ci: cache test IV

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.7.6
+current_version = 0.7.1
 commit = True
 tag = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)

.ci/python310.Dockerfile

@@ -0,0 +1,7 @@
+FROM python:3.9
+
+RUN adduser --uid 1000 jenkins
+
+USER jenkins
+
+RUN mkdir -p /home/jenkins/.cache/pip

.ci/python36.Dockerfile

@@ -0,0 +1,7 @@
+FROM python:3.6
+
+RUN adduser --uid 1000 jenkins
+
+USER jenkins
+
+RUN mkdir -p /home/jenkins/.cache/pip

.codacy.yml

@@ -0,0 +1,15 @@
+# To validate the contents of your configuration file
+# run the following command in the folder where the configuration file is located:
+# codacy-analysis-cli validate-configuration --directory `pwd`
+# To analyse, run:
+# codacy-analysis-cli analyse --tool remark-lint --directory `pwd`
+---
+engines:
+  pylintpython3:
+    exclude_paths:
+      - config/engines.yml
+  remark-lint:
+    exclude_paths:
+      - config/engines.yml
+exclude_paths:
+  - 'tests/**'

.codecov.yml

@@ -0,0 +1,2 @@
+comment:
+  require_changes: yes

.github/workflows/pythonapp.yml

@@ -5,71 +5,33 @@ name: tests
 
 on:
   push:
+    branches: [ master, dev ]
   pull_request:
-    branches: [master]
+    branches: [ master ]
 
 jobs:
-  style:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install .[all]
-      - uses: pre-commit/action@v3.0.0
-  compatibility:
-    needs: style
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
-        os: [ubuntu-latest, windows-latest]
-        exclude:
-          - os: windows-latest
-            python-version: "3.8"
-          - os: windows-latest
-            python-version: "3.9"
-          - os: windows-latest
-            python-version: "3.10"
+  build:
+
+    runs-on: ubuntu-latest
 
-    runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v1
       with:
-          python-version: ${{ matrix.python-version }}
+        python-version: 3.9
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install .[all]
+    - name: Lint with flake8
+      run: |
+        pip install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
+        pip install pytest
         pytest
-  publish_pypi:
-    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
-    needs: compatibility
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install .[all]
-          pip install wheel
-      - name: Build package
-        run: python setup.py sdist bdist_wheel
-      - name: Publish a Python distribution to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __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: v4.4.0
+  rev: v4.0.1
   hooks:
   - id: trailing-whitespace
   - id: end-of-file-fixer
@@ -13,36 +13,36 @@ repos:
   - id: check-case-conflict
 
 - repo: https://github.com/myint/autoflake
-  rev: v2.1.1
+  rev: v1.4
   hooks:
   - id: autoflake
 
 - repo: http://github.com/PyCQA/isort
-  rev: 5.12.0
+  rev: 5.8.0
   hooks:
   - id: isort
 
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.3.0
+  rev: v0.902
   hooks:
   - id: mypy
     files: prototorch
     additional_dependencies: [types-pkg_resources]
 
 - repo: https://github.com/pre-commit/mirrors-yapf
-  rev: v0.32.0
+  rev: v0.31.0
   hooks:
   - id: yapf
 
 - repo: https://github.com/pre-commit/pygrep-hooks
-  rev: v1.10.0
+  rev: v1.9.0
   hooks:
   - id: python-use-type-annotations
   - id: python-no-log-warn
   - id: python-check-blanket-noqa
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.7.0
+  rev: v2.19.4
   hooks:
   - id: pyupgrade
 

Jenkinsfile

@@ -0,0 +1,41 @@
+pipeline {
+  agent none
+  stages {
+    stage('Unit Tests') {
+      parallel {
+        stage('3.6'){
+          agent{
+            dockerfile {
+              filename 'python36.Dockerfile'
+              dir '.ci'
+              args '-v pip-cache:/home/jenkins/.cache/pip'
+            }
+          }
+          steps {
+              sh 'pip install pip --upgrade --progress-bar off'
+              sh 'pip install .[all] --progress-bar off'
+              sh '~/.local/bin/pytest -v --junitxml=reports/result.xml --cov=prototorch/ --cov-report=xml:reports/coverage.xml'
+              cobertura coberturaReportFile: 'reports/coverage.xml'
+              junit 'reports/**/*.xml'
+          }
+        }
+        stage('3.10'){
+          agent{
+            dockerfile {
+              filename 'python310.Dockerfile'
+              dir '.ci'
+              args '-v pip-cache:/home/jenkins/.cache/pip'
+            }
+          }
+          steps {
+            sh 'pip install pip --upgrade --progress-bar off'
+            sh 'pip install .[all] --progress-bar off'
+            sh '~/.local/bin/pytest -v --junitxml=reports/result.xml --cov=prototorch/ --cov-report=xml:reports/coverage.xml'
+            cobertura coberturaReportFile: 'reports/coverage.xml'
+            junit 'reports/**/*.xml'
+        }
+        }
+      }
+    }
+  }
+}

LICENSE

@@ -1,7 +1,6 @@
 MIT License
 
-Copyright (c) 2020 Saxon Institute for Computational Intelligence and Machine
-Learning (SICIM)
+Copyright (c) 2020 si-cim
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -2,9 +2,12 @@
 
 ![ProtoTorch Logo](https://prototorch.readthedocs.io/en/latest/_static/horizontal-lockup.png)
 
+[![Build Status](https://api.travis-ci.com/si-cim/prototorch.svg?branch=master)](https://travis-ci.com/github/si-cim/prototorch)
 ![tests](https://github.com/si-cim/prototorch/workflows/tests/badge.svg)
 [![GitHub tag (latest by date)](https://img.shields.io/github/v/tag/si-cim/prototorch?color=yellow&label=version)](https://github.com/si-cim/prototorch/releases)
 [![PyPI](https://img.shields.io/pypi/v/prototorch)](https://pypi.org/project/prototorch/)
+[![codecov](https://codecov.io/gh/si-cim/prototorch/branch/master/graph/badge.svg)](https://codecov.io/gh/si-cim/prototorch)
+[![Codacy Badge](https://api.codacy.com/project/badge/Grade/76273904bf9343f0a8b29cd8aca242e7)](https://www.codacy.com/gh/si-cim/prototorch?utm_source=github.com&utm_medium=referral&utm_content=si-cim/prototorch&utm_campaign=Badge_Grade)
 [![GitHub license](https://img.shields.io/github/license/si-cim/prototorch)](https://github.com/si-cim/prototorch/blob/master/LICENSE)
 
