build: bump version 0.7.5 → 0.7.6

it was necessary to update the pre-commit definition for a successfull
commit.

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.7.3
+current_version = 0.7.6
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)

.github/workflows/pythonapp.yml

@@ -6,70 +6,70 @@ name: tests
 on:
   push:
   pull_request:
-    branches: [ master ]
+    branches: [master]
 
 jobs:
   style:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
-    - name: Set up Python 3.10
+      - name: Set up Python 3.11
-      uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
-      with:
+        with:
-        python-version: "3.10"
+          python-version: "3.11"
-    - name: Install dependencies
+      - name: Install dependencies
-      run: |
+        run: |
-        python -m pip install --upgrade pip
+          python -m pip install --upgrade pip
-        pip install .[all]
+          pip install .[all]
-    - uses: pre-commit/action@v2.0.3
+      - uses: pre-commit/action@v3.0.0
   compatibility:
     needs: style
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
         os: [ubuntu-latest, windows-latest]
         exclude:
-        - os: windows-latest
+          - os: windows-latest
-          python-version: "3.7"
+            python-version: "3.8"
-        - os: windows-latest
+          - os: windows-latest
-          python-version: "3.8"
+            python-version: "3.9"
-        - os: windows-latest
+          - os: windows-latest
-          python-version: "3.9"
+            python-version: "3.10"
 
     runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
+      - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
-      with:
+        with:
-        python-version: ${{ matrix.python-version }}
+          python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+      - name: Install dependencies
-      run: |
+        run: |
-        python -m pip install --upgrade pip
+          python -m pip install --upgrade pip
-        pip install .[all]
+          pip install .[all]
-    - name: Test with pytest
+      - name: Test with pytest
-      run: |
+        run: |
-        pytest
+          pytest
   publish_pypi:
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     needs: compatibility
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
-    - name: Set up Python 3.10
+      - name: Set up Python 3.10
-      uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
-      with:
+        with:
-        python-version: "3.10"
+          python-version: "3.11"
-    - name: Install dependencies
+      - name: Install dependencies
-      run: |
+        run: |
-        python -m pip install --upgrade pip
+          python -m pip install --upgrade pip
-        pip install .[all]
+          pip install .[all]
-        pip install wheel
+          pip install wheel
-    - name: Build package
+      - name: Build package
-      run: python setup.py sdist bdist_wheel
+        run: python setup.py sdist bdist_wheel
-    - name: Publish a Python distribution to PyPI
+      - name: Publish a Python distribution to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@release/v1
-      with:
+        with:
-        user: __token__
+          user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+          password: ${{ secrets.PYPI_API_TOKEN }}

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.1.0
+  rev: v4.4.0
   hooks:
   - id: trailing-whitespace
   - id: end-of-file-fixer
@@ -13,17 +13,17 @@ repos:
   - id: check-case-conflict
 
 - repo: https://github.com/myint/autoflake
-  rev: v1.4
+  rev: v2.1.1
   hooks:
   - id: autoflake
 
 - repo: http://github.com/PyCQA/isort
-  rev: 5.10.1
+  rev: 5.12.0
   hooks:
   - id: isort
 
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v0.931
+  rev: v1.3.0
   hooks:
   - id: mypy
     files: prototorch
@@ -35,14 +35,14 @@ repos:
   - id: yapf
 
 - repo: https://github.com/pre-commit/pygrep-hooks
-  rev: v1.9.0
+  rev: v1.10.0
   hooks:
   - id: python-use-type-annotations
   - id: python-no-log-warn
   - id: python-check-blanket-noqa
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: v2.31.0
+  rev: v3.7.0
   hooks:
   - id: pyupgrade
 

docs/source/conf.py

@@ -23,7 +23,7 @@ author = "Jensun Ravichandran"
 
 # The full version, including alpha/beta/rc tags
 #
-release = "0.7.3"
+release = "0.7.6"
 
 # -- General configuration ---------------------------------------------------
 

examples/cbc_iris.py

@@ -1,5 +1,7 @@
 """ProtoTorch CBC example using 2D Iris data."""
 
