masster 0.2.5__py3-none-any.whl → 0.3.1__py3-none-any.whl

masster/study/__init__.py

@@ -1,9 +1,9 @@
-"""
-Study module for masster.
-
-This module provides the Sample class for handling mass spectrometry data.
-"""
-
-from .study import Study
-
-__all__ = ["Study"]
+"""
+Study module for masster.
+
+This module provides the Sample class for handling mass spectrometry data.
+"""
+
+from .study import Study
+
+__all__ = ["Study"]

masster/study/defaults/__init__.py

@@ -1,19 +1,21 @@
-"""Study defaults initialization."""
-
-from .align_def import align_defaults
-from .export_def import export_mgf_defaults  
-from .fill_chrom_def import fill_chrom_defaults
-from .find_consensus_def import find_consensus_defaults
-from .find_ms2_def import find_ms2_defaults
-from .integrate_chrom_def import integrate_chrom_defaults
-from .study_def import study_defaults
-
-__all__ = [
-    "align_defaults",
-    "export_mgf_defaults", 
-    "fill_chrom_defaults",
-    "find_consensus_defaults",
-    "find_ms2_defaults", 
-    "integrate_chrom_defaults",
-    "study_defaults",
-]
+"""Study defaults initialization."""
+
+from .align_def import align_defaults
+from .export_def import export_mgf_defaults
+from .fill_def import fill_defaults
+from .find_consensus_def import find_consensus_defaults
+from .find_ms2_def import find_ms2_defaults
+from .integrate_def import integrate_defaults
+from .merge_def import merge_defaults
+from .study_def import study_defaults
+
+__all__ = [
+    "align_defaults",
+    "export_mgf_defaults",
+    "fill_defaults",
+    "find_consensus_defaults",
+    "find_ms2_defaults",
+    "integrate_defaults",
+    "merge_defaults",
+    "study_defaults",
+]

masster/study/defaults/align_def.py

@@ -1,267 +1,267 @@
-"""Parameter class for Study align method."""
-
-from dataclasses import dataclass, field
-from typing import Any
-
-
-@dataclass
-class align_defaults:
-    """
-    Parameter class for Study align method.
-
-    This class encapsulates parameters for feature alignment across samples,
-    including retention time and m/z tolerances, warping parameters, and
-    alignment algorithm settings.
-
-    Attributes:
-        rt_max_diff (float): Maximum retention time difference for alignment. Default is 60.0.
-        mz_max_diff (float): Maximum m/z difference for alignment. Default is 0.01.
-        rt_pair_distance_frac (float): Fraction of RT difference for pair distance. Default is 0.2.
-        mz_pair_max_distance (float): Maximum m/z pair distance. Default is 0.01.
-        num_used_points (int): Number of points used for alignment. Default is 1000.
-        save_features (bool): Whether to save features after alignment. Default is True.
-        skip_blanks (bool): Whether to skip blank samples. Default is True.
-    """
-
-    rt_max_diff: float = 60.0
-    mz_max_diff: float = 0.01
-    rt_pair_distance_frac: float = 0.2
-    mz_pair_max_distance: float = 0.01
-    num_used_points: int = 1000
-    save_features: bool = True
-    skip_blanks: bool = True
-
-    _param_metadata: dict[str, dict[str, Any]] = field(
-        default_factory=lambda: {
-            "rt_max_diff": {
-                "dtype": float,
-                "description": "Maximum retention time difference for alignment (seconds)",
-                "default": 60.0,
-                "min_value": 1.0,
-                "max_value": 300.0,
-            },
-            "mz_max_diff": {
-                "dtype": float,
-                "description": "Maximum m/z difference for alignment (Da)",
-                "default": 0.01,
-                "min_value": 0.001,
-                "max_value": 1.0,
-            },
-            "rt_pair_distance_frac": {
-                "dtype": float,
-                "description": "Fraction of RT difference for pair distance calculation",
-                "default": 0.2,
-                "min_value": 0.1,
-                "max_value": 1.0,
-            },
-            "mz_pair_max_distance": {
-                "dtype": float,
-                "description": "Maximum m/z pair distance (Da)",
-                "default": 0.01,
-                "min_value": 0.001,
-                "max_value": 0.1,
-            },
-            "num_used_points": {
-                "dtype": int,
-                "description": "Number of points used for alignment",
-                "default": 1000,
-                "min_value": 10,
-                "max_value": 100000,
-            },
-            "save_features": {
-                "dtype": bool,
-                "description": "Whether to save features after alignment",
-                "default": True,
-            },
-            "skip_blanks": {
-                "dtype": bool,
-                "description": "Whether to skip blank samples during alignment",
-                "default": True,
-            },
-        },
-        repr=False,
-    )
-
-    def get_info(self, param_name: str) -> dict[str, Any]:
-        """
-        Get information about a specific parameter.