 *Tensorflow users, see:* [ProtoFlow](https://github.com/si-cim/protoflow)

deprecated.travis.yml

@@ -0,0 +1,46 @@
+dist: bionic
+sudo: false
+language: python
+python:
+  - 3.9
+  - 3.8
+  - 3.7
+  - 3.6
+cache:
+  directories:
+  - "$HOME/.cache/pip"
+  - "./tests/artifacts"
+  - "$HOME/datasets"
+install:
+- pip install .[all] --progress-bar off
+
+# Generate code coverage report
+script:
+- coverage run -m pytest
+
+# Push the results to codecov
+after_success:
+- bash <(curl -s https://codecov.io/bash)
+
+# Publish on PyPI
+jobs:
+  include:
+    - stage: build
+      python: 3.9
+      script: echo "Starting Pypi build"
+      deploy:
+        provider: pypi
+        username: __token__
+        distributions: "sdist bdist_wheel"
+        password:
+          secure: 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
+        on:
+          tags: true
+          skip_existing: true
+
+# The password is encrypted with:
+# `cd prototorch && travis encrypt your-pypi-api-token --add deploy.password`
+# See https://docs.travis-ci.com/user/deployment/pypi and
+# https://github.com/travis-ci/travis.rb#installation
+# for more details
+# Note: The encrypt command does not work well in ZSH.

docs/source/conf.py

@@ -23,7 +23,7 @@ author = "Jensun Ravichandran"
 
 # The full version, including alpha/beta/rc tags
 #
-release = "0.7.6"
+release = "0.7.1"
 
 # -- General configuration ---------------------------------------------------
 
@@ -120,7 +120,7 @@ html_css_files = [
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = "prototorchdoc"
+htmlhelp_basename = "protoflowdoc"
 
 # -- Options for LaTeX output ---------------------------------------------
 

examples/cbc_iris.py

@@ -1,7 +1,5 @@
 """ProtoTorch CBC example using 2D Iris data."""
 
-import logging
-
 import torch
 from matplotlib import pyplot as plt
 
@@ -9,7 +7,6 @@ import prototorch as pt
 
 
 class CBC(torch.nn.Module):
-
     def __init__(self, data, **kwargs):
         super().__init__(**kwargs)
         self.components_layer = pt.components.ReasoningComponents(
@@ -26,7 +23,6 @@ class CBC(torch.nn.Module):
 
 
 class VisCBC2D():
-
     def __init__(self, model, data):
         self.model = model
         self.x_train, self.y_train = pt.utils.parse_data_arg(data)
@@ -36,7 +32,7 @@ class VisCBC2D():
         self.resolution = 100
         self.cmap = "viridis"
 
-    def on_train_epoch_end(self):
+    def on_epoch_end(self):
         x_train, y_train = self.x_train, self.y_train
         _components = self.model.components_layer._components.detach()
         ax = self.fig.gca()
@@ -96,5 +92,5 @@ if __name__ == "__main__":
             correct += (y_pred.argmax(1) == y).float().sum(0)
 
         acc = 100 * correct / len(train_ds)
-        logging.info(f"Epoch: {epoch} Accuracy: {acc:05.02f}%")
-        vis.on_train_epoch_end()
+        print(f"Epoch: {epoch} Accuracy: {acc:05.02f}%")
+        vis.on_epoch_end()

examples/gmlvq.py

@@ -1,76 +0,0 @@
-"""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

@@ -1,23 +1,28 @@
 """ProtoTorch package"""
 
 import pkgutil
+from typing import List
 
 import pkg_resources
 
-from . import datasets  # noqa: F401
-from . import nn  # noqa: F401
-from . import utils  # noqa: F401
-from .core import competitions  # noqa: F401
-from .core import components  # noqa: F401
-from .core import distances  # noqa: F401
-from .core import initializers  # noqa: F401
-from .core import losses  # noqa: F401
-from .core import pooling  # noqa: F401
-from .core import similarities  # noqa: F401
-from .core import transforms  # noqa: F401
+from . import (
+    datasets,
+    nn,
+    utils,
+)
+from .core import (
+    competitions,
+    components,
+    distances,
+    initializers,
+    losses,
+    pooling,
+    similarities,
+    transforms,
+)
 
 # Core Setup
-__version__ = "0.7.6"
+__version__ = "0.7.1"
 
 __all_core__ = [
     "competitions",
@@ -35,7 +40,7 @@ __all_core__ = [
 ]
 
 # Plugin Loader
-__path__ = pkgutil.extend_path(__path__, __name__)
+__path__: List[str] = pkgutil.extend_path(__path__, __name__)
 
 
 def discover_plugins():

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) + 1e-8)
+    probs = numerator / (pk + nk).sum(1)
     return probs
 
 
@@ -48,7 +48,6 @@ class WTAC(torch.nn.Module):
     Thin wrapper over the `wtac` function.
 
     """
-
     def forward(self, distances, labels):  # pylint: disable=no-self-use
         return wtac(distances, labels)
 
@@ -59,7 +58,6 @@ class LTAC(torch.nn.Module):
     Thin wrapper over the `wtac` function.
 
     """
-
     def forward(self, probs, labels):  # pylint: disable=no-self-use
         return wtac(-1.0 * probs, labels)
 
@@ -70,7 +68,6 @@ class KNNC(torch.nn.Module):
     Thin wrapper over the `knnc` function.
 
     """
-
     def __init__(self, k=1, **kwargs):
         super().__init__(**kwargs)
         self.k = k
@@ -88,6 +85,5 @@ class CBCC(torch.nn.Module):
     Thin wrapper over the `cbcc` function.
 
