Buildsystem overhaul - #316
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Remove the generated _version.py and versioneer dependency. Version is now derived from git tags via setuptools-scm at build time and read via importlib.metadata at runtime.
- Replace scikit-build (legacy) + setuptools with scikit-build-core as build backend. This fixes broken editable installs and removes the need for SETUPTOOLS_ENABLE_FEATURES=legacy-editable. - Delete setup.py — scikit-build-core is configured entirely via pyproject.toml. - Simplify CMakeLists.txt: remove SKBUILD/non-SKBUILD branching and LIBRARY_OUTPUT_DIRECTORY hack. scikit-build-core handles pybind11 discovery and editable install redirects natively. - Pre-cythonize eig_qr.pyx to eig_qr.c, replacing scikit-build's add_cython_target() with Python_add_library(). This removes Cython as a build-time dependency. - Install destinations now include the full deeptime/ prefix since scikit-build-core installs to the wheel root (no cmake_install_dir).
Move the package from deeptime/ to src/deeptime/ to prevent the source tree from shadowing the installed package during testing. Update CMakeLists.txt add_subdirectory() paths and install destination relative path calculations accordingly.
- Add tests.yml: matrix of (ubuntu/macos/windows) x (3.9-3.13), with coverage upload on ubuntu/3.12 and a separate C++ test job. - Add wheels.yml: cibuildwheel on tag push with PyPI trusted publishing. - Remove all Azure Pipelines configuration.
The nox-based test runner existed primarily to work around broken editable installs with scikit-build (legacy). With scikit-build-core and src/ layout, the development workflow is simply: pip install -e ".[tests,plotting,units]" pytest tests/ -vv --pyargs deeptime --doctest-modules Also remove devtools/cmake/ helper scripts that were only used by the nox cpp test path (now handled by GitHub Actions directly).
Replace Azure Pipelines build badge with GitHub Actions badge. Update release checklist to reflect automated wheel building via GitHub Actions trusted publishing instead of manual Azure Pipelines + twine workflow.
Use Development.Module instead of Development (which requires Development.Embed / static Python library, often unavailable). Disable editable.rebuild since the auto-rebuild uses system cmake which may lack proper environment setup from scikit-build-core.
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Catch2 v3.0.1 is missing #include <cstdint> which causes build failures with newer GCC versions on GitHub Actions runners.
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Use setup-python's built-in pip cache to avoid re-downloading torch + CUDA libs (~2GB) on every run.
The pre-cythonized eig_qr.c inlines all scipy types as typedefs — no scipy headers are needed at compile time. LAPACK function pointers are resolved at runtime via Cython's import mechanism. Removes scipy from build-system requires and the scipy.get_include() call from CMakeLists.txt (which broke with newer scipy that removed get_include()).
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