aisp 0.3.2__py3-none-any.whl → 0.4.0__py3-none-any.whl

aisp/utils/display.py

@@ -0,0 +1,185 @@
+"""Utility functions for displaying algorithm information."""
+
+from __future__ import annotations
+
+import locale
+import sys
+import time
+from typing import Mapping, Union
+
+
+def _supports_box_drawing() -> bool:
+    """
+    Check if the terminal supports boxed characters.
+
+    Returns
+    -------
+    bool
+        True if the terminal likely supports boxed characters, False otherwise.
+    """
+    enc = (sys.stdout.encoding or locale.getpreferredencoding(False)).lower()
+    if not enc.startswith("utf"):
+        return False
+    try:
+        "┌".encode(enc)
+    except UnicodeEncodeError:
+        return False
+    return True
+
+
+class TableFormatter:
+    """
+    Format tabular data into strings for display in the console.
+
+    Parameters
+    ----------
+    headers : Mapping[str, int]
+        Mapping of column names to their respective widths, in the format
+        {column_name: column_width}.
+    """
+
+    def __init__(self, headers: Mapping[str, int]) -> None:
+        if not headers or not isinstance(headers, Mapping):
+            raise ValueError("'headers' must be a non-empty dictionary.")
+        self.headers: Mapping[str, int] = headers
+        self._ascii_only = not _supports_box_drawing()
+
+    def _border(self, left: str, middle: str, right: str, line: str, new_line: bool = True) -> str:
+        """
+        Create a horizontal border for the table.
+
+        Parameters
+        ----------
+        left: str
+            Character on the left side of the border.
+        middle: str
+            Character separator between columns.
+        right: str
+            Character on the right side of the border.
+        line: str
+            Character used to fill the border.
+        new_line: bool, optional
+            If True, adds a line break before the border (default is True).
+
+        Returns
+        -------
+        str
+            String representing the horizontal border.
+        """
+        nl = '\n' if new_line else ''
+        return f"{nl}{left}{middle.join(line * w for w in self.headers.values())}{right}"
+
+    def get_header(self):
+        """
+        Generate the table header, including the top border, column headings, and separator line.
+
+        Returns
+        -------
+        str
+            Formatted string of the table header.
+        """
+        if self._ascii_only:
+            top = self._border("+", "+", "+", "-")
+            sep = self._border("+", "+", "+", "-")
+            cell_border = "|"
+        else:
+            top = self._border("┌", "┬", "┐", "─")
+            sep = self._border("├", "┼", "┤", "─")
+            cell_border = "│"
+
+        titles = '\n' + cell_border + cell_border.join(
+            f"{h:^{self.headers[h]}}" for h in self.headers
+        ) + cell_border
+
+        return top + titles + sep
+
+    def get_row(self, values: Mapping[str, Union[str, int, float]]):
+        """
+        Generate a formatted row for the table data.
+
+        Parameters
+        ----------
+        values : Mapping[str, Union[str, int, float]]
+            Dictionary with values for each column, in the format
+            {column_name: value}.
+
+        Returns
+        -------
+        str
+        Formatted string of the table row.
+        """
+        border = "|" if self._ascii_only else "│"
+        row = border + border.join(
+            f"{values.get(h, ''):^{self.headers[h]}}" for h in self.headers
+        ) + border
+
+        return row
+
+    def get_bottom(self, new_line: bool = False):
+        """
+        Generate the table's bottom border.
+
+        Parameters
+        ----------
+        new_line : bool, Optional
+            If True, adds a line break before the border (default is False).
+
+        Returns
+        -------
+        str
+            Formatted string for the bottom border.
+        """
+        if self._ascii_only:
+            bottom = self._border("+", "+", "+", "-", new_line)
+        else:
+            bottom = self._border("└", "┴", "┘", "─", new_line)
+        return bottom
+
+
+class ProgressTable(TableFormatter):
+    """
+    Display a formatted table in the console to track the algorithm's progress.
+
+    Parameters
+    ----------
+    headers : Mapping[str, int]
+        Mapping {column_name: column_width}.
+    verbose : bool, default=True
+        If False, prints nothing to the terminal.
+    """
+
+    def __init__(self, headers: Mapping[str, int], verbose: bool = True) -> None:
+        super().__init__(headers)
+        if not headers or not isinstance(headers, Mapping):
+            raise ValueError("'headers' must be a non-empty dictionary.")
+        self.verbose: bool = verbose
+        self.headers: Mapping[str, int] = headers
+        self._ascii_only = not _supports_box_drawing()
+        if self.verbose:
+            self._print_header()
+            self._start = time.perf_counter()
+
+    def _print_header(self) -> None:
+        """Print the table header."""
+        print(self.get_header())
+
+    def update(self, values: Mapping[str, Union[str, int, float]]) -> None:
+        """
+        Add a new row of values to the table.
+
+        Parameters
+        ----------
+        values: Mapping[str, Union[str, int, float]]
+            Keys must match the columns defined in headers.
+        """
+        if not self.verbose:
+            return
+        print(self.get_row(values))
+
+    def finish(self) -> None:
+        """End the table display, printing the bottom border and total time."""
+        if not self.verbose:
+            return
+
+        print(self.get_bottom())
+        print(f"Total time: {time.perf_counter() - self._start:.6f} seconds")

