return nan<T>();
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}
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};
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}
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template <class T>
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XSIMD_INLINE constexpr T allbits() noexcept
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{
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return T(detail::allbits_impl<typename T::value_type>::get_value());
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}
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/*****************************
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* mask1frexp implementation *
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*****************************/
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template <class T>
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XSIMD_INLINE constexpr as_integer_t<T> mask1frexp() noexcept
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{
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return as_integer_t<T>(mask1frexp<typename T::value_type>());
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}
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template <>
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XSIMD_INLINE constexpr int32_t mask1frexp<float>() noexcept
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{
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return 0x7f800000;
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}
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template <>
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XSIMD_INLINE constexpr int64_t mask1frexp<double>() noexcept
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{
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return 0x7ff0000000000000;
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}
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/*****************************
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* mask2frexp implementation *
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*****************************/
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template <class T>
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XSIMD_INLINE constexpr as_integer_t<T> mask2frexp() noexcept
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{
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return as_integer_t<T>(mask2frexp<typename T::value_type>());
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}
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template <>
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XSIMD_INLINE constexpr int32_t mask2frexp<float>() noexcept
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{
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return 0x3f000000;
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}
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template <>
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XSIMD_INLINE constexpr int64_t mask2frexp<double>() noexcept
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{
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return 0x3fe0000000000000;
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}
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/******************************
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* maxexponent implementation *
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******************************/
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template <class T>
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XSIMD_INLINE constexpr as_integer_t<T> maxexponent() noexcept
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{
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return as_integer_t<T>(maxexponent<typename T::value_type>());
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}
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template <>
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XSIMD_INLINE constexpr int32_t maxexponent<float>() noexcept
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{
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return 127;
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}
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template <>
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XSIMD_INLINE constexpr int64_t maxexponent<double>() noexcept
