ci: cache test IV

Classes are used as common interface and connection to pytorch.

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.6.0
+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

.github/ISSUE_TEMPLATE/bug_report.md

@@ -10,21 +10,28 @@ 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 '...'
+**Steps to reproduce the behavior**
+1. ...
+2. Run script '...' or this snippet:
+```python
+import prototorch as pt
+
+...
+```
 3. See errors
 
 **Expected behavior**
 A clear and concise description of what you expected to happen.
 
+**Observed behavior**
+A clear and concise description of what actually happened.
+
 **Screenshots**
 If applicable, add screenshots to help explain your problem.
 
-**Desktop (please complete the following information):**
+**System and version information**
 - OS: [e.g. Ubuntu 20.10]
-- Prototorch Version: [e.g. v0.4.0]
+- ProtoTorch Version: [e.g. 0.4.0]
 - Python Version: [e.g. 3.9.5]
 
 **Additional context**

.travis.yml

@@ -1,36 +0,0 @@
-dist: bionic
-sudo: false
-language: python
-python: 3.9
-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
-deploy:
-  provider: pypi
-  username: __token__
-  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.

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'
+        }
+        }
+      }
+    }
+  }
+}

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 = "0.6.0"
+release = "0.7.1"
 
 # -- General configuration ---------------------------------------------------
 

prototorch/__init__.py

@@ -22,7 +22,7 @@ from .core import (
 )
 
 # Core Setup
-__version__ = "0.6.0"
+__version__ = "0.7.1"
 
 __all_core__ = [
     "competitions",

prototorch/core/competitions.py

@@ -48,7 +48,7 @@ class WTAC(torch.nn.Module):
     Thin wrapper over the `wtac` function.
 
     """
-    def forward(self, distances, labels):
+    def forward(self, distances, labels):  # pylint: disable=no-self-use
         return wtac(distances, labels)
 
 
@@ -58,7 +58,7 @@ class LTAC(torch.nn.Module):
     Thin wrapper over the `wtac` function.
 
     """
-    def forward(self, probs, labels):
+    def forward(self, probs, labels):  # pylint: disable=no-self-use
         return wtac(-1.0 * probs, labels)
 
 
@@ -85,5 +85,5 @@ class CBCC(torch.nn.Module):
     Thin wrapper over the `cbcc` function.
 
     """
-    def forward(self, detections, reasonings):
+    def forward(self, detections, reasonings):  # pylint: disable=no-self-use
         return cbcc(detections, reasonings)

prototorch/core/components.py

@@ -253,8 +253,10 @@ class Reasonings(torch.nn.Module):
         self,
         distribution: Union[dict, list, tuple],
         initializer:
-        AbstractReasoningsInitializer = RandomReasoningsInitializer()):
+        AbstractReasoningsInitializer = RandomReasoningsInitializer(),
+    ):
         super().__init__()
+        self.add_reasonings(distribution, initializer)
 
     @property
     def num_classes(self):

prototorch/core/distances.py

@@ -41,9 +41,6 @@ def euclidean_distance_v2(x, y):
     # batch diagonal. See:
     # https://pytorch.org/docs/stable/generated/torch.diagonal.html
     distances = torch.diagonal(pairwise_distances, dim1=-2, dim2=-1)
-    # print(f"{diff.shape=}")  # (nx, ny, ndim)
-    # print(f"{pairwise_distances.shape=}")  # (nx, ny, ny)
-    # print(f"{distances.shape=}")  # (nx, ny)
     return distances
 
 

prototorch/core/initializers.py

@@ -303,17 +303,18 @@ class OneHotLabelsInitializer(LabelsInitializer):
 
 
 # Reasonings
-class AbstractReasoningsInitializer(ABC):
-    """Abstract class for all reasonings initializers."""
-    def __init__(self, components_first: bool = True):
-        self.components_first = components_first
-
-    def compute_shape(self, distribution):
+def compute_distribution_shape(distribution):
     distribution = parse_distribution(distribution)
     num_components = sum(distribution.values())
     num_classes = len(distribution.keys())
     return (num_components, num_classes, 2)
 
+
+class AbstractReasoningsInitializer(ABC):
+    """Abstract class for all reasonings initializers."""
+    def __init__(self, components_first: bool = True):
+        self.components_first = components_first
+
     def generate_end_hook(self, reasonings):
         if not self.components_first:
             reasonings = reasonings.permute(2, 1, 0)
@@ -349,7 +350,7 @@ class LiteralReasoningsInitializer(AbstractReasoningsInitializer):
 class ZerosReasoningsInitializer(AbstractReasoningsInitializer):
     """Reasonings are all initialized with zeros."""
     def generate(self, distribution: Union[dict, list, tuple]):
-        shape = self.compute_shape(distribution)
+        shape = compute_distribution_shape(distribution)
         reasonings = torch.zeros(*shape)
         reasonings = self.generate_end_hook(reasonings)
         return reasonings
@@ -358,7 +359,7 @@ class ZerosReasoningsInitializer(AbstractReasoningsInitializer):
 class OnesReasoningsInitializer(AbstractReasoningsInitializer):
     """Reasonings are all initialized with ones."""
     def generate(self, distribution: Union[dict, list, tuple]):
-        shape = self.compute_shape(distribution)
+        shape = compute_distribution_shape(distribution)
         reasonings = torch.ones(*shape)
         reasonings = self.generate_end_hook(reasonings)
         return reasonings
@@ -372,7 +373,7 @@ class RandomReasoningsInitializer(AbstractReasoningsInitializer):
         self.maximum = maximum
 