     """
-
     def forward(self, detections, reasonings):  # pylint: disable=no-self-use
         return cbcc(detections, reasonings)

prototorch/core/components.py

@@ -6,8 +6,7 @@ from typing import Union
 import torch
 from torch.nn.parameter import Parameter
 
-from prototorch.utils import parse_distribution
-
+from ..utils import parse_distribution
 from .initializers import (
     AbstractClassAwareCompInitializer,
     AbstractComponentsInitializer,
@@ -64,7 +63,6 @@ def get_cikwargs(init, distribution):
 
 class AbstractComponents(torch.nn.Module):
     """Abstract class for all components modules."""
-
     @property
     def num_components(self):
         """Current number of components."""
@@ -87,7 +85,6 @@ class AbstractComponents(torch.nn.Module):
 
 class Components(AbstractComponents):
     """A set of adaptable Tensors."""
-
     def __init__(self, num_components: int,
                  initializer: AbstractComponentsInitializer):
         super().__init__()
@@ -115,7 +112,6 @@ class Components(AbstractComponents):
 
 class AbstractLabels(torch.nn.Module):
     """Abstract class for all labels modules."""
-
     @property
     def labels(self):
         return self._labels.cpu()
@@ -156,7 +152,6 @@ class AbstractLabels(torch.nn.Module):
 
 class Labels(AbstractLabels):
     """A set of standalone labels."""
-
     def __init__(self,
                  distribution: Union[dict, list, tuple],
                  initializer: AbstractLabelsInitializer = LabelsInitializer()):
@@ -187,7 +182,6 @@ class Labels(AbstractLabels):
 
 class LabeledComponents(AbstractComponents):
     """A set of adaptable components and corresponding unadaptable labels."""
-
     def __init__(
         self,
         distribution: Union[dict, list, tuple],
@@ -255,7 +249,6 @@ class Reasonings(torch.nn.Module):
     The `reasonings` tensor is of shape [num_components, num_classes, 2].
 
     """
-
     def __init__(
         self,
         distribution: Union[dict, list, tuple],
@@ -315,7 +308,6 @@ class ReasoningComponents(AbstractComponents):
     three element probability distribution.
 
     """
-
     def __init__(
         self,
         distribution: Union[dict, list, tuple],

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/initializers.py

@@ -11,7 +11,7 @@ from typing import (
 
 import torch
 
-from prototorch.utils import parse_data_arg, parse_distribution
+from ..utils import parse_data_arg, parse_distribution
 
 
 # Components
@@ -26,18 +26,11 @@ class LiteralCompInitializer(AbstractComponentsInitializer):
     Use this to 'generate' pre-initialized components elsewhere.
 
     """
-
     def __init__(self, components):
         self.components = components
 
     def generate(self, num_components: int = 0):
         """Ignore `num_components` and simply return `self.components`."""
-        provided_num_components = len(self.components)
-        if provided_num_components != num_components:
-            wmsg = f"The number of components ({provided_num_components}) " \
-                f"provided to {self.__class__.__name__} " \
-                f"does not match the expected number ({num_components})."
-            warnings.warn(wmsg)
         if not isinstance(self.components, torch.Tensor):
             wmsg = f"Converting components to {torch.Tensor}..."
             warnings.warn(wmsg)
@@ -47,7 +40,6 @@ class LiteralCompInitializer(AbstractComponentsInitializer):
 
 class ShapeAwareCompInitializer(AbstractComponentsInitializer):
     """Abstract class for all dimension-aware components initializers."""
-
     def __init__(self, shape: Union[Iterable, int]):
         if isinstance(shape, Iterable):
             self.component_shape = tuple(shape)
@@ -61,7 +53,6 @@ class ShapeAwareCompInitializer(AbstractComponentsInitializer):
 
 class ZerosCompInitializer(ShapeAwareCompInitializer):
     """Generate zeros corresponding to the components shape."""
-
     def generate(self, num_components: int):
         components = torch.zeros((num_components, ) + self.component_shape)
         return components
@@ -69,7 +60,6 @@ class ZerosCompInitializer(ShapeAwareCompInitializer):
 
 class OnesCompInitializer(ShapeAwareCompInitializer):
     """Generate ones corresponding to the components shape."""
-
     def generate(self, num_components: int):
         components = torch.ones((num_components, ) + self.component_shape)
         return components
@@ -77,7 +67,6 @@ class OnesCompInitializer(ShapeAwareCompInitializer):
 
 class FillValueCompInitializer(OnesCompInitializer):
     """Generate components with the provided `fill_value`."""
-
     def __init__(self, shape, fill_value: float = 1.0):
         super().__init__(shape)
         self.fill_value = fill_value
@@ -90,7 +79,6 @@ class FillValueCompInitializer(OnesCompInitializer):
 
 class UniformCompInitializer(OnesCompInitializer):
     """Generate components by sampling from a continuous uniform distribution."""
-
     def __init__(self, shape, minimum=0.0, maximum=1.0, scale=1.0):
         super().__init__(shape)
         self.minimum = minimum
@@ -105,7 +93,6 @@ class UniformCompInitializer(OnesCompInitializer):
 
 class RandomNormalCompInitializer(OnesCompInitializer):
     """Generate components by sampling from a standard normal distribution."""
-
     def __init__(self, shape, shift=0.0, scale=1.0):
         super().__init__(shape)
         self.shift = shift
@@ -126,7 +113,6 @@ class AbstractDataAwareCompInitializer(AbstractComponentsInitializer):
     `data` has to be a torch tensor.
 
     """
-
     def __init__(self,
                  data: torch.Tensor,
                  noise: float = 0.0,
@@ -151,7 +137,6 @@ class AbstractDataAwareCompInitializer(AbstractComponentsInitializer):
 
 class DataAwareCompInitializer(AbstractDataAwareCompInitializer):
     """'Generate' the components from the provided data."""
-
     def generate(self, num_components: int = 0):
         """Ignore `num_components` and simply return transformed `self.data`."""
         components = self.generate_end_hook(self.data)
@@ -160,7 +145,6 @@ class DataAwareCompInitializer(AbstractDataAwareCompInitializer):
 
 class SelectionCompInitializer(AbstractDataAwareCompInitializer):
     """Generate components by uniformly sampling from the provided data."""
-
     def generate(self, num_components: int):
         indices = torch.LongTensor(num_components).random_(0, len(self.data))
         samples = self.data[indices]
@@ -170,7 +154,6 @@ class SelectionCompInitializer(AbstractDataAwareCompInitializer):
 
 class MeanCompInitializer(AbstractDataAwareCompInitializer):
     """Generate components by computing the mean of the provided data."""
-
     def generate(self, num_components: int):
         mean = self.data.mean(dim=0)
         repeat_dim = [num_components] + [1] * len(mean.shape)
@@ -189,7 +172,6 @@ class AbstractClassAwareCompInitializer(AbstractComponentsInitializer):
     target tensors.
 
