sequenzo 0.1.21__cp312-cp312-macosx_11_0_arm64.whl
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- 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 +467 -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-312-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 +196 -0
- sequenzo/clustering/__init__.py +30 -0
- sequenzo/clustering/clustering_c_code.cpython-312-darwin.so +0 -0
- sequenzo/clustering/hierarchical_clustering.py +1380 -0
- sequenzo/clustering/src/KMedoid.cpp +262 -0
- sequenzo/clustering/src/PAM.cpp +236 -0
- sequenzo/clustering/src/PAMonce.cpp +234 -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-312-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-312-darwin.so +0 -0
- sequenzo/dissimilarity_measures/utils/seqconc.cpython-312-darwin.so +0 -0
- sequenzo/dissimilarity_measures/utils/seqdss.cpython-312-darwin.so +0 -0
- sequenzo/dissimilarity_measures/utils/seqdur.cpython-312-darwin.so +0 -0
- sequenzo/dissimilarity_measures/utils/seqlength.cpython-312-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 +937 -0
- sequenzo/visualization/plot_single_medoid.py +153 -0
- sequenzo/visualization/plot_state_distribution.py +613 -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-0.1.21.dist-info/METADATA +308 -0
- sequenzo-0.1.21.dist-info/RECORD +254 -0
- sequenzo-0.1.21.dist-info/WHEEL +5 -0
- sequenzo-0.1.21.dist-info/licenses/LICENSE +28 -0
- sequenzo-0.1.21.dist-info/top_level.txt +1 -0
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/***************************************************************************
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* Copyright (c) Johan Mabille, Sylvain Corlay, Wolf Vollprecht and *
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* Martin Renou *
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* Copyright (c) QuantStack *
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* Copyright (c) Serge Guelton *
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* *
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* Distributed under the terms of the BSD 3-Clause License. *
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* *
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* The full license is in the file LICENSE, distributed with this software. *
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****************************************************************************/
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#include "xsimd/xsimd.hpp"
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#ifndef XSIMD_NO_SUPPORTED_ARCHITECTURE
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#include "test_utils.hpp"
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template <class B>
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struct complex_power_test
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{
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using batch_type = B;
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using real_batch_type = typename B::real_batch;
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using value_type = typename B::value_type;
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using real_value_type = typename value_type::value_type;
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static constexpr size_t size = B::size;
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using vector_type = std::vector<value_type>;
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using real_vector_type = std::vector<real_value_type>;
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size_t nb_input;
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real_vector_type lhs_p;
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vector_type lhs_nn;
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vector_type lhs_pn;
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vector_type lhs_np;
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vector_type lhs_pp;
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vector_type rhs;
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vector_type expected;
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vector_type res;
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complex_power_test()
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{
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nb_input = 10000 * size;
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lhs_p.resize(nb_input);
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lhs_nn.resize(nb_input);
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lhs_pn.resize(nb_input);
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lhs_np.resize(nb_input);
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lhs_pp.resize(nb_input);
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rhs.resize(nb_input);
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for (size_t i = 0; i < nb_input; ++i)
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{
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real_value_type real = (real_value_type(i) / 4 + real_value_type(1.2) * std::sqrt(real_value_type(i + 0.25))) / 100;
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real_value_type imag = (real_value_type(i) / 7 + real_value_type(1.7) * std::sqrt(real_value_type(i + 0.37))) / 100;
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lhs_p[i] = real;
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lhs_nn[i] = value_type(-real, -imag);
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lhs_pn[i] = value_type(real, -imag);
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lhs_np[i] = value_type(-real, imag);
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lhs_pp[i] = value_type(real, imag);
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rhs[i] = value_type(real_value_type(10.2) / (i + 2) + real_value_type(0.25),
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real_value_type(9.1) / (i + 3) + real_value_type(0.45));
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}
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expected.resize(nb_input);
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res.resize(nb_input);
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}
