Add CI and release workflows

.github/workflows/ci.yml

@@ -0,0 +1,64 @@
+name: CI
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+
+      # Pin ruff to the version used by the pre-commit hooks so CI matches the
+      # project's lint baseline.
+      - name: Lint with ruff
+        run: |
+          uvx ruff@0.11.12 check .
+          uvx ruff@0.11.12 format --check .
+
+  test:
+    needs: lint
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --extra dev
+
+      # GEFF fixtures, model weights, and a Gurobi license are not provisioned in
+      # CI, so the data/model/solver tests skip; the unit tests and the
+      # download mechanism (served from a local HTTP server) still run.
+      - name: Run tests with coverage
+        run: uv run pytest --cov=hoct --cov-report=xml -q
+
+      - name: Upload coverage to Codecov
+        if: matrix.python-version == '3.12' && github.repository == 'royerlab/hoct'
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false

.github/workflows/release.yml

@@ -0,0 +1,108 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - "v*"
+  workflow_dispatch:
+    inputs:
+      test_release:
+        description: 'Test release (skips PyPI publish)'
+        required: false
+        default: false
+        type: boolean
+
+permissions:
+  contents: write
+  id-token: write
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 0  # required for hatch-vcs to read git tags/history
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: uv sync --extra dev
+
+      - name: Run tests
+        run: uv run pytest -q
+
+      - name: Build package
+        run: uv build
+
+      - name: Upload build artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  release:
+    needs: build
+    runs-on: ubuntu-latest
+    # Only publish from the main repo and not for dry-run releases.
+    if: github.repository == 'royerlab/hoct' && github.event.inputs.test_release != 'true'
+    environment:
+      name: pypi
+      url: https://pypi.org/p/hoct
+    steps:
+      - name: Download build artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          attestations: true
+
+  test-release:
+    needs: build
+    runs-on: ubuntu-latest
+    # Dry run for workflow_dispatch test releases or forks.
+    if: github.event.inputs.test_release == 'true' || github.repository != 'royerlab/hoct'
+    steps:
+      - name: Download build artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Test PyPI upload (dry run)
+        run: |
+          echo "🧪 This would upload to PyPI:"
+          ls -la dist/
+          echo "✅ Test release completed successfully!"
+
+  github-release:
+    needs: build
+    runs-on: ubuntu-latest
+    if: github.repository == 'royerlab/hoct' && github.event.inputs.test_release != 'true'
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+
+      - name: Download build artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@v2
+        with:
+          files: dist/*
+          generate_release_notes: true
+          draft: false
+          prerelease: ${{ contains(github.ref, 'alpha') || contains(github.ref, 'beta') || contains(github.ref, 'rc') }}

.gitignore

@@ -36,6 +36,7 @@ env/
 # Testing
 .pytest_cache/
 .coverage
+coverage.xml
 htmlcov/
 .tox/
 

src/hoct/features/features.py

@@ -57,8 +57,21 @@ def normalize_image(
     clip: bool = False,
     uq: float = 0.999,
 ) -> NDArray:
-    """
-    Normalize an image to [0, 1] using the quantile.
+    """Normalize an image to ``[0, 1]`` using an upper quantile.
+
+    Parameters
+    ----------
+    image : NDArray
+        Image to normalize.
+    clip : bool, default=False
+        If True, clip the normalized values to ``[0, 1]``.
+    uq : float, default=0.999
+        Upper quantile used as the normalization maximum (robust to outliers).
+
+    Returns
+    -------
+    NDArray
+        The normalized image as ``float32``.
     """
     image = np.asarray(image, dtype=np.float32)
 

src/hoct/features/graph.py

@@ -1,4 +1,5 @@
 from functools import partial
+from typing import Any
 
 import dask.array as da
 import numpy as np
@@ -9,7 +10,7 @@
 from tracksdata.utils._multiprocessing import multiprocessing_apply
 
 from hoct.features.constants import EDGE_GT_KEY, REGIONPROPS
-from hoct.features.features import add_border_dist, add_delta_t, add_is_div
+from hoct.features.features import add_border_dist, add_delta_t, add_is_div, normalize_image
 
 
 def convert_to_3d(graph: td.graph.RustWorkXGraph) -> None:
@@ -69,6 +70,8 @@ def create_graph(
     delta_t: float,
     scale: tuple[float, ...] | None = None,
     images: ArrayLike | None = None,
+    normalize_images: bool = True,
+    normalize_kwargs: dict[str, Any] | None = None,
     gt_graph: td.graph.BaseGraph | None = None,
     out_graph: td.graph.BaseGraph | None = None,
 ) -> td.graph.InMemoryGraph:
@@ -92,6 +95,13 @@ def create_graph(
     images : ArrayLike | None
         Optional intensity images of shape (T, [Z,] Y, X).
         If None, only geometric features are computed.
+    normalize_images : bool, default=True
+        If True and ``images`` is provided, normalize each time point with
+        :func:`hoct.features.normalize_image` before extracting intensity
+        features. Has no effect when ``images`` is None.
+    normalize_kwargs : dict[str, Any] | None
+        Keyword arguments forwarded to :func:`hoct.features.normalize_image`
+        (e.g. ``clip``, ``uq``). Defaults to an empty dict.
     gt_graph : td.graph.BaseGraph | None
         Optional ground truth graph for training. If provided, adds ground truth edge labels.
         If None (inference mode), skips ground truth-related features.
@@ -123,6 +133,12 @@ def create_graph(
     if images is not None and not isinstance(images, da.Array):
         images = da.from_array(images)
 
+    if images is not None and normalize_images:
+        images = images.rechunk((1, *images.shape[1:]))
+        if normalize_kwargs is None:
+            normalize_kwargs = {}
+        images = images.map_blocks(normalize_image, **normalize_kwargs)
+
     if scale is None:
         scale = (1.0,) * labels.ndim
 

src/hoct/tracking/_tracklet_solver.py

@@ -157,8 +157,6 @@ def _tracklet_graph(
             list(tracklet_edges_df.iter_rows(named=True)),
         )
 
-        tracklet_graph.summary(attrs_stats=True)
-
         tracklet_invalid_edges = tracklet_graph.edge_attrs().filter(pl.col("delta_t") <= 0)
         if len(tracklet_invalid_edges) > 0:
             raise ValueError(