     """
-
     def __init__(self,
                  data,
                  noise: float = 0.0,
@@ -217,7 +199,6 @@ class AbstractClassAwareCompInitializer(AbstractComponentsInitializer):
 
 class ClassAwareCompInitializer(AbstractClassAwareCompInitializer):
     """'Generate' components from provided data and requested distribution."""
-
     def generate(self, distribution: Union[dict, list, tuple]):
         """Ignore `distribution` and simply return transformed `self.data`."""
         components = self.generate_end_hook(self.data)
@@ -226,7 +207,6 @@ class ClassAwareCompInitializer(AbstractClassAwareCompInitializer):
 
 class AbstractStratifiedCompInitializer(AbstractClassAwareCompInitializer):
     """Abstract class for all stratified components initializers."""
-
     @property
     @abstractmethod
     def subinit_type(self) -> Type[AbstractDataAwareCompInitializer]:
@@ -237,8 +217,6 @@ class AbstractStratifiedCompInitializer(AbstractClassAwareCompInitializer):
         components = torch.tensor([])
         for k, v in distribution.items():
             stratified_data = self.data[self.targets == k]
-            if len(stratified_data) == 0:
-                raise ValueError(f"No data available for class {k}.")
             initializer = self.subinit_type(
                 stratified_data,
                 noise=self.noise,
@@ -251,7 +229,6 @@ class AbstractStratifiedCompInitializer(AbstractClassAwareCompInitializer):
 
 class StratifiedSelectionCompInitializer(AbstractStratifiedCompInitializer):
     """Generate components using stratified sampling from the provided data."""
-
     @property
     def subinit_type(self):
         return SelectionCompInitializer
@@ -259,7 +236,6 @@ class StratifiedSelectionCompInitializer(AbstractStratifiedCompInitializer):
 
 class StratifiedMeanCompInitializer(AbstractStratifiedCompInitializer):
     """Generate components at stratified means of the provided data."""
-
     @property
     def subinit_type(self):
         return MeanCompInitializer
@@ -268,7 +244,6 @@ class StratifiedMeanCompInitializer(AbstractStratifiedCompInitializer):
 # Labels
 class AbstractLabelsInitializer(ABC):
     """Abstract class for all labels initializers."""
-
     @abstractmethod
     def generate(self, distribution: Union[dict, list, tuple]):
         ...
@@ -280,7 +255,6 @@ class LiteralLabelsInitializer(AbstractLabelsInitializer):
     Use this to 'generate' pre-initialized labels elsewhere.
 
     """
-
     def __init__(self, labels):
         self.labels = labels
 
@@ -299,7 +273,6 @@ class LiteralLabelsInitializer(AbstractLabelsInitializer):
 
 class DataAwareLabelsInitializer(AbstractLabelsInitializer):
     """'Generate' the labels from a torch Dataset."""
-
     def __init__(self, data):
         self.data, self.targets = parse_data_arg(data)
 
@@ -310,7 +283,6 @@ class DataAwareLabelsInitializer(AbstractLabelsInitializer):
 
 class LabelsInitializer(AbstractLabelsInitializer):
     """Generate labels from `distribution`."""
-
     def generate(self, distribution: Union[dict, list, tuple]):
         distribution = parse_distribution(distribution)
         labels_list = []
@@ -322,7 +294,6 @@ class LabelsInitializer(AbstractLabelsInitializer):
 
 class OneHotLabelsInitializer(LabelsInitializer):
     """Generate one-hot-encoded labels from `distribution`."""
-
     def generate(self, distribution: Union[dict, list, tuple]):
         distribution = parse_distribution(distribution)
         num_classes = len(distribution.keys())
@@ -341,7 +312,6 @@ def compute_distribution_shape(distribution):
 
 class AbstractReasoningsInitializer(ABC):
     """Abstract class for all reasonings initializers."""
-
     def __init__(self, components_first: bool = True):
         self.components_first = components_first
 
@@ -362,7 +332,6 @@ class LiteralReasoningsInitializer(AbstractReasoningsInitializer):
     Use this to 'generate' pre-initialized reasonings elsewhere.
 
     """
-
     def __init__(self, reasonings, **kwargs):
         super().__init__(**kwargs)
         self.reasonings = reasonings
@@ -380,7 +349,6 @@ class LiteralReasoningsInitializer(AbstractReasoningsInitializer):
 
 class ZerosReasoningsInitializer(AbstractReasoningsInitializer):
     """Reasonings are all initialized with zeros."""
-
     def generate(self, distribution: Union[dict, list, tuple]):
         shape = compute_distribution_shape(distribution)
         reasonings = torch.zeros(*shape)
@@ -390,7 +358,6 @@ class ZerosReasoningsInitializer(AbstractReasoningsInitializer):
 
 class OnesReasoningsInitializer(AbstractReasoningsInitializer):
     """Reasonings are all initialized with ones."""
-
     def generate(self, distribution: Union[dict, list, tuple]):
         shape = compute_distribution_shape(distribution)
         reasonings = torch.ones(*shape)
@@ -400,7 +367,6 @@ class OnesReasoningsInitializer(AbstractReasoningsInitializer):
 
 class RandomReasoningsInitializer(AbstractReasoningsInitializer):
     """Reasonings are randomly initialized."""
-
     def __init__(self, minimum=0.4, maximum=0.6, **kwargs):
         super().__init__(**kwargs)
         self.minimum = minimum
@@ -415,7 +381,6 @@ class RandomReasoningsInitializer(AbstractReasoningsInitializer):
 
 class PurePositiveReasoningsInitializer(AbstractReasoningsInitializer):
     """Each component reasons positively for exactly one class."""
-
     def generate(self, distribution: Union[dict, list, tuple]):
         num_components, num_classes, _ = compute_distribution_shape(
             distribution)
@@ -434,7 +399,6 @@ class AbstractTransformInitializer(ABC):
 
 class AbstractLinearTransformInitializer(AbstractTransformInitializer):
     """Abstract class for all linear transform initializers."""
-
     def __init__(self, out_dim_first: bool = False):
         self.out_dim_first = out_dim_first
 