+import logging
+
 import torch
 from matplotlib import pyplot as plt
 
@@ -34,7 +36,7 @@ class VisCBC2D():
         self.resolution = 100
         self.cmap = "viridis"
 
-    def on_epoch_end(self):
+    def on_train_epoch_end(self):
         x_train, y_train = self.x_train, self.y_train
         _components = self.model.components_layer._components.detach()
         ax = self.fig.gca()
@@ -94,5 +96,5 @@ if __name__ == "__main__":
             correct += (y_pred.argmax(1) == y).float().sum(0)
 
         acc = 100 * correct / len(train_ds)
-        print(f"Epoch: {epoch} Accuracy: {acc:05.02f}%")
+        logging.info(f"Epoch: {epoch} Accuracy: {acc:05.02f}%")
-        vis.on_epoch_end()
+        vis.on_train_epoch_end()

examples/gmlvq.py

@@ -0,0 +1,76 @@
+"""ProtoTorch GMLVQ example using Iris data."""
+
+import torch
+
+import prototorch as pt
+
+
+class GMLVQ(torch.nn.Module):
+    """
+    Implementation of Generalized Matrix Learning Vector Quantization.
+    """
+
+    def __init__(self, data, **kwargs):
+        super().__init__(**kwargs)
+
+        self.components_layer = pt.components.LabeledComponents(
+            distribution=[1, 1, 1],
+            components_initializer=pt.initializers.SMCI(data, noise=0.1),
+        )
+
+        self.backbone = pt.transforms.Omega(
+            len(data[0][0]),
+            len(data[0][0]),
+            pt.initializers.RandomLinearTransformInitializer(),
+        )
+
+    def forward(self, data):
+        """
+        Forward function that returns a tuple of dissimilarities and label information.
+        Feed into GLVQLoss to get a complete GMLVQ model.
+        """
+        components, label = self.components_layer()
+
+        latent_x = self.backbone(data)
+        latent_components = self.backbone(components)
+
+        distance = pt.distances.squared_euclidean_distance(
+            latent_x, latent_components)
+
+        return distance, label
+
+    def predict(self, data):
+        """
+        The GMLVQ has a modified prediction step, where a competition layer is applied.
+        """
+        components, label = self.components_layer()
+        distance = pt.distances.squared_euclidean_distance(data, components)
+        winning_label = pt.competitions.wtac(distance, label)
+        return winning_label
+
+
+if __name__ == "__main__":
+    train_ds = pt.datasets.Iris()
+
+    train_loader = torch.utils.data.DataLoader(train_ds, batch_size=32)
+
+    model = GMLVQ(train_ds)
+    optimizer = torch.optim.Adam(model.parameters(), lr=0.05)
+    criterion = pt.losses.GLVQLoss()
+
+    for epoch in range(200):
+        correct = 0.0
+        for x, y in train_loader:
+            d, labels = model(x)
+            loss = criterion(d, y, labels).mean(0)
+
+            optimizer.zero_grad()
+            loss.backward()
+            optimizer.step()
+
+            with torch.no_grad():
+                y_pred = model.predict(x)
+                correct += (y_pred == y).float().sum(0)
+
+        acc = 100 * correct / len(train_ds)
+        print(f"Epoch: {epoch} Accuracy: {acc:05.02f}%")

prototorch/__init__.py

@@ -17,7 +17,7 @@ from .core import similarities  # noqa: F401
 from .core import transforms  # noqa: F401
 
 # Core Setup
-__version__ = "0.7.3"
+__version__ = "0.7.6"
 
 __all_core__ = [
     "competitions",

prototorch/core/competitions.py

@@ -38,7 +38,7 @@ def cbcc(detections: torch.Tensor, reasonings: torch.Tensor):
     pk = A
     nk = (1 - A) * B
     numerator = (detections @ (pk - nk).T) + nk.sum(1)
-    probs = numerator / (pk + nk).sum(1)
+    probs = numerator / ((pk + nk).sum(1) + 1e-8)
     return probs
 