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{
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return 1023;
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}
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/******************************
|
|
245
|
+
* maxexponent implementation *
|
|
246
|
+
******************************/
|
|
247
|
+
|
|
248
|
+
template <class T>
|
|
249
|
+
XSIMD_INLINE constexpr as_integer_t<T> maxexponentm1() noexcept
|
|
250
|
+
{
|
|
251
|
+
return as_integer_t<T>(maxexponentm1<typename T::value_type>());
|
|
252
|
+
}
|
|
253
|
+
|
|
254
|
+
template <>
|
|
255
|
+
XSIMD_INLINE constexpr int32_t maxexponentm1<float>() noexcept
|
|
256
|
+
{
|
|
257
|
+
return 126;
|
|
258
|
+
}
|
|
259
|
+
|
|
260
|
+
template <>
|
|
261
|
+
XSIMD_INLINE constexpr int64_t maxexponentm1<double>() noexcept
|
|
262
|
+
{
|
|
263
|
+
return 1022;
|
|
264
|
+
}
|
|
265
|
+
|
|
266
|
+
/**********************
|
|
267
|
+
* nmb implementation *
|
|
268
|
+
**********************/
|
|
269
|
+
|
|
270
|
+
template <class T>
|
|
271
|
+
XSIMD_INLINE constexpr int32_t nmb() noexcept
|
|
272
|
+
{
|
|
273
|
+
return nmb<typename T::value_type>();
|
|
274
|
+
}
|
|
275
|
+
|
|
276
|
+
template <>
|
|
277
|
+
XSIMD_INLINE constexpr int32_t nmb<float>() noexcept
|
|
278
|
+
{
|
|
279
|
+
return 23;
|
|
280
|
+
}
|
|
281
|
+
|
|
282
|
+
template <>
|
|
283
|
+
XSIMD_INLINE constexpr int32_t nmb<double>() noexcept
|
|
284
|
+
{
|
|
285
|
+
return 52;
|
|
286
|
+
}
|
|
287
|
+
|
|
288
|
+
/***********************
|
|
289
|
+
* zero implementation *
|
|
290
|
+
***********************/
|
|
291
|
+
|
|
292
|
+
template <class T>
|
|
293
|
+
XSIMD_INLINE constexpr T zero() noexcept
|
|
294
|
+
{
|
|
295
|
+
return T(typename T::value_type(0));
|
|
296
|
+
}
|
|
297
|
+
|
|
298
|
+
/***************************
|
|
299
|
+
* minvalue implementation *
|
|
300
|
+
***************************/
|
|
301
|
+
|
|
302
|
+
namespace detail
|
|
303
|
+
{
|
|
304
|
+
template <class T>
|
|
305
|
+
struct minvalue_impl
|
|
306
|
+
{
|
|
307
|
+
static constexpr T get_value() noexcept
|
|
308
|
+
{
|
|
309
|
+
return std::numeric_limits<typename T::value_type>::min();
|
|
310
|
+
}
|
|
311
|
+
};
|
|
312
|
+
|
|
313
|
+
template <class T>
|
|
314
|
+
struct minvalue_common
|
|
315
|
+
{
|
|
316
|
+
static constexpr T get_value() noexcept
|
|
317
|
+
{
|
|
318
|
+
return std::numeric_limits<T>::min();
|
|
319
|
+
}
|
|
320
|
+
};
|
|
321
|
+
|
|
322
|
+
template <>
|
|
323
|
+
struct minvalue_impl<int8_t> : minvalue_common<int8_t>
|
|
324
|
+
{
|
|
325
|
+
};
|
|
326
|
+
template <>
|
|
327
|
+
struct minvalue_impl<uint8_t> : minvalue_common<uint8_t>
|
|
328
|
+
{
|
|
329
|
+
};
|
|
330
|
+
template <>
|
|
331
|
+
struct minvalue_impl<int16_t> : minvalue_common<int16_t>
|
|
332
|
+
{
|
|
333
|
+
};
|
|
334
|
+
template <>
|
|
335
|
+
struct minvalue_impl<uint16_t> : minvalue_common<uint16_t>
|
|
336
|
+
{
|
|
337
|
+
};
|
|
338
|
+
template <>
|
|
339
|
+
struct minvalue_impl<int32_t> : minvalue_common<int32_t>
|
|
340
|
+
{
|
|
341
|
+
};
|
|
342
|
+
template <>
|
|
343
|
+
struct minvalue_impl<uint32_t> : minvalue_common<uint32_t>
|
|
344
|
+
{
|
|
345
|
+
};
|
|
346
|
+
template <>
|
|
347
|
+
struct minvalue_impl<int64_t> : minvalue_common<int64_t>
|
|
348
|
+
{
|
|
349
|
+
};
|
|
350
|
+
template <>
|
|
351
|
+
struct minvalue_impl<uint64_t> : minvalue_common<uint64_t>
|
|
352
|
+
{
|
|
353
|
+
};
|
|
354
|
+
|
|
355
|
+
template <>
|
|
356
|
+
struct minvalue_impl<float>
|
|
357
|
+
{
|
|
358
|
+
XSIMD_INLINE static float get_value() noexcept
|
|
359
|
+
{
|
|
360
|
+
return bit_cast<float>((uint32_t)0xff7fffff);
|
|
361
|
+
}
|
|
362
|
+
};
|
|
363
|
+
|
|
364
|
+
template <>
|
|
365
|
+
struct minvalue_impl<double>
|
|
366
|
+
{
|
|
367
|
+
XSIMD_INLINE static double get_value() noexcept
|
|
368
|
+
{
|
|
369
|
+
return bit_cast<double>((uint64_t)0xffefffffffffffff);
|
|
370
|
+
}
|
|
371
|
+
};
|
|
372
|
+
}
|
|
373
|
+
|
|
374
|
+
template <class T>
|
|
375
|
+
constexpr T minvalue() noexcept
|
|
376
|
+
{
|
|
377
|
+
return T(detail::minvalue_impl<typename T::value_type>::get_value());
|
|
378
|
+
}
|
|
379
|
+
|
|
380
|
+
/***************************
|
|
381
|
+
* maxvalue implementation *
|
|
382
|
+
***************************/
|
|
383
|
+
|
|
384
|
+
template <class T>
|
|
385
|
+
constexpr T maxvalue() noexcept
|
|
386
|
+
{
|
|
387
|
+
return T(std::numeric_limits<typename T::value_type>::max());
|
|
388
|
+
}
|
|
389
|
+
}
|
|
390
|
+
|
|
391
|
+
}
|
|
392
|
+
|
|
393
|
+
#endif
|