Support NumPy 2

.github/workflows/release.yml

@@ -37,24 +37,17 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        arch: [auto, aarch64, universal2]
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+        arch: [auto, aarch64]
         py: [cp38, cp39, cp310, cp311, cp312]
         exclude:
           - os: windows-latest
             arch: aarch64
-          - os: windows-latest
-            arch: universal2
-          - os: macos-latest
+          - os: macos-13
+            arch: aarch64
+          - os: macos-14
             arch: aarch64
-          - os: macos-latest
-            arch: auto
-          - os: ubuntu-latest
-            arch: universal2
-
-    env:
-      CIBW_BUILD: ${{ matrix.py }}-*
-      CIBW_ARCHS_LINUX: ${{ matrix.arch }}
+
     steps:
       - uses: actions/checkout@v4
         with:
@@ -63,7 +56,7 @@ jobs:
       - if: ${{ matrix.arch == 'aarch64' }}
         uses: docker/setup-qemu-action@v3
 
-      - uses: pypa/cibuildwheel@v2.16.5
+      - uses: pypa/cibuildwheel@v2.17.0
         env:
           CIBW_BUILD: ${{ matrix.py }}-*
           CIBW_ARCHS: ${{ matrix.arch }}

.github/workflows/test.yml

@@ -18,15 +18,19 @@ jobs:
 
     strategy:
       matrix:
-        os: [windows-latest, macos-latest, ubuntu-latest]
         include:
           # version number must be string, otherwise 3.10 becomes 3.1
           - os: windows-latest
             python-version: "3.11"
+            installs: "numpy>=2.0.0rc1"
           - os: macos-latest
             python-version: "3.8"
+            installs: "'numpy==1.21.0'"
           - os: ubuntu-latest
             python-version: "pypy-3.8"
+          - os: ubuntu-latest
+            python-version: "3.12"
+            installs: "'numpy>=2.0.0rc1' scipy matplotlib"
       fail-fast: false
     steps:
     - uses: actions/checkout@v4
@@ -41,8 +45,8 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - run: python -m pip install --upgrade pip wheel
     # python -m pip install .[test] is not used here to test minimum (faster),
-    # the cov workflow runs all tests
-    - run: python -m pip install -v . pytest
+    # the cov workflow runs all tests.
+    - run: python -m pip install -v . pytest ${{ matrix.installs }}
     - run: python -m pytest
 
   # aarch64:

.pre-commit-config.yaml

@@ -68,3 +68,14 @@ repos:
     additional_dependencies: [numpy]
     args: [src]
     pass_filenames: false
+
+- repo: https://github.com/python-jsonschema/check-jsonschema
+  rev: 0.28.0
+  hooks:
+  - id: check-readthedocs
+  - id: check-github-workflows
+
+- repo: https://github.com/henryiii/validate-pyproject-schema-store
+  rev: 2024.03.25
+  hooks:
+  - id: validate-pyproject

doc/notebooks/hesse_and_minos.ipynb

@@ -1,5 +1,5 @@
 {
- "cells": [
+  "cells": [
   {
    "attachments": {},
    "cell_type": "markdown",

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["scikit-build-core[pyproject]>=0.3", "pybind11"]
+requires = ["scikit-build-core[pyproject]>=0.5", "pybind11>=2.12"]
 build-backend = "scikit_build_core.build"
 
 [project]
@@ -33,7 +33,7 @@ classifiers = [
     "Operating System :: Unix",
     "Operating System :: MacOS",
 ]
-dependencies = ["numpy >= 1.21", "typing_extensions;python_version < '3.9'"]
+dependencies = ["numpy >=1.21", "typing_extensions >=3.7.4; python_version<'3.9'"]
 
 [project.urls]
 repository = "http://github.com/scikit-hep/iminuit"
@@ -75,7 +75,7 @@ doc = [
 ]
 
