Merge branch 'master' into kernel_distances

.bumpversion.cfg

@@ -1,20 +1,11 @@
 [bumpversion]
-current_version = 0.3.0-dev0
+current_version = 0.4.2
 commit = True
 tag = True
-parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)
 serialize = 
-	{major}.{minor}.{patch}-{release}{build}
 	{major}.{minor}.{patch}
 
-[bumpversion:part:release]
-optional_value = prod
-first_value = dev
-values = 
-	dev
-	rc
-	prod
-
 [bumpversion:file:setup.py]
 
 [bumpversion:file:./prototorch/__init__.py]

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,31 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Install Prototorch by running '...'
+2. Run script '...'
+3. See errors
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. Ubuntu 20.10]
+ - Prototorch Version: [e.g. v0.4.0]
+ - Python Version: [e.g. 3.9.5]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/pythonapp.yml

@@ -23,10 +23,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install .
-    - name: Install extras
-      run: |
-        pip install -r requirements.txt
+        pip install .[all]
     - name: Lint with flake8
       run: |
         pip install flake8

.travis.yml

@@ -5,10 +5,8 @@ python: 3.8
 cache:
   directories:
   - "./tests/artifacts"
-  # - "$HOME/.prototorch/datasets"
 install:
-- pip install . --progress-bar off
-- pip install -r requirements.txt
+- pip install .[all] --progress-bar off
 
 # Generate code coverage report
 script:
@@ -25,8 +23,8 @@ deploy:
   password:
     secure: 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
   on:
-  tags: true
-  skip_existing: true
+    tags: true
+    skip_existing: true
 
