Merge pull request #33 from sigma-py/up

some updates

.github/workflows/release.yml

@@ -0,0 +1,33 @@
+name: Release
+
+on:
+  release:
+    types: [released]
+
+jobs:
+  build-upload:
+    name: Build and upload to PyPI
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write # required for pypi upload
+      contents: read # required for checkout
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Build stubs
+        run: |
+          pip install mypy
+          stubgen --include-docstrings src/ -o src/
+
+      - name: Build wheels
+        run: |
+          pip install build
+          python3 -m build --wheel
+
+      - name: Upload to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

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

@@ -13,26 +13,28 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repo
-        uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/checkout@v4
       - name: Run pre-commit
-        uses: pre-commit/action@v2.0.3
+        uses: pre-commit/action@v3.0.0
 
   build:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.7", "3.12"]
     steps:
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - uses: actions/checkout@v2
+          allow-prereleases: true
+
+      - uses: actions/checkout@v4
+
       - name: Test with tox
         run: |
           pip install tox
           tox -- --cov npx --cov-report xml --cov-report term
+
       - name: Submit to codecov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v4
         if: ${{ matrix.python-version == '3.9' }}

.pre-commit-config.yaml

@@ -1,16 +1,23 @@
 repos:
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.1.15
     hooks:
-      - id: isort
+      - id: ruff
 
-  - repo: https://github.com/psf/black
-    rev: 22.1.0
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.1.0
     hooks:
-      - id: black
-        language_version: python3
+      - id: prettier
 
-  - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
     hooks:
-      - id: flake8
+      - id: codespell
+        # args: ["-L", "sur,nd"]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.8.0
+    hooks:
+      - id: mypy
+        files: src
+        args: ["--install-types", "--non-interactive"]

CODE_OF_CONDUCT.md

@@ -14,21 +14,21 @@ appearance, race, religion, or sexual identity and orientation.
 Examples of behavior that contributes to creating a positive environment
 include:
 
-* Using welcoming and inclusive language
-* Being respectful of differing viewpoints and experiences
-* Gracefully accepting constructive criticism
-* Focusing on what is best for the community
-* Showing empathy towards other community members
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
+- Showing empathy towards other community members
 
 Examples of unacceptable behavior by participants include:
 
-* The use of sexualized language or imagery and unwelcome sexual attention or
+- The use of sexualized language or imagery and unwelcome sexual attention or
   advances
-* Trolling, insulting/derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or electronic
+- Trolling, insulting/derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or electronic
   address, without explicit permission
-* Other conduct which could reasonably be considered inappropriate in a
+- Other conduct which could reasonably be considered inappropriate in a
   professional setting
 
 ## Our Responsibilities
@@ -74,4 +74,3 @@ available at https://www.contributor-covenant.org/version/1/4/code-of-conduct/
 
 For answers to common questions about this code of conduct, see
 https://www.contributor-covenant.org/faq/
-

CONTRIBUTING.md

@@ -1,7 +1,7 @@
 # npx contributing guidelines
 
 The npx community appreciates your contributions via issues and
-pull requests.  Note that the [code of conduct](CODE_OF_CONDUCT.md)
+pull requests. Note that the [code of conduct](CODE_OF_CONDUCT.md)
 applies to all interactions with the npx project, including
 issues and pull requests.
 

LICENSE

@@ -1,4 +1,4 @@
-Copyright 2021-2022 Nico Schlömer
+Copyright 2021-present Nico Schlömer
 
 Redistribution and use in source and binary forms, with or without modification, are
 permitted provided that the following conditions are met:

README.md

@@ -4,11 +4,11 @@
 [![PyPI pyversions](https://img.shields.io/pypi/pyversions/npx.svg?style=flat-square)](https://pypi.org/project/npx/)
 [![GitHub stars](https://img.shields.io/github/stars/nschloe/npx.svg?style=flat-square&logo=github&label=Stars&logoColor=white)](https://github.com/nschloe/npx)
 [![Downloads](https://pepy.tech/badge/npx/month?style=flat-square)](https://pepy.tech/project/npx)
+
 <!--[![PyPi downloads](https://img.shields.io/pypi/dm/npx.svg?style=flat-square)](https://pypistats.org/packages/npx)-->
 