 

prototorch/core/distances.py

@@ -11,7 +11,7 @@ def squared_euclidean_distance(x, y):
     **Alias:**
     ``prototorch.functions.distances.sed``
     """
-    x, y = [arr.view(arr.size(0), -1) for arr in (x, y)]
+    x, y = (arr.view(arr.size(0), -1) for arr in (x, y))
     expanded_x = x.unsqueeze(dim=1)
     batchwise_difference = y - expanded_x
     differences_raised = torch.pow(batchwise_difference, 2)
@@ -27,14 +27,14 @@ def euclidean_distance(x, y):
     :returns: Distance Tensor of shape :math:`X \times Y`
     :rtype: `torch.tensor`
     """
-    x, y = [arr.view(arr.size(0), -1) for arr in (x, y)]
+    x, y = (arr.view(arr.size(0), -1) for arr in (x, y))
     distances_raised = squared_euclidean_distance(x, y)
     distances = torch.sqrt(distances_raised)
     return distances
 
 
 def euclidean_distance_v2(x, y):
-    x, y = [arr.view(arr.size(0), -1) for arr in (x, y)]
+    x, y = (arr.view(arr.size(0), -1) for arr in (x, y))
     diff = y - x.unsqueeze(1)
     pairwise_distances = (diff @ diff.permute((0, 2, 1))).sqrt()
     # Passing `dim1=-2` and `dim2=-1` to `diagonal()` takes the
@@ -54,7 +54,7 @@ def lpnorm_distance(x, y, p):
 
     :param p: p parameter of the lp norm
     """
-    x, y = [arr.view(arr.size(0), -1) for arr in (x, y)]
+    x, y = (arr.view(arr.size(0), -1) for arr in (x, y))
     distances = torch.cdist(x, y, p=p)
     return distances
 
@@ -66,7 +66,7 @@ def omega_distance(x, y, omega):
 
     :param `torch.tensor` omega: Two dimensional matrix
     """
-    x, y = [arr.view(arr.size(0), -1) for arr in (x, y)]
+    x, y = (arr.view(arr.size(0), -1) for arr in (x, y))
     projected_x = x @ omega
     projected_y = y @ omega
     distances = squared_euclidean_distance(projected_x, projected_y)
@@ -80,7 +80,7 @@ def lomega_distance(x, y, omegas):
 
     :param `torch.tensor` omegas: Three dimensional matrix
     """
-    x, y = [arr.view(arr.size(0), -1) for arr in (x, y)]
+    x, y = (arr.view(arr.size(0), -1) for arr in (x, y))
     projected_x = x @ omegas
     projected_y = torch.diagonal(y @ omegas).T
     expanded_y = torch.unsqueeze(projected_y, dim=1)

prototorch/core/similarities.py

@@ -21,7 +21,7 @@ def cosine_similarity(x, y):
     Expected dimension of x is 2.
     Expected dimension of y is 2.
     """
-    x, y = [arr.view(arr.size(0), -1) for arr in (x, y)]
+    x, y = (arr.view(arr.size(0), -1) for arr in (x, y))
     norm_x = x.pow(2).sum(1).sqrt()
     norm_y = y.pow(2).sum(1).sqrt()
     norm_mat = norm_x.unsqueeze(-1) @ norm_y.unsqueeze(-1).T

prototorch/datasets/abstract.py

@@ -20,7 +20,7 @@ class Dataset(torch.utils.data.Dataset):
     _repr_indent = 2
 
     def __init__(self, root):
-        if isinstance(root, torch._six.string_classes):
+        if isinstance(root, str):
             root = os.path.expanduser(root)
         self.root = root
 

prototorch/datasets/sklearn.py

@@ -5,8 +5,10 @@ URL:
 
 """
 
+from __future__ import annotations
+
 import warnings
-from typing import Sequence, Union
+from typing import Sequence
 
 from sklearn.datasets import (
     load_iris,
@@ -41,9 +43,9 @@ class Iris(NumpyDataset):
     :param dims: select a subset of dimensions
     """
 
-    def __init__(self, dims: Sequence[int] = None):
+    def __init__(self, dims: Sequence[int] | None = None):
         x, y = load_iris(return_X_y=True)
-        if dims:
+        if dims is not None:
             x = x[:, dims]
         super().__init__(x, y)
 