-
-        Args:
-            param_name: Name of the parameter
-
-        Returns:
-            Dictionary containing parameter metadata
-
-        Raises:
-            KeyError: If parameter name is not found
-        """
-        if param_name not in self._param_metadata:
-            raise KeyError(f"Parameter '{param_name}' not found")
-        return self._param_metadata[param_name]
-
-    def get_description(self, param_name: str) -> str:
-        """
-        Get description for a specific parameter.
-
-        Args:
-            param_name: Name of the parameter
-
-        Returns:
-            Parameter description string
-        """
-        return str(self.get_info(param_name)["description"])
-
-    def validate(self, param_name: str, value: Any) -> bool:
-        """
-        Validate a parameter value against its constraints.
-
-        Args:
-            param_name: Name of the parameter
-            value: Value to validate
-
-        Returns:
-            True if value is valid, False otherwise
-        """
-        if param_name not in self._param_metadata:
-            return False
-
-        metadata = self._param_metadata[param_name]
-        expected_dtype = metadata["dtype"]
-
-        # Type checking
-        if expected_dtype is int:
-            if not isinstance(value, int):
-                try:
-                    value = int(value)
-                except (ValueError, TypeError):
-                    return False
-        elif expected_dtype is float:
-            if not isinstance(value, (int, float)):
-                try:
-                    value = float(value)
-                except (ValueError, TypeError):
-                    return False
-        elif expected_dtype is bool:
-            if not isinstance(value, bool):
-                return False
-
-        # Range validation for numeric types
-        if expected_dtype in (int, float) and isinstance(value, (int, float)):
-            if "min_value" in metadata and value < metadata["min_value"]:
-                return False
-            if "max_value" in metadata and value > metadata["max_value"]:
-                return False
-
-        return True
-
-    def set(self, param_name: str, value: Any, validate: bool = True) -> bool:
-        """
-        Set a parameter value with optional validation.
-
-        Args:
-            param_name: Name of the parameter
-            value: New value for the parameter
-            validate: Whether to validate the value before setting
-
-        Returns:
-            True if parameter was set successfully, False otherwise
-        """
-        if not hasattr(self, param_name):
-            return False
-
-        if validate and not self.validate(param_name, value):
-            return False
-
-        # Convert to expected type if needed
-        if param_name in self._param_metadata:
-            expected_dtype = self._param_metadata[param_name]["dtype"]
-
-            if expected_dtype is int and not isinstance(value, int):
-                try:
-                    value = int(value)
-                except (ValueError, TypeError):
-                    if validate:
-                        return False
-            elif expected_dtype is float and not isinstance(value, float):
-                try:
-                    value = float(value)
-                except (ValueError, TypeError):
-                    if validate:
-                        return False
-
-        setattr(self, param_name, value)
-        return True
-
-    def get(self, param_name: str) -> Any:
-        """
-        Get the value of a parameter by name.
-
-        Args:
-            param_name: Name of the parameter
-
-        Returns:
-            Current value of the parameter
-        """
-        if not hasattr(self, param_name):
-            raise KeyError(f"Parameter '{param_name}' not found")
-        return getattr(self, param_name)
-
-    def set_from_dict(
-        self,
-        param_dict: dict[str, Any],
-        validate: bool = True,
-    ) -> list[str]:
-        """
-        Update multiple parameters from a dictionary.
-
-        Args:
-            param_dict: Dictionary of parameter names and values
-            validate: Whether to validate values before setting
-
-        Returns:
-            List of parameter names that could not be set
-        """
-        failed_params = []
-
-        for param_name, value in param_dict.items():
-            if not self.set(param_name, value, validate):
-                failed_params.append(param_name)
-
-        return failed_params
-
-    def to_dict(self) -> dict[str, Any]:
-        """
-        Convert parameters to dictionary, excluding metadata.