     def generate(self, distribution: Union[dict, list, tuple]):
-        shape = self.compute_shape(distribution)
+        shape = compute_distribution_shape(distribution)
         reasonings = torch.ones(*shape).uniform_(self.minimum, self.maximum)
         reasonings = self.generate_end_hook(reasonings)
         return reasonings
@@ -381,7 +382,8 @@ 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, _ = self.compute_shape(distribution)
+        num_components, num_classes, _ = compute_distribution_shape(
+            distribution)
         A = OneHotLabelsInitializer().generate(distribution)
         B = torch.zeros(num_components, num_classes)
         reasonings = torch.stack([A, B], dim=-1)

prototorch/core/losses.py

@@ -106,17 +106,16 @@ def margin_loss(y_pred, y_true, margin=0.3):
 
 
 class GLVQLoss(torch.nn.Module):
-    def __init__(self, margin=0.0, squashing="identity", beta=10, **kwargs):
+    def __init__(self, margin=0.0, transfer_fn="identity", beta=10, **kwargs):
         super().__init__(**kwargs)
         self.margin = margin
-        self.squashing = get_activation(squashing)
+        self.transfer_fn = get_activation(transfer_fn)
         self.beta = torch.tensor(beta)
 
-    def forward(self, outputs, targets):
-        distances, plabels = outputs
-        mu = glvq_loss(distances, targets, prototype_labels=plabels)
-        batch_loss = self.squashing(mu + self.margin, beta=self.beta)
-        return torch.sum(batch_loss, dim=0)
+    def forward(self, outputs, targets, plabels):
+        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):

prototorch/core/pooling.py

@@ -82,23 +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):
+    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):
+    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):
+    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):
+    def forward(self, values, labels):  # pylint: disable=no-self-use
         return stratified_max_pooling(values, labels)

prototorch/core/transforms.py

@@ -36,7 +36,7 @@ class LinearTransform(torch.nn.Module):
         self._register_weights(weights)
 
     def forward(self, x):
-        return x @ self.weights.T
+        return x @ self.weights
 
 
 # Aliases

prototorch/datasets/__init__.py

@@ -1,6 +1,6 @@
 """ProtoTorch datasets"""
 
-from .abstract import NumpyDataset
+from .abstract import CSVDataset, NumpyDataset
 from .sklearn import (
     Blobs,
     Circles,
@@ -10,3 +10,4 @@ from .sklearn import (
 )
 from .spiral import Spiral
 from .tecator import Tecator
+from .xor import XOR

prototorch/datasets/abstract.py

@@ -10,6 +10,7 @@ https://github.com/pytorch/vision/blob/master/torchvision/datasets/mnist.py
 
 import os
 
+import numpy as np
 import torch
 
 
@@ -97,3 +98,16 @@ class NumpyDataset(torch.utils.data.TensorDataset):
         self.targets = torch.LongTensor(targets)
         tensors = [self.data, self.targets]
         super().__init__(*tensors)
+
+
+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,
+            delimiter=delimiter,
+            skip_header=skip_header,
+        )
+        data = np.delete(raw, 1, target_col)
+        targets = raw[:, target_col]
+        super().__init__(data, targets)

prototorch/datasets/xor.py

@@ -0,0 +1,18 @@
+"""Exclusive-or (XOR) dataset for binary classification."""
+
+import torch
+
+
+def make_xor(num_samples=500):
+    x = torch.rand(num_samples, 2)
+    y = torch.zeros(num_samples)
+    y[torch.logical_and(x[:, 0] > 0.5, x[:, 1] < 0.5)] = 1
+    y[torch.logical_and(x[:, 1] > 0.5, x[:, 0] < 0.5)] = 1
+    return x, y
+
+
+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/utils/utils.py

@@ -1,8 +1,12 @@
 """ProtoFlow utilities"""
 
 import warnings
-from collections.abc import Iterable
-from typing import Union
+from typing import (
+    Dict,
+    Iterable,
+    List,
+    Union,
+)
 
 import numpy as np
 import torch
@@ -24,7 +28,7 @@ def mesh2d(x=None, border: float = 1.0, resolution: int = 100):
     return mesh, xx, yy
 
 
-def distribution_from_list(list_dist: list[int],
+def distribution_from_list(list_dist: List[int],
                            clabels: Iterable[int] = None):
     clabels = clabels or list(range(len(list_dist)))
     distribution = dict(zip(clabels, list_dist))
@@ -32,7 +36,7 @@ def distribution_from_list(list_dist: list[int],
 
 
 def parse_distribution(user_distribution,
-                       clabels: Iterable[int] = None) -> dict[int, int]:
+                       clabels: Iterable[int] = None) -> Dict[int, int]:
     """Parse user-provided distribution.
 