 [![gh-actions](https://img.shields.io/github/workflow/status/nschloe/npx/ci?style=flat-square)](https://github.com/nschloe/npx/actions?query=workflow%3Aci)
 [![codecov](https://img.shields.io/codecov/c/github/nschloe/npx.svg?style=flat-square)](https://app.codecov.io/gh/nschloe/npx)
-[![LGTM](https://img.shields.io/lgtm/grade/python/github/nschloe/npx.svg?style=flat-square)](https://lgtm.com/projects/g/nschloe/npx)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg?style=flat-square)](https://github.com/psf/black)
 
 [NumPy](https://numpy.org/) is a large library used everywhere in scientific computing.
@@ -57,7 +57,7 @@ Solves a linear equation system with a matrix of shape `(n, n)` and an array of
 
 #### `sum_at`/`add_at`
 
-<!--pytest-codeblocks:skip-->
+<!--pytest.mark.skip-->
 
 ```python
 npx.sum_at(a, idx, minlength=0)
@@ -78,7 +78,6 @@ Relevant issue reports:
 - [ufunc.at (and possibly other methods)
   slow](https://github.com/numpy/numpy/issues/11156)
 
-
 #### `unique`
 
 ```python
@@ -95,8 +94,8 @@ npx's `unique()` works just like NumPy's, except that it provides a parameter
 is essentially partitioned into bins of size `tol` and at most one
 representative of each bin is returned.
 
