aisp 0.3.1__tar.gz → 0.3.21__tar.gz

{aisp-0.3.1 → aisp-0.3.21}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aisp
-Version: 0.3.1
+Version: 0.3.21
 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>
@@ -83,12 +83,12 @@ Artificial Immune Systems (AIS) are inspired by the vertebrate immune system, cr
 
 ##### Algorithms implemented:
 
-> - [x] [**Negative Selection.**](https://ais-package.github.io/docs/aisp-techniques/Negative%20Selection/)
-> - [x] [**Clonal Selection Algorithms.**](https://ais-package.github.io/docs/aisp-techniques/Clonal%20Selection%20Algorithms/)
->     * [AIRS - Artificial Immune Recognition System](https://ais-package.github.io/docs/aisp-techniques/Clonal%20Selection%20Algorithms/airs/)
+> - [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/)
 > - [ ] *Danger Theory.*
-> - [x] [*Immune Network Theory.*](https://ais-package.github.io/docs/aisp-techniques/Immune%20Network%20Theory)
->   - [AiNet - Artificial Immune Network para Clustering and Compression](https://ais-package.github.io/docs/aisp-techniques/Immune%20Network%20Theory/ainet)
+> - [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)
 
 </section>
 

{aisp-0.3.1 → aisp-0.3.21}/README.md

@@ -48,12 +48,12 @@ Artificial Immune Systems (AIS) are inspired by the vertebrate immune system, cr
 
 ##### Algorithms implemented:
 
-> - [x] [**Negative Selection.**](https://ais-package.github.io/docs/aisp-techniques/Negative%20Selection/)
-> - [x] [**Clonal Selection Algorithms.**](https://ais-package.github.io/docs/aisp-techniques/Clonal%20Selection%20Algorithms/)
->     * [AIRS - Artificial Immune Recognition System](https://ais-package.github.io/docs/aisp-techniques/Clonal%20Selection%20Algorithms/airs/)
+> - [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/)
 > - [ ] *Danger Theory.*
-> - [x] [*Immune Network Theory.*](https://ais-package.github.io/docs/aisp-techniques/Immune%20Network%20Theory)
->   - [AiNet - Artificial Immune Network para Clustering and Compression](https://ais-package.github.io/docs/aisp-techniques/Immune%20Network%20Theory/ainet)
+> - [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)
 
 </section>
 

{aisp-0.3.1 → aisp-0.3.21}/aisp/__init__.py

@@ -14,11 +14,11 @@ https://ais-package.github.io/docs/intro
 """
 
 from . import csa
-from . import nsa
 from . import ina
+from . import nsa
 
 __author__ = "AISP Development Team"
-__version__ = "0.3.1"
+__version__ = "0.3.2"
 __all__ = [
     'csa',
     'nsa',

{aisp-0.3.1 → aisp-0.3.21}/aisp/base/__init__.py

@@ -1,7 +1,7 @@
 """Base class modules."""
 
+from ._base import set_seed_numba
 from ._classifier import BaseClassifier
 from ._clusterer import BaseClusterer
-from ._base import set_seed_numba
 
 __all__ = ['BaseClassifier', 'BaseClusterer', 'set_seed_numba']

{aisp-0.3.1 → aisp-0.3.21}/aisp/base/_classifier.py

@@ -1,6 +1,7 @@
 """Base class for classification algorithm."""
 
 from __future__ import annotations
+
 from abc import ABC, abstractmethod
 from typing import Optional, Union
 

{aisp-0.3.1 → aisp-0.3.21}/aisp/base/_clusterer.py

@@ -1,6 +1,7 @@
 """Base class for clustering algorithms."""
 
 from __future__ import annotations
+
 from abc import ABC, abstractmethod
 from typing import Optional
 

{aisp-0.3.1 → aisp-0.3.21}/aisp/base/mutation.py

@@ -122,8 +122,8 @@ def clone_and_mutate_ranged(
         position_mutations = np.random.permutation(n_features)[:n_mutations]
         for j in range(n_mutations):
             idx = position_mutations[j]
-            min_limit = bounds[idx, 0]
-            max_limit = bounds[idx, 1]
+            min_limit = bounds[0][idx]
+            max_limit = bounds[1][idx]
             clone[idx] = np.random.uniform(min_limit, max_limit)
         clone_set[i] = clone
 