 # The password is encrypted with:
 # `cd prototorch && travis encrypt your-pypi-api-token --add deploy.password`

README.md

@@ -31,15 +31,15 @@ To also install the extras, use
 pip install -U prototorch[all]
 ```
 
-*Note: If you're using [ZSH](https://www.zsh.org/), the square brackets `[ ]`
-have to be escaped like so: `\[\]`, making the install command `pip install -U
-prototorch\[all\]`.*
+*Note: If you're using [ZSH](https://www.zsh.org/) (which is also the default
+shell on MacOS now), the square brackets `[ ]` have to be escaped like so:
+`\[\]`, making the install command `pip install -U prototorch\[all\]`.*
 
 To install the bleeding-edge features and improvements:
 ```bash
 git clone https://github.com/si-cim/prototorch.git
-git checkout dev
 cd prototorch
+git checkout dev
 pip install -e .[all]
 ```
 

docs/source/conf.py

@@ -23,7 +23,7 @@ author = "Jensun Ravichandran"
 
 # The full version, including alpha/beta/rc tags
 #
-release = "0.3.0-dev0"
+release = "0.4.2"
 
 # -- General configuration ---------------------------------------------------
 

examples/new_components.py

@@ -1,6 +1,9 @@
-#
+"""This example script shows the usage of the new components architecture.
+
+Serialization/deserialization also works as expected.
+"""
+
 # DATASET
-#
 import torch
 from sklearn.datasets import load_iris
 from sklearn.preprocessing import StandardScaler
@@ -15,9 +18,7 @@ x_train = torch.Tensor(x_train)
 y_train = torch.Tensor(y_train)
 num_classes = len(torch.unique(y_train))
 
-#
 # CREATE NEW COMPONENTS
-#
 from prototorch.components import *
 from prototorch.components.initializers import *
 
@@ -32,9 +33,7 @@ components = ReasoningComponents(
     (3, 6), StratifiedSelectionInitializer(x_train, y_train))
 print(components())
 
-#
 # TEST SERIALIZATION
-#
 import io
 
 save = io.BytesIO()
@@ -52,8 +51,8 @@ serialized_prototypes = torch.load(save)
 
 assert torch.all(prototypes.components == serialized_prototypes.components
                  ), "Serialization of Components failed."
-assert torch.all(prototypes.labels == serialized_prototypes.labels
-                 ), "Serialization of Components failed."
+assert torch.all(prototypes.component_labels == serialized_prototypes.
+                 component_labels), "Serialization of Components failed."
 
 save = io.BytesIO()
 torch.save(components, save)

prototorch/__init__.py

@@ -1,9 +1,7 @@
 """ProtoTorch package."""
 
-# #############################################
 # Core Setup
-# #############################################
-__version__ = "0.3.0-dev0"
+__version__ = "0.4.2"
 
 __all_core__ = [
     "datasets",
@@ -11,9 +9,9 @@ __all_core__ = [
     "modules",
 ]
 
-# #############################################
+from .datasets import *
+
 # Plugin Loader
-# #############################################
 import pkgutil
 
 import pkg_resources

prototorch/components/__init__.py

@@ -1,11 +1,2 @@
-from prototorch.components.components import (
-    Components,
-    LabeledComponents,
-    ReasoningComponents,
-)
-
-__all__ = [
-    "Components",
-    "LabeledComponents",
-    "ReasoningComponents",
-]
+from prototorch.components.components import *
+from prototorch.components.initializers import *

prototorch/components/components.py

@@ -1,48 +1,52 @@
 """ProtoTorch components modules."""
 
 import warnings
+from typing import Tuple
 
 import torch
+from prototorch.components.initializers import (ClassAwareInitializer,
+                                                ComponentsInitializer,
+                                                EqualLabelsInitializer,
+                                                UnequalLabelsInitializer,
+                                                ZeroReasoningsInitializer)
+from prototorch.functions.initializers import get_initializer
 from torch.nn.parameter import Parameter
 
-from prototorch.components.initializers import (
-    EqualLabelInitializer,
-    ZeroReasoningsInitializer,
-)
-
 
 class Components(torch.nn.Module):
-    """
-    Components is a set of learnable Tensors.
-    """
-    def __init__(
-        self,
-        number_of_components=None,
-        initializer=None,
-        *,
-        initialized_components=None,
-        dtype=torch.float32,
-    ):
+    """Components is a set of learnable Tensors."""
+    def __init__(self,
+                 number_of_components=None,
+                 initializer=None,
+                 *,
+                 initialized_components=None,
+                 dtype=torch.float32):
         super().__init__()
 
         # Ignore all initialization settings if initialized_components is given.
         if initialized_components is not None:
             self._components = Parameter(initialized_components)
