sequenzo 0.1.31__cp310-cp310-macosx_10_9_x86_64.whl

sequenzo/__init__.py

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+"""
+@Author  : Yuqi Liang 梁彧祺
+@File    : __init__.py
+@Time    : 11/02/2025 16:41
+@Desc    : 
+"""
+from .datasets import load_dataset, list_datasets
+
+# Import the core functions that should be directly available from the sequenzo package
+
+from .data_preprocessing import helpers
+from .data_preprocessing.helpers import (assign_unique_ids,
+                                         wide_to_long_format_data,
+                                         long_to_wide_format_data,
+                                         summarize_missing_values,
+                                         replace_cluster_id_by_labels)
+
+from sequenzo.define_sequence_data import *
+
+from .visualization import (plot_sequence_index,
+                            plot_most_frequent_sequences,
+                            plot_single_medoid,
+                            plot_state_distribution,
+                            plot_modal_state,
+                            plot_relative_frequency,
+                            plot_mean_time,
+                            plot_transition_matrix,
+                            )
+
+from .dissimilarity_measures.get_distance_matrix import get_distance_matrix
+from .dissimilarity_measures.get_substitution_cost_matrix import get_substitution_cost_matrix
+from .dissimilarity_measures.utils.get_LCP_length_for_2_seq import get_LCP_length_for_2_seq
+
+from .clustering import Cluster, ClusterResults, ClusterQuality
+from .clustering.KMedoids import KMedoids
+from .big_data.clara.clara import clara
+from .big_data.clara.visualization import plot_scores_from_dataframe
+
+from .multidomain import (create_idcd_sequence_from_csvs,
+                          compute_cat_distance_matrix,
+                          compute_dat_distance_matrix,
+                          get_interactive_combined_typology,
+                          merge_sparse_combt_types,
+                          get_association_between_domains,
+                          linked_polyadic_sequence_analysis
+                          )
+
+from .prefix_tree import (
+    build_prefix_tree,
+    compute_prefix_count,
+    IndividualDivergence,
+    extract_sequences,
+    get_state_space,
+    compute_branching_factor,
+    compute_js_divergence,
+    convert_to_prefix_tree_data,
+    plot_system_indicators,
+    plot_system_indicators_multiple_comparison,
+    plot_prefix_rarity_distribution,
+    plot_individual_indicators_correlation,
+    # Spell-based (mode="spell")
+    SpellPrefixTree,
+    build_spell_prefix_tree,
+    compute_js_divergence_spell,
+    convert_seqdata_to_spells,
+    SpellIndividualDivergence,
+)
+
+from .suffix_tree import (
+    build_suffix_tree,
+    get_depth_stats,
+    compute_suffix_count,
+    compute_merging_factor,
+    compute_js_convergence,
+    IndividualConvergence,
+    convert_to_suffix_tree_data,
+    plot_system_indicators,
+    plot_system_indicators_multiple_comparison,
+    plot_suffix_rarity_distribution,
+    # Spell-based (mode="spell")
+    SpellSuffixTree,
+    build_spell_suffix_tree,
+    compute_js_convergence_spell,
+    SpellIndividualConvergence,
+)
+
+from .sequence_characteristics import (
+    get_subsequences_in_single_sequence,
+    get_subsequences_all_sequences,
+    get_number_of_transitions,
+
+    get_turbulence,
+    get_complexity_index,
+    get_within_sequence_entropy,
+    get_spell_duration_variance,
+    get_state_freq_and_entropy_per_seq,
+
+    get_cross_sectional_entropy,
+    plot_cross_sectional_characteristics,
