Moved to uv

.github/workflows/ci_checks.yml

@@ -3,23 +3,28 @@ name: CI checks
 on:
   pull_request:
     branches: ["*"]
-  push:
-    branches: [ master ]
 
 jobs:
   code-coverage:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
-      with:
-        python-version: '3.12'
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+
+    - name: Set up Python
+      run: uv python install
+
     - name: Install
       run: |
-        pip install .[dev]
+        uv sync --dev
+
     - name: Unit-tests with coverage
       run: |
-        pytest --cov=./ --cov-report=xml
+        uv run pytest --cov=./ --cov-report=xml
+
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v4
       with:
@@ -28,29 +33,22 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
-      with:
-        python-version: '3.12'
-    - name: Install dev dependencies
-      run: |
-        pip install .[dev]
-    - uses: pre-commit/action@v3.0.1
+      - name: Checkout
+        uses: actions/checkout@v4
 
-  run_lint:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
-      with:
-        python-version: '3.12'
-    - name: Install dev dependencies
-      run: |
-        pip install .[dev]
-    - name: Run linting
-      shell: bash
-      run: |
-        bash scripts/ci_checks.sh
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Set up Python
+        run: uv python install
+
+      - name: Install
+        run: |
+          uv sync --dev
+
+      - name: Run pre-commit hooks
+        run: |
+          uv run pre-commit run --all-files
 
   unit-tests:
     runs-on: ${{ matrix.os }}
@@ -59,14 +57,18 @@ jobs:
         python-version: ['3.9', '3.10', '3.11', '3.12']
         os: [ubuntu-latest, windows-latest, macos-latest]
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install
       run: |
-        pip install .[dev]
+        uv sync --dev
+
     - name: Unit-tests with coverage
       run: |
-        pytest tests/
+        uv run pytest tests/

.github/workflows/upload_pypi.yml

@@ -12,15 +12,18 @@ jobs:
     permissions:
       id-token: write
     steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
-      with:
-        python-version: '3.12'
-    - name: Install
-      run: |
-        pip install .[dev]
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+
+    - name: Set up Python
+      run: uv python install
+
     - name: Create package
       run: |
-        python3 -m build
+        uv build
+
     - name: Publish package distributions to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1

.pre-commit-config.yaml

@@ -4,16 +4,7 @@ repos:
     hooks:
       - id: ruff
         args: [ --fix ]
-
-  - repo: https://github.com/psf/black
-    rev: 24.10.0
-    hooks:
-      - id: black
-
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.13.2
-    hooks:
-      - id: isort
+      - id: ruff-format
 
   - repo: local
     hooks:
@@ -31,4 +22,3 @@ repos:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
-      - id: requirements-txt-fixer

.python-version

@@ -0,0 +1 @@
+3.12.11

denstream/den_stream.py

@@ -308,7 +308,7 @@ def _cluster_evaluate(self, iteration: int) -> None:
             if len(self.label_metrics_list) > 0:
                 metrics += self._compute_label_metrics(predicted_labels)
             if len(self.no_label_metrics_list) > 0:
-                # Checking that we have atleast two clusters (exluding outlier clusters, i.e. label=-1).
+                # Checking that we have at-least two clusters (excluding outlier clusters, i.e. label=-1).
                 if len(set(predicted_labels[predicted_labels != -1])) > 1:
                     metrics += self._compute_no_label_metric(predicted_labels)
                 else:
@@ -318,7 +318,7 @@ def _cluster_evaluate(self, iteration: int) -> None:
         else:
             self.metrics_results.append({"iteration": iteration, "metrics": None})
 
-    def _request_clustering(self) -> FloatArrayType:
+    def _request_clustering(self) -> IntArrayType:
         """
         Clustering based on self.model for the p-micro-clusters.
 
@@ -328,14 +328,14 @@ def _request_clustering(self) -> FloatArrayType:
         if len(self.p_micro_clusters) > 0:
             center_array = np.concatenate([c.center for c in self.p_micro_clusters], axis=0)
         else:
-            return np.empty(0, dtype=np.float32)
+            return np.empty(0, dtype=np.int32)
 
         # TODO: Should the new clusters be connected? I.e. if micro-cluster 1 and 2 and connected, should they be merged
         local_model = sklearn.base.clone(self.model)
-        predicted_labels: FloatArrayType = local_model.fit_predict(center_array)
+        predicted_labels: IntArrayType = local_model.fit_predict(center_array)
         return predicted_labels
 
-    def _compute_label_metrics(self, predicted_labels: FloatArrayType) -> List[MetricsDict]:
+    def _compute_label_metrics(self, predicted_labels: IntArrayType) -> List[MetricsDict]:
         """
         Compute the label metrics given the predicted labels.
 