             if number_of_components is not None or initializer is not None:
-                warnings.warn(
-                    "Arguments ignored while initializing Components")
+                wmsg = "Arguments ignored while initializing Components"
+                warnings.warn(wmsg)
         else:
             self._initialize_components(number_of_components, initializer)
 
+    def _precheck_initializer(self, initializer):
+        if not isinstance(initializer, ComponentsInitializer):
+            emsg = f"`initializer` has to be some subtype of " \
+                f"{ComponentsInitializer}. " \
+                f"You have provided: {initializer=} instead."
+            raise TypeError(emsg)
+
     def _initialize_components(self, number_of_components, initializer):
+        self._precheck_initializer(initializer)
         self._components = Parameter(
             initializer.generate(number_of_components))
 
     @property
     def components(self):
-        """
-        Tensor containing the component tensors.
-        """
+        """Tensor containing the component tensors."""
         return self._components.detach().cpu()
 
     def forward(self):
@@ -53,12 +57,12 @@ class Components(torch.nn.Module):
 
 
 class LabeledComponents(Components):
-    """
-    LabeledComponents generate a set of components and a set of labels.
+    """LabeledComponents generate a set of components and a set of labels.
+
     Every Component has a label assigned.
     """
     def __init__(self,
-                 labels=None,
+                 distribution=None,
                  initializer=None,
                  *,
                  initialized_components=None):
@@ -66,22 +70,32 @@ class LabeledComponents(Components):
             super().__init__(initialized_components=initialized_components[0])
             self._labels = initialized_components[1]
         else:
-            self._initialize_labels(labels, initializer)
+            self._initialize_labels(distribution)
             super().__init__(number_of_components=len(self._labels),
                              initializer=initializer)
 
-    def _initialize_labels(self, labels, initializer):
-        if type(labels) == tuple:
-            num_classes, prototypes_per_class = labels
-            labels = EqualLabelInitializer(num_classes, prototypes_per_class)
+    def _initialize_components(self, number_of_components, initializer):
+        if isinstance(initializer, ClassAwareInitializer):
+            self._precheck_initializer(initializer)
+            self._components = Parameter(
+                initializer.generate(number_of_components, self.distribution))
+        else:
+            super()._initialize_components(self, number_of_components,
+                                           initializer)
 
+    def _initialize_labels(self, distribution):
+        if type(distribution) == tuple:
+            num_classes, prototypes_per_class = distribution
+            labels = EqualLabelsInitializer(num_classes, prototypes_per_class)
+        elif type(distribution) == list:
+            labels = UnequalLabelsInitializer(distribution)
+
+        self.distribution = labels.distribution
         self._labels = labels.generate()
 
     @property
-    def labels(self):
-        """
-        Tensor containing the component tensors.
-        """
+    def component_labels(self):
+        """Tensor containing the component tensors."""
         return self._labels.detach().cpu()
 
     def forward(self):
@@ -89,16 +103,19 @@ class LabeledComponents(Components):
 
 
 class ReasoningComponents(Components):
-    """
-    ReasoningComponents generate a set of components and a set of reasoning matrices.
+    """ReasoningComponents generate a set of components and a set of reasoning matrices.
+
     Every Component has a reasoning matrix assigned.
 
-    A reasoning matrix is a Nx2 matrix, where N is the number of Classes.
-    The first element is called positive reasoning :math:`p`, the second negative reasoning :math:`n`.
-    A components can reason in favour (positive) of a class, against (negative) a class or not at all (neutral).
+    A reasoning matrix is a Nx2 matrix, where N is the number of Classes. The
+    first element is called positive reasoning :math:`p`, the second negative
+    reasoning :math:`n`. A components can reason in favour (positive) of a
+    class, against (negative) a class or not at all (neutral).
+
+    It holds that :math:`0 \leq n \leq 1`, :math:`0 \leq p \leq 1` and :math:`0
+    \leq n+p \leq 1`. Therefore :math:`n` and :math:`p` are two elements of a
+    three element probability distribution.
 
-    It holds that :math:`0 \leq n \leq 1`, :math:`0 \leq p \leq 1` and :math:`0 \leq n+p \leq 1`.