aisp/utils/distance.py

@@ -40,7 +40,7 @@ def hamming(u: npt.NDArray[np.bool_], v: npt.NDArray[np.bool_]) -> float64:
 def euclidean(u: npt.NDArray[np.float64], v: npt.NDArray[np.float64]) -> float64:
     """Calculate the normalized Euclidean distance between two points.
     
-    √( (x₁ – x₂)² + (y₁ – y₂)² + ... + (yn – yn)²)
+    √( (x₁ - x₂)² + (y₁ - y₂)² + ... + (yn - yn)²)
 
     Parameters
     ----------
@@ -61,7 +61,7 @@ def euclidean(u: npt.NDArray[np.float64], v: npt.NDArray[np.float64]) -> float64
 def cityblock(u: npt.NDArray[float64], v: npt.NDArray[float64]) -> float64:
     """Calculate the normalized Manhattan distance between two points.
     
-    (|x₁ – x₂| + |y₁ – y₂| + ... + |yn – yn|) / n
+    (|x₁ - x₂| + |y₁ - y₂| + ... + |yn - yn|) / n
 
     Parameters
     ----------
@@ -86,7 +86,7 @@ def cityblock(u: npt.NDArray[float64], v: npt.NDArray[float64]) -> float64:
 def minkowski(u: npt.NDArray[float64], v: npt.NDArray[float64], p: float = 2.0) -> float64:
     """Calculate the normalized Minkowski distance between two points.
     
-    (( |X₁ – Y₁|p + |X₂ – Y₂|p + ... + |Xn – Yn|p) ¹/ₚ.) / n
+    (( |X₁ - Y₁|p + |X₂ - Y₂|p + ... + |Xn - Yn|p) ¹/ₚ.) / n
 
     Parameters
     ----------
@@ -124,7 +124,7 @@ def compute_metric_distance(
     u: npt.NDArray[float64],
     v: npt.NDArray[float64],
     metric: int,
-    p: float64 = 2.0
+    p: float = 2.0
 ) -> float64:
     """Calculate the distance between two points by the chosen metric.
 

aisp/utils/sanitizers.py

@@ -1,6 +1,9 @@
 """Utility functions for validation and treatment of parameters."""
 
-from typing import TypeVar, Iterable, Callable, Any, Optional
+from typing import TypeVar, Iterable, Callable, Any, Optional, Dict
+
+import numpy as np
+import numpy.typing as npt
 
 T = TypeVar('T')
 
@@ -62,3 +65,52 @@ def sanitize_seed(seed: Any) -> Optional[int]:
         The original seed if it is a non-negative integer, or None if it is invalid.
     """
     return seed if isinstance(seed, int) and seed >= 0 else None
+
+
+def sanitize_bounds(bounds: Any, problem_size: int) -> Dict[str, npt.NDArray[np.float64]]:
+    """Validate and normalize feature bounds.
+
+    Parameters
+    ----------
+    bounds : Any
+        The input bounds, which must be either None or a dictionary with 'low'
+        and 'high' keys.
+    problem_size : int
+        The expected length for the normalized bounds lists, corresponding to
+        the number of features in the problem.
+
+    Returns
+    -------
+    Dict[str, list]
+        Dictionary {'low': [low_1, ..., low_N], 'high': [high_1, ..., high_N]}.
+
+    Raises
+    ------
+    TypeError
+        If `bounds` is not None and not a dict with 'low'/'high', or if items are non-numeric.
+    ValueError
+        If provided iterables have the wrong length.
+    """
+    if bounds is None or not isinstance(bounds, dict) or set(bounds.keys()) != {'low', 'high'}:
+        raise ValueError("bounds expects a dict with keys 'low' and 'high'")
+    result = {}
+
+    for key in ['low', 'high']:
+        value = bounds[key]
+        if isinstance(value, (float, int)):
+            result[key] = np.array([value] * problem_size).astype(dtype=np.float64)
+        else:
+            if not isinstance(value, (list, np.ndarray)):
+                raise TypeError(
+                    f"{key} must be a list or numpy array, got {type(value).__name__}"
+                )
+            if not all(isinstance(i, (float, int)) for i in value):
+                raise TypeError(f"All elements of {key} must be numeric")
+
+            value = np.array(value).astype(dtype=np.float64)
+            if len(value) != problem_size:
+                raise ValueError(
+                    f"The size of {key} must be equal to the size of the problem ({problem_size})"
+                )
+            result[key] = value
+    return result