+    plot_longitudinal_characteristics
+
+)
+
+# Event History Analysis (SAMM)
+from .with_event_history_analysis import (
+    SAMM,
+    sequence_analysis_multi_state_model,
+    plot_samm,
+    seqsammseq,
+    set_typology,
+    seqsammeha,
+    # Keep old names for backward compatibility
+    seqsamm
+)
+
+# Hidden Markov Models (HMM)
+from .seqhmm import (
+    HMM,
+    build_hmm,
+    fit_model,
+    predict,
+    posterior_probs,
+    plot_hmm,
+    # Mixture HMM
+    MHMM,
+    build_mhmm,
+    fit_mhmm,
+    predict_mhmm,
+    posterior_probs_mhmm,
+    plot_mhmm,
+    # Non-homogeneous HMM
+    NHMM,
+    build_nhmm,
+    fit_nhmm,
+    # Model comparison
+    aic,
+    bic,
+    compare_models,
+    # Simulation
+    simulate_hmm,
+    simulate_mhmm,
+    # Bootstrap
+    bootstrap_model,
+    # Advanced optimization
+    fit_model_advanced,
+    # Formulas
+    Formula,
+    create_model_matrix
+)
+
+# Define `__all__` to specify the public API when using `from sequenzo import *`
+__all__ = [
+    # Datasets
+    "load_dataset",
+    "list_datasets",
+
+    # Data preprocessing
+    "helpers",
+    "assign_unique_ids",
+    "wide_to_long_format_data",
+    "long_to_wide_format_data",
+    "summarize_missing_values",
+    "replace_cluster_id_by_labels",
+
+    "SequenceData",
+
+    # Visualization
+    "plot_sequence_index",
+    "plot_most_frequent_sequences",
+    "plot_single_medoid",
+    "plot_state_distribution",
+    "plot_modal_state",
+    "plot_relative_frequency",
+    "plot_mean_time",
+    "plot_transition_matrix",
+
+    # Dissimilarity measures
+    "get_distance_matrix",
+    "get_substitution_cost_matrix",
+    "get_LCP_length_for_2_seq",
+
+    # Hierarchical clustering
+    "Cluster",
+    "ClusterResults",
+    "ClusterQuality",
+    "KMedoids",
+
+    # Big data
+    "clara",
+    "plot_scores_from_dataframe",
+
+    # Multi-domain sequence analysis
+    "create_idcd_sequence_from_csvs",
+    "compute_cat_distance_matrix",
+    "compute_dat_distance_matrix",
+    "get_interactive_combined_typology",
+    "merge_sparse_combt_types",
+    "get_association_between_domains",
+    "linked_polyadic_sequence_analysis",
+
+    # Prefix Tree
+    "build_prefix_tree",
+    "compute_prefix_count",
+    "IndividualDivergence",
+    "extract_sequences",
+    "get_state_space",
+    "compute_branching_factor",
+    "compute_js_divergence",
+    "convert_to_prefix_tree_data",
+    "plot_system_indicators",
+    "plot_system_indicators_multiple_comparison",
+    "plot_prefix_rarity_distribution",
+    "plot_individual_indicators_correlation",
+    "SpellPrefixTree",
+    "build_spell_prefix_tree",
+    "compute_js_divergence_spell",
+    "convert_seqdata_to_spells",
+    "SpellIndividualDivergence",
+
+    # Suffix Tree
+    "build_suffix_tree",
+    "get_depth_stats",
+    "compute_suffix_count",
+    "compute_merging_factor",
+    "compute_js_convergence",
+    "IndividualConvergence",
+    "convert_to_suffix_tree_data",
+    "plot_system_indicators",
+    "plot_system_indicators_multiple_comparison",
+    "plot_suffix_rarity_distribution",
+    "SpellSuffixTree",
+    "build_spell_suffix_tree",
+    "compute_js_convergence_spell",
+    "SpellIndividualConvergence",
+
+    # Sequence characteristics
+    "get_subsequences_in_single_sequence",
+    "get_subsequences_all_sequences",
+    "get_number_of_transitions",
+    "get_turbulence",
+    "get_complexity_index",
+    "get_within_sequence_entropy",
+    "get_spell_duration_variance",
+    "get_state_freq_and_entropy_per_seq",
+    "get_cross_sectional_entropy",
+    "plot_longitudinal_characteristics",
