Deprecate add at

.github/workflows/release.yml

@@ -13,21 +13,16 @@ jobs:
       contents: read # required for checkout
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
-      - uses: actions/setup-python@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
         with:
-          python-version: "3.11"
+          enable-cache: true
 
-      - name: Build stubs
-        run: |
-          pip install mypy
-          stubgen --include-docstrings src/ -o src/
+      - name: Build package
+        run: uv build
 
-      - name: Build wheels
-        run: |
-          pip install build
-          python3 -m build --wheel
-
-      - name: Upload to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+      - name: Publish to PyPI
+        # uv publish automatically detects the OIDC token in GitHub Actions
+        run: uv publish

.github/workflows/tests.yml

@@ -13,28 +13,24 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repo
-        uses: actions/checkout@v4
-      - name: Run pre-commit
-        uses: pre-commit/action@v3.0.1
+        uses: actions/checkout@v6
+      - name: Run prek
+        uses: j178/prek-action@v2
 
   build:
+    needs: [lint]
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.12"]
+        python-version: ["3.10", "3.14"]
     steps:
-      - uses: actions/setup-python@v5
+      - uses: actions/checkout@v6
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
         with:
           python-version: ${{ matrix.python-version }}
-          allow-prereleases: true
-
-      - uses: actions/checkout@v4
 
-      - name: Test with tox
+      - name: Test
         run: |
-          pip install tox
-          tox -- --cov npx --cov-report xml --cov-report term
-
-      - name: Submit to codecov
-        uses: codecov/codecov-action@v4
-        if: ${{ matrix.python-version == '3.9' }}
+          uv run pytest --cov npx --cov-report term

.pre-commit-config.yaml

@@ -1,22 +1,23 @@
 repos:
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.4.10
+    rev: v0.15.12
     hooks:
-      - id: ruff
+      - id: ruff-check
+      - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: v3.1.0
     hooks:
       - id: prettier
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.2
     hooks:
       - id: codespell
         # args: ["-L", "sur,nd"]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.10.0
+    rev: v1.20.2
     hooks:
       - id: mypy
         files: src

justfile

@@ -12,9 +12,12 @@ clean:
 	@rm -rf src/*.egg-info/ build/ dist/ .tox/ .mypy_cache/
 
 format:
-	ruff --fix src/ tests/
-	black src/ tests/
+	ruff format src/ tests/
+	ruff check --fix src/ tests/
 	blacken-docs README.md
 
 lint:
-	pre-commit run --all
+	prek run --all-files
+
+test *args:
+  uv run pytest -W error {{args}}

pyproject.toml

@@ -4,47 +4,56 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "npx"
-version = "0.1.6"
-authors = [{name = "Nico Schlömer", email = "nico.schloemer@gmail.com"}]
+version = "0.1.7"
+authors = [{ name = "Nico Schlömer", email = "nico.schloemer@gmail.com" }]
 description = "Some useful extensions for NumPy"
 readme = "README.md"
-license = {file = "LICENSE"}
+license = { file = "LICENSE" }
 classifiers = [
   "Development Status :: 4 - Beta",
   "Intended Audience :: Science/Research",
   "License :: OSI Approved :: BSD License",
   "Operating System :: OS Independent",
   "Programming Language :: Python",
   "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.7",
-  "Programming Language :: Python :: 3.8",
-  "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
   "Topic :: Scientific/Engineering",
   "Topic :: Utilities",
 ]
-requires-python = ">=3.7"
+requires-python = ">=3.10"
 dependencies = [
   "numpy >= 1.20.0",
   # "scipy >= 1.8",
 ]
 
+[dependency-groups]
+dev = ["pytest", "pytest-cov"]
+
 [project.urls]
 Code = "https://github.com/sigma-py/npx"
 Issues = "https://github.com/sigma-py/npx/issues"
 
 [tool.ruff]
 src = ["src", "tests"]
 line-length = 88
-select = ["ALL"]
-ignore = [
-  "ANN", "S101", "D", "T201", "ERA", "N803", "PLR2004"
-#   "ANN", "C901", "D", "E741", "ERA", "FBT", "INP001",
-#   "N", "PLR", "S101", "T201", "TID252", "TD", "FIX002"
+lint.select = ["ALL"]
+lint.ignore = [
+  "ANN",
+  "COM812",
+  "S101",
+  "D",
+  "T201",
+  "ERA",
+  "N803",
+  "PLR2004",
+  #   "ANN", "C901", "D", "E741", "ERA", "FBT", "INP001",
+  #   "N", "PLR", "S101", "T201", "TID252", "TD", "FIX002"
 ]
-target-version = "py38"
+target-version = "py310"
 
