From dbc924f08ef5f70d1a9605e8a172d74371fca6d2 Mon Sep 17 00:00:00 2001 From: Mehdi Samsami Date: Fri, 17 Jan 2025 15:27:10 +0330 Subject: [PATCH 1/8] use uv for package management, remove setup.py, add ruff to dev dependencies --- pyproject.toml | 20 +- requirements-dev.txt | 6 +- setup.py | 54 --- uv.lock | 1052 ++++++++++++++++++++++++++++++++++++++++++ 4 files changed, 1064 insertions(+), 68 deletions(-) delete mode 100644 setup.py create mode 100644 uv.lock diff --git a/pyproject.toml b/pyproject.toml index 028fbb5..4e7951e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -39,21 +39,22 @@ dependencies = [ "scipy>=1.8.0", "scikit-learn>=1.0.2", "typing-extensions>=4.8.0; python_full_version < '3.11'", + "black>=24.8.0", ] -[project.urls] -Homepage = "https://github.com/msamsami/wnb" -Source = "https://github.com/msamsami/wnb" - -[project.optional-dependencies] +[dependency-groups] dev = [ + "isort", + "pre-commit>=3.5.0", "pytest>=7.0.0", - "black>=24.8.0", + "ruff>=0.9.2", "tqdm", - "pre-commit>=3.5.0", - "isort", ] +[project.urls] +Homepage = "https://github.com/msamsami/wnb" +Source = "https://github.com/msamsami/wnb" + [tool.hatch.version] path = "wnb/__init__.py" @@ -63,9 +64,6 @@ packages = ["wnb"] [tool.hatch.metadata] allow-direct-references = true -[tool.hatch.build.targets.sdist] -include = ["/README.md", "/wnb"] - [tool.pytest.ini_options] testpaths = ["tests"] filterwarnings = ["ignore"] diff --git a/requirements-dev.txt b/requirements-dev.txt index fe249be..1140451 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -1,5 +1,5 @@ +isort +pre-commit>=3.5.0 pytest>=7.0.0 -black>=24.8.0 +ruff>=0.9.2 tqdm -pre-commit>=3.5.0 -isort diff --git a/setup.py b/setup.py deleted file mode 100644 index 7175641..0000000 --- a/setup.py +++ /dev/null @@ -1,54 +0,0 @@ -import codecs -from os import path - -from setuptools import find_packages, setup - -from wnb import __version__ - -setup( - name="wnb", - version=__version__, - description="Python library for the implementations of general and weighted naive Bayes (WNB) classifiers.", - keywords=["python", "machine learning", "bayes", "naive bayes", "classifier"], - author="Mehdi Samsami", - author_email="mehdisamsami@live.com", - license="BSD License", - url="https://github.com/msamsami/wnb", - long_description=codecs.open( - path.join(path.abspath(path.dirname(__file__)), "README.md"), encoding="utf-8" - ).read(), - long_description_content_type="text/markdown", - include_package_data=True, - packages=find_packages(exclude=["tests*"]), - classifiers=[ - "Intended Audience :: Science/Research", - "Intended Audience :: Developers", - "Topic :: Scientific/Engineering", - "Topic :: Scientific/Engineering :: Artificial Intelligence", - "Topic :: Scientific/Engineering :: Information Analysis", - "Topic :: Software Development :: Libraries :: Python Modules", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 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">=7.0.0" }, + { name = "ruff", specifier = ">=0.9.2" }, + { name = "tqdm" }, +] From 7b93016b135798f9260288de854c4ecafc41eda7 Mon Sep 17 00:00:00 2001 From: Mehdi Samsami Date: Fri, 17 Jan 2025 15:28:18 +0330 Subject: [PATCH 2/8] minor changes to fix lint and format issues --- LICENSE | 2 +- tests/benchmarks/utils.py | 5 ++++- wnb/_utils.py | 7 ++++++- wnb/dist.py | 2 +- wnb/gwnb.py | 2 +- wnb/stats/__init__.py | 31 ++++++++++++++++++++++++++++--- wnb/stats/base.py | 6 +++++- wnb/typing.py | 2 +- 8 files changed, 47 insertions(+), 10 deletions(-) diff --git a/LICENSE b/LICENSE index a0f1f87..94991e8 100644 --- a/LICENSE +++ b/LICENSE @@ -1,7 +1,7 @@ BSD License =========== -Copyright (c) 2024 by Mehdi Samsami. +Copyright (c) 2025 by Mehdi Samsami. All rights reserved. Redistribution and use in source and binary forms, with or without diff --git a/tests/benchmarks/utils.py b/tests/benchmarks/utils.py index 388f15f..c8bb84d 100644 --- a/tests/benchmarks/utils.py +++ b/tests/benchmarks/utils.py @@ -10,7 +10,10 @@ try: from tqdm import tqdm except ModuleNotFoundError: - tqdm = lambda iterable, *args, **kwargs: iterable + + def tqdm(iterable, *args, **kwargs): + return iterable + warnings.filterwarnings("ignore") diff --git a/wnb/_utils.py b/wnb/_utils.py index 1ee850a..0686d0d 100644 --- a/wnb/_utils.py +++ b/wnb/_utils.py @@ -4,7 +4,12 @@ from packaging import version from sklearn.utils import check_array -__all__ = ["SKLEARN_V1_6_OR_LATER", "validate_data", "_check_n_features", "_check_feature_names"] +__all__ = [ + "SKLEARN_V1_6_OR_LATER", + "validate_data", + "_check_n_features", + "_check_feature_names", +] SKLEARN_V1_6_OR_LATER = version.parse(sklearn.__version__) >= version.parse("1.6") diff --git a/wnb/dist.py b/wnb/dist.py index c9b26a9..294c707 100644 --- a/wnb/dist.py +++ b/wnb/dist.py @@ -1,6 +1,6 @@ import warnings -from wnb.stats import * +from wnb.stats import * # noqa: F403 warnings.warn( "The `wnb.dist` module is deprecated and will be removed in a future release. " diff --git a/wnb/gwnb.py b/wnb/gwnb.py index cd206ef..89d93e1 100644 --- a/wnb/gwnb.py +++ b/wnb/gwnb.py @@ -12,7 +12,7 @@ from scipy.stats import norm from sklearn.base import BaseEstimator, ClassifierMixin from sklearn.exceptions import DataConversionWarning -from sklearn.utils import as_float_array, deprecated +from sklearn.utils import as_float_array from sklearn.utils.multiclass import check_classification_targets, type_of_target from sklearn.utils.validation import check_is_fitted diff --git a/wnb/stats/__init__.py b/wnb/stats/__init__.py index 4b27bba..3df8721 100644 --- a/wnb/stats/__init__.py +++ b/wnb/stats/__init__.py @@ -1,6 +1,17 @@ from .base import DistMixin -from .continuous import * -from .discrete import * +from .continuous import ( + BetaDist, + ChiSquaredDist, + ExponentialDist, + GammaDist, + LognormalDist, + NormalDist, + ParetoDist, + RayleighDist, + TDist, + UniformDist, +) +from .discrete import BernoulliDist, CategoricalDist, GeometricDist, PoissonDist from .enums import Distribution _all_distribution_classes = { @@ -13,7 +24,21 @@ NonNumericDistributions = [Distribution.CATEGORICAL] -__all__ = list(_all_distribution_classes.keys()) + [ +__all__ = [ + "NormalDist", + "LognormalDist", + "ExponentialDist", + "UniformDist", + "ParetoDist", + "GammaDist", + "BetaDist", + "ChiSquaredDist", + "TDist", + "RayleighDist", + "BernoulliDist", + "CategoricalDist", + "GeometricDist", + "PoissonDist", "Distribution", "AllDistributions", "NonNumericDistributions", diff --git a/wnb/stats/base.py b/wnb/stats/base.py index a94fc8e..2cc2495 100644 --- a/wnb/stats/base.py +++ b/wnb/stats/base.py @@ -118,7 +118,11 @@ def __repr__(self) -> str: ) -def vectorize(otypes: str | None = None, excluded: set[int | str] = None, signature: str | None = None): +def vectorize( + otypes: str | None = None, + excluded: set[int | str] = None, + signature: str | None = None, +): """ Numpy vectorization wrapper that works with class methods. """ diff --git a/wnb/typing.py b/wnb/typing.py index a70db3d..52ee752 100644 --- a/wnb/typing.py +++ b/wnb/typing.py @@ -6,7 +6,7 @@ import pandas as pd from scipy.sparse import spmatrix -__all__ = ["MatrixLike", "ArrayLike", "Int", "Float", "DistributionLike"] +__all__ = ["MatrixLike", "ArrayLike", "Int", "Float", "DistributionLike"] # noqa: F822 ArrayLike = numpy.typing.ArrayLike From b5c1c50de0371a3b31405e63063fbb15c97cb376 Mon Sep 17 00:00:00 2001 From: Mehdi Samsami Date: Fri, 17 Jan 2025 15:28:50 +0330 Subject: [PATCH 3/8] refactor workflows, make changes to use uv, add ci workflow --- .github/workflows/black.yml | 20 ---------------- .github/workflows/build.yml | 30 +++++++++++------------- .github/workflows/ci.yml | 41 +++++++++++++++++++++++++++++++++ .github/workflows/run-tests.yml | 36 ----------------------------- 4 files changed, 55 insertions(+), 72 deletions(-) delete mode 100644 .github/workflows/black.yml create mode 100644 .github/workflows/ci.yml delete mode 100644 .github/workflows/run-tests.yml diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml deleted file mode 100644 index 38a6cca..0000000 --- a/.github/workflows/black.yml +++ /dev/null @@ -1,20 +0,0 @@ -# This workflow will check if code is formatted using Black - -name: Check Code Format - -on: - workflow_dispatch: - pull_request: - branches: [ main ] - -jobs: - BlackFormatCheck: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ["3.8"] - steps: - - uses: actions/checkout@v3 - - uses: psf/black@stable - with: - options: "--check --diff --verbose" diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 9d00072..d3de525 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -1,5 +1,3 @@ -# This workflow will upload a Python Package using Twine when a release is created - name: build on: @@ -10,31 +8,31 @@ permissions: contents: read jobs: - test: - uses: ./.github/workflows/run-tests.yml + ci: + uses: ./.github/workflows/ci.yml publish: runs-on: ubuntu-latest - needs: test + needs: ci steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v3 + uses: actions/setup-python@v5 with: - python-version: '3.x' + python-version: '3.8' + + - name: Set up uv + uses: astral-sh/setup-uv@v5 - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install build - pip install -r requirements.txt + run: uv sync - - name: Build the package - run: python -m build + - name: Build + run: uv build - - name: Publish the package - uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29 + - name: Publish + uses: pypa/gh-action-pypi-publish@release/v1 with: user: __token__ password: ${{ secrets.PYPI_API_TOKEN }} diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 0000000..35814fd --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,41 @@ +name: CI + +on: + pull_request: + branches: [ main ] + workflow_call: + workflow_dispatch: + +permissions: + contents: read + +jobs: + ci: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"] + + steps: + - uses: actions/checkout@v4 + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + - name: Set up uv + uses: astral-sh/setup-uv@v5 + + - name: Install dependencies + run: uv sync + + - name: Run ruff linter + run: uv run ruff check --output-format=github . + + - name: Run black format check + uses: psf/black@stable + with: + options: "--check --diff" + + - name: Run tests + run: uv run pytest -vv diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml deleted file mode 100644 index f31e6d0..0000000 --- a/.github/workflows/run-tests.yml +++ /dev/null @@ -1,36 +0,0 @@ -# This workflow will run the unit tests on a PR - -name: Run Tests - -on: - pull_request: - branches: [ main ] - workflow_call: - -permissions: - contents: read - -jobs: - build-and-test: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"] - - steps: - - uses: actions/checkout@v3 - - name: Set up Python - uses: actions/setup-python@v3 - with: - python-version: ${{ matrix.python-version }} - - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install build - pip install -r requirements.txt - pip install -r requirements-dev.txt - - - name: Run tests - run: | - pytest From b55fd74c4f49ea6eb026c111303a8cbfdd59a127 Mon Sep 17 00:00:00 2001 From: Mehdi Samsami Date: Fri, 17 Jan 2025 17:19:17 +0330 Subject: [PATCH 4/8] move black to dev dependencies, was among the main dependencies by mistake --- pyproject.toml | 2 +- requirements-dev.txt | 1 + uv.lock | 6 +++--- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 4e7951e..2dc8f14 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -39,11 +39,11 @@ dependencies = [ "scipy>=1.8.0", "scikit-learn>=1.0.2", "typing-extensions>=4.8.0; python_full_version < '3.11'", - "black>=24.8.0", ] [dependency-groups] dev = [ + "black>=24.8.0", "isort", "pre-commit>=3.5.0", "pytest>=7.0.0", diff --git a/requirements-dev.txt b/requirements-dev.txt index 1140451..3f24f13 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -1,3 +1,4 @@ +black>=24.8.0 isort pre-commit>=3.5.0 pytest>=7.0.0 diff --git a/uv.lock b/uv.lock index f7fe3c8..65e9492 100644 --- a/uv.lock +++ b/uv.lock @@ -1011,8 +1011,6 @@ name = "wnb" version = "0.5.0" source = { editable = "." } dependencies = [ - { name = "black", version = "24.8.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.9'" }, - { name = "black", version = "24.10.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.9'" }, { name = "pandas", version = "2.0.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.9'" }, { name = "pandas", version = "2.2.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.9'" }, { name = "scikit-learn", version = "1.3.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.9'" }, @@ -1025,6 +1023,8 @@ dependencies = [ [package.dev-dependencies] dev = [ + { name = "black", version = "24.8.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.9'" }, + { name = "black", version = "24.10.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.9'" }, { name = "isort" }, { name = "pre-commit", version = "3.5.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.9'" }, { name = "pre-commit", version = "4.0.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.9'" }, @@ -1035,7 +1035,6 @@ dev = [ [package.metadata] requires-dist = [ - { name = "black", specifier = ">=24.8.0" }, { name = "pandas", specifier = ">=1.4.1" }, { name = "scikit-learn", specifier = ">=1.0.2" }, { name = "scipy", specifier = ">=1.8.0" }, @@ -1044,6 +1043,7 @@ requires-dist = [ [package.metadata.requires-dev] dev = [ + { name = "black", specifier = ">=24.8.0" }, { name = "isort" }, { name = "pre-commit", specifier = ">=3.5.0" }, { name = "pytest", specifier = ">=7.0.0" }, From f9b7de979e70e32c2d19adea756284f77ed90140 Mon Sep 17 00:00:00 2001 From: Mehdi Samsami Date: Fri, 17 Jan 2025 17:20:11 +0330 Subject: [PATCH 5/8] use local command to run black format check --- .github/workflows/ci.yml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 35814fd..a2fc7ce 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -10,7 +10,7 @@ permissions: contents: read jobs: - ci: + test: runs-on: ubuntu-latest strategy: matrix: @@ -33,9 +33,7 @@ jobs: run: uv run ruff check --output-format=github . - name: Run black format check - uses: psf/black@stable - with: - options: "--check --diff" + run: uv run black --check --diff . - name: Run tests run: uv run pytest -vv From 845326ccd29947f4cd65f11b294b76a260da9981 Mon Sep 17 00:00:00 2001 From: Mehdi Samsami Date: Fri, 17 Jan 2025 17:23:30 +0330 Subject: [PATCH 6/8] bump version -> v0.5.1 --- README.md | 18 +++--------------- uv.lock | 2 +- wnb/__init__.py | 2 +- 3 files changed, 5 insertions(+), 17 deletions(-) diff --git a/README.md b/README.md index 50088b3..ba484e7 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@