@@ -362,7 +362,7 @@ def _compute_label_metrics(self, predicted_labels: FloatArrayType) -> List[Metri
             results.append(result_dict)
         return results
 
-    def _compute_no_label_metric(self, predicted_labels: FloatArrayType) -> List[MetricsDict]:
+    def _compute_no_label_metric(self, predicted_labels: IntArrayType) -> List[MetricsDict]:
         """
         Compute the no-label metrics given the predicted labels.
 

denstream/preprocessing.py

@@ -20,13 +20,13 @@ def __init__(self, dim: Tuple[int, ...], eps: float = 1e-10):
         """
 
         self.dim = dim
-        self.mean = np.zeros(self.dim)
+        self.mean = np.zeros(self.dim, dtype=np.float32)
 
-        self.variance = np.zeros(self.dim)
-        self.sse = np.zeros(self.dim)
+        self.variance = np.zeros(self.dim, dtype=np.float32)
+        self.sse = np.zeros(self.dim, dtype=np.float32)
 
-        self.num_data_points = 0
-        self.eps = eps
+        self.num_data_points = np.float32(0.0)
+        self.eps = np.float32(eps)
 
     def update_statistics(self, x: FloatArrayType) -> None:
         """
@@ -37,7 +37,7 @@ def update_statistics(self, x: FloatArrayType) -> None:
         :return:
         """
 
-        self.num_data_points += 1
+        self.num_data_points += np.float32(1.0)
 
         old_mean = self.mean
         self.mean = self.mean + (x - self.mean) / self.num_data_points

denstream/utils.py

@@ -13,7 +13,7 @@ def fading_function(lambd: float, time: IntArrayType) -> FloatArrayType:
     :return: The calculated fading array.
     """
 
-    return np.power(2, -lambd * time, dtype=np.float32)
+    return np.power(2, -lambd * time, dtype=np.float32)  # type: ignore
 
 
 def numpy_cf1(x: FloatArrayType, fading_array: FloatArrayType) -> FloatArrayType:

examples/user_guide.ipynb

@@ -79,7 +79,9 @@
     "T = np.concatenate([t_1, t_2, t_3, t_4], axis=0).astype(int)\n",
     "\n",
     "# Sorting data s.t. they come in time order.\n",
-    "idx = np.argsort(T, axis=0).reshape(T.shape[0],)\n",
+    "idx = np.argsort(T, axis=0).reshape(\n",
+    "    T.shape[0],\n",
+    ")\n",
     "X = X[idx, :]\n",
     "Y = Y[idx, :]\n",
     "T = T[idx, :]"
@@ -161,11 +163,8 @@
    "source": [
     "def generator(X, Y, T):\n",
     "    for i in range(0, X.shape[0]):\n",
-    "        yield {\n",
-    "            \"time\": int(T[i, :]),\n",
-    "            \"feature_array\": X[i, :].reshape((1, X.shape[1])),\n",
-    "            \"label\": int(Y[i, :])\n",
-    "        }\n",
+    "        yield {\"time\": int(T[i, :]), \"feature_array\": X[i, :].reshape((1, X.shape[1])), \"label\": int(Y[i, :])}\n",
+    "\n",
     "\n",
     "gen = generator(X, Y, T)\n",
     "\n",

pyproject.toml

@@ -1,34 +1,32 @@
 [build-system]
-build-backend = "setuptools.build_meta"
-requires = ["setuptools>=61.0", "wheel>=0.37.1"]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
 
 [project]
 name = "denstream"
-version = "0.1.1"
+version = "0.1.4"
 description = "Implementation of the DenStream algorithm"
 readme = "README.md"
-requires-python = ">=3.9, <3.13"
+requires-python = ">=3.9, <3.14"
 authors = [
     {name = "MrParosk"}
 ]
 
 dependencies = [
-    "numba>=0.56.2",
-    "numpy>=1.23,<3.0",
+    "numba>=0.56",
+    "numpy>=2.0",
     "scikit-learn>=1.0",
+    "typing-extensions>=4.14.0",
 ]
 
-[project.optional-dependencies]
+
+[dependency-groups]
 dev = [
-    "black==24.10.0",
-    "isort==5.13.2",
-    "mypy==1.13.0",
-    "pre-commit==4.0.1",
-    "pytest==8.3.3",
-    "pytest-cov==6.0.0",
-    "ruff==0.7.3",
-    "build==1.2.2",
-    "twine==5.1.1",
+    "mypy>=1.16.0",
+    "pre-commit>=4.2.0",
+    "pytest>=8.4.0",
+    "pytest-cov>=6.2.0",
+    "ruff>=0.12.0",
 ]
 
 [tool.mypy]
@@ -39,12 +37,5 @@ exclude = [
     "tests"
 ]
 
-[tool.black]
-line-length = 128
-
-[tool.isort]
-line_length = 128
-profile = "black"
-
 [tool.ruff]
 line-length = 128