@@ -451,7 +415,6 @@ class AbstractLinearTransformInitializer(AbstractTransformInitializer):
 
 class ZerosLinearTransformInitializer(AbstractLinearTransformInitializer):
     """Initialize a matrix with zeros."""
-
     def generate(self, in_dim: int, out_dim: int):
         weights = torch.zeros(in_dim, out_dim)
         return self.generate_end_hook(weights)
@@ -459,23 +422,13 @@ class ZerosLinearTransformInitializer(AbstractLinearTransformInitializer):
 
 class OnesLinearTransformInitializer(AbstractLinearTransformInitializer):
     """Initialize a matrix with ones."""
-
     def generate(self, in_dim: int, out_dim: int):
         weights = torch.ones(in_dim, out_dim)
         return self.generate_end_hook(weights)
 
 
-class RandomLinearTransformInitializer(AbstractLinearTransformInitializer):
-    """Initialize a matrix with random values."""
-
-    def generate(self, in_dim: int, out_dim: int):
-        weights = torch.rand(in_dim, out_dim)
-        return self.generate_end_hook(weights)
-
-
-class EyeLinearTransformInitializer(AbstractLinearTransformInitializer):
+class EyeTransformInitializer(AbstractLinearTransformInitializer):
     """Initialize a matrix with the largest possible identity matrix."""
-
     def generate(self, in_dim: int, out_dim: int):
         weights = torch.zeros(in_dim, out_dim)
         I = torch.eye(min(in_dim, out_dim))
@@ -485,7 +438,6 @@ class EyeLinearTransformInitializer(AbstractLinearTransformInitializer):
 
 class AbstractDataAwareLTInitializer(AbstractLinearTransformInitializer):
     """Abstract class for all data-aware linear transform initializers."""
-
     def __init__(self,
                  data: torch.Tensor,
                  noise: float = 0.0,
@@ -506,19 +458,11 @@ class AbstractDataAwareLTInitializer(AbstractLinearTransformInitializer):
 
 class PCALinearTransformInitializer(AbstractDataAwareLTInitializer):
     """Initialize a matrix with Eigenvectors from the data."""
-
     def generate(self, in_dim: int, out_dim: int):
         _, _, weights = torch.pca_lowrank(self.data, q=out_dim)
         return self.generate_end_hook(weights)
 
 
-class LiteralLinearTransformInitializer(AbstractDataAwareLTInitializer):
-    """'Generate' the provided weights."""
-
-    def generate(self, in_dim: int, out_dim: int):
-        return self.generate_end_hook(self.data)
-
-
 # Aliases - Components
 CACI = ClassAwareCompInitializer
 DACI = DataAwareCompInitializer
@@ -547,9 +491,7 @@ RRI = RandomReasoningsInitializer
 ZRI = ZerosReasoningsInitializer
 
 # Aliases - Transforms
-ELTI = Eye = EyeLinearTransformInitializer
+Eye = EyeTransformInitializer
 OLTI = OnesLinearTransformInitializer
-RLTI = RandomLinearTransformInitializer
 ZLTI = ZerosLinearTransformInitializer
 PCALTI = PCALinearTransformInitializer
-LLTI = LiteralLinearTransformInitializer

prototorch/core/losses.py

@@ -2,7 +2,7 @@
 
 import torch
 
-from prototorch.nn.activations import get_activation
+from ..nn.activations import get_activation
 
 
 # Helpers
@@ -106,31 +106,19 @@ def margin_loss(y_pred, y_true, margin=0.3):
 
 
 class GLVQLoss(torch.nn.Module):
-
-    def __init__(self,
-                 margin=0.0,
-                 transfer_fn="identity",
-                 beta=10,
-                 add_dp=False,
-                 **kwargs):
+    def __init__(self, margin=0.0, transfer_fn="identity", beta=10, **kwargs):
         super().__init__(**kwargs)
         self.margin = margin
         self.transfer_fn = get_activation(transfer_fn)
         self.beta = torch.tensor(beta)
-        self.add_dp = add_dp
 
     def forward(self, outputs, targets, plabels):
-        # mu = glvq_loss(outputs, targets, plabels)
-        dp, dm = _get_dp_dm(outputs, targets, plabels)
-        mu = (dp - dm) / (dp + dm)
-        if self.add_dp:
-            mu = mu + dp
+        mu = glvq_loss(outputs, targets, prototype_labels=plabels)
         batch_loss = self.transfer_fn(mu + self.margin, beta=self.beta)
         return batch_loss.sum()
 
 
 class MarginLoss(torch.nn.modules.loss._Loss):
-
     def __init__(self,
                  margin=0.3,
                  size_average=None,
@@ -144,7 +132,6 @@ class MarginLoss(torch.nn.modules.loss._Loss):
 
 
 class NeuralGasEnergy(torch.nn.Module):
-
     def __init__(self, lm, **kwargs):
         super().__init__(**kwargs)
         self.lm = lm
@@ -165,7 +152,6 @@ class NeuralGasEnergy(torch.nn.Module):
 
 
 class GrowingNeuralGasEnergy(NeuralGasEnergy):
-
     def __init__(self, topology_layer, **kwargs):
         super().__init__(**kwargs)
         self.topology_layer = topology_layer

prototorch/core/pooling.py

@@ -82,27 +82,23 @@ def stratified_prod_pooling(values: torch.Tensor,
 
 class StratifiedSumPooling(torch.nn.Module):
     """Thin wrapper over the `stratified_sum_pooling` function."""
-
     def forward(self, values, labels):  # pylint: disable=no-self-use
         return stratified_sum_pooling(values, labels)
 
 
 class StratifiedProdPooling(torch.nn.Module):
     """Thin wrapper over the `stratified_prod_pooling` function."""
-
     def forward(self, values, labels):  # pylint: disable=no-self-use
         return stratified_prod_pooling(values, labels)
 
 
 class StratifiedMinPooling(torch.nn.Module):
     """Thin wrapper over the `stratified_min_pooling` function."""
-
     def forward(self, values, labels):  # pylint: disable=no-self-use
         return stratified_min_pooling(values, labels)
 
 
 class StratifiedMaxPooling(torch.nn.Module):
     """Thin wrapper over the `stratified_max_pooling` function."""
-
     def forward(self, values, labels):  # pylint: disable=no-self-use
         return stratified_max_pooling(values, labels)