-    Therefore :math:`n` and  :math:`p` are two elements of a three element probability distribution.
     """
     def __init__(self,
                  reasonings=None,
@@ -123,10 +140,10 @@ class ReasoningComponents(Components):
 
     @property
     def reasonings(self):
-        """
-        Returns Reasoning Matrix.
+        """Returns Reasoning Matrix.
 
         Dimension NxCx2
+
         """
         return self._reasonings.detach().cpu()
 

prototorch/components/initializers.py

@@ -1,12 +1,33 @@
+"""ProtoTroch Initializers."""
+import warnings
 from collections.abc import Iterable
+from itertools import chain
 
 import torch
+from torch.utils.data import DataLoader, Dataset
+
+
+def parse_init_arg(arg):
+    if isinstance(arg, Dataset):
+        data, labels = next(iter(DataLoader(arg, batch_size=len(arg))))
+        # data = data.view(len(arg), -1)  # flatten
+    else:
+        data, labels = arg
+        if not isinstance(data, torch.Tensor):
+            wmsg = f"Converting data to {torch.Tensor}."
+            warnings.warn(wmsg)
+            data = torch.Tensor(data)
+        if not isinstance(labels, torch.Tensor):
+            wmsg = f"Converting labels to {torch.Tensor}."
+            warnings.warn(wmsg)
+            labels = torch.Tensor(labels)
+    return data, labels
 
 
 # Components
-class ComponentsInitializer:
+class ComponentsInitializer(object):
     def generate(self, number_of_components):
-        pass
+        raise NotImplementedError("Subclasses should implement this!")
 
 
 class DimensionAwareInitializer(ComponentsInitializer):
@@ -39,7 +60,7 @@ class UniformInitializer(DimensionAwareInitializer):
 
     def generate(self, length):
         gen_dims = (length, ) + self.components_dims
-        return torch.FloatTensor(gen_dims).uniform_(self.min, self.max)
+        return torch.ones(gen_dims).uniform_(self.min, self.max)
 
 
 class PositionAwareInitializer(ComponentsInitializer):
@@ -62,58 +83,95 @@ class MeanInitializer(PositionAwareInitializer):
 
 
 class ClassAwareInitializer(ComponentsInitializer):
-    def __init__(self, positions, classes):
+    def __init__(self, arg):
         super().__init__()
-        self.data = positions
-        self.classes = classes
+        data, labels = parse_init_arg(arg)
+        self.data = data
+        self.labels = labels
 
-        self.names = torch.unique(self.classes)
-        self.num_classes = len(self.names)
+        self.clabels = torch.unique(self.labels)
+        self.num_classes = len(self.clabels)
+
+    def _get_samples_from_initializer(self, length, dist):
+        if not dist:
+            per_class = length // self.num_classes
+            dist = self.num_classes * [per_class]
+        samples_list = [
+            init.generate(n) for init, n in zip(self.initializers, dist)
+        ]
+        return torch.vstack(samples_list)
 
 
 class StratifiedMeanInitializer(ClassAwareInitializer):
-    def __init__(self, positions, classes):
-        super().__init__(positions, classes)
+    def __init__(self, arg):
+        super().__init__(arg)
 
         self.initializers = []
-        for name in self.names:
-            class_data = self.data[self.classes == name]
+        for clabel in self.clabels:
+            class_data = self.data[self.labels == clabel]
             class_initializer = MeanInitializer(class_data)
             self.initializers.append(class_initializer)
 
-    def generate(self, length):
-        per_class = length // self.num_classes
-        return torch.vstack(
-            [init.generate(per_class) for init in self.initializers])
+    def generate(self, length, dist=[]):
+        samples = self._get_samples_from_initializer(length, dist)
+        return samples
 
 
 class StratifiedSelectionInitializer(ClassAwareInitializer):
-    def __init__(self, positions, classes):
-        super().__init__(positions, classes)
+    def __init__(self, arg, *, noise=None):
+        super().__init__(arg)
+        self.noise = noise
 
         self.initializers = []
-        for name in self.names:
-            class_data = self.data[self.classes == name]
+        for clabel in self.clabels:
+            class_data = self.data[self.labels == clabel]
             class_initializer = SelectionInitializer(class_data)
             self.initializers.append(class_initializer)
 
-    def generate(self, length):
-        per_class = length // self.num_classes
-        return torch.vstack(
-            [init.generate(per_class) for init in self.initializers])
+    def add_noise(self, x):
+        """Shifts some dimensions of the data randomly."""
+        n1 = torch.rand_like(x)
+        n2 = torch.rand_like(x)
