Fix compilation warnings#691
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October 13, 2025 21:57
force_all_finite has been deprecated in scikit-learn 1.6.0 and will be removed in the upcoming 1.8.0
Mokto
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The published wheels haven't kept up: the Linux job pinned `cython<3` inside a `manylinux2014` container and built only cp38-cp311, leaving no upstream wheels for 3.12+ and producing artifacts incompatible with NumPy 2.x. This PR brings the build chain forward. Build system - `[build-system]` now requires `cython>=3.0.11,<4` and `numpy>=2.0,<3` so any source build (CI, conda-forge, end-user `pip install`) targets current Cython/NumPy. - `requires-python = ">=3.10"` matches the supported matrix; 3.8 reached EOL on 2024-10-07 and 3.9 on 2025-10-31. - Adds the `Programming Language :: Python :: 3.14` classifier. Cython 3 source updates - Reorders `nogil except -1` -> `except -1 nogil` across `.pyx`/`.pxd` (Cython 3 syntax requirement). - Adds `# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION` to silence NumPy deprecated-API warnings at compile time. These rebases the still-relevant source-file hunks of scikit-learn-contrib#691 onto current master; scikit-learn-contrib#691's pyproject/setup.py hunks have been superseded by master. Wheel CI (`.github/workflows/pythonpublish_wheel.yml`) - Linux: bumps the manylinux image from `manylinux2014_x86_64` to `manylinux_2_28_x86_64` (Python 3.14 needs glibc >= 2.28), pins `cython>=3.0.11,<4` and `numpy>=2.0` in the build env, installs `setuptools` + `wheel` (the cp314 image doesn't ship them by default), and extends the matrix to cp310-cp314. - Windows/macOS: replaces the deprecated `oldest-supported-numpy` with `numpy>=2.0`, bumps `actions/checkout`@v1->v4 and `actions/setup-python`@v1->v5 (v1 doesn't support recent Pythons), retires the EOL `windows-2019`/`macos-11` runners (now `windows-2022` + `macos-14` -- macOS 14 already produces universal2 wheels covering both arm64 and x86_64), extends the matrix to 3.10-3.14, and enables `allow-prereleases: true` in case 3.14 isn't GA on a runner yet. - Disables `fail-fast` on both matrices so one failure doesn't cancel the rest. Verification - All 15 build jobs (Linux cp310-cp314, Windows + macOS for 3.10-3.14) go green on a workflow_dispatch run on the fork. - Locally on Python 3.14.4 with Cython 3.2.4 + NumPy 2.4.4: every extension cythonizes and compiles cleanly, and `HDBSCAN().fit(X)` runs end-to-end. This is consistent with how conda-forge already ships working py314 builds of this package. Closes scikit-learn-contrib#688 (missing wheels for 3.13), scikit-learn-contrib#686 (Linux wheel for 3.12). Supersedes scikit-learn-contrib#691 for the parts still needed.
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Just a couple of very minor tweaks to address warnings during builds:
nogilat the end of the declaration#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSIONto ensure we're not building against deprecated functions and fail in case they are usedtest_suiteandtest_requireshave been deprecated for a while and have been removed from setup.py