@@ -56,15 +58,19 @@ class Blobs(NumpyDataset):
 
     """
 
-    def __init__(self,
+    def __init__(
-                 num_samples: int = 300,
+        self,
-                 num_features: int = 2,
+        num_samples: int = 300,
-                 seed: Union[None, int] = 0):
+        num_features: int = 2,
-        x, y = make_blobs(num_samples,
+        seed: None | int = 0,
-                          num_features,
+    ):
-                          centers=None,
+        x, y = make_blobs(
-                          random_state=seed,
+            num_samples,
-                          shuffle=False)
+            num_features,
+            centers=None,
+            random_state=seed,
+            shuffle=False,
+        )
         super().__init__(x, y)
 
 
@@ -77,29 +83,33 @@ class Random(NumpyDataset):
     Note: n_classes * n_clusters_per_class <= 2**n_informative must satisfy.
     """
 
-    def __init__(self,
+    def __init__(
-                 num_samples: int = 300,
+        self,
-                 num_features: int = 2,
+        num_samples: int = 300,
-                 num_classes: int = 2,
+        num_features: int = 2,
-                 num_clusters: int = 2,
+        num_classes: int = 2,
-                 num_informative: Union[None, int] = None,
+        num_clusters: int = 2,
-                 separation: float = 1.0,
+        num_informative: None | int = None,
-                 seed: Union[None, int] = 0):
+        separation: float = 1.0,
+        seed: None | int = 0,
+    ):
         if not num_informative:
             import math
             num_informative = math.ceil(math.log2(num_classes * num_clusters))
             if num_features < num_informative:
                 warnings.warn("Generating more features than requested.")
                 num_features = num_informative
-        x, y = make_classification(num_samples,
+        x, y = make_classification(
-                                   num_features,
+            num_samples,
-                                   n_informative=num_informative,
+            num_features,
-                                   n_redundant=0,
+            n_informative=num_informative,
-                                   n_classes=num_classes,
+            n_redundant=0,
-                                   n_clusters_per_class=num_clusters,
+            n_classes=num_classes,
-                                   class_sep=separation,
+            n_clusters_per_class=num_clusters,
-                                   random_state=seed,
+            class_sep=separation,
-                                   shuffle=False)
+            random_state=seed,
+            shuffle=False,
+        )
         super().__init__(x, y)
 
 
@@ -113,16 +123,20 @@ class Circles(NumpyDataset):
 
     """
 
-    def __init__(self,
+    def __init__(
-                 num_samples: int = 300,
+        self,
-                 noise: float = 0.3,
+        num_samples: int = 300,
-                 factor: float = 0.8,
+        noise: float = 0.3,
-                 seed: Union[None, int] = 0):
+        factor: float = 0.8,
-        x, y = make_circles(num_samples,
+        seed: None | int = 0,
-                            noise=noise,
+    ):
-                            factor=factor,
+        x, y = make_circles(
-                            random_state=seed,
+            num_samples,
-                            shuffle=False)
+            noise=noise,
+            factor=factor,
+            random_state=seed,
+            shuffle=False,
+        )
         super().__init__(x, y)
 
 
@@ -136,12 +150,16 @@ class Moons(NumpyDataset):
 
     """
 
-    def __init__(self,
+    def __init__(
-                 num_samples: int = 300,
+        self,
-                 noise: float = 0.3,
+        num_samples: int = 300,
-                 seed: Union[None, int] = 0):
+        noise: float = 0.3,
-        x, y = make_moons(num_samples,
+        seed: None | int = 0,
-                          noise=noise,
+    ):
-                          random_state=seed,
+        x, y = make_moons(
-                          shuffle=False)
+            num_samples,
+            noise=noise,
+            random_state=seed,
+            shuffle=False,
+        )
         super().__init__(x, y)

prototorch/datasets/tecator.py

@@ -36,6 +36,7 @@ Description:
     are determined by analytic chemistry.
 """
 