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void test_abs()
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{
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real_vector_type real_expected(nb_input), real_res(nb_input);
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std::transform(lhs_np.cbegin(), lhs_np.cend(), real_expected.begin(),
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[](const value_type& v)
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{ using std::abs; return abs(v); });
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batch_type in;
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real_batch_type out;
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for (size_t i = 0; i < nb_input; i += size)
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{
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detail::load_batch(in, lhs_np, i);
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out = abs(in);
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detail::store_batch(out, real_res, i);
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}
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size_t diff = detail::get_nb_diff(real_res, real_expected);
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CHECK_EQ(diff, 0);
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}
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void test_arg()
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{
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real_vector_type real_expected(nb_input), real_res(nb_input);
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std::transform(lhs_np.cbegin(), lhs_np.cend(), real_expected.begin(),
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[](const value_type& v)
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{ using std::arg; return arg(v); });
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batch_type in;
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real_batch_type out;
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for (size_t i = 0; i < nb_input; i += size)
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{
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detail::load_batch(in, lhs_np, i);
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out = arg(in);
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detail::store_batch(out, real_res, i);
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}
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size_t diff = detail::get_nb_diff(real_res, real_expected);
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CHECK_EQ(diff, 0);
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}
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void test_pow()
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{
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std::transform(lhs_np.cbegin(), lhs_np.cend(), rhs.cbegin(), expected.begin(),
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[](const value_type& l, const value_type& r)
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{ using std::pow; return pow(l, r); });
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batch_type lhs_in, rhs_in, out;
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for (size_t i = 0; i < nb_input; i += size)
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{
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detail::load_batch(lhs_in, lhs_np, i);
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detail::load_batch(rhs_in, rhs, i);
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out = pow(lhs_in, rhs_in);
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detail::store_batch(out, res, i);
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}
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size_t diff = detail::get_nb_diff_near(res, expected, std::numeric_limits<real_value_type>::epsilon());
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CHECK_EQ(diff, 0);
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}
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void test_pow_real_complex()
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{
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std::transform(lhs_p.cbegin(), lhs_p.cend(), lhs_pp.cbegin(), expected.begin(),
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[](const real_value_type& l, const value_type& r)
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{ using std::pow; return pow(l, r); });
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batch_type rhs_in, out;
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real_batch_type lhs_in;
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for (size_t i = 0; i < nb_input; i += size)
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{
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detail::load_batch(lhs_in, lhs_p, i);
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detail::load_batch(rhs_in, lhs_pp, i);
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out = pow(lhs_in, rhs_in);
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detail::store_batch(out, res, i);
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}
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size_t diff = detail::get_nb_diff_near(res, expected, std::numeric_limits<real_value_type>::epsilon());
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CHECK_EQ(diff, 0);
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}
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void test_pow_complex_real()
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{
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std::transform(lhs_pp.cbegin(), lhs_pp.cend(), lhs_p.cbegin(), expected.begin(),
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[](const value_type& l, const real_value_type& r)
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{ using std::pow; return pow(l, r); });
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batch_type rhs_in, out;
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real_batch_type lhs_in;
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for (size_t i = 0; i < nb_input; i += size)
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{