+        mask = torch.bernoulli(n1) - torch.bernoulli(n2)
+        return x + (self.noise * mask)
+
+    def generate(self, length, dist=[]):
+        samples = self._get_samples_from_initializer(length, dist)
+        if self.noise is not None:
+            # samples = self.add_noise(samples)
+            samples = samples + self.noise
+        return samples
 
 
 # Labels
 class LabelsInitializer:
     def generate(self):
-        pass
+        raise NotImplementedError("Subclasses should implement this!")
 
 
-class EqualLabelInitializer(LabelsInitializer):
+class UnequalLabelsInitializer(LabelsInitializer):
+    def __init__(self, dist):
+        self.dist = dist
+
+    @property
+    def distribution(self):
+        return self.dist
+
+    def generate(self):
+        clabels = range(len(self.dist))
+        labels = list(chain(*[[i] * n for i, n in zip(clabels, self.dist)]))
+        return torch.tensor(labels)
+
+
+class EqualLabelsInitializer(LabelsInitializer):
     def __init__(self, classes, per_class):
         self.classes = classes
         self.per_class = per_class
 
+    @property
+    def distribution(self):
+        return self.classes * [self.per_class]
+
     def generate(self):
         return torch.arange(self.classes).repeat(self.per_class, 1).T.flatten()
 
@@ -121,7 +179,7 @@ class EqualLabelInitializer(LabelsInitializer):
 # Reasonings
 class ReasoningsInitializer:
     def generate(self, length):
-        pass
+        raise NotImplementedError("Subclasses should implement this!")
 
 
 class ZeroReasoningsInitializer(ReasoningsInitializer):
@@ -131,3 +189,9 @@ class ZeroReasoningsInitializer(ReasoningsInitializer):
 
     def generate(self):
         return torch.zeros((self.length, self.classes, 2))
+
+
+# Aliases
+SSI = StratifiedSampleInitializer = StratifiedSelectionInitializer
+SMI = StratifiedMeanInitializer
+Random = RandomInitializer = UniformInitializer

prototorch/datasets/__init__.py

@@ -1,7 +1,11 @@
 """ProtoTorch datasets."""
 
+from .abstract import NumpyDataset
+from .spiral import Spiral
 from .tecator import Tecator
 
 __all__ = [
+    "NumpyDataset",
+    "Spiral",
     "Tecator",
 ]

prototorch/datasets/abstract.py

@@ -13,6 +13,7 @@ import torch
 
 
 class NumpyDataset(torch.utils.data.TensorDataset):
+    """Create a PyTorch TensorDataset from NumPy arrays."""
     def __init__(self, *arrays):
         tensors = [torch.Tensor(arr) for arr in arrays]
         super().__init__(*tensors)

prototorch/datasets/spiral.py

@@ -0,0 +1,33 @@
+"""Spiral dataset for binary classification."""
+
+import numpy as np
+import torch
+
+
+def make_spiral(n_samples=500, noise=0.3):
+    def get_samples(n, delta_t):
+        points = []
+        for i in range(n):
+            r = i / n_samples * 5
+            t = 1.75 * i / n * 2 * np.pi + delta_t
+            x = r * np.sin(t) + np.random.rand(1) * noise
+            y = r * np.cos(t) + np.random.rand(1) * noise
+            points.append([x, y])
+        return points
+
+    n = n_samples // 2
+    positive = get_samples(n=n, delta_t=0)
+    negative = get_samples(n=n, delta_t=np.pi)
+    x = np.concatenate(
+        [np.array(positive).reshape(n, -1),
+         np.array(negative).reshape(n, -1)],
+        axis=0)
+    y = np.concatenate([np.zeros(n), np.ones(n)])
+    return x, y
+
+
+class Spiral(torch.utils.data.TensorDataset):
+    """Spiral dataset for binary classification."""
+    def __init__(self, n_samples=500, noise=0.3):
+        x, y = make_spiral(n_samples, noise)
+        super().__init__(torch.Tensor(x), torch.LongTensor(y))

prototorch/datasets/tecator.py

@@ -52,7 +52,7 @@ class Tecator(ProtoDataset):
     """
 
     _resources = [
-        ("1MMuUK8V41IgNpnPDbg3E-QAL6wlErTk0",
+        ("1P9WIYnyxFPh6f1vqAbnKfK8oYmUgyV83",
          "ba5607c580d0f91bb27dc29d13c2f8df"),
     ]  # (google_storage_id, md5hash)
     classes = ["0 - low_fat", "1 - high_fat"]

prototorch/functions/activations.py

@@ -16,40 +16,43 @@ def register_activation(function):
 
 @register_activation
 # @torch.jit.script
-def identity(x, beta=torch.tensor(0)):
+def identity(x, beta=0.0):
     """Identity activation function.
 
     Definition:
     :math:`f(x) = x`
+
+    Keyword Arguments:
+        beta (`float`): Ignored.
     """
     return x
 
 
 @register_activation
 # @torch.jit.script
-def sigmoid_beta(x, beta=torch.tensor(10)):
+def sigmoid_beta(x, beta=10.0):
     r"""Sigmoid activation function with scaling.
 
     Definition:
     :math:`f(x) = \frac{1}{1 + e^{-\beta x}}`
 
     Keyword Arguments:
-        beta (`torch.tensor`): Scaling parameter :math:`\beta`
+        beta (`float`): Scaling parameter :math:`\beta`
     """
-    out = torch.reciprocal(1.0 + torch.exp(-int(beta.item()) * x))