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/core/transforms.py

@@ -5,18 +5,17 @@ from torch.nn.parameter import Parameter
 
 from .initializers import (
     AbstractLinearTransformInitializer,
-    EyeLinearTransformInitializer,
+    EyeTransformInitializer,
 )
 
 
 class LinearTransform(torch.nn.Module):
-
     def __init__(
         self,
         in_dim: int,
         out_dim: int,
         initializer:
-        AbstractLinearTransformInitializer = EyeLinearTransformInitializer()):
+        AbstractLinearTransformInitializer = EyeTransformInitializer()):
         super().__init__()
         self.set_weights(in_dim, out_dim, initializer)
 
@@ -32,15 +31,12 @@ class LinearTransform(torch.nn.Module):
         in_dim: int,
         out_dim: int,
         initializer:
-        AbstractLinearTransformInitializer = EyeLinearTransformInitializer()):
+        AbstractLinearTransformInitializer = EyeTransformInitializer()):
         weights = initializer.generate(in_dim, out_dim)
         self._register_weights(weights)
 
     def forward(self, x):
-        return x @ self._weights
-
-    def extra_repr(self):
-        return f"weights: (shape: {tuple(self._weights.shape)})"
+        return x @ self.weights
 
 
 # Aliases

prototorch/datasets/abstract.py

@@ -20,7 +20,7 @@ class Dataset(torch.utils.data.Dataset):
     _repr_indent = 2
 
     def __init__(self, root):
-        if isinstance(root, str):
+        if isinstance(root, torch._six.string_classes):
             root = os.path.expanduser(root)
         self.root = root
 
@@ -93,7 +93,6 @@ class ProtoDataset(Dataset):
 
 class NumpyDataset(torch.utils.data.TensorDataset):
     """Create a PyTorch TensorDataset from NumPy arrays."""
-
     def __init__(self, data, targets):
         self.data = torch.Tensor(data)
         self.targets = torch.LongTensor(targets)
@@ -103,7 +102,6 @@ class NumpyDataset(torch.utils.data.TensorDataset):
 
 class CSVDataset(NumpyDataset):
     """Create a Dataset from a CSV file."""
-
     def __init__(self, filepath, target_col=-1, delimiter=',', skip_header=0):
         raw = np.genfromtxt(
             filepath,

prototorch/datasets/sklearn.py

@@ -5,18 +5,11 @@ URL:
 
 """
 
-from __future__ import annotations
-
 import warnings
-from typing import Sequence
+from typing import Sequence, Union
 
-from sklearn.datasets import (
-    load_iris,
-    make_blobs,
-    make_circles,
-    make_classification,
-    make_moons,
-)
+from sklearn.datasets import (load_iris, make_blobs, make_circles,
+                              make_classification, make_moons)
 
 from prototorch.datasets.abstract import NumpyDataset
 
@@ -42,10 +35,9 @@ class Iris(NumpyDataset):
 
     :param dims: select a subset of dimensions
     """
-
-    def __init__(self, dims: Sequence[int] | None = None):
+    def __init__(self, dims: Sequence[int] = None):
         x, y = load_iris(return_X_y=True)
-        if dims is not None:
+        if dims:
             x = x[:, dims]
         super().__init__(x, y)
 
@@ -57,20 +49,15 @@ class Blobs(NumpyDataset):
     https://scikit-learn.org/stable/datasets/sample_generators.html#sample-generators.
 
     """
-
-    def __init__(
-        self,
+    def __init__(self,
                  num_samples: int = 300,
                  num_features: int = 2,
-        seed: None | int = 0,
-    ):
-        x, y = make_blobs(
-            num_samples,
+                 seed: Union[None, int] = 0):
+        x, y = make_blobs(num_samples,
                           num_features,
                           centers=None,
                           random_state=seed,
-            shuffle=False,
-        )
+                          shuffle=False)
         super().__init__(x, y)
 
 
@@ -82,25 +69,21 @@ class Random(NumpyDataset):
 
     Note: n_classes * n_clusters_per_class <= 2**n_informative must satisfy.
     """
-
-    def __init__(
-        self,
+    def __init__(self,
                  num_samples: int = 300,
                  num_features: int = 2,
                  num_classes: int = 2,
                  num_clusters: int = 2,
-        num_informative: None | int = None,
+                 num_informative: Union[None, int] = None,
                  separation: float = 1.0,
-        seed: None | int = 0,
-    ):
+                 seed: Union[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_samples,
                                    num_features,
                                    n_informative=num_informative,
                                    n_redundant=0,
@@ -108,8 +91,7 @@ class Random(NumpyDataset):
                                    n_clusters_per_class=num_clusters,
                                    class_sep=separation,
                                    random_state=seed,
-            shuffle=False,
-        )
+                                   shuffle=False)
         super().__init__(x, y)
 
 
@@ -122,21 +104,16 @@ class Circles(NumpyDataset):
     https://scikit-learn.org/stable/modules/generated/sklearn.datasets.make_circles.html
 
     """
-
-    def __init__(
-        self,
+    def __init__(self,
                  num_samples: int = 300,
                  noise: float = 0.3,
                  factor: float = 0.8,
-        seed: None | int = 0,
-    ):
-        x, y = make_circles(
-            num_samples,
+                 seed: Union[None, int] = 0):
+        x, y = make_circles(num_samples,
                             noise=noise,
                             factor=factor,
                             random_state=seed,
-            shuffle=False,
-        )
+                            shuffle=False)
         super().__init__(x, y)
 