{aisp-0.3.1 → aisp-0.3.21}/aisp/csa/_ai_recognition_sys.py

@@ -1,6 +1,7 @@
 """Artificial Immune Recognition System (AIRS)."""
 
 from __future__ import annotations
+
 import random
 from collections import Counter
 from heapq import nlargest
@@ -12,13 +13,13 @@ import numpy.typing as npt
 from scipy.spatial.distance import pdist
 from tqdm import tqdm
 
-from ..base import set_seed_numba
+from ._base import BaseAIRS
 from ._cell import Cell
-from ..utils.sanitizers import sanitize_param, sanitize_seed, sanitize_choice
+from ..base import set_seed_numba
 from ..utils.distance import hamming, compute_metric_distance, get_metric_code
+from ..utils.sanitizers import sanitize_param, sanitize_seed, sanitize_choice
 from ..utils.types import FeatureType, MetricType
 from ..utils.validation import detect_vector_data_type
-from ._base import BaseAIRS
 
 
 class _ARB(Cell):
@@ -110,13 +111,13 @@ class AIRS(BaseAIRS):
         Way to calculate the distance between the detector and the sample:
 
         * ``'Euclidean'`` ➜ 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.
 
         * ``'manhattan'`` ➜ The calculation of the distance is given by the expression:
-            ( |x₁ – x₂| + |y₁ – y₂| + ... + |yn – yn|).
+            ( |x₁ - x₂| + |y₁ - y₂| + ... + |yn - yn|).
 
     seed : int
         Seed for the random generation of detector values. Defaults to None.
@@ -138,7 +139,7 @@ class AIRS(BaseAIRS):
 
     References
     ----------
-    .. [1] Brabazon, A., O’Neill, M., & McGarraghy, S. (2015). Natural Computing Algorithms. In
+    .. [1] Brabazon, A., O'Neill, M., & McGarraghy, S. (2015). Natural Computing Algorithms. In
         Natural Computing Series. Springer Berlin Heidelberg.
         https://doi.org/10.1007/978-3-662-43631-8
 
@@ -194,6 +195,7 @@ class AIRS(BaseAIRS):
         self.affinity_threshold = 0.0
         self.classes = []
         self._bounds: Optional[npt.NDArray[np.float64]] = None
+        self._n_features: Optional[int] = None
 
     @property
     def cells_memory(self) -> Optional[Dict[str, list[Cell]]]:
@@ -234,6 +236,7 @@ class AIRS(BaseAIRS):
                 self._bounds = np.vstack([np.min(X, axis=0), np.max(X, axis=0)])
 
         self.classes = np.unique(y)
+        self._n_features = X.shape[1]
         sample_index = self._slice_index_list_by_class(y)
         progress = tqdm(
             total=len(y),
@@ -329,11 +332,11 @@ class AIRS(BaseAIRS):
             An ndarray of the form ``C`` [``N samples``], containing the predicted classes for
             ``X``. or ``None``: If there are no detectors for the prediction.
         """
-        if self._all_class_cell_vectors is None:
+        if self._all_class_cell_vectors is None or self._n_features is None:
             return None
 
         super()._check_and_raise_exceptions_predict(
-            X, len(self._cells_memory[self.classes[0]][0].vector), self._feature_type
+            X, self._n_features, self._feature_type
         )
 
         c: list = []
@@ -379,7 +382,7 @@ class AIRS(BaseAIRS):
 
         References
         ----------
-        .. [1] Brabazon, A., O’Neill, M., & McGarraghy, S. (2015).
+        .. [1] Brabazon, A., O'Neill, M., & McGarraghy, S. (2015).
                 Natural Computing Algorithms. Natural Computing Series.
                 Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-662-43631-8
         """
@@ -440,7 +443,7 @@ class AIRS(BaseAIRS):
             distances = pdist(antigens_list, metric="hamming")
         else:
             metric_kwargs = {'p': self.p} if self.metric == 'minkowski' else {}
-            distances = pdist(antigens_list, metric=self.metric, **metric_kwargs)
+            distances = pdist(antigens_list, metric=self.metric, **metric_kwargs) # type: ignore
 
         n = antigens_list.shape[0]
         sum_affinity = np.sum(1.0 - (distances / (1.0 + distances)))

{aisp-0.3.1 → aisp-0.3.21}/aisp/csa/_base.py

@@ -5,9 +5,9 @@ from abc import ABC
 import numpy as np
 import numpy.typing as npt
 
