add github actions, format, lint, update version number

Author: pattonw

.github/workflows/publish.yaml

@@ -0,0 +1,37 @@
+name: Publish
+
+permissions:
+  id-token: write
+
+on:
+  push:
+    tags: "*"
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.11"
+      - name: Install pypa/build
+        run: >-
+          python -m
+          pip install
+          build
+          --user
+      - name: Build a binary wheel and a source tarball
+        run: >-
+          python -m
+          build
+          --sdist
+          --wheel
+          --outdir dist/
+      - name: Publish distribution 📦 to PyPI
+        if: startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/ruff.yaml

@@ -0,0 +1,17 @@
+name: Python Ruff
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    name: Python Lint
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup checkout
+        uses: actions/checkout@master
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Lint with ruff
+        run: uvx ruff check src tests

.github/workflows/tests.yaml

@@ -0,0 +1,28 @@
+name: Test
+
+on:
+  push:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+        resolution: ["highest", "lowest-direct"]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+
+    - name: pytest
+      run: uv run --extra dev --resolution ${{ matrix.resolution }} --python ${{ matrix.python-version}} pytest --cov=src tests
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v2
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        fail_ci_if_error: false

.github/workflows/ty.yaml

@@ -0,0 +1,17 @@
+name: ty
+
+on: [push, pull_request]
+
+jobs:
+  static-analysis:
+    name: ty
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup checkout
+        uses: actions/checkout@v2
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: ty
+        run: uv run --extra dev ty check

pyproject.toml

@@ -21,19 +21,17 @@ requires-python = ">=3.11"
 dependencies = ["funlib.geometry>=0.3", "scipy>=1.15.3"]
 
 [project.optional-dependencies]
-dev = ["pytest>=8.0", "pytest-cov>=5.0", "mypy>=1.0", "ruff>=0.6"]
-scratch = [
-    "dacapo-toolbox>=1.0.0",
-    "lsds",
-    "matplotlib>=3.10.6",
+dev = [
+    "pytest>=8.0",
+    "pytest-cov>=5.0",
+    "ruff>=0.6",
+    "ty>=0.0.1a21",
 ]
+scratch = ["dacapo-toolbox>=1.0.0", "lsds", "matplotlib>=3.10.6"]
 
 [tool.setuptools.dynamic]
 version = { attr = "lsd_lite.__version__" }
 
-[tool.setuptools.packages.find]
-include = ["lsd_lite*"]
-
 [tool.ruff]
 lint.select = ["F", "W", "I001"]
 

lsd_lite/__init__.py renamed to src/lsd_lite/__init__.py

@@ -3,5 +3,5 @@
 
 __all__ = ["get_affs", "get_lsds"]
 
-__version__ = "0.0.0"
+__version__ = "1.0.0"
 __version_info__ = tuple(int(i) for i in __version__.split("."))

lsd_lite/affs.py renamed to src/lsd_lite/affs.py

@@ -1,6 +1,7 @@
-from numpy.typing import ArrayLike, NDArray
 from typing import Callable, Sequence
+
 import numpy as np
+from numpy.typing import ArrayLike, NDArray
 
 
 def eq(x: NDArray, y: NDArray) -> NDArray:

lsd_lite/lsds.py renamed to src/lsd_lite/lsds.py

@@ -1,10 +1,11 @@
+import functools
+import logging
 from collections.abc import Sequence
+
+import numpy as np
 from funlib.geometry import Coordinate
 from numpy.lib.stride_tricks import as_strided
 from scipy.ndimage import convolve, gaussian_filter
-import functools
-import logging
-import numpy as np
 
 logger = logging.getLogger(__name__)
 
@@ -181,15 +182,13 @@ def get_lsds(
             variance[d] /= sigma[d] ** 2
 
         # reset 0 mass regions (this was set to 1 above to avoid nans)
-        mass = (mass * ~mass_mask)
+        mass = mass * ~mass_mask
 
         if dims == 3 and use_paper_ordering:
             # rearrange for backwards compatibility
             pearson = pearson[[0, 2, 1]]
 
-        descriptor = np.concatenate(
-            (mean_offset, variance, pearson, mass[None, :])
-        )
+        descriptor = np.concatenate((mean_offset, variance, pearson, mass[None, :]))
         descriptor = upsample(descriptor, df)
         label_descriptors.append(descriptor * (segmentation == label)[None, ...])
 

tests/conftest.py

@@ -1,4 +1,5 @@
 from pathlib import Path
+
 import numpy as np
 import pytest
 

tests/test_affs.py

@@ -1,7 +1,8 @@
-from lsd_lite import get_affs
 import numpy as np
 import pytest
 
+from lsd_lite import get_affs
+
 NEIGHBORHOODS = {
     "1d": [[1], [0]],
     "2d": [[1, 0], [0, 1]],