added cassiopeia dependencies to do preprocess

laml_libs/mixins/__init__.py

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+from .errors import *
+from .logging import logger
+from .utilities import *
+from .warnings import *

laml_libs/mixins/errors.py

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+class AutocorrelationError(Exception):
+    """An Exception for the tools.autocorrelation methods."""
+
+    pass
+
+
+class CassiopeiaError(Exception):
+    """An general exception for the Cassiopeia software."""
+
+    pass
+
+
+class CassiopeiaTreeError(Exception):
+    """An Exception class for the CassiopeiaTree class."""
+
+    pass
+
+
+class DataSimulatorError(Exception):
+    """Generic error for the DataSimulator subclasses"""
+
+    pass
+
+
+class DistanceSolverError(Exception):
+    """An Exception class for all DistanceSolver subclasses."""
+
+    pass
+
+class ecDNABirthDeathSimulatorError(Exception):
+    """An ExceptionClass for ecDNABirthDeathSimulator class."""
+
+    pass
+
+class FitchCountError(Exception):
+    """An ExceptionClass for FitchCount."""
+
+    pass
+
+
+class GreedySolverError(Exception):
+    pass
+
+
+class HybridSolverError(Exception):
+    """An Exception class for all HybridSolver subclasses."""
+
+    pass
+
+
+class ILPSolverError(Exception):
+    """An Exception class for all ILPError subclasses."""
+
+    pass
+
+
+class iTOLError(Exception):
+    pass
+
+
+class LeafSubsamplerError(Exception):
+    """An Exception class for the LeafSubsampler class."""
+
+    pass
+
+
+class PreprocessError(Exception):
+    pass
+
+
+class PriorTransformationError(Exception):
+    """An Exception class for generating weights from priors."""
+
+    pass
+
+
+class SharedMutationJoiningSolverError(Exception):
+    """An Exception class for SharedMutationJoiningSolver."""
+
+    pass
+
+
+class TreeSimulatorError(Exception):
+    """An Exception class for all exceptions generated by
+    TreeSimulator or a subclass of TreeSimulator
+    """
+
+    pass
+
+
+class UnknownCigarStringError(Exception):
+    pass
+
+
+class UnspecifiedConfigParameterError(Exception):
+    pass
+
+
+class BranchLengthEstimatorError(Exception):
+    """An Exception class for the BranchLengthEstimator class."""
+
+    pass
+
+
+class IIDExponentialMLEError(BranchLengthEstimatorError):
+    pass
+
+
+class TreeMetricError(Exception):
+    """An Exception class for calculating tree metrics"""
+
+    pass
+
+
+class ParameterEstimateError(Exception):
+    """An Exception class for the estimation and retrieval of tree parameters"""
+
+    pass
+
+
+class PlottingError(Exception):
+    pass

laml_libs/mixins/logging.py

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+import logging
+
+import ngs_tools as ngs
+
+logger = ngs.logging.Logger(__name__)
+logger.setLevel(logging.INFO)

laml_libs/mixins/utilities.py

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+import functools
+import importlib
+from types import ModuleType
+from typing import Dict, List, Optional, Tuple, Union
+
+import numpy as np
+
+
+def is_ambiguous_state(state: Union[int, Tuple[int, ...]]) -> bool:
+    """Determine whether the provided state is ambiguous.
+
+    Note that this function operates on a single (indel) state.
+
+    Args:
+        state: Single, possibly ambiguous, character state
+
+    Returns:
+        True if the state is ambiguous, False otherwise.
+    """
+    return isinstance(state, tuple)
+
+
+def try_import(module: str) -> Optional[ModuleType]:
+    """Helper function to import a possibly not-installed module.
+
+    Args:
+        module: Module to try and import
+
+    Returns:
+        The imported module, if the module exists, or None
+    """
+    try:
+        return importlib.import_module(module)
+    except ModuleNotFoundError:
+        return None
+
+
+def unravel_ambiguous_states(
+    state_array: List[Union[int, Tuple[int, ...]]]
+) -> List[int]:
+    """Helper function to unravel ambiguous states.
+
+    Args:
+        A list of states, potentially containing ambiguous states.
+
+    Returns:
+        A list of unique states contained in the list.
+    """
+    all_states = [
+        list(state) if is_ambiguous_state(state) else [state]
+        for state in state_array
+    ]
+    return functools.reduce(lambda a, b: a + b, all_states)
+
+def find_duplicate_groups(character_matrix) -> Dict[str, Tuple[str, ...]]:
+    """Maps duplicated indices in character matrix to groups.
+
+    Groups together samples in a character matrix if they have the same
+    character states.
+
+    Args:
+        character_matrix: Character matrix, potentially with ambiguous states.
+
+    Returns:
+        A mapping of a single sample name to the set of of samples that have
+            the same character states.
+    """
+
+    character_matrix.index.name = "index"
+
+     # convert to sets to support ambiguous states
+    character_matrix_sets = character_matrix.copy()
+    character_matrix_sets = character_matrix_sets.apply(
+            lambda x: [
+                set(s) if is_ambiguous_state(s) else set([s])
+                for s in x.values
+            ],
+            axis=0,
+        ).apply(tuple, axis=1)
+    is_duplicated = (
+        character_matrix_sets.duplicated(keep=False)
+    )
+    unique_states = np.unique(character_matrix_sets[is_duplicated])
+    duplicate_groups = [character_matrix_sets[character_matrix_sets == val].index.values for val in unique_states]
+    duplicate_mappings =  {g[0]: tuple(g) for g in duplicate_groups}
+
+    return duplicate_mappings

laml_libs/mixins/warnings.py

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+class CassiopeiaTreeWarning(UserWarning):
+    """A Warning for the CassiopeiaTree class."""
+
+    pass
+
+class DataSimulatorWarning(UserWarning):
+    pass
+
+
+class PreprocessWarning(UserWarning):
+    pass
+
+
+class SharedMutationJoiningSolverWarning(UserWarning):
+    """A warning class for SharedMutationJoiningSolver."""
+
+    pass
+
+
+class ParameterEstimateWarning(UserWarning):
+    """An warning class for the estimation and retrieval of tree parameters"""
+
+    pass
+
+
+class PlottingWarning(UserWarning):
+    pass
+
+class LeafSubsamplerWarning(UserWarning):
+
+    pass