+from ..base import BaseClassifier
 from ..exceptions import FeatureDimensionMismatch
 from ..utils.types import FeatureType
-from ..base import BaseClassifier
 
 
 class BaseAIRS(BaseClassifier, ABC):

{aisp-0.3.1 → aisp-0.3.21}/aisp/ina/_ai_network.py

@@ -1,6 +1,7 @@
 """Artificial Immune Network (AiNet)."""
 
 from __future__ import annotations
+
 from collections import Counter
 from heapq import nlargest
 from typing import Optional
@@ -15,8 +16,8 @@ from ._base import BaseAiNet
 from ..base import set_seed_numba
 from ..base.mutation import clone_and_mutate_binary, clone_and_mutate_continuous, \
     clone_and_mutate_ranged
-from ..utils.sanitizers import sanitize_choice, sanitize_param, sanitize_seed
 from ..utils.distance import hamming, compute_metric_distance, get_metric_code
+from ..utils.sanitizers import sanitize_choice, sanitize_param, sanitize_seed
 from ..utils.types import FeatureType, MetricType
 from ..utils.validation import detect_vector_data_type
 
@@ -28,7 +29,7 @@ class AiNet(BaseAiNet):
     clustering and data compression tasks. The aiNet algorithm uses principles from immune
     network theory, clonal selection, and affinity maturation to compress high-dimensional
     datasets. [1]_
-    For clustering, the class uses SciPy’s implementation of the **Minimum Spanning Tree**
+    For clustering, the class uses SciPy's implementation of the **Minimum Spanning Tree**
     (MST) to remove the most distant nodes and separate the groups. [2]_
 
     Parameters
@@ -57,13 +58,13 @@ class AiNet(BaseAiNet):
         Way to calculate the distance between the detector and the sample:
 
         * ``'Euclidean'`` ➜ 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.
 
         * ``'manhattan'`` ➜ The calculation of the distance is given by the expression:
-            ( |x₁ – x₂| + |y₁ – y₂| + ... + |yn – yn|).
+            ( |x₁ - x₂| + |y₁ - y₂| + ... + |yn - yn|).
 
     seed : Optional[int]
         Seed for the random generation of detector values. Defaults to None.
@@ -454,7 +455,7 @@ class AiNet(BaseAiNet):
         """
         u = np.reshape(u, (1, -1))
         v = np.atleast_2d(v)
-        distances = cdist(u, v, metric=self.metric, **self._metric_params)[0]
+        distances = cdist(u, v, metric=self.metric, **self._metric_params)[0] # type: ignore
 
         return 1 - (distances / (1 + distances))
 
@@ -522,6 +523,8 @@ class AiNet(BaseAiNet):
         ------
         ValueError
             If the Minimum Spanning Tree (MST) has not yet been created
+            If Population of antibodies is empty
+            If MST statistics (mean or std) are not available.
 
         Updates
         -------
@@ -533,6 +536,12 @@ class AiNet(BaseAiNet):
         if self._mst_structure is None:
             raise ValueError("The Minimum Spanning Tree (MST) has not yet been created.")
 
+        if self._population_antibodies is None or len(self._population_antibodies) == 0:
+            raise ValueError("Population of antibodies is empty")
+
+        if self._mst_mean_distance is None or self._mst_std_distance is None:
+            raise ValueError("MST statistics (mean or std) are not available.")
+
         if mst_inconsistency_factor is not None:
             self.mst_inconsistency_factor = mst_inconsistency_factor
 

{aisp-0.3.1 → aisp-0.3.21}/aisp/ina/_base.py

@@ -3,9 +3,8 @@
 from abc import ABC
 from typing import Optional
 
-from numpy import typing as npt
-
 import numpy as np
+from numpy import typing as npt
 
 from ..base import BaseClusterer
 from ..exceptions import FeatureDimensionMismatch

{aisp-0.3.1 → aisp-0.3.21}/aisp/nsa/_binary_negative_selection.py

@@ -1,19 +1,20 @@
 """Negative Selection Algorithm."""
 
 from __future__ import annotations
+
 from typing import Dict, Literal, Optional, Union
-from tqdm import tqdm
 
 import numpy as np
 import numpy.typing as npt
+from tqdm import tqdm
 
+from ._base import BaseNSA
 from ._ns_core import (
     check_detector_bnsa_validity,
     bnsa_class_prediction
 )
 from ..exceptions import MaxDiscardsReachedError
 from ..utils.sanitizers import sanitize_seed, sanitize_param
-from ._base import BaseNSA
 
 
 class BNSA(BaseNSA):
@@ -236,4 +237,4 @@ class BNSA(BaseNSA):
             else:
                 class_differences[_class_] = distances.sum() / self.N
 