     Return a dictionary with integer keys that represent the class labels and

setup.py

@@ -20,7 +20,7 @@ with open("README.md", "r") as fh:
 
 INSTALL_REQUIRES = [
     "torch>=1.3.1",
-    "torchvision>=0.6.0",
+    "torchvision>=0.7.1",
     "numpy>=1.9.1",
     "sklearn",
 ]
@@ -43,12 +43,15 @@ EXAMPLES = [
     "matplotlib",
     "torchinfo",
 ]
-TESTS = ["codecov", "pytest"]
+TESTS = [
+    "pytest-cov",
+    "pytest",
+]
 ALL = DATASETS + DEV + DOCS + EXAMPLES + TESTS
 
 setup(
     name="prototorch",
-    version="0.6.0",
+    version="0.7.1",
     description="Highly extensible, GPU-supported "
     "Learning Vector Quantization (LVQ) toolbox "
     "built using PyTorch and its nn API.",
@@ -59,7 +62,7 @@ setup(
     url=PROJECT_URL,
     download_url=DOWNLOAD_URL,
     license="MIT",
-    python_requires=">=3.9",
+    python_requires=">=3.6",
     install_requires=INSTALL_REQUIRES,
     extras_require={
         "datasets": DATASETS,
@@ -70,18 +73,22 @@ setup(
         "all": ALL,
     },
     classifiers=[
-        "Development Status :: 2 - Pre-Alpha",
         "Environment :: Console",
+        "Natural Language :: English",
+        "Development Status :: 4 - Beta",
         "Intended Audience :: Developers",
         "Intended Audience :: Education",
         "Intended Audience :: Science/Research",
-        "License :: OSI Approved :: MIT License",
-        "Natural Language :: English",
-        "Programming Language :: Python :: 3.9",
-        "Operating System :: OS Independent",
         "Topic :: Scientific/Engineering :: Artificial Intelligence",
         "Topic :: Software Development :: Libraries",
         "Topic :: Software Development :: Libraries :: Python Modules",
+        "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",
     ],
     packages=find_packages(),
     zip_safe=False,

tests/test_core.py

@@ -265,13 +265,25 @@ def test_eye_transform_init_wide():
 
 
 # Transforms
-def test_linear_transform():
+def test_linear_transform_default_eye_init():
     l = pt.transforms.LinearTransform(2, 4)
     actual = l.weights
     desired = torch.Tensor([[1, 0, 0, 0], [0, 1, 0, 0]])
     assert torch.allclose(actual, desired)
 
 
+def test_linear_transform_forward():
+    l = pt.transforms.LinearTransform(4, 2)
+    actual_weights = l.weights
+    desired_weights = torch.Tensor([[1, 0], [0, 1], [0, 0], [0, 0]])
+    assert torch.allclose(actual_weights, desired_weights)
+    actual_outputs = l(torch.Tensor([[1.1, 2.2, 3.3, 4.4], \
+                                     [1.1, 2.2, 3.3, 4.4], \
+                                     [5.5, 6.6, 7.7, 8.8]]))
+    desired_outputs = torch.Tensor([[1.1, 2.2], [1.1, 2.2], [5.5, 6.6]])
+    assert torch.allclose(actual_outputs, desired_outputs)
+
+
 def test_linear_transform_zeros_init():
     l = pt.transforms.LinearTransform(
         in_dim=2,

tests/test_datasets.py

@@ -49,6 +49,23 @@ class TestNumpyDataset(unittest.TestCase):
         self.assertEqual(len(ds), 3)
 
 
+class TestCSVDataset(unittest.TestCase):
+    def setUp(self):
+        data = np.random.rand(100, 4)
+        targets = np.random.randint(2, size=(100, 1))
+        arr = np.hstack([data, targets])
+        if not os.path.exists("./artifacts"):
+            os.mkdir("./artifacts")
+        np.savetxt("./artifacts/test.csv", arr, delimiter=",")
+
+    def test_len(self):
+        ds = pt.datasets.CSVDataset("./artifacts/test.csv")
+        self.assertEqual(len(ds), 100)
+
+    def tearDown(self):
+        os.remove("./artifacts/test.csv")
+
+
 class TestSpiral(unittest.TestCase):
     def test_init(self):
         ds = pt.datasets.Spiral(num_samples=10)