masster 0.2.5__py3-none-any.whl → 0.3.0__py3-none-any.whl

masster/study/defaults/export_def.py

@@ -1,40 +1,41 @@
-"""Export defaults for study-level operations."""
-
-from dataclasses import dataclass
-from typing import Optional
-
-
-@dataclass
-class export_mgf_defaults:
-    """Default parameters for exporting study results."""
-    
-    filename: str = "features.mgf"
-    selection: str = "best"  # "best" or "all"
-    split_energy: bool = True
-    merge: bool = False
-    mz_start: Optional[float] = None
-    mz_end: Optional[float] = None
-    rt_start: Optional[float] = None
-    rt_end: Optional[float] = None
-    centroid: bool = True
-    inty_min: Optional[float] = None
-    deisotope: bool = True
-    verbose: bool = False
-    precursor_trim: float = -10
-    centroid_algo: str = "lmp"
-
-    def get(self, key: str):
-        """Get parameter value by key."""
-        return getattr(self, key, None)
-    
-    def set(self, key: str, value, validate: bool = True) -> bool:
-        """Set parameter value with optional validation."""
-        if hasattr(self, key):
-            setattr(self, key, value)
-            return True
-        return False
-    
-    def to_dict(self) -> dict:
-        """Convert to dictionary."""
-        from dataclasses import asdict
-        return asdict(self)
+"""Export defaults for study-level operations."""
+
+from dataclasses import dataclass
+from typing import Optional
+
+
+@dataclass
+class export_mgf_defaults:
+    """Default parameters for exporting study results."""
+
+    filename: str = "features.mgf"
+    selection: str = "best"  # "best" or "all"
+    split_energy: bool = True
+    merge: bool = False
+    mz_start: Optional[float] = None
+    mz_end: Optional[float] = None
+    rt_start: Optional[float] = None
+    rt_end: Optional[float] = None
+    centroid: bool = True
+    inty_min: Optional[float] = None
+    deisotope: bool = True
+    verbose: bool = False
+    precursor_trim: float = -10
+    centroid_algo: str = "lmp"
+
+    def get(self, key: str):
+        """Get parameter value by key."""
+        return getattr(self, key, None)
+
+    def set(self, key: str, value, validate: bool = True) -> bool:
+        """Set parameter value with optional validation."""
+        if hasattr(self, key):
+            setattr(self, key, value)
+            return True
+        return False
+
+    def to_dict(self) -> dict:
+        """Convert to dictionary."""
+        from dataclasses import asdict
+
+        return asdict(self)