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detail::load_batch(lhs_in, lhs_p, i);
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detail::load_batch(rhs_in, lhs_pp, i);
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out = pow(lhs_in, rhs_in);
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detail::store_batch(out, res, i);
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}
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size_t diff = detail::get_nb_diff_near(res, expected, std::numeric_limits<real_value_type>::epsilon());
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CHECK_EQ(diff, 0);
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}
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void test_sqrt_nn()
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{
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std::transform(lhs_nn.cbegin(), lhs_nn.cend(), expected.begin(),
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[](const value_type& v)
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{ using std::sqrt; return sqrt(v); });
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batch_type in, out;
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for (size_t i = 0; i < nb_input; i += size)
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{
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detail::load_batch(in, lhs_nn, i);
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out = sqrt(in);
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detail::store_batch(out, res, i);
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}
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size_t diff = detail::get_nb_diff(res, expected);
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CHECK_EQ(diff, 0);
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}
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void test_sqrt_pn()
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{
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std::transform(lhs_pn.cbegin(), lhs_pn.cend(), expected.begin(),
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[](const value_type& v)
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{ using std::sqrt; return sqrt(v); });
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batch_type in, out;
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for (size_t i = 0; i < nb_input; i += size)
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{
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detail::load_batch(in, lhs_pn, i);
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out = sqrt(in);
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detail::store_batch(out, res, i);
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}
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size_t diff = detail::get_nb_diff(res, expected);
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CHECK_EQ(diff, 0);
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}
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void test_sqrt_np()
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{
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std::transform(lhs_np.cbegin(), lhs_np.cend(), expected.begin(),
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[](const value_type& v)
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{ using std::sqrt; return sqrt(v); });
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batch_type in, out;
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for (size_t i = 0; i < nb_input; i += size)
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{
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detail::load_batch(in, lhs_np, i);
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out = sqrt(in);
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detail::store_batch(out, res, i);
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}
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size_t diff = detail::get_nb_diff(res, expected);
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CHECK_EQ(diff, 0);
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}
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void test_sqrt_pp()
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{
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std::transform(lhs_pp.cbegin(), lhs_pp.cend(), expected.begin(),
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[](const value_type& v)
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{ using std::sqrt; return sqrt(v); });
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batch_type in, out;
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for (size_t i = 0; i < nb_input; i += size)
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{
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detail::load_batch(in, lhs_pp, i);
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out = sqrt(in);
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detail::store_batch(out, res, i);
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}
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size_t diff = detail::get_nb_diff(res, expected);
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CHECK_EQ(diff, 0);
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}
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};
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TEST_CASE_TEMPLATE("[complex power]", B, BATCH_COMPLEX_TYPES)
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{
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complex_power_test<B> Test;
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SUBCASE("abs")
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{
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Test.test_abs();
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}
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SUBCASE("arg")
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{
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Test.test_arg();
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}
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SUBCASE("pow")
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{
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Test.test_pow();