 
@@ -149,17 +126,12 @@ class Moons(NumpyDataset):
     https://scikit-learn.org/stable/modules/generated/sklearn.datasets.make_moons.html
 
     """
-
-    def __init__(
-        self,
+    def __init__(self,
                  num_samples: int = 300,
                  noise: float = 0.3,
-        seed: None | int = 0,
-    ):
-        x, y = make_moons(
-            num_samples,
+                 seed: Union[None, int] = 0):
+        x, y = make_moons(num_samples,
                           noise=noise,
                           random_state=seed,
-            shuffle=False,
-        )
+                          shuffle=False)
         super().__init__(x, y)

prototorch/datasets/spiral.py

@@ -9,7 +9,6 @@ def make_spiral(num_samples=500, noise=0.3):
 
     For use in Prototorch use `prototorch.datasets.Spiral` instead.
     """
-
     def get_samples(n, delta_t):
         points = []
         for i in range(n):
@@ -53,7 +52,6 @@ class Spiral(torch.utils.data.TensorDataset):
     :param num_samples: number of random samples
     :param noise: noise added to the spirals
     """
-
     def __init__(self, num_samples: int = 500, noise: float = 0.3):
         x, y = make_spiral(num_samples, noise)
         super().__init__(torch.Tensor(x), torch.LongTensor(y))

prototorch/datasets/tecator.py

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

prototorch/datasets/xor.py

@@ -13,7 +13,6 @@ def make_xor(num_samples=500):
 
 class XOR(torch.utils.data.TensorDataset):
     """Exclusive-or (XOR) dataset for binary classification."""
-
     def __init__(self, num_samples: int = 500):
         x, y = make_xor(num_samples)
         super().__init__(x, y)

prototorch/nn/wrappers.py

@@ -4,7 +4,6 @@ import torch
 
 
 class LambdaLayer(torch.nn.Module):
-
     def __init__(self, fn, name=None):
         super().__init__()
         self.fn = fn
@@ -18,7 +17,6 @@ class LambdaLayer(torch.nn.Module):
 
 
 class LossLayer(torch.nn.modules.loss._Loss):
-
     def __init__(self,
                  fn,
                  name=None,

prototorch/utils/__init__.py

@@ -1,11 +1,6 @@
-"""ProtoTorch utils module"""
+"""ProtoFlow utils module"""
 
-from .colors import (
-    get_colors,
-    get_legend_handles,
-    hex_to_rgb,
-    rgb_to_hex,
-)
+from .colors import hex_to_rgb, rgb_to_hex
 from .utils import (
     mesh2d,
     parse_data_arg,

prototorch/utils/colors.py

@@ -1,13 +1,4 @@
-"""ProtoTorch color utilities"""
-
-import matplotlib.lines as mlines
-import torch
-from matplotlib import cm
-from matplotlib.colors import (
-    Normalize,
-    to_hex,
-    to_rgb,
-)
+"""ProtoFlow color utilities"""
 
 
 def hex_to_rgb(hex_values):
@@ -22,39 +13,3 @@ def rgb_to_hex(rgb_values):
     for v in rgb_values:
         c = "%02x%02x%02x" % tuple(v)
         yield c
-
-
-def get_colors(vmax, vmin=0, cmap="viridis"):
-    cmap = cm.get_cmap(cmap)
-    colornorm = Normalize(vmin=vmin, vmax=vmax)
-    colors = dict()
-    for c in range(vmin, vmax + 1):
-        colors[c] = to_hex(cmap(colornorm(c)))
-    return colors
-
-
-def get_legend_handles(colors, labels, marker="dots", zero_indexed=False):
-    handles = list()
-    for color, label in zip(colors.values(), labels):
-        if marker == "dots":
-            handle = mlines.Line2D(
-                xdata=[],
-                ydata=[],
-                label=label,
-                color="white",
-                markerfacecolor=color,
-                marker="o",
-                markersize=10,
-                markeredgecolor="k",
-            )
-        else:
-            handle = mlines.Line2D(
-                xdata=[],
-                ydata=[],
-                label=label,
-                color=color,
-                marker="",
-                markersize=15,
-            )
-        handles.append(handle)
-    return handles

prototorch/utils/utils.py

@@ -1,11 +1,10 @@
-"""ProtoTorch utilities"""
+"""ProtoFlow utilities"""
 
 import warnings
 from typing import (
     Dict,
     Iterable,
     List,
-    Optional,
     Union,
 )
 
@@ -14,32 +13,6 @@ import torch
 from torch.utils.data import DataLoader, Dataset
 
 
-def generate_mesh(
-    minima: torch.TensorType,
-    maxima: torch.TensorType,
-    border: float = 1.0,
-    resolution: int = 100,
-    device: Optional[torch.device] = None,
-):
-    # Apply Border
-    ptp = maxima - minima
-    shift = border * ptp
-    minima -= shift
-    maxima += shift
-
-    # Generate Mesh
-    minima = minima.to(device).unsqueeze(1)
-    maxima = maxima.to(device).unsqueeze(1)
-
-    factors = torch.linspace(0, 1, resolution, device=device)
-    marginals = factors * maxima + ((1 - factors) * minima)
-
-    single_dimensions = torch.meshgrid(*marginals)
-    mesh_input = torch.stack([dim.ravel() for dim in single_dimensions], dim=1)
-
-    return mesh_input, single_dimensions
-
-
 def mesh2d(x=None, border: float = 1.0, resolution: int = 100):
     if x is not None:
         x_shift = border * np.ptp(x[:, 0])
@@ -56,15 +29,14 @@ def mesh2d(x=None, border: float = 1.0, resolution: int = 100):
 
 
 def distribution_from_list(list_dist: List[int],
-                           clabels: Optional[Iterable[int]] = None):
+                           clabels: Iterable[int] = None):
     clabels = clabels or list(range(len(list_dist)))
     distribution = dict(zip(clabels, list_dist))
     return distribution
 
 
-def parse_distribution(
-        user_distribution,
-        clabels: Optional[Iterable[int]] = None) -> Dict[int, int]:
+def parse_distribution(user_distribution,
+                       clabels: Iterable[int] = None) -> Dict[int, int]:
     """Parse user-provided distribution.
 
