Fixes for numpy-2.0 (#81)

This patch fixes a couple of deprecations/dependency changes. * Resolved issues with numpy-2.0: replaced numpy.VisibleDeprecationWarning, upgraded pybind11 to 2.13.2 * Fixed issues with clang-format, which destroyed the jupyter notebooks * Updated CI scripts analog to iminuit * Dropped support for python-3.8 --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
scikit-hep · Oct 10, 2024 · 997dfc6 · 997dfc6
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commit 997dfc6
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Showing 18 changed files with 159 additions and 123 deletions.
diff --git a/.clang-format-ignore b/.clang-format-ignore
@@ -0,0 +1,2 @@
+docs/examples/*
+extern/*
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -14,24 +14,24 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-      with:
-        submodules: true
-        fetch-depth: 0  # needed for setuptools_scm
-    # must come after checkout
-    - uses: hendrikmuhs/[email protected]
-      with:
-        key: ${{ github.job }}-${{ matrix.os }}-${{ matrix.python-version }}
-    - uses: actions/setup-python@v4
-      with:
-        python-version: "3.9"
-    - run: sudo apt-get install pandoc
-    - run: python -m pip install --prefer-binary -v .[doc]
-    - run: python -m ipykernel install --user --name python3
-    - run: python docs/build.py
-    - uses: actions/upload-pages-artifact@v1
-      with:
-        path: 'docs/_build/html'
+      - uses: actions/checkout@v3
+        with:
+          submodules: true
+          fetch-depth: 0 # needed for setuptools_scm
+      # must come after checkout
+      - uses: hendrikmuhs/[email protected]
+        with:
+          key: ${{ github.job }}-${{ matrix.os }}-${{ matrix.python-version }}
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+      - run: sudo apt-get install pandoc
+      - run: python -m pip install --prefer-binary -v .[doc]
+      - run: python -m ipykernel install --user --name python3
+      - run: python docs/build.py
+      - uses: actions/upload-pages-artifact@v1
+        with:
+          path: "docs/_build/html"
 
   deploy:
     if: github.ref_type == 'tag' || github.ref_name == 'main'
@@ -49,5 +49,5 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/configure-pages@v2
-    - uses: actions/deploy-pages@v1
+      - uses: actions/configure-pages@v2
+      - uses: actions/deploy-pages@v1
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -3,9 +3,9 @@ name: Test
 on:
   pull_request:
     paths-ignore:
-      - 'docs/**'
-      - '*.rst'
-      - '*.md'
+      - "docs/**"
+      - "*.rst"
+      - "*.md"
   workflow_dispatch:
 
 concurrency:
@@ -22,27 +22,31 @@ jobs:
           # version number must be string, otherwise 3.10 becomes 3.1
           - os: windows-latest
             python-version: "3.11"
-          - os: macos-13
-            python-version: "3.8"
+            installs: "numpy>=2"
+          - os: macos-14
+            python-version: "3.9"
+            installs: "numpy==1.21.0"
           - os: ubuntu-latest
-            python-version: "pypy-3.8"
+            python-version: "3.13"
+            installs: "'numpy>=2' scipy matplotlib"
       fail-fast: false
     steps:
-    - uses: actions/checkout@v3
-      with:
-        submodules: true
-        fetch-depth: 3
-    # must come after checkout
-    - uses: hendrikmuhs/[email protected]
-      with:
-        key: ${{ github.job }}-${{ matrix.os }}-${{ matrix.python-version }}
-    - uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-    - run: python -m pip install --upgrade pip
-    - run: python -m pip install --prefer-binary -v .[test]
-      env:
-        DEBUG: 1
-    - uses: ts-graphviz/setup-graphviz@v1
-      if: ${{ matrix.os != 'macos-13' }}
-    - run: python -m pytest
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+          fetch-depth: 3
+      # must come after checkout
+      - uses: hendrikmuhs/[email protected]
+        with:
+          key: ${{ github.job }}-${{ matrix.os }}-${{ matrix.python-version }}
+      - uses: astral-sh/setup-uv@v3
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          allow-prereleases: true
+      - uses: ts-graphviz/setup-graphviz@v1
+        if: ${{ matrix.os != 'macos-13' }}
+      - run: uv pip install --system .[test] ${{ matrix.installs }}
+        env:
+          DEBUG: 1
+      - run: python -m pytest
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -3,7 +3,7 @@ name: Wheels
 on:
   push:
     tags:
-      - '**'
+      - "**"
   workflow_dispatch:
 