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}
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SUBCASE("pow real complex")
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{
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Test.test_pow_real_complex();
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}
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SUBCASE("pow complex real")
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{
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Test.test_pow_complex_real();
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}
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SUBCASE("sqrt_nn")
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{
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Test.test_sqrt_nn();
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}
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SUBCASE("sqrt_pn")
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{
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Test.test_sqrt_pn();
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}
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SUBCASE("sqrt_np")
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{
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Test.test_sqrt_np();
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}
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SUBCASE("sqrt_pp")
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{
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Test.test_sqrt_pp();
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}
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}
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#endif
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@@ -0,0 +1,236 @@
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/***************************************************************************
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2
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* Copyright (c) Johan Mabille, Sylvain Corlay, Wolf Vollprecht and *
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3
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* Martin Renou *
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4
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* Copyright (c) QuantStack *
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5
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* Copyright (c) Serge Guelton *
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* *
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7
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* Distributed under the terms of the BSD 3-Clause License. *
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* *
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9
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* The full license is in the file LICENSE, distributed with this software. *
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10
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****************************************************************************/
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11
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12
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#include "xsimd/xsimd.hpp"
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13
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14
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#ifndef XSIMD_NO_SUPPORTED_ARCHITECTURE
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15
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16
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#include "test_utils.hpp"
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17
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18
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template <class B>
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19
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struct complex_trigonometric_test
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20
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{
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using batch_type = B;
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using real_batch_type = typename B::real_batch;
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using value_type = typename B::value_type;
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using real_value_type = typename value_type::value_type;
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25
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static constexpr size_t size = B::size;
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26
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using vector_type = std::vector<value_type>;
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27
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28
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size_t nb_input;
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29
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vector_type input;
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30
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vector_type ainput;
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31
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vector_type atan_input;
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32
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vector_type expected;
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33
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vector_type res;
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34
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+
|
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35
|
+
complex_trigonometric_test()
|
|
36
|
+
{
|
|
37
|
+
nb_input = size * 10000;
|
|
38
|
+
input.resize(nb_input);
|
|
39
|
+
ainput.resize(nb_input);
|
|
40
|
+
atan_input.resize(nb_input);
|
|
41
|
+
for (size_t i = 0; i < nb_input; ++i)
|
|
42
|
+
{
|
|
43
|
+
input[i] = value_type(real_value_type(0.) + i * real_value_type(80.) / nb_input,
|
|
44
|
+
real_value_type(0.1) + i * real_value_type(56.) / nb_input);
