Merge pull request #42 from msamsami/use-uv-refactor-workflows

patch: use `uv` for package management, refactor github workflows, fix bug in handling complex arrays

.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 }}

.github/workflows/run-tests.yml → .github/workflows/ci.yml

@@ -1,36 +1,39 @@
-# This workflow will run the unit tests on a PR
-
-name: Run Tests
+name: CI
 
 on:
   pull_request:
     branches: [ main ]
   workflow_call:
+  workflow_dispatch:
 
 permissions:
     contents: read
 
 jobs:
-  build-and-test:
+  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
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v3
+      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: |
-        python -m pip install --upgrade pip
-        pip install build
-        pip install -r requirements.txt
-        pip install -r requirements-dev.txt
+      run: uv sync
+
+    - name: Run ruff linter
+      run: uv run ruff check --output-format=github .
+
+    - name: Run black format check
+      run: uv run black --check --diff .
 
     - name: Run tests
-      run: |
-        pytest
+      run: uv run pytest -vv

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

README.md

@@ -7,7 +7,7 @@
 
 <div align="center">
 
-![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)<br>
 ![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 ⚡️

pyproject.toml

@@ -41,19 +41,20 @@ dependencies = [
     "typing-extensions>=4.8.0; python_full_version < '3.11'",
 ]
 
-[project.urls]
-Homepage = "https://github.com/msamsami/wnb"
-Source = "https://github.com/msamsami/wnb"
-
-[project.optional-dependencies]
+[dependency-groups]
 dev = [
-    "pytest>=7.0.0",
     "black>=24.8.0",
-    "tqdm",
-    "pre-commit>=3.5.0",
     "isort",
+    "pre-commit>=3.5.0",
+    "pytest>=7.0.0",
+    "ruff>=0.9.2",
+    "tqdm",
 ]
 
+[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"]

requirements-dev.txt

@@ -1,5 +1,6 @@
-pytest>=7.0.0
 black>=24.8.0
-tqdm
-pre-commit>=3.5.0
 isort
+pre-commit>=3.5.0
+pytest>=7.0.0
+ruff>=0.9.2
+tqdm

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")
 

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`.

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