 concurrency:
@@ -22,40 +22,33 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-13]
-        arch: [auto, aarch64, universal2]
-        py: [cp38, cp39, cp310, cp311, cp312]
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+        arch: [auto, aarch64]
+        py: [cp39, cp310, cp311, cp312, cp313]
         exclude:
           - os: windows-latest
             arch: aarch64
-          - os: windows-latest
-            arch: universal2
           - os: macos-13
             arch: aarch64
-          - os: ubuntu-latest
-            arch: universal2
-          # some unrelated error with installing pillow
-          - os: ubuntu-latest
-            py: cp38
-    env:
-      CIBW_BUILD: ${{ matrix.py }}-*
-      CIBW_ARCHS_LINUX: ${{ matrix.arch }}
+          - os: macos-14
+            arch: aarch64
     steps:
       - uses: actions/checkout@v4
         with:
           submodules: true
-          fetch-depth: 0  # needed by setuptools_scm
+          fetch-depth: 0 # needed by setuptools_scm
 
       - if: ${{ matrix.arch == 'aarch64' }}
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
 
-      - uses: pypa/cibuildwheel@v2.16.5
+      - uses: pypa/cibuildwheel@v2.21
         env:
           CIBW_BUILD: ${{ matrix.py }}-*
           CIBW_ARCHS: ${{ matrix.arch }}
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: wheel-${{ matrix.py }}-${{ matrix.os }}-${{ matrix.arch }}
           path: ./wheelhouse/*.whl
 
   sdist:
@@ -65,28 +58,39 @@ jobs:
       - uses: actions/checkout@v4
         with:
           submodules: true
-          fetch-depth: 0  # needed by setuptools_scm
+          fetch-depth: 0 # needed by setuptools_scm
 
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.11'
+          python-version: "3.11"
 
-      - run: python -m pip install --upgrade pip setuptools wheel
-      - run: python setup.py sdist
+      - run: pipx run build --sdist
+      - run: python -m pip install --upgrade pip setuptools
       - run: python -m pip install -v $(echo dist/*)'[test]'
       - run: python -m pytest
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: sdist
           path: dist/*.tar.gz
 
   upload:
+    if: github.event_name == 'push' && contains(github.event.ref, '/tags/')
     needs: [wheels, sdist]
     runs-on: ubuntu-latest
-    if: github.event_name == 'push' && contains(github.event.ref, '/tags/')
+
+    environment:
+      name: pypi
+      url: https://pypi.org/project/pyhepmc/
+
+    permissions:
+      id-token: write
+      attestations: write
+
     steps:
       - uses: actions/[email protected]
         with:
+          pattern: "*"
           name: artifact
           path: dist
 

diff --git a/.gitignore b/.gitignore
@@ -4,9 +4,10 @@ var
 build
 dist
 *.pyc
+*.pyd
 *.so
 *.egg-info
-tests/__pycache__
+__pycache__
 .eggs
 .cache
 .compiler_support_cache
@@ -17,6 +18,7 @@ py??
 py???
 .ci_bak
 venv
+.venv
 .coverage
 htmlcov
 src/pyhepmc/_version.py

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -15,7 +15,7 @@
 repos:
 # Standard hooks
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.6.0
+  rev: v5.0.0
   hooks:
   - id: check-case-conflict
   - id: check-docstring-first
@@ -35,20 +35,20 @@ repos:
 
 # Python formatting
 - repo: https://github.com/psf/black-pre-commit-mirror
-  rev: 24.4.2
+  rev: 24.10.0
   hooks:
   - id: black
 