-![Lastest Release](https://img.shields.io/badge/release-v0.5.0-green) +![Lastest Release](https://img.shields.io/badge/release-v0.5.1-green) [![PyPI Version](https://img.shields.io/pypi/v/wnb)](https://pypi.org/project/wnb/) ![Python Versions](https://img.shields.io/badge/python-3.8%20%7C%203.9%20%7C%203.10%20%7C%203.11%20%7C%203.12%20%7C%203.13-blue)
![GitHub Workflow Status (build)](https://github.com/msamsami/wnb/actions/workflows/build.yml/badge.svg) @@ -36,21 +36,9 @@ Ensure that Python 3.8 or higher is installed on your machine before installing pip install wnb ``` -### Poetry +### uv ```bash -poetry add wnb -``` - -### GitHub -```bash -# Clone the repository -git clone https://github.com/msamsami/wnb.git - -# Navigate into the project directory -cd wnb - -# Install the package -pip install . +uv add wnb ``` ## Getting started ⚡️ diff --git a/uv.lock b/uv.lock index 65e9492..c9eb14f 100644 --- a/uv.lock +++ b/uv.lock @@ -1008,7 +1008,7 @@ wheels = [ [[package]] name = "wnb" -version = "0.5.0" +version = "0.5.1" source = { editable = "." } dependencies = [ { name = "pandas", version = "2.0.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.9'" }, diff --git a/wnb/__init__.py b/wnb/__init__.py index 207c00a..3523c4e 100644 --- a/wnb/__init__.py +++ b/wnb/__init__.py @@ -2,7 +2,7 @@ Python library for the implementations of general and weighted naive Bayes (WNB) classifiers. """ -__version__ = "0.5.0" +__version__ = "0.5.1" __author__ = "Mehdi Samsami" From e79ee0fc212f67806b9752da32247c2faf405b83 Mon Sep 17 00:00:00 2001 From: Mehdi Samsami Date: Fri, 17 Jan 2025 18:22:25 +0330 Subject: [PATCH 7/8] fix bug in handling array with complex values --- wnb/gnb.py | 10 +++------- wnb/gwnb.py | 7 ++----- 2 files changed, 5 insertions(+), 12 deletions(-) diff --git a/wnb/gnb.py b/wnb/gnb.py index 0058837..5a0b2fc 100644 --- a/wnb/gnb.py +++ b/wnb/gnb.py @@ -12,7 +12,7 @@ from sklearn.exceptions import DataConversionWarning from sklearn.utils import as_float_array from sklearn.utils.multiclass import check_classification_targets -from sklearn.utils.validation import check_is_fitted +from sklearn.utils.validation import _ensure_no_complex_data, check_is_fitted if sys.version_info >= (3, 11): from typing import Self @@ -139,10 +139,6 @@ def _check_inputs(self, X, y) -> None: ensure_min_features=1, ) - # Check if X contains complex values - if np.iscomplex(X).any() or np.iscomplex(y).any(): - raise ValueError("Complex data not supported") - # Check that the number of samples and labels are compatible if X.shape[0] != y.shape[0]: raise ValueError("X.shape[0]=%d and y.shape[0]=%d are incompatible." % (X.shape[0], y.shape[0])) @@ -155,6 +151,7 @@ def _prepare_X_y(self, X=None, y=None, from_fit: bool = False): # Convert to NumPy array if X is Pandas DataFrame if isinstance(X, pd.DataFrame): X = X.values + _ensure_no_complex_data(X) X = ( X if any(d in self._get_distributions() for d in NonNumericDistributions) @@ -259,10 +256,9 @@ def fit(self, X: MatrixLike, y: ArrayLike) -> Self: y = y_ self._prepare_parameters() + self.epsilon_ = 0.0 if np.all(np.isreal(X)): self.epsilon_ = self.var_smoothing * np.var(X, axis=0).max() - else: - self.epsilon_ = 0.0 self.likelihood_params_: dict[int, list[DistMixin]] = { c: [ diff --git a/wnb/gwnb.py b/wnb/gwnb.py index 89d93e1..7ed510d 100644 --- a/wnb/gwnb.py +++ b/wnb/gwnb.py @@ -14,7 +14,7 @@ from sklearn.exceptions import DataConversionWarning from sklearn.utils import as_float_array from sklearn.utils.multiclass import check_classification_targets, type_of_target -from sklearn.utils.validation import check_is_fitted +from sklearn.utils.validation import _ensure_no_complex_data, check_is_fitted if sys.version_info >= (3, 11): from typing import Self @@ -162,10 +162,6 @@ def _check_inputs(self, X, y) -> None: ensure_min_features=1, ) - # Check if X contains complex values - if np.iscomplex(X).any() or np.iscomplex(y).any(): - raise ValueError("Complex data not supported") - # Check that the number of samples and labels are compatible if self.__n_samples != y.shape[0]: raise ValueError("X.shape[0]=%d and y.shape[0]=%d are incompatible." % (X.shape[0], y.shape[0])) @@ -211,6 +207,7 @@ def _prepare_X_y(self, X=None, y=None, from_fit: bool = False): # Convert to NumPy array if X is Pandas DataFrame if isinstance(X, pd.DataFrame): X = X.values + _ensure_no_complex_data(X) X = as_float_array(X) if y is not None: From 61d33d00bb5c2ea74551722ebfd335c05afda2a0 Mon Sep 17 00:00:00 2001 From: Mehdi Samsami Date: Fri, 17 Jan 2025 18:22:59 +0330 Subject: [PATCH 8/8] add unit tests for epsilon in normal dist and var_smoothing in generalnb --- tests/test_dist.py | 15 +++++++++++++++ tests/test_gnb.py | 34 ++++++++++++++++++++++++++++++++++ 2 files changed, 49 insertions(+) diff --git a/tests/test_dist.py b/tests/test_dist.py index bd8fb4b..b2013d6 100644 --- a/tests/test_dist.py +++ b/tests/test_dist.py @@ -62,6 +62,21 @@ def test_normal_pdf(): assert_array_almost_equal(norm_wnb(X), norm_scipy.pdf(X), decimal=10) +@pytest.mark.parametrize("epsilon", [1e-10, 1e-9, 1e-6, 1e-3]) +def test_normal_with_epsilon(epsilon: float): + """ + Test whether epsilon is correctly applied for `NormalDist`. + """ + norm_1 = NormalDist(mu=1, sigma=0) + norm_2 = NormalDist(mu=1, sigma=0, epsilon=epsilon) + norm_3 = NormalDist(mu=1, sigma=np.sqrt(epsilon)) + assert norm_1.sigma == norm_2.sigma == 0 + assert norm_3.sigma == np.sqrt(epsilon) + X = np.random.uniform(-100, 100, size=10000) + assert np.isnan(norm_1(X)).all() + assert_array_almost_equal(norm_2(X), norm_3(X), decimal=10) + + def test_lognormal_pdf(random_uniform): """ Test whether pdf method of `LognormalDist` returns the same result as pdf method of `scipy.stats.lognorm`. diff --git a/tests/test_gnb.py b/tests/test_gnb.py index c1e365a..d6f2801 100644 --- a/tests/test_gnb.py +++ b/tests/test_gnb.py @@ -247,3 +247,37 @@ def test_gnb_invalid_dist(): msg = r"Distribution .* is not supported" with pytest.raises(ValueError, match=msg): clf.fit(X, y) + + +def test_gnb_var_smoothing(): + """ + Test whether var_smoothing parameter properly affects the variances of normal distributions. + """ + X = np.array([[1, 0], [2, 0], [3, 0], [4, 0], [5, 0]]) # First feature has variance 2.0 + y = np.array([1, 1, 2, 2, 2]) + + clf1 = GeneralNB(var_smoothing=0.0) + clf1.fit(X, y) + + clf2 = GeneralNB(var_smoothing=1.0) + clf2.fit(X, y) + + test_point = np.array([[2.5, 0]]) + prob1 = clf1.predict_proba(test_point) + prob2 = clf2.predict_proba(test_point) + + assert not np.allclose(prob1, prob2) + assert clf1.epsilon_ == 0.0 + assert clf2.epsilon_ > clf1.epsilon_ + + +def test_gnb_var_smoothing_non_numeric(): + """ + Test that var_smoothing is ignored for non-numeric features. + """ + X = np.array([["a", 1], ["b", 2], ["a", 2], ["b", 1]]) + y = np.array([1, 1, 2, 2]) + + clf = GeneralNB(distributions=[D.CATEGORICAL, D.CATEGORICAL], var_smoothing=1e-6) + clf.fit(X, y) + assert clf.epsilon_ == 0