 [tool.mypy]
 ignore_missing_imports = true

src/npx/__init__.py

@@ -4,15 +4,14 @@
 from ._unique import unique, unique_rows
 
 __all__ = [
+    "add_at",
     "dot",
+    "isin_rows",
+    "mean",
     "outer",
     "solve",
-    "sum_at",
-    "add_at",
     "subtract_at",
-    "unique_rows",
-    "isin_rows",
-    "mean",
+    "sum_at",
     "unique",
     "unique_rows",
 ]

src/npx/_helpers.py

@@ -0,0 +1,18 @@
+import warnings
+from functools import wraps
+
+
+def deprecated(reason: str):
+    def decorator(func):
+        @wraps(func)
+        def wrapper(*args, **kwargs):
+            warnings.warn(
+                f"{func.__name__}() is deprecated: {reason}",
+                DeprecationWarning,
+                stacklevel=2,
+            )
+            return func(*args, **kwargs)
+
+        return wrapper
+
+    return decorator

src/npx/_main.py

@@ -1,14 +1,9 @@
-from functools import reduce
-from operator import mul
+from math import prod
 
 import numpy as np
 from numpy.typing import ArrayLike
 
-
-# math.prod in 3.8
-# https://docs.python.org/3/library/math.html#math.prod
-def _prod(a):
-    return reduce(mul, a, 1)
+from ._helpers import deprecated
 
 
 def dot(a: ArrayLike, b: np.ndarray) -> np.ndarray:
@@ -36,6 +31,7 @@ def solve(A: np.ndarray, x: np.ndarray) -> np.ndarray:
     return np.linalg.solve(A, x.reshape(x.shape[0], -1)).reshape(x.shape)
 
 
+@deprecated("np.add.at is now equally fast. Use that.")
 def sum_at(a: ArrayLike, indices: ArrayLike, minlength: int):
     """Sums up values `a` with `indices` into an output array of at least
     length `minlength` while treating dimensionality correctly. It's a lot
@@ -49,6 +45,10 @@ def sum_at(a: ArrayLike, indices: ArrayLike, minlength: int):
     `indices` may have arbitrary shape, too, but then `a` has to start out the
     same. (Those dimensions are flattened out in the computation.)
     """
+    return _sum_at(a, indices, minlength)
+
+
+def _sum_at(a: ArrayLike, indices: ArrayLike, minlength: int):
     a = np.asarray(a)
     indices = np.asarray(indices)
 
@@ -65,7 +65,7 @@ def sum_at(a: ArrayLike, indices: ArrayLike, minlength: int):
     out_shape = (minlength, *a.shape[m:])
 
     indices = indices.reshape(-1)
-    a = a.reshape(_prod(a.shape[:m]), _prod(a.shape[m:]))
+    a = a.reshape(prod(a.shape[:m]), prod(a.shape[m:]))
 
     # Cast to int; bincount doesn't work for uint64 yet
     # https://github.com/numpy/numpy/issues/17760
@@ -79,16 +79,22 @@ def sum_at(a: ArrayLike, indices: ArrayLike, minlength: int):
     ).T.reshape(out_shape)
 
 
+@deprecated("np.add.at is now equally fast. Use that.")
 def add_at(a: ArrayLike, indices: ArrayLike, b: ArrayLike):
+    return _add_at(a, indices, b)
+
+
+def _add_at(a: ArrayLike, indices: ArrayLike, b: ArrayLike):
     a = np.asarray(a)
     indices = np.asarray(indices)
     b = np.asarray(b)
 
     m = len(indices.shape)
     assert a.shape[1:] == b.shape[m:]
-    a += sum_at(b, indices, a.shape[0])
+    a += _sum_at(b, indices, a.shape[0])
 
 
+@deprecated("np.subtract.at is now equally fast. Use that.")
 def subtract_at(a: ArrayLike, indices: ArrayLike, b: ArrayLike):
     b = np.asarray(b)
-    add_at(a, indices, -b)
+    _add_at(a, indices, -b)

src/npx/_unique.py

@@ -1,10 +1,12 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Callable
+from typing import TYPE_CHECKING
 
 import numpy as np
 
 if TYPE_CHECKING:
+    from collections.abc import Callable
+
     from numpy.typing import ArrayLike
 
 
@@ -49,6 +51,7 @@ def unique(
 
 
 def unique_rows(a: ArrayLike, **kwargs) -> np.ndarray | tuple[np.ndarray, ...]:
+    # return np.unique(a, axis=0, **kwargs)
     # The numpy alternative `np.unique(a, axis=0)` is slow; cf.
     # <https://github.com/numpy/numpy/issues/11136>.
     a = np.asarray(a)

tests/speedtest.py

@@ -1,3 +1,10 @@
+# /// script
+# dependencies = [
+#   "npx",
+#   "numpy",
+#   "perfplot",
+# ]
+# ///
 import numpy as np
 import perfplot
 
@@ -9,33 +16,34 @@
 
 
 def setup(n):
-    idx = rng.randomint(0, m, n)
+    idx = rng.integers(0, m, size=n)
     b = rng.random(n)
     return idx, b
 
 
-def np_add_at(data):
+def np_add_at(idx, b):
     a = np.zeros(m)
-    idx, b = data
     np.add.at(a, idx, b)
     return a
 
 
-def npx_add_at(data):
+def npx_add_at(idx, b):
     a = np.zeros(m)
-    idx, b = data
     npx.add_at(a, idx, b)
     return a
 
 
-def npx_sum_at(data):
-    idx, b = data
+def npx_sum_at(idx, b):
     return npx.sum_at(b, idx, minlength=m)
 
 
+def bincount(idx, b):
+    return np.bincount(idx, weights=b, minlength=m)
+
+
 b = perfplot.bench(
     setup=setup,
-    kernels=[np_add_at, npx_add_at, npx_sum_at],
+    kernels=[np_add_at, npx_add_at, npx_sum_at, bincount],
     n_range=[2**k for k in range(23)],
 )
-b.save("perf-add-at.svg")
+b.save("perf-add-at.png", transparent=False)