 # Ruff linter, replacement for flake8, pydocstyle, isort
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: 'v0.4.5'
+  rev: 'v0.6.9'
   hooks:
     - id: ruff
       args: [--fix, --show-fixes]
 
 # C++ formatting
 - repo: https://github.com/pre-commit/mirrors-clang-format
-  rev: v18.1.5
+  rev: v19.1.1
   hooks:
   - id: clang-format
 
@@ -63,7 +63,7 @@ repos:
 
 # Python type checking
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: 'v1.10.0'
+  rev: 'v1.11.2'
   hooks:
   - id: mypy
     # additional_dependencies: [numpy]

diff --git a/docs/conf.py b/docs/conf.py
@@ -6,7 +6,6 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 import pyhepmc
-import os
 
 project = "pyhepmc"
 copyright = "2022, Hans Dembinski"
@@ -30,13 +29,7 @@
 
 html_static_path = ["_static"]
 
-on_rtd = os.environ.get("READTHEDOCS", None) == "True"
-if not on_rtd:
-    # Import and set the theme if we're building docs locally
-    import sphinx_rtd_theme
-
-    html_theme = "sphinx_rtd_theme"
-    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+html_theme = "sphinx_rtd_theme"
 
 # Autodoc options
 autodoc_member_order = "groupwise"

diff --git a/extern/pybind11 b/extern/pybind11
diff --git a/pyproject.toml b/pyproject.toml
@@ -10,12 +10,9 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "pyhepmc"
 description = "Pythonic interface to the HepMC3 C++ library licensed under LGPL-v3."
-maintainers = [
-    { name = "Hans Dembinski" },
-    { email = "[email protected]" },
-]
+maintainers = [{ name = "Hans Dembinski", email = "[email protected]" }]
 readme = "README.rst"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 license = { text = "BSD 3-Clause License" }
 classifiers = [
     "Development Status :: 5 - Production/Stable",
@@ -27,7 +24,7 @@ classifiers = [
     "Topic :: Scientific/Engineering",
     "Intended Audience :: Developers",
 ]
-dependencies = ["numpy"]
+dependencies = ["numpy>=1.21", "packaging"]
 dynamic = ["version"]
 
 [project.urls]
@@ -54,8 +51,9 @@ testpaths = ["tests"]
 log_cli_level = "INFO"
 xfail_strict = true
 filterwarnings = [
+    "error::PendingDeprecationWarning",
     "error::DeprecationWarning",
-    "error::numpy.VisibleDeprecationWarning",
+    "error::FutureWarning",
 ]
 
 [tool.coverage.run]
@@ -66,10 +64,10 @@ source = ["pyhepmc"]
 exclude_lines = ["pragma: no cover"]
 
 [tool.ruff]
-src = ["src"]
+exclude = ["docs/examples/*"]
 
 [tool.ruff.lint]
-select = [
+extend-select = [
     "E",
     "F", # flake8
     "D", # pydocstyle

diff --git a/src/equal.cpp b/src/equal.cpp
@@ -9,10 +9,21 @@
 #include <HepMC3/GenParticle.h>
 #include <HepMC3/GenRunInfo.h>
 #include <HepMC3/GenVertex.h>
+#include <type_traits>
 
 namespace HepMC3 {
 
+template <class...>
+using void_t = void;
+
+template <class, class = void>
+struct has_unequal_op : std::false_type {};
+
 template <class T>
+struct has_unequal_op<T, void_t<decltype(std::declval<T>() != std::declval<T>())>>
+    : std::true_type {};
+
+template <class T, class = std::enable_if_t<!has_unequal_op<T>::value>>
 bool operator!=(const T& a, const T& b) {
   return !operator==(a, b);
 }

diff --git a/src/io.cpp b/src/io.cpp
@@ -70,7 +70,7 @@ void register_io(py::module& m) {
       .def(py::init<>())
       .def(py::init<std::string>())
       .def("__str__",
-           (std::string(std::stringstream::*)() const) & std::stringstream::str);
+           (std::string(std::stringstream::*)() const)&std::stringstream::str);
 
   py::class_<Reader>(m, "Reader")
       // clang-format off