aisp/utils/types.py

@@ -8,24 +8,32 @@ FeatureType : Literal["binary-features", "continuous-features", "ranged-features
     - "binary-features": Features with binary values (e.g., 0 or 1).
     - "continuous-features": Features with continuous numeric values.
     - "ranged-features": Features represented by ranges or intervals.
+FeatureTypeAll : Literal["binary-features", "continuous-features", "ranged-features"]
+    Specifies the type of features in the input data. Can be one of:
+    - "binary-features": Features with binary values (e.g., 0 or 1).
+    - "continuous-features": Features with continuous numeric values.
+    - "ranged-features": Features represented by ranges or intervals.
+    - "permutation-features": Features represented by permutation.
 
 MetricType : Literal["manhattan", "minkowski", "euclidean"]
     Specifies the distance metric to use for calculations. Possible values:
     - "manhattan": The calculation of the distance is given by the expression:
-            √( (x₁ – x₂)² + (y₁ – y₂)² + ... + (yn – yn)²).
+            √( (x₁ - x₂)² + (y₁ - y₂)² + ... + (yn - yn)²).
     - "minkowski": The calculation of the distance is given by the expression:
-            ( |X₁ – Y₁|p + |X₂ – Y₂|p + ... + |Xn – Yn|p) ¹/ₚ.
+            ( |X₁ - Y₁|p + |X₂ - Y₂|p + ... + |Xn - Yn|p) ¹/ₚ.
     - "euclidean": The calculation of the distance is given by the expression:
-            ( |x₁ – x₂| + |y₁ – y₂| + ... + |yn – yn|).
+            ( |x₁ - x₂| + |y₁ - y₂| + ... + |yn - yn|).
 """
 
 
-from typing import Literal, TypeAlias
-
+from typing import Literal, TypeAlias, Union
 
 FeatureType: TypeAlias = Literal[
     "binary-features",
     "continuous-features",
     "ranged-features"
 ]
+
+FeatureTypeAll: TypeAlias = Union[FeatureType, Literal["permutation-features"]]
+
 MetricType: TypeAlias = Literal["manhattan", "minkowski", "euclidean"]

{aisp-0.3.2.dist-info → aisp-0.4.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aisp
-Version: 0.3.2
+Version: 0.4.0
 Summary: Package with techniques of artificial immune systems.
 Author-email: João Paulo da Silva Barros <jpsilvabarr@gmail.com>
 Maintainer-email: Alison Zille Lopes <alisonzille@gmail.com>
@@ -86,6 +86,7 @@ Artificial Immune Systems (AIS) are inspired by the vertebrate immune system, cr
 > - [x] [**Negative Selection.**](https://ais-package.github.io/docs/aisp-techniques/negative-selection/)
 > - [x] [**Clonal Selection Algorithms.**](https://ais-package.github.io/docs/aisp-techniques/clonal-selection-algorithms/)
 >     * [AIRS - Artificial Immune Recognition System](https://ais-package.github.io/docs/aisp-techniques/clonal-selection-algorithms/airs/)
+>     * [CLONALG - Clonal Selection Algorithm](https://ais-package.github.io/docs/aisp-techniques/clonal-selection-algorithms/clonalg)
 > - [ ] *Danger Theory.*
 > - [x] [*Immune Network Theory.*](https://ais-package.github.io/docs/aisp-techniques/immune-network-theory/)
 >   - [AiNet - Artificial Immune Network para Clustering and Compression](https://ais-package.github.io/docs/aisp-techniques/immune-network-theory/ainet)

aisp-0.4.0.dist-info/RECORD

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aisp-0.3.2.dist-info/RECORD

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