-        c.append(max(class_differences, key=class_differences.get))
+        c.append(max(class_differences, key=class_differences.get)) # type: ignore

{aisp-0.3.1 → aisp-0.3.21}/aisp/nsa/_negative_selection.py

@@ -1,14 +1,16 @@
 """Negative Selection Algorithm."""
 
 from __future__ import annotations
+
 from typing import Any, Dict, Literal, Optional, Union
-from tqdm import tqdm
 
 import numpy as np
 import numpy.typing as npt
+from tqdm import tqdm
 
-from ..base import set_seed_numba
+from ._base import BaseNSA, Detector
 from ._ns_core import check_detector_rnsa_validity
+from ..base import set_seed_numba
 from ..exceptions import MaxDiscardsReachedError
 from ..utils.distance import (
     min_distance_to_class_vectors,
@@ -16,7 +18,6 @@ from ..utils.distance import (
     compute_metric_distance,
 )
 from ..utils.sanitizers import sanitize_seed, sanitize_choice, sanitize_param
-from ._base import BaseNSA, Detector
 
 
 class RNSA(BaseNSA):
@@ -39,11 +40,11 @@ class RNSA(BaseNSA):
         Way to calculate the distance between the detector and the sample:
 
         + ``'Euclidean'`` ➜ 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.
         + ``'manhattan'`` ➜ The calculation of the distance is given by the expression:
-            ( |x₁ – x₂| + |y₁ – y₂| + ... + |yn – yn|) .
+            ( |x₁ - x₂| + |y₁ - y₂| + ... + |yn - yn|) .
     max_discards : int, default=1000
         This parameter indicates the maximum number of consecutive detector discards, aimed at
         preventing a possible infinite loop in case a radius is defined that cannot generate
@@ -259,7 +260,7 @@ class RNSA(BaseNSA):
                     average_distance[_class_] = np.average(
                         [self.__distance(detector, line) for detector in detectores]
                     )
-                c.append(max(average_distance, key=average_distance.get))
+                c.append(max(average_distance, key=average_distance.get)) # type: ignore
         return np.array(c)
 
     def __checks_valid_detector(

{aisp-0.3.1 → aisp-0.3.21}/aisp/utils/_multiclass.py

@@ -1,6 +1,7 @@
 """Utility functions for handling classes with multiple categories."""
 
 from typing import Union
+
 import numpy as np
 import numpy.typing as npt
 

{aisp-0.3.1 → aisp-0.3.21}/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-0.3.1 → aisp-0.3.21}/aisp/utils/types.py

@@ -12,11 +12,11 @@ FeatureType : Literal["binary-features", "continuous-features", "ranged-features
 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|).
 """
 
 

{aisp-0.3.1 → aisp-0.3.21}/aisp.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aisp
-Version: 0.3.1
+Version: 0.3.21
 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>
@@ -83,12 +83,12 @@ Artificial Immune Systems (AIS) are inspired by the vertebrate immune system, cr
 
 ##### Algorithms implemented:
 
-> - [x] [**Negative Selection.**](https://ais-package.github.io/docs/aisp-techniques/Negative%20Selection/)
-> - [x] [**Clonal Selection Algorithms.**](https://ais-package.github.io/docs/aisp-techniques/Clonal%20Selection%20Algorithms/)
->     * [AIRS - Artificial Immune Recognition System](https://ais-package.github.io/docs/aisp-techniques/Clonal%20Selection%20Algorithms/airs/)
+> - [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/)
 > - [ ] *Danger Theory.*
-> - [x] [*Immune Network Theory.*](https://ais-package.github.io/docs/aisp-techniques/Immune%20Network%20Theory)
->   - [AiNet - Artificial Immune Network para Clustering and Compression](https://ais-package.github.io/docs/aisp-techniques/Immune%20Network%20Theory/ainet)
+> - [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)
 
 </section>
 

{aisp-0.3.1 → aisp-0.3.21}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "aisp"
-version = "0.3.1"
+version = "0.3.21"
 authors = [
   { name="João Paulo da Silva Barros", email="jpsilvabarr@gmail.com" },
 ]