From 997dfc676d70e67c00e25fcc8e33ab8f043fc1b3 Mon Sep 17 00:00:00 2001
From: Hans Dembinski <HDembinski@users.noreply.github.com>
Date: Thu, 10 Oct 2024 14:37:12 +0200
Subject: [PATCH] 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>
---
 .clang-format-ignore         |  2 ++
 .github/workflows/docs.yml   | 40 +++++++++++++--------------
 .github/workflows/test.yml   | 52 +++++++++++++++++++-----------------
 .github/workflows/wheels.yml | 52 +++++++++++++++++++-----------------
 .gitignore                   |  4 ++-
 .pre-commit-config.yaml      | 10 +++----
 docs/conf.py                 |  9 +------
 extern/pybind11              |  2 +-
 pyproject.toml               | 16 +++++------
 src/equal.cpp                | 11 ++++++++
 src/io.cpp                   |  2 +-
 src/pyhepmc/__init__.py      |  3 +--
 src/pyhepmc/_deprecated.py   | 34 +++++++++++++----------
 src/pyhepmc/_graphviz.py     |  7 +++--
 src/pyhepmc/view.py          | 14 +++++-----
 tests/test_deprecated.py     | 15 ++++++++---
 tests/test_io.py             |  3 +--
 tests/test_view.py           |  6 ++++-
 18 files changed, 159 insertions(+), 123 deletions(-)
 create mode 100644 .clang-format-ignore

diff --git a/.clang-format-ignore b/.clang-format-ignore
new file mode 100644
index 0000000..d229323
--- /dev/null
+++ b/.clang-format-ignore
@@ -0,0 +1,2 @@
+docs/examples/*
+extern/*
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 635dfcc..1d01a53 100644
--- 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/ccache-action@v1.2
-      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/ccache-action@v1.2
+        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
index 44384dd..5030e1b 100644
--- 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/ccache-action@v1.2
-      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/ccache-action@v1.2
+        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
index e0d852c..72623fe 100644
--- 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/download-artifact@v4.1.7
         with:
+          pattern: "*"
           name: artifact
           path: dist
 
diff --git a/.gitignore b/.gitignore
index 9c39faf..def7a53 100644
--- 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
index 34c7624..bbdd6af 100644
--- 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
index 5f8378c..8a79ca3 100644
--- 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
index 914c06f..a2e59f0 160000
--- a/extern/pybind11
+++ b/extern/pybind11
@@ -1 +1 @@
-Subproject commit 914c06fb252b6cc3727d0eedab6736e88a3fcb01
+Subproject commit a2e59f0e7065404b44dfe92a28aca47ba1378dc4
diff --git a/pyproject.toml b/pyproject.toml
index 07dee11..c12e57e 100644
--- 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 = "hans.dembinski@gmail.com" },
-]
+maintainers = [{ name = "Hans Dembinski", email = "hans.dembinski@gmail.com" }]
 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
index cd7767a..cd67790 100644
--- 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
index 2da7c9e..38f907e 100644
--- 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
diff --git a/src/pyhepmc/__init__.py b/src/pyhepmc/__init__.py
index 3aa7131..0de189b 100644
--- a/src/pyhepmc/__init__.py
+++ b/src/pyhepmc/__init__.py
@@ -109,13 +109,12 @@
 def __getattr__(name: str) -> Any:
     from . import io
     import warnings
-    from numpy import VisibleDeprecationWarning
 
     if name in dir(io):
         warnings.warn(
             f"importing {name} from pyhepmc is deprecated, "
             "please import from pyhepmc.io",
-            category=VisibleDeprecationWarning,
+            category=DeprecationWarning,
             stacklevel=2,
         )
         return getattr(io, name)
diff --git a/src/pyhepmc/_deprecated.py b/src/pyhepmc/_deprecated.py
index 917ed6c..3f3809f 100644
--- a/src/pyhepmc/_deprecated.py
+++ b/src/pyhepmc/_deprecated.py
@@ -1,23 +1,29 @@
 import warnings
-from numpy import VisibleDeprecationWarning
-import typing as _tp
+from typing import Callable, Any
+from importlib.metadata import version
+from packaging.version import Version
+
+
+CURRENT_VERSION = Version(version("pyhepmc"))
 
 
 class deprecated:
-    def __init__(self, reason: str):
-        if not isinstance(reason, str):
-            raise ValueError("argument `reason: str` is required")
-        self._reason = reason
+    def __init__(self, reason: str, removal: str = ""):
+        assert isinstance(reason, str)
+        self.reason = reason
+        self.removal = Version(removal) if removal else None
+
+    def __call__(self, func: Callable[..., Any]) -> Callable[..., Any]:
+        category: Any = DeprecationWarning
+        extra = ""
+        if self.removal and CURRENT_VERSION < self.removal:
+            extra = f" and will be removed in version {self.removal}"
+        msg = f"{func.__name__} is deprecated{extra}: {self.reason}"
 