-
-        Returns:
-            Dictionary of parameter names and values
-        """
-        return {k: v for k, v in self.__dict__.items() if not k.startswith("_")}
-
-    def list_parameters(self) -> list[str]:
-        """
-        Get list of all parameter names.
-
-        Returns:
-            List of parameter names
-        """
-        return [k for k in self.__dict__.keys() if not k.startswith("_")]
-
-    def validate_all(self) -> tuple[bool, list[str]]:
-        """
-        Validate all parameters in the instance.
-
-        Returns:
-            Tuple of (all_valid, list_of_invalid_params)
-            - all_valid: True if all parameters are valid, False otherwise
-            - list_of_invalid_params: List of parameter names that failed validation
-        """
-        invalid_params = []
-
-        for param_name in self.list_parameters():
-            if param_name in self._param_metadata:
-                current_value = getattr(self, param_name)
-                if not self.validate(param_name, current_value):
-                    invalid_params.append(param_name)
-
-        return len(invalid_params) == 0, invalid_params
+"""Parameter class for Study align method."""
+
+from dataclasses import dataclass, field
+from typing import Any
+
+
+@dataclass
+class align_defaults:
+    """
+    Parameter class for Study align method.
+
+    This class encapsulates parameters for feature alignment across samples,
+    including retention time and m/z tolerances, warping parameters, and
+    alignment algorithm settings.
+
+    Attributes:
+        rt_max_diff (float): Maximum retention time difference for alignment. Default is 60.0.
+        mz_max_diff (float): Maximum m/z difference for alignment. Default is 0.01.
+        rt_pair_distance_frac (float): Fraction of RT difference for pair distance. Default is 0.2.
+        mz_pair_max_distance (float): Maximum m/z pair distance. Default is 0.01.
+        num_used_points (int): Number of points used for alignment. Default is 1000.
+        save_features (bool): Whether to save features after alignment. Default is True.
+        skip_blanks (bool): Whether to skip blank samples. Default is True.
+    """
+
+    rt_max_diff: float = 60.0
+    mz_max_diff: float = 0.01
+    rt_pair_distance_frac: float = 0.2
+    mz_pair_max_distance: float = 0.01
+    num_used_points: int = 1000
+    save_features: bool = True
+    skip_blanks: bool = True
+
+    _param_metadata: dict[str, dict[str, Any]] = field(
+        default_factory=lambda: {
+            "rt_max_diff": {
+                "dtype": float,
+                "description": "Maximum retention time difference for alignment (seconds)",
+                "default": 60.0,
+                "min_value": 1.0,
+                "max_value": 300.0,
+            },
+            "mz_max_diff": {
+                "dtype": float,
+                "description": "Maximum m/z difference for alignment (Da)",
+                "default": 0.01,
+                "min_value": 0.001,
+                "max_value": 1.0,
+            },
+            "rt_pair_distance_frac": {
+                "dtype": float,
+                "description": "Fraction of RT difference for pair distance calculation",
+                "default": 0.2,
+                "min_value": 0.1,
+                "max_value": 1.0,
+            },
+            "mz_pair_max_distance": {
+                "dtype": float,
+                "description": "Maximum m/z pair distance (Da)",
+                "default": 0.01,
+                "min_value": 0.001,
+                "max_value": 0.1,
+            },
+            "num_used_points": {
+                "dtype": int,
+                "description": "Number of points used for alignment",
+                "default": 1000,
+                "min_value": 10,
+                "max_value": 100000,
+            },
+            "save_features": {
+                "dtype": bool,
+                "description": "Whether to save features after alignment",
+                "default": True,
+            },
+            "skip_blanks": {
+                "dtype": bool,
+                "description": "Whether to skip blank samples during alignment",
+                "default": True,
+            },
+        },
+        repr=False,
+    )
+
+    def get_info(self, param_name: str) -> dict[str, Any]:
+        """
+        Get information about a specific parameter.
+
+        Args:
+            param_name: Name of the parameter
+
+        Returns:
+            Dictionary containing parameter metadata
+
+        Raises:
+            KeyError: If parameter name is not found
+        """
+        if param_name not in self._param_metadata:
+            raise KeyError(f"Parameter '{param_name}' not found")
+        return self._param_metadata[param_name]
+
+    def get_description(self, param_name: str) -> str:
+        """
+        Get description for a specific parameter.