-
 #### `unique_rows`
+
 ```python
 import npx
 import numpy as np

justfile

@@ -1,22 +1,20 @@
-version := `python3 -c "from src.npx.__about__ import __version__; print(__version__)"`
+version := `python -c "import tomllib; print(tomllib.load(open('pyproject.toml', 'rb'))['project']['version'])"`
 
 default:
 	@echo "\"just publish\"?"
 
 publish:
 	@if [ "$(git rev-parse --abbrev-ref HEAD)" != "main" ]; then exit 1; fi
 	gh release create "v{{version}}"
-	flit publish
 
 clean:
 	@find . | grep -E "(__pycache__|\.pyc|\.pyo$)" | xargs rm -rf
-	@rm -rf src/*.egg-info/ build/ dist/ .tox/
+	@rm -rf src/*.egg-info/ build/ dist/ .tox/ .mypy_cache/
 
 format:
-	isort .
-	black .
+	ruff --fix src/ tests/
+	black src/ tests/
 	blacken-docs README.md
 
 lint:
-	black --check .
-	flake8 .
+	pre-commit run --all

pyproject.toml

@@ -1,12 +1,10 @@
 [build-system]
-requires = ["flit_core >=3.2,<4"]
-build-backend = "flit_core.buildapi"
-
-[tool.isort]
-profile = "black"
+requires = ["setuptools>=61"]
+build-backend = "setuptools.build_meta"
 
 [project]
 name = "npx"
+version = "0.1.2"
 authors = [{name = "Nico Schlömer", email = "nico.schloemer@gmail.com"}]
 description = "Some useful extensions for NumPy"
 readme = "README.md"
@@ -22,14 +20,31 @@ classifiers = [
   "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",
   "Topic :: Scientific/Engineering",
   "Topic :: Utilities",
 ]
-dynamic = ["version"]
 requires-python = ">=3.7"
-dependencies = ["numpy >= 1.20.0"]
+dependencies = [
+  "numpy >= 1.20.0",
+  # "scipy >= 1.8",
+]
 
 [project.urls]
-Code = "https://github.com/nschloe/npx"
-Issues = "https://github.com/nschloe/npx/issues"
-Funding = "https://github.com/sponsors/nschloe"
+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"
+]
+target-version = "py38"
+
+[tool.mypy]
+ignore_missing_imports = true

src/npx/__init__.py

@@ -1,11 +1,9 @@
-from .__about__ import __version__
 from ._isin import isin_rows
 from ._main import add_at, dot, outer, solve, subtract_at, sum_at
 from ._mean import mean
 from ._unique import unique, unique_rows
 
 __all__ = [
-    "__version__",
     "dot",
     "outer",
     "solve",

src/npx/_isin.py

@@ -6,18 +6,20 @@ def isin_rows(a: ArrayLike, b: ArrayLike) -> np.ndarray:
     a = np.asarray(a)
     b = np.asarray(b)
     if not np.issubdtype(a.dtype, np.integer):
-        raise ValueError(f"Input array must be integer type, got {a.dtype}.")
+        msg = f"Input array must be integer type, got {a.dtype}."
+        raise ValueError(msg)
     if not np.issubdtype(b.dtype, np.integer):
-        raise ValueError(f"Input array must be integer type, got {b.dtype}.")
+        msg = f"Input array must be integer type, got {b.dtype}."
+        raise ValueError(msg)
 
     a = a.reshape(a.shape[0], np.prod(a.shape[1:], dtype=int))
     b = b.reshape(b.shape[0], np.prod(b.shape[1:], dtype=int))
 
     a_view = np.ascontiguousarray(a).view(
-        np.dtype((np.void, a.dtype.itemsize * a.shape[1]))
+        np.dtype((np.void, a.dtype.itemsize * a.shape[1])),
     )
     b_view = np.ascontiguousarray(b).view(
-        np.dtype((np.void, b.dtype.itemsize * b.shape[1]))
+        np.dtype((np.void, b.dtype.itemsize * b.shape[1])),
     )
 
     out = np.isin(a_view, b_view)

src/npx/_main.py

@@ -11,9 +11,9 @@ def _prod(a):
     return reduce(mul, a, 1)
 
 
-def dot(a: np.ndarray, b: np.ndarray) -> np.ndarray:
-    """Take arrays `a` and `b` and form the dot product between the last axis of `a` and
-    the first of `b`.
+def dot(a: ArrayLike, b: np.ndarray) -> np.ndarray:
+    """Take arrays `a` and `b` and form the dot product between the last axis
+    of `a` and the first of `b`.
     """
     return np.tensordot(a, b, 1)
 
@@ -37,26 +37,27 @@ def solve(A: np.ndarray, x: np.ndarray) -> np.ndarray:
 
 
 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 faster than numpy's
-    own np.add.at (see
+    """Sums up values `a` with `indices` into an output array of at least
+    length `minlength` while treating dimensionality correctly. It's a lot
+    faster than numpy's own np.add.at (see
     https://github.com/numpy/numpy/issues/5922#issuecomment-511477435).
 
     Typically, `indices` will be a one-dimensional array; `a` can have any
     dimensionality. In this case, the output array will have shape (minlength,
     a.shape[1:]).
 
-    `indices` may have arbitrary shape, too, but then `a` has to start out the same.
-    (Those dimensions are flattened out in the computation.)
+    `indices` may have arbitrary shape, too, but then `a` has to start out the
+    same. (Those dimensions are flattened out in the computation.)
     """
     a = np.asarray(a)
     indices = np.asarray(indices)
 
     if len(a.shape) < len(indices.shape):
-        raise RuntimeError(
+        msg = (
             f"a.shape = {a.shape}, indices.shape = {indices.shape}, "
             "but len(a.shape) >= len(indices.shape) is required."
         )
+        raise RuntimeError(msg)
 
     m = len(indices.shape)
     assert indices.shape == a.shape[:m]
@@ -74,7 +75,7 @@ def sum_at(a: ArrayLike, indices: ArrayLike, minlength: int):
         [
             np.bincount(indices, weights=a[:, k], minlength=minlength)
             for k in range(a.shape[1])
-        ]
+        ],
     ).T.reshape(out_shape)