-    def __call__(self, func: _tp.Callable[..., _tp.Any]) -> _tp.Callable[..., _tp.Any]:
-        def decorated_func(*args: _tp.Any, **kwargs: _tp.Any) -> _tp.Any:
-            warnings.warn(
-                f"{func.__name__} is deprecated: {self._reason}",
-                category=VisibleDeprecationWarning,
-                stacklevel=2,
-            )
+        def decorated_func(*args: Any, **kwargs: Any) -> Any:
+            warnings.warn(msg, category=category, stacklevel=2)
             return func(*args, **kwargs)
 
         decorated_func.__name__ = func.__name__
-        decorated_func.__doc__ = "deprecated: " + self._reason
+        decorated_func.__doc__ = msg
         return decorated_func
diff --git a/src/pyhepmc/_graphviz.py b/src/pyhepmc/_graphviz.py
index a9d7111..c92d544 100644
--- a/src/pyhepmc/_graphviz.py
+++ b/src/pyhepmc/_graphviz.py
@@ -125,8 +125,11 @@ def pipe(self, *, format: str, encoding: str = None) -> Union[str, bytes]:
         return r.stdout
 
     def _repr_svg_(self) -> str:
-        s = self.pipe(format="svg", encoding="utf-8")
-        assert isinstance(s, str)
+        try:
+            s = self.pipe(format="svg", encoding="utf-8")
+            assert isinstance(s, str)
+        except FileNotFoundError as e:
+            return f"SVG view not available: {e.args[0]}"
         return s
 
     def _repr_png_(self) -> bytes:
diff --git a/src/pyhepmc/view.py b/src/pyhepmc/view.py
index dfad4c9..57ec2c8 100644
--- a/src/pyhepmc/view.py
+++ b/src/pyhepmc/view.py
@@ -6,7 +6,7 @@
 from pyhepmc import Units, GenEvent
 import numpy as np
 import os
-from pathlib import PurePath
+from pathlib import Path
 from typing import BinaryIO, Union, Set, Any, Optional, Tuple
 
 
@@ -245,15 +245,17 @@ def savefig(
         Other arguments are forwarded to pyhepmc.view.to_dot.
     """
     if isinstance(fname, (str, os.PathLike)):
-        p = PurePath(fname)
+        p = Path(fname)
         if format is None:
             format = "".join(p.suffixes)[1:]
-        if format in SUPPORTED_FORMATS:
+        try:
+            # unknown format raises exception in nested call
             with open(p, "wb") as fo:
                 savefig(event, fo, format=format, **kwargs)
-        # unknown format raises exception in nested call
-        with open(os.devnull, "wb") as fo:
-            savefig(event, fo, format=format, **kwargs)
+        except ValueError:
+            if p.exists():
+                p.unlink()
+            raise
         return
 
     # if we arrive here, fname is a file-like object
diff --git a/tests/test_deprecated.py b/tests/test_deprecated.py
index 3345449..bf0d171 100644
--- a/tests/test_deprecated.py
+++ b/tests/test_deprecated.py
@@ -1,6 +1,5 @@
 from pyhepmc._deprecated import deprecated
 import pytest
-import numpy as np
 
 
 class Foo:
@@ -8,15 +7,25 @@ class Foo:
     def bar(self):
         return 0
 
+    @deprecated("use baz", removal="1000.0.0")
+    def foo(self):
+        return 0
+
 
 def test_deprecated():
     foo = Foo()
 
-    with pytest.raises(ValueError, match="reason.*required"):
+    with pytest.raises(AssertionError):
 
         @deprecated
         def bad(self):
             return 0
 
-    with pytest.warns(np.VisibleDeprecationWarning, match="bar is deprecated: use baz"):
+    with pytest.warns(DeprecationWarning, match="bar is deprecated: use baz"):
         foo.bar()
+
+    with pytest.warns(
+        DeprecationWarning,
+        match="foo is deprecated and will be removed in version 1000.0.0: use baz",
+    ):
+        foo.foo()
diff --git a/tests/test_io.py b/tests/test_io.py
index 31d6ec8..66f5aaa 100644
--- a/tests/test_io.py
+++ b/tests/test_io.py
@@ -6,7 +6,6 @@
 from pyhepmc._core import stringstream, pyiostream
 from io import BytesIO
 from pathlib import Path
-import numpy as np
 import typing
 import gzip
 from sys import version_info
@@ -476,7 +475,7 @@ def test_open_standalone(evt):  # noqa
 
 
 def test_deprecated_import():
-    with pytest.warns(np.VisibleDeprecationWarning):
+    with pytest.warns(DeprecationWarning):
         from pyhepmc import ReaderAscii  # noqa F401
 
 
diff --git a/tests/test_view.py b/tests/test_view.py
index ae6580d..e8c2186 100644
--- a/tests/test_view.py
+++ b/tests/test_view.py
@@ -121,13 +121,17 @@ def test_savefig_1(evt, ext):
             assert np.sum(a1[:size] != a2[:size]) < 150
 
 
-def test_savefig_2(evt):
+def test_savefig_2a(evt):
     with pytest.raises(ValueError):
         view.savefig(evt, "foo")
 
+
+def test_savefig_2b(evt):
     with pytest.raises(ValueError):
         view.savefig(evt, "foo.foo")
 
+
+def test_savefig_2c(evt):
     with pytest.raises(ValueError):
         with io.BytesIO() as f:
             view.savefig(evt, f)