+
+        Args:
+            param_name: Name of the parameter
+
+        Returns:
+            Parameter description string
+        """
+        return str(self.get_info(param_name)["description"])
+
+    def validate(self, param_name: str, value: Any) -> bool:
+        """
+        Validate a parameter value against its constraints.
+
+        Args:
+            param_name: Name of the parameter
+            value: Value to validate
+
+        Returns:
+            True if value is valid, False otherwise
+        """
+        if param_name not in self._param_metadata:
+            return False
+
+        metadata = self._param_metadata[param_name]
+        expected_dtype = metadata["dtype"]
+
+        # Type checking
+        if expected_dtype is int:
+            if not isinstance(value, int):
+                try:
+                    value = int(value)
+                except (ValueError, TypeError):
+                    return False
+        elif expected_dtype is float:
+            if not isinstance(value, (int, float)):
+                try:
+                    value = float(value)
+                except (ValueError, TypeError):
+                    return False
+        elif expected_dtype is bool:
+            if not isinstance(value, bool):
+                return False
+
+        # Range validation for numeric types
+        if expected_dtype in (int, float) and isinstance(value, (int, float)):
+            if "min_value" in metadata and value < metadata["min_value"]:
+                return False
+            if "max_value" in metadata and value > metadata["max_value"]:
+                return False
+
+        return True
+
+    def set(self, param_name: str, value: Any, validate: bool = True) -> bool:
+        """
+        Set a parameter value with optional validation.
+
+        Args:
+            param_name: Name of the parameter
+            value: New value for the parameter
+            validate: Whether to validate the value before setting
+
+        Returns:
+            True if parameter was set successfully, False otherwise
+        """
+        if not hasattr(self, param_name):
+            return False
+
+        if validate and not self.validate(param_name, value):
+            return False
+
+        # Convert to expected type if needed
+        if param_name in self._param_metadata:
+            expected_dtype = self._param_metadata[param_name]["dtype"]
+
+            if expected_dtype is int and not isinstance(value, int):
+                try:
+                    value = int(value)
+                except (ValueError, TypeError):
+                    if validate:
+                        return False
+            elif expected_dtype is float and not isinstance(value, float):
+                try:
+                    value = float(value)
+                except (ValueError, TypeError):
+                    if validate:
+                        return False
+
+        setattr(self, param_name, value)
+        return True
+
+    def get(self, param_name: str) -> Any:
+        """
+        Get the value of a parameter by name.
+
+        Args:
+            param_name: Name of the parameter
+
+        Returns:
+            Current value of the parameter
+        """
+        if not hasattr(self, param_name):
+            raise KeyError(f"Parameter '{param_name}' not found")
+        return getattr(self, param_name)
+
+    def set_from_dict(
+        self,
+        param_dict: dict[str, Any],
+        validate: bool = True,
+    ) -> list[str]:
+        """
+        Update multiple parameters from a dictionary.
+
+        Args:
+            param_dict: Dictionary of parameter names and values
+            validate: Whether to validate values before setting
+
+        Returns:
+            List of parameter names that could not be set
+        """
+        failed_params = []
+
+        for param_name, value in param_dict.items():
+            if not self.set(param_name, value, validate):
+                failed_params.append(param_name)
+
+        return failed_params
+
+    def to_dict(self) -> dict[str, Any]:
+        """
+        Convert parameters to dictionary, excluding metadata.
+
+        Returns:
+            Dictionary of parameter names and values
+        """
+        return {k: v for k, v in self.__dict__.items() if not k.startswith("_")}
+
+    def list_parameters(self) -> list[str]:
+        """
+        Get list of all parameter names.
+
+        Returns:
+            List of parameter names
+        """
+        return [k for k in self.__dict__.keys() if not k.startswith("_")]
+
+    def validate_all(self) -> tuple[bool, list[str]]:
+        """
+        Validate all parameters in the instance.
+
+        Returns:
+            Tuple of (all_valid, list_of_invalid_params)
+            - all_valid: True if all parameters are valid, False otherwise
+            - list_of_invalid_params: List of parameter names that failed validation
+        """
+        invalid_params = []
+
+        for param_name in self.list_parameters():
+            if param_name in self._param_metadata:
+                current_value = getattr(self, param_name)
+                if not self.validate(param_name, current_value):
+                    invalid_params.append(param_name)
+
+        return len(invalid_params) == 0, invalid_params