 [tool.scikit-build]
-minimum-version = "0.3"
+minimum-version = "0.5"
 build-dir = "build/{wheel_tag}"
 sdist.exclude = ["extern/root"]
 sdist.include = ["extern/root/math/minuit2/inc", "extern/root/math/minuit2/src"]
@@ -87,7 +87,7 @@ log_cli_level = "INFO"
 testpaths = ["tests"]
 xfail_strict = true
 filterwarnings = [
-    "error::numpy.VisibleDeprecationWarning",
+    "error::iminuit._exceptions.VisibleDeprecationWarning",
     "error::PendingDeprecationWarning",
     "error::DeprecationWarning",
     "error::FutureWarning",
@@ -126,7 +126,7 @@ no_implicit_optional = false
 
 [tool.cibuildwheel]
 # update skip when numpy wheels become available
-skip = ["*-musllinux_*", "cp31?-win32", "cp31?-manylinux_i686"]
+skip = ["*-musllinux_*", "cp31?-manylinux_i686"]
 test-requires = "pytest"
 test-command = "python -m pytest {package}/tests"
 test-skip = ["*universal2:arm64"]

src/iminuit/_deprecated.py

@@ -1,5 +1,5 @@
 import warnings
-from numpy import VisibleDeprecationWarning
+from ._exceptions import VisibleDeprecationWarning
 
 
 class deprecated:

src/iminuit/_exceptions.py

@@ -0,0 +1,7 @@
+# NumPy 2 and recent 1.x place this in exceptions
+try:
+    from numpy.exceptions import VisibleDeprecationWarning
+except ImportError:
+    from numpy import VisibleDeprecationWarning
+
+__all__ = ["VisibleDeprecationWarning"]

src/iminuit/cost.py

@@ -92,6 +92,7 @@ class documentation for details.
     is_positive_definite,
 )
 from .typing import Model, ModelGradient, LossFunction
+from ._exceptions import VisibleDeprecationWarning
 import numpy as np
 from numpy.typing import NDArray, ArrayLike
 from collections.abc import Sequence as ABCSequence
@@ -1521,7 +1522,7 @@ def __init__(self, n, xe, model, verbose, grad, use_pdf):
                 self._model_xm = self._model_xe[:-1] + 0.5 * dx
         else:
             self._xe_shape = tuple(len(xei) for xei in self.xe)
-            self._model_xe = np.row_stack(
+            self._model_xe = np.vstack(
                 [x.flatten() for x in np.meshgrid(*self.xe, indexing="ij")]
             )
             if use_pdf == "approximate":
@@ -1754,7 +1755,7 @@ def __init__(
         if method == "hpd":
             warnings.warn(
                 "key 'hpd' is deprecated, please use 'da' instead",
-                category=np.VisibleDeprecationWarning,
+                category=VisibleDeprecationWarning,
                 stacklevel=2,
             )
 
@@ -1765,7 +1766,7 @@ def __init__(
             self._model_xe = _norm(self.xe)
         else:
             self._xe_shape = tuple(len(xei) for xei in self.xe)
-            self._model_xe = np.row_stack(
+            self._model_xe = np.vstack(
                 [x.flatten() for x in np.meshgrid(*self.xe, indexing="ij")]
             )
         self._model_len = np.prod(self._xe_shape)
@@ -2473,7 +2474,11 @@ def _normalize_output(x, kind, *shape, msg=None):
     if x.ndim < len(shape):
         return x.reshape(*shape)
     elif x.shape != shape:
-        msg = f"output of {kind} has shape {x.shape!r}, but {shape!r} is required"
+        # NumPy 2 uses a numpy int here
+        pretty_shape = tuple(int(i) for i in shape)
+        msg = (
+            f"output of {kind} has shape {x.shape!r}, but {pretty_shape!r} is required"
+        )
         raise ValueError(msg)
     return x
 
@@ -2504,7 +2509,7 @@ def __getattr__(name: str) -> Any:
         new_name, obj = _deprecated_content[name]
         warnings.warn(
             f"{name} was renamed to {new_name}, please import {new_name} instead",
-            np.VisibleDeprecationWarning,
+            VisibleDeprecationWarning,
             stacklevel=2,
         )
         return obj

tests/test_cost.py

@@ -18,6 +18,7 @@
 )
 from iminuit.util import describe
 from iminuit.typing import Annotated, Gt, Lt
+from iminuit._exceptions import VisibleDeprecationWarning
 from typing import Sequence
 import pickle
 