+    "plot_cross_sectional_characteristics",
+
+    # Event History Analysis (SAMM)
+    "SAMM",
+    "sequence_analysis_multi_state_model",
+    "plot_samm",
+    "seqsammseq",
+    "set_typology",
+    "seqsammeha",
+    # Keep old names for backward compatibility
+    "seqsamm",
+    
+    # Hidden Markov Models (HMM)
+    "HMM",
+    "build_hmm",
+    "fit_model",
+    "predict",
+    "posterior_probs",
+    "plot_hmm",
+    # Mixture HMM
+    "MHMM",
+    "build_mhmm",
+    "fit_mhmm",
+    "predict_mhmm",
+    "posterior_probs_mhmm",
+    "plot_mhmm",
+    # Non-homogeneous HMM
+    "NHMM",
+    "build_nhmm",
+    "fit_nhmm",
+    # Model comparison
+    "aic",
+    "bic",
+    "compare_models",
+    # Simulation
+    "simulate_hmm",
+    "simulate_mhmm",
+    # Bootstrap
+    "bootstrap_model",
+    # Advanced optimization
+    "fit_model_advanced",
+    # Formulas
+    "Formula",
+    "create_model_matrix"
+]
+
+# Auto-setup OpenMP on Apple Silicon (runs on import)
+def _setup_openmp_if_needed():
+    """
+    Automatically setup OpenMP dependencies on Apple Silicon Macs.
+    This function runs on import to ensure OpenMP is available.
+    """
+    import sys
+    import os
+    import platform
+    
+    # Only run on macOS
+    if sys.platform != 'darwin':
+        return
+    
+    # Only run on Apple Silicon
+    if platform.machine() != 'arm64':
+        return
+    
+    # Check if we're in a conda environment (don't interfere)
+    if os.environ.get('CONDA_DEFAULT_ENV'):
+        return
+    
+    # Try to import and run the OpenMP setup
+    try:
+        from .openmp_setup import ensure_openmp_support
+        ensure_openmp_support()
+    except ImportError:
+        # OpenMP setup module not available, skip
+        pass
+    except Exception:
+        # Any other error, skip silently
+        pass
+
+# Run the setup function
+_setup_openmp_if_needed()
+
+# Clean up the setup function from the module namespace
+del _setup_openmp_if_needed
+
+# Version check: Check for updates asynchronously (non-blocking)
+def _check_version_update():
+    """
+    Check if a newer version of Sequenzo is available.
+    This runs asynchronously to avoid blocking the import process.
+    """
+    try:
+        from .version_check import check_version_update_async
+        check_version_update_async()
+    except Exception:
+        # Silently fail - version checks should never break imports
+        pass
+
+# Run version check in background
+_check_version_update()
+
+# Clean up the version check function from the module namespace
+del _check_version_update

sequenzo/big_data/__init__.py

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+"""
+@Author  : 李欣怡
+@File    : __init__.py.py
+@Time    : 2025/2/28 00:30
+@Desc    : 
+"""
+
+from .clara.clara import clara
+
+__all__ = [
+    'clara'
+]

sequenzo/big_data/clara/__init__.py

@@ -0,0 +1,26 @@
+"""
+@Author  : 李欣怡
+@File    : __init__.py
+@Time    : 2025/2/28 00:38
+@Desc    : 
+"""
+from .clara import clara
+from .visualization import plot_scores_from_dataframe
+
+
+def _import_c_code():
+    """Lazily import the c_code module to avoid circular dependencies during installation"""
+    try:
+        from sequenzo.clustering import clustering_c_code
+        return clustering_c_code
+    except ImportError:
+        # If the C extension cannot be imported, return None
+        print(
+            "Warning: The C++ extension (c_code) could not be imported. Please ensure the extension module is compiled correctly.")
+        return None
+
+
+__all__ = [
+    'clara',
+    'plot_scores_from_dataframe'
+]