masster/study/defaults/fill_chrom_def.py

@@ -1,264 +1,264 @@
-"""Parameter class for Study fill_chrom method."""
-
-from dataclasses import dataclass, field
-from typing import Optional, Any
-
-
-@dataclass
-class fill_chrom_defaults:
-    """
-    Parameter class for Study fill_chrom method.
-
-    This class encapsulates parameters for filling missing chromatograms
-    by extracting them from raw data across samples.
-
-    Attributes:
-        uids (Optional[list]): List of consensus UIDs to process. Default is None (all).
-        mz_tol (float): m/z tolerance for chromatogram extraction (Da). Default is 0.010.
-        rt_tol (float): RT tolerance for chromatogram extraction (seconds). Default is 10.0.
-        min_samples_rel (float): Minimum relative samples threshold. Default is 0.05.
-        min_samples_abs (int): Minimum absolute samples threshold. Default is 5.
-    """
-
-    uids: Optional[list] = None
-    mz_tol: float = 0.010
-    rt_tol: float = 10.0
-    min_samples_rel: float = 0.05
-    min_samples_abs: int = 5
-
-    _param_metadata: dict[str, dict[str, Any]] = field(
-        default_factory=lambda: {
-            "uids": {
-                "dtype": "Optional[list]",
-                "description": "List of consensus UIDs to process (None for all)",
-                "default": None,
-            },
-            "mz_tol": {
-                "dtype": float,
-                "description": "m/z tolerance for chromatogram extraction (Da)",
-                "default": 0.010,
-                "min_value": 0.001,
-                "max_value": 0.1,
-            },
-            "rt_tol": {
-                "dtype": float,
-                "description": "RT tolerance for chromatogram extraction (seconds)",
-                "default": 10.0,
-                "min_value": 1.0,
-                "max_value": 300.0,
-            },
-            "min_samples_rel": {
-                "dtype": float,
-                "description": "Minimum relative samples threshold (fraction)",
-                "default": 0.05,
-                "min_value": 0.01,
-                "max_value": 1.0,
-            },
-            "min_samples_abs": {
-                "dtype": int,
-                "description": "Minimum absolute samples threshold",
-                "default": 5,
-                "min_value": 1,
-                "max_value": 100,
-            },
-        },
-        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"]
-
-        # Handle optional types
-        if isinstance(expected_dtype, str) and expected_dtype.startswith("Optional"):
-            if value is None:
-                return True
-            # Extract the inner type for validation
-            if "list" in expected_dtype:
-                expected_dtype = list
-
-        # 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 list:
-            if not isinstance(value, list):
-                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"]
-
-            # Handle optional types
-            if (
-                isinstance(expected_dtype, str)
-                and expected_dtype.startswith("Optional")
-                and value is not None
-            ):
-                if "int" in expected_dtype and not isinstance(value, int):
-                    try:
-                        value = int(value)
-                    except (ValueError, TypeError):
-                        if validate:
-                            return False
-                elif "float" in expected_dtype 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 fill_chrom method."""
+
+from dataclasses import dataclass, field
+from typing import Optional, Any
+
+
+@dataclass
+class fill_chrom_defaults:
+    """
+    Parameter class for Study fill_chrom method.
+
+    This class encapsulates parameters for filling missing chromatograms
+    by extracting them from raw data across samples.
+
+    Attributes:
+        uids (Optional[list]): List of consensus UIDs to process. Default is None (all).
+        mz_tol (float): m/z tolerance for chromatogram extraction (Da). Default is 0.010.
+        rt_tol (float): RT tolerance for chromatogram extraction (seconds). Default is 10.0.
+        min_samples_rel (float): Minimum relative samples threshold. Default is 0.05.
+        min_samples_abs (int): Minimum absolute samples threshold. Default is 5.
+    """
+
+    uids: Optional[list] = None
+    mz_tol: float = 0.010
+    rt_tol: float = 10.0
+    min_samples_rel: float = 0.05
+    min_samples_abs: int = 5
+
+    _param_metadata: dict[str, dict[str, Any]] = field(
+        default_factory=lambda: {
+            "uids": {
+                "dtype": "Optional[list]",
+                "description": "List of consensus UIDs to process (None for all)",
+                "default": None,
+            },
+            "mz_tol": {
+                "dtype": float,
+                "description": "m/z tolerance for chromatogram extraction (Da)",
+                "default": 0.010,
+                "min_value": 0.001,
+                "max_value": 0.1,
+            },
+            "rt_tol": {
+                "dtype": float,
+                "description": "RT tolerance for chromatogram extraction (seconds)",
+                "default": 10.0,
+                "min_value": 1.0,
+                "max_value": 300.0,
+            },
+            "min_samples_rel": {
+                "dtype": float,
+                "description": "Minimum relative samples threshold (fraction)",
+                "default": 0.05,
+                "min_value": 0.01,
+                "max_value": 1.0,
+            },
+            "min_samples_abs": {
+                "dtype": int,
+                "description": "Minimum absolute samples threshold",
+                "default": 5,
+                "min_value": 1,
+                "max_value": 100,
+            },
+        },
+        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"]
+
+        # Handle optional types
+        if isinstance(expected_dtype, str) and expected_dtype.startswith("Optional"):
+            if value is None:
+                return True
+            # Extract the inner type for validation
+            if "list" in expected_dtype:
+                expected_dtype = list
+
+        # 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 list:
+            if not isinstance(value, list):
+                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"]
+
+            # Handle optional types
+            if (
+                isinstance(expected_dtype, str)
+                and expected_dtype.startswith("Optional")
+                and value is not None
+            ):
+                if "int" in expected_dtype and not isinstance(value, int):
+                    try:
+                        value = int(value)
+                    except (ValueError, TypeError):
+                        if validate:
+                            return False
+                elif "float" in expected_dtype 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