@@ -320,9 +321,7 @@ def test_UnbinnedNLL_visualize(log):
     # manual spacing
     c.visualize((1, 2), model_points=np.linspace(1, 1000))
 
-    with pytest.warns(
-        np.VisibleDeprecationWarning, match="keyword 'nbins' is deprecated"
-    ):
+    with pytest.warns(VisibleDeprecationWarning, match="keyword 'nbins' is deprecated"):
         c.visualize((1, 2), nbins=20)
 
 
@@ -1909,23 +1908,23 @@ def test_Template_pulls():
 def test_deprecated():
     from iminuit import cost
 
-    with pytest.warns(np.VisibleDeprecationWarning):
+    with pytest.warns(VisibleDeprecationWarning):
         from iminuit.cost import BarlowBeestonLite
     assert BarlowBeestonLite is cost.Template
 
-    with pytest.warns(np.VisibleDeprecationWarning):
+    with pytest.warns(VisibleDeprecationWarning):
         from iminuit.cost import barlow_beeston_lite_chi2_jsc
     assert barlow_beeston_lite_chi2_jsc is cost.template_chi2_jsc
 
-    with pytest.warns(np.VisibleDeprecationWarning):
+    with pytest.warns(VisibleDeprecationWarning):
         from iminuit.cost import barlow_beeston_lite_chi2_hpd
     assert barlow_beeston_lite_chi2_hpd is cost.template_chi2_da
 
 
 def test_deprecated_Template_method():
     from iminuit import cost
 
-    with pytest.warns(np.VisibleDeprecationWarning):
+    with pytest.warns(VisibleDeprecationWarning):
         t = Template([1], [2, 3], [[1], [2]], method="hpd")
         t._impl is cost.template_chi2_da
 
@@ -1967,7 +1966,7 @@ def cdf(xye, a):
 def test_BohmZechTransform():
     from iminuit.cost import BohmZechTransform
 
-    with pytest.warns(np.VisibleDeprecationWarning):
+    with pytest.warns(VisibleDeprecationWarning):
         val = np.array([1.0, 2.0])
         var = np.array([3.0, 4.0])
         tr = BohmZechTransform(val, var)

tests/test_deprecated.py

@@ -1,14 +1,14 @@
 from iminuit._deprecated import deprecated, deprecated_parameter
+from iminuit._exceptions import VisibleDeprecationWarning
 import pytest
-import numpy as np
 
 
 def test_deprecated_func():
     @deprecated("bla")
     def func(x):
         pass
 
-    with pytest.warns(np.VisibleDeprecationWarning, match="func is deprecated: bla"):
+    with pytest.warns(VisibleDeprecationWarning, match="func is deprecated: bla"):
         func(1)
 
 
@@ -20,7 +20,7 @@ def some_function(x, y, foo):
     some_function(1, 2, foo=3)
 
     with pytest.warns(
-        np.VisibleDeprecationWarning,
+        VisibleDeprecationWarning,
         match="keyword 'bar' is deprecated, please use 'foo'",
     ):
         some_function(1, 2, bar=3)

tests/test_describe.py

@@ -1,5 +1,6 @@
 from iminuit.util import describe, make_func_code
 from iminuit.typing import Annotated, Gt, Lt, Ge, Le, Interval
+from iminuit._exceptions import VisibleDeprecationWarning
 from math import ldexp
 import platform
 from functools import wraps
@@ -94,7 +95,7 @@ def __init__(self):
         def __call__(self, *args):
             pass
 
-    with pytest.warns(np.VisibleDeprecationWarning):
+    with pytest.warns(VisibleDeprecationWarning):
         assert describe(A()) == ["x", "y"]
 
 

tests/test_minuit.py

@@ -6,6 +6,7 @@
 from iminuit.util import Param, make_func_code
 from iminuit.warnings import IMinuitWarning, ErrordefAlreadySetWarning
 from iminuit.typing import Annotated
+from iminuit._exceptions import VisibleDeprecationWarning
 from pytest import approx
 from argparse import Namespace
 
@@ -193,7 +194,7 @@ def test_Func1():
 
 
 def test_Func2():
-    with pytest.warns(np.VisibleDeprecationWarning):
+    with pytest.warns(VisibleDeprecationWarning):
         func_test_helper(Func2())