+import logging
 import os
 
 import numpy as np
@@ -81,13 +82,11 @@ class Tecator(ProtoDataset):
         if self._check_exists():
             return
 
-        if self.verbose:
+        logging.debug("Making directories...")
-            print("Making directories...")
         os.makedirs(self.raw_folder, exist_ok=True)
         os.makedirs(self.processed_folder, exist_ok=True)
 
-        if self.verbose:
+        logging.debug("Downloading...")
-            print("Downloading...")
         for fileid, md5 in self._resources:
             filename = "tecator.npz"
             download_file_from_google_drive(fileid,
@@ -95,8 +94,7 @@ class Tecator(ProtoDataset):
                                             filename=filename,
                                             md5=md5)
 
-        if self.verbose:
+        logging.debug("Processing...")
-            print("Processing...")
         with np.load(os.path.join(self.raw_folder, "tecator.npz"),
                      allow_pickle=False) as f:
             x_train, y_train = f["x_train"], f["y_train"]
@@ -117,5 +115,4 @@ class Tecator(ProtoDataset):
                   "wb") as f:
             torch.save(test_set, f)
 
-        if self.verbose:
+        logging.debug("Done!")
-            print("Done!")

prototorch/utils/utils.py

@@ -5,6 +5,7 @@ from typing import (
     Dict,
     Iterable,
     List,
+    Optional,
     Union,
 )
 
@@ -18,7 +19,7 @@ def generate_mesh(
     maxima: torch.TensorType,
     border: float = 1.0,
     resolution: int = 100,
-    device: torch.device = None,
+    device: Optional[torch.device] = None,
 ):
     # Apply Border
     ptp = maxima - minima
@@ -55,14 +56,15 @@ def mesh2d(x=None, border: float = 1.0, resolution: int = 100):
 
 
 def distribution_from_list(list_dist: List[int],
-                           clabels: Iterable[int] = None):
+                           clabels: Optional[Iterable[int]] = None):
     clabels = clabels or list(range(len(list_dist)))
     distribution = dict(zip(clabels, list_dist))
     return distribution
 
 
-def parse_distribution(user_distribution,
+def parse_distribution(
-                       clabels: Iterable[int] = None) -> Dict[int, int]:
+        user_distribution,
+        clabels: Optional[Iterable[int]] = None) -> Dict[int, int]:
     """Parse user-provided distribution.
 
     Return a dictionary with integer keys that represent the class labels and

setup.py

@@ -15,14 +15,14 @@ from setuptools import find_packages, setup
 PROJECT_URL = "https://github.com/si-cim/prototorch"
 DOWNLOAD_URL = "https://github.com/si-cim/prototorch.git"
 
-with open("README.md", "r") as fh:
+with open("README.md", encoding="utf-8") as fh:
     long_description = fh.read()
 
 INSTALL_REQUIRES = [
-    "torch>=1.3.1",
+    "torch>=2.0.0",
-    "torchvision>=0.7.3",
+    "torchvision",
-    "numpy>=1.9.1",
+    "numpy",
-    "sklearn",
+    "scikit-learn",
     "matplotlib",
 ]
 DATASETS = [
@@ -51,7 +51,7 @@ ALL = DATASETS + DEV + DOCS + EXAMPLES + TESTS
 
 setup(
     name="prototorch",
-    version="0.7.3",
+    version="0.7.6",
     description="Highly extensible, GPU-supported "
     "Learning Vector Quantization (LVQ) toolbox "
     "built using PyTorch and its nn API.",
@@ -62,7 +62,7 @@ setup(
     url=PROJECT_URL,
     download_url=DOWNLOAD_URL,
     license="MIT",
-    python_requires=">=3.7",
+    python_requires=">=3.8",
     install_requires=INSTALL_REQUIRES,
     extras_require={
         "datasets": DATASETS,
@@ -85,10 +85,10 @@ setup(
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
     ],
     packages=find_packages(),
     zip_safe=False,

tests/test_datasets.py

@@ -1,7 +1,6 @@
 """ProtoTorch datasets test suite"""
 
 import os
-import shutil
 import unittest
 
 import numpy as np