|
|
45
|
+
ainput[i] = value_type(real_value_type(-1.) + real_value_type(2.) * i / nb_input,
|
|
46
|
+
real_value_type(-1.1) + real_value_type(2.1) * i / nb_input);
|
|
47
|
+
atan_input[i] = value_type(real_value_type(-10.) + i * real_value_type(20.) / nb_input,
|
|
48
|
+
real_value_type(-9.) + i * real_value_type(21.) / nb_input);
|
|
49
|
+
}
|
|
50
|
+
expected.resize(nb_input);
|
|
51
|
+
res.resize(nb_input);
|
|
52
|
+
}
|
|
53
|
+
|
|
54
|
+
void test_sin()
|
|
55
|
+
{
|
|
56
|
+
std::transform(input.cbegin(), input.cend(), expected.begin(),
|
|
57
|
+
[](const value_type& v)
|
|
58
|
+
{ using std::sin; return sin(v); });
|
|
59
|
+
batch_type in, out;
|
|
60
|
+
for (size_t i = 0; i < nb_input; i += size)
|
|
61
|
+
{
|
|
62
|
+
detail::load_batch(in, input, i);
|
|
63
|
+
out = sin(in);
|
|
64
|
+
detail::store_batch(out, res, i);
|
|
65
|
+
}
|
|
66
|
+
size_t diff = detail::get_nb_diff(res, expected);
|
|
67
|
+
CHECK_EQ(diff, 0);
|
|
68
|
+
}
|
|
69
|
+
|
|
70
|
+
void test_cos()
|
|
71
|
+
{
|
|
72
|
+
std::transform(input.cbegin(), input.cend(), expected.begin(),
|
|
73
|
+
[](const value_type& v)
|
|
74
|
+
{ using std::cos; return cos(v); });
|
|
75
|
+
batch_type in, out;
|
|
76
|
+
for (size_t i = 0; i < nb_input; i += size)
|
|
77
|
+
{
|
|
78
|
+
detail::load_batch(in, input, i);
|
|
79
|
+
out = cos(in);
|
|
80
|
+
detail::store_batch(out, res, i);
|
|
81
|
+
}
|
|
82
|
+
size_t diff = detail::get_nb_diff(res, expected);
|
|
83
|
+
CHECK_EQ(diff, 0);
|
|
84
|
+
}
|
|
85
|
+
|
|
86
|
+
void test_sincos()
|
|
87
|
+
{
|
|
88
|
+
vector_type expected2(nb_input), res2(nb_input);
|
|
89
|
+
std::transform(input.cbegin(), input.cend(), expected.begin(),
|
|
90
|
+
[](const value_type& v)
|
|
91
|
+
{ using std::sin; return sin(v); });
|
|
92
|
+
std::transform(input.cbegin(), input.cend(), expected2.begin(),
|
|
93
|
+
[](const value_type& v)
|
|
94
|
+
{ using std::cos; return cos(v); });
|
|
95
|
+
batch_type in, out1, out2;
|
|
96
|
+
for (size_t i = 0; i < nb_input; i += size)
|
|
97
|
+
{
|
|
98
|
+
detail::load_batch(in, input, i);
|
|
99
|
+
std::tie(out1, out2) = sincos(in);
|
|
100
|
+
detail::store_batch(out1, res, i);
|
|
101
|
+
detail::store_batch(out2, res2, i);
|
|
102
|
+
}
|
|
103
|
+
size_t diff = detail::get_nb_diff(res, expected);
|
|
104
|
+
CHECK_EQ(diff, 0);
|
|
105
|
+
diff = detail::get_nb_diff(res2, expected2);
|
|
106
|
+
CHECK_EQ(diff, 0);
|
|
107
|
+
}
|
|
108
|
+
|
|
109
|
+
void test_tan()
|
|
110
|
+
{
|
|
111
|
+
test_conditional_tan<real_value_type>();
|
|
112
|
+
}
|
|
113
|
+
|
|
114
|
+
void test_asin()
|
|
115
|
+
{
|
|
116
|
+
std::transform(ainput.cbegin(), ainput.cend(), expected.begin(),
|
|
117
|
+
[](const value_type& v)
|
|
118
|
+
{ using std::asin; return asin(v); });
|
|
119
|
+
batch_type in, out;
|
|
120
|
+
for (size_t i = 0; i < nb_input; i += size)
|
|
121
|
+
{
|
|
122
|
+
detail::load_batch(in, ainput, i);
|
|
123
|
+
out = asin(in);
|
|
124
|
+
detail::store_batch(out, res, i);
|
|
125
|
+
}
|
|
126
|
+
size_t diff = detail::get_nb_diff(res, expected);
|
|
127
|
+
CHECK_EQ(diff, 0);
|
|
128
|
+
}
|
|
129
|
+
|
|
130
|
+
void test_acos()
|
|
131
|
+
{
|
|
132
|
+
std::transform(ainput.cbegin(), ainput.cend(), expected.begin(),
|
|
133
|
+
[](const value_type& v)
|
|
134
|
+
{ using std::acos; return acos(v); });
|
|
135
|
+
batch_type in, out;
|
|
136
|
+
for (size_t i = 0; i < nb_input; i += size)
|
|
137
|
+
{
|
|
138
|
+
detail::load_batch(in, ainput, i);
|
|
139
|
+
out = acos(in);
|
|
140
|
+
detail::store_batch(out, res, i);
|
|
141
|
+
}
|
|
142
|
+
size_t diff = detail::get_nb_diff(res, expected);
|
|
143
|
+
CHECK_EQ(diff, 0);
|
|
144
|
+
}
|
|
145
|
+
|
|
146
|
+
void test_atan()
|
|
147
|
+
{
|
|
148
|
+
std::transform(atan_input.cbegin(), atan_input.cend(), expected.begin(),
|
|
149
|
+
[](const value_type& v)
|
|
150
|
+
{ using std::atan; return atan(v); });
|
|
151
|
+
batch_type in, out;
|
|
152
|
+
for (size_t i = 0; i < nb_input; i += size)
|
|
153
|
+
{
|
|
154
|
+
detail::load_batch(in, atan_input, i);
|
|
155
|
+
out = atan(in);
|
|
156
|
+
detail::store_batch(out, res, i);
|
|
157
|
+
}
|
|
158
|
+
size_t diff = detail::get_nb_diff(res, expected);
|
|
159
|
+
CHECK_EQ(diff, 0);
|
|
160
|
+
}
|
|
161
|
+
|
|
162
|
+
private:
|
|
163
|
+
void test_tan_impl()
|
|
164
|
+
{
|
|
165
|
+
std::transform(input.cbegin(), input.cend(), expected.begin(),
|
|
166
|
+
[](const value_type& v)
|
|
167
|
+
{ using std::tan; return tan(v); });
|
|
168
|
+
batch_type in, out;
|
|
169
|
+
for (size_t i = 0; i < nb_input; i += size)
|
|
170
|
+
{
|
|
171
|
+
detail::load_batch(in, input, i);
|
|
172
|
+
out = tan(in);
|
|
173
|
+
detail::store_batch(out, res, i);
|
|
174
|
+
}
|
|
175
|
+
size_t diff = detail::get_nb_diff(res, expected);
|
|
176
|
+
CHECK_EQ(diff, 0);
|
|
177
|
+
}
|
|
178
|
+
|
|
179
|
+
template <class T, typename std::enable_if<!std::is_same<T, float>::value, int>::type = 0>
|
|
180
|
+
void test_conditional_tan()
|
|
181
|
+
{
|
|
182
|
+
test_tan_impl();
|
|
183
|
+
}
|
|
184
|
+
|
|
185
|
+
template <class T, typename std::enable_if<std::is_same<T, float>::value, int>::type = 0>
|
|
186
|
+
void test_conditional_tan()
|
|
187
|
+
{
|
|
188
|
+
#if (XSIMD_ARM_INSTR_SET >= XSIMD_ARM7_NEON_VERSION)
|
|
189
|
+
#if DEBUG_ACCURACY
|
|
190
|
+
test_tan_impl();
|
|
191
|
+
#endif
|
|
192
|
+
#else
|
|
193
|
+
test_tan_impl();
|
|
194
|
+
#endif
|
|
195
|
+
}
|
|
196
|
+
};
|
|
197
|
+
|
|
198
|
+
TEST_CASE_TEMPLATE("[complex trigonometric]", B, BATCH_COMPLEX_TYPES)
|
|
199
|
+
{
|
|
200
|
+
complex_trigonometric_test<B> Test;
|
|
201
|
+
SUBCASE("sin")
|
|
202
|
+
{
|
|
203
|
+
Test.test_sin();
|
|
204
|
+
}
|
|
205
|
+
|
|
206
|
+
SUBCASE("cos")
|
|
207
|
+
{
|
|
208
|
+
Test.test_cos();
|
|
209
|
+
}
|
|
210
|
+
|
|
211
|
+
SUBCASE("sincos")
|
|
212
|
+
{
|
|
213
|
+
Test.test_sincos();
|
|
214
|
+
}
|
|
215
|
+
|
|
216
|
+
SUBCASE("tan")
|
|
217
|
+
{
|
|
218
|
+
Test.test_tan();
|
|
219
|
+
}
|
|
220
|
+
|
|
221
|
+
SUBCASE("asin")
|
|
222
|
+
{
|
|
223
|
+
Test.test_asin();
|
|
224
|
+
}
|
|
225
|
+
|
|
226
|
+
SUBCASE("acos")
|
|
227
|
+
{
|
|
228
|
+
Test.test_acos();
|
|
229
|
+
}
|
|
230
|
+
|
|
231
|
+
SUBCASE("atan")
|
|
232
|
+
{
|
|
233
|
+
Test.test_atan();
|
|
234
|
+
}
|
|
235
|
+
}
|
|
236
|
+
#endif
|