     Return a dictionary with integer keys that represent the class labels and

setup.cfg

@@ -4,7 +4,6 @@ disable =
     too-few-public-methods,
     fixme,
 
-
 [pycodestyle]
 max-line-length = 79
 

setup.py

@@ -15,22 +15,21 @@ 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", encoding="utf-8") as fh:
+with open("README.md", "r") as fh:
     long_description = fh.read()
 
 INSTALL_REQUIRES = [
-    "torch>=2.0.0",
-    "torchvision",
-    "numpy",
-    "scikit-learn",
-    "matplotlib",
+    "torch>=1.3.1",
+    "torchvision>=0.7.1",
+    "numpy>=1.9.1",
+    "sklearn",
 ]
 DATASETS = [
     "requests",
     "tqdm",
 ]
 DEV = [
-    "bump2version",
+    "bumpversion",
     "pre-commit",
 ]
 DOCS = [
@@ -41,17 +40,18 @@ DOCS = [
     "sphinx-autodoc-typehints",
 ]
 EXAMPLES = [
+    "matplotlib",
     "torchinfo",
 ]
 TESTS = [
-    "flake8",
+    "pytest-cov",
     "pytest",
 ]
 ALL = DATASETS + DEV + DOCS + EXAMPLES + TESTS
 
 setup(
     name="prototorch",
-    version="0.7.6",
+    version="0.7.1",
     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=">=3.8",
+    python_requires=">=3.6",
     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 :: 3.6",
+        "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_core.py

@@ -245,20 +245,20 @@ def test_random_reasonings_init_channels_not_first():
 
 # Transform initializers
 def test_eye_transform_init_square():
-    t = pt.initializers.EyeLinearTransformInitializer()
+    t = pt.initializers.EyeTransformInitializer()
     I = t.generate(3, 3)
     assert torch.allclose(I, torch.eye(3))
 
 
 def test_eye_transform_init_narrow():
-    t = pt.initializers.EyeLinearTransformInitializer()
+    t = pt.initializers.EyeTransformInitializer()
     actual = t.generate(3, 2)
     desired = torch.Tensor([[1, 0], [0, 1], [0, 0]])
     assert torch.allclose(actual, desired)
 
 
 def test_eye_transform_init_wide():
-    t = pt.initializers.EyeLinearTransformInitializer()
+    t = pt.initializers.EyeTransformInitializer()
     actual = t.generate(2, 3)
     desired = torch.Tensor([[1, 0, 0], [0, 1, 0]])
     assert torch.allclose(actual, desired)
@@ -404,7 +404,6 @@ def test_glvq_loss_one_hot_unequal():
 
 # Activations
 class TestActivations(unittest.TestCase):
-
     def setUp(self):
         self.flist = ["identity", "sigmoid_beta", "swish_beta"]
         self.x = torch.randn(1024, 1)
@@ -419,7 +418,6 @@ class TestActivations(unittest.TestCase):
             self.assertTrue(iscallable)
 
     def test_callable_deserialization(self):
-
         def dummy(x, **kwargs):
             return x
 
@@ -464,7 +462,6 @@ class TestActivations(unittest.TestCase):
 
 # Competitions
 class TestCompetitions(unittest.TestCase):
-
     def setUp(self):
         pass
 
@@ -518,7 +515,6 @@ class TestCompetitions(unittest.TestCase):
 
 # Pooling
 class TestPooling(unittest.TestCase):
-
     def setUp(self):
         pass
 
@@ -619,7 +615,6 @@ class TestPooling(unittest.TestCase):
 
 # Distances
 class TestDistances(unittest.TestCase):
-
     def setUp(self):
         self.nx, self.mx = 32, 2048
         self.ny, self.my = 8, 2048

tests/test_datasets.py

@@ -1,6 +1,7 @@
 """ProtoTorch datasets test suite"""
 
 import os
+import shutil
 import unittest
 
 import numpy as np
@@ -11,7 +12,6 @@ from prototorch.datasets.abstract import Dataset, ProtoDataset
 
 
 class TestAbstract(unittest.TestCase):
-
     def setUp(self):
         self.ds = Dataset("./artifacts")
 
@@ -28,7 +28,6 @@ class TestAbstract(unittest.TestCase):
 
 
 class TestProtoDataset(unittest.TestCase):
-
     def test_download(self):
         with self.assertRaises(NotImplementedError):
             _ = ProtoDataset("./artifacts", download=True)
@@ -39,7 +38,6 @@ class TestProtoDataset(unittest.TestCase):
 
 
 class TestNumpyDataset(unittest.TestCase):
-
     def test_list_init(self):
         ds = pt.datasets.NumpyDataset([1], [1])
         self.assertEqual(len(ds), 1)
@@ -52,7 +50,6 @@ class TestNumpyDataset(unittest.TestCase):
 
 
 class TestCSVDataset(unittest.TestCase):
-
     def setUp(self):
         data = np.random.rand(100, 4)
         targets = np.random.randint(2, size=(100, 1))
@@ -70,14 +67,12 @@ class TestCSVDataset(unittest.TestCase):
 
 
 class TestSpiral(unittest.TestCase):
-
     def test_init(self):
         ds = pt.datasets.Spiral(num_samples=10)
         self.assertEqual(len(ds), 10)
 
 
 class TestIris(unittest.TestCase):
-
     def setUp(self):
         self.ds = pt.datasets.Iris()
 
@@ -93,28 +88,24 @@ class TestIris(unittest.TestCase):
 
 
 class TestBlobs(unittest.TestCase):
-
     def test_size(self):
         ds = pt.datasets.Blobs(num_samples=10)
         self.assertEqual(len(ds), 10)
 
 
 class TestRandom(unittest.TestCase):
-
     def test_size(self):
         ds = pt.datasets.Random(num_samples=10)
         self.assertEqual(len(ds), 10)
 
 
 class TestCircles(unittest.TestCase):
-
     def test_size(self):
         ds = pt.datasets.Circles(num_samples=10)
         self.assertEqual(len(ds), 10)
 
 
 class TestMoons(unittest.TestCase):
-
     def test_size(self):
         ds = pt.datasets.Moons(num_samples=10)
         self.assertEqual(len(ds), 10)