+    out = 1.0 / (1.0 + torch.exp(-1.0 * beta * x))
     return out
 
 
 @register_activation
 # @torch.jit.script
-def swish_beta(x, beta=torch.tensor(10)):
+def swish_beta(x, beta=10.0):
     r"""Swish activation function with scaling.
 
     Definition:
     :math:`f(x) = \frac{x}{1 + e^{-\beta x}}`
 
     Keyword Arguments:
-        beta (`torch.tensor`): Scaling parameter :math:`\beta`
+        beta (`float`): Scaling parameter :math:`\beta`
     """
     out = x * sigmoid_beta(x, beta=beta)
     return out

prototorch/functions/losses.py

@@ -3,12 +3,19 @@
 import torch
 
 
-def _get_dp_dm(distances, targets, plabels):
-    matcher = torch.eq(targets.unsqueeze(dim=1), plabels)
-    if plabels.ndim == 2:
+def _get_matcher(targets, labels):
+    """Returns a boolean tensor."""
+    matcher = torch.eq(targets.unsqueeze(dim=1), labels)
+    if labels.ndim == 2:
         # if the labels are one-hot vectors
         nclasses = targets.size()[1]
         matcher = torch.eq(torch.sum(matcher, dim=-1), nclasses)
+    return matcher
+
+
+def _get_dp_dm(distances, targets, plabels):
+    """Returns the d+ and d- values for a batch of distances."""
+    matcher = _get_matcher(targets, plabels)
     not_matcher = torch.bitwise_not(matcher)
 
     inf = torch.full_like(distances, fill_value=float("inf"))
@@ -24,3 +31,26 @@ def glvq_loss(distances, target_labels, prototype_labels):
     dp, dm = _get_dp_dm(distances, target_labels, prototype_labels)
     mu = (dp - dm) / (dp + dm)
     return mu
+
+
+def lvq1_loss(distances, target_labels, prototype_labels):
+    """LVQ1 loss function with support for one-hot labels.
+
+    See Section 4 [Sado&Yamada]
+    https://papers.nips.cc/paper/1995/file/9c3b1830513cc3b8fc4b76635d32e692-Paper.pdf
+    """
+    dp, dm = _get_dp_dm(distances, target_labels, prototype_labels)
+    mu = dp
+    mu[dp > dm] = -dm[dp > dm]
+    return mu
+
+
+def lvq21_loss(distances, target_labels, prototype_labels):
+    """LVQ2.1 loss function with support for one-hot labels.
+    
+    See Section 4 [Sado&Yamada]
+    https://papers.nips.cc/paper/1995/file/9c3b1830513cc3b8fc4b76635d32e692-Paper.pdf
+    """
+    dp, dm = _get_dp_dm(distances, target_labels, prototype_labels)
+    mu = dp - dm
+    return mu

requirements.txt

@@ -1,5 +0,0 @@
-matplotlib==3.1.2
-pytest==5.3.4
-requests==2.22.0
-codecov==2.0.22
-tqdm==4.44.1

setup.py

@@ -21,27 +21,28 @@ INSTALL_REQUIRES = [
     "torchvision>=0.5.0",
     "numpy>=1.9.1",
 ]
+DATASETS = [
+    "requests",
+    "tqdm",
+]
+DEV = ["bumpversion"]
 DOCS = [
     "recommonmark",
     "sphinx",
     "sphinx_rtd_theme",
     "sphinxcontrib-katex",
 ]
-DATASETS = [
-    "requests",
-    "tqdm",
-]
 EXAMPLES = [
     "sklearn",
     "matplotlib",
     "torchinfo",
 ]
-TESTS = ["pytest"]
-ALL = DOCS + DATASETS + EXAMPLES + TESTS
+TESTS = ["codecov", "pytest"]
+ALL = DATASETS + DEV + DOCS + EXAMPLES + TESTS
 
 setup(
     name="prototorch",
-    version="0.3.0-dev0",
+    version="0.4.2",
     description="Highly extensible, GPU-supported "
     "Learning Vector Quantization (LVQ) toolbox "
     "built using PyTorch and its nn API.",
@@ -71,6 +72,7 @@ setup(
         "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
         "Operating System :: OS Independent",
         "Topic :: Scientific/Engineering :: Artificial Intelligence",
         "Topic :: Software Development :: Libraries",

tests/test_functions.py

@@ -57,7 +57,7 @@ class TestActivations(unittest.TestCase):
         self.assertIsNone(mismatch)
 
     def test_sigmoid_beta1(self):
-        actual = activations.sigmoid_beta(self.x, beta=torch.tensor(1))
+        actual = activations.sigmoid_beta(self.x, beta=1.0)
         desired = torch.sigmoid(self.x)
         mismatch = np.testing.assert_array_almost_equal(actual,
                                                         desired,
@@ -65,7 +65,7 @@ class TestActivations(unittest.TestCase):
         self.assertIsNone(mismatch)
 
     def test_swish_beta1(self):
-        actual = activations.swish_beta(self.x, beta=torch.tensor(1))
+        actual = activations.swish_beta(self.x, beta=1.0)
         desired = self.x * torch.sigmoid(self.x)
         mismatch = np.testing.assert_array_almost_equal(actual,
                                                         desired,

tox.ini

@@ -1,15 +0,0 @@
-# tox (https://tox.readthedocs.io/) is a tool for running tests
-# in multiple virtualenvs. This configuration file will run the
-# test suite on all supported python versions. To use it, "pip install tox"
-# and then run "tox" from this directory.
-
-[tox]
-envlist = py36,py37,py38
-
-[testenv]
-deps =
-    pytest
-    coverage
-commands =
-    pip install -e .
-    coverage run -m pytest