nixpkgs/pkgs/development/python-modules/scipy/default.nix

{
  lib,
  stdenv,
  fetchurl,
  writeText,
  python,
  buildPythonPackage,
  fetchFromGitHub,
  fetchpatch,

  # build-system
  cython,
  gfortran,
  meson-python,
  nukeReferences,
  pythran,
  pkg-config,
  setuptools,
  xcbuild,

  # buildInputs
  # Upstream has support for using Darwin's Accelerate package. However this
  # requires a Darwin user to work on a nice way to do that via an override.
  # See:
  # https://github.com/scipy/scipy/blob/v1.14.0/scipy/meson.build#L194-L211
  blas,
  lapack,
  pybind11,
  pooch,
  xsimd,

  # dependencies
  numpy,

  # tests
  hypothesis,
  pytestCheckHook,
  pytest-xdist,

  # Reverse dependency
  sage,
}:

let
  pname = "scipy";
  # DON'T UPDATE THESE ATTRIBUTES MANUALLY - USE:
  #
  #     nix-shell maintainers/scripts/update.nix --argstr package python3.pkgs.scipy
  #
  # The update script uses sed regexes to replace them with the updated hashes.
  version = "1.16.0";
  srcHash = "sha256-PFWUq7RsqMgBK1bTw52y1renoPygWNreikNTFHWE2Ig=";
  datasetsHashes = {
    ascent = "1qjp35ncrniq9rhzb14icwwykqg2208hcssznn3hz27w39615kh3";
    ecg = "1bwbjp43b7znnwha5hv6wiz3g0bhwrpqpi75s12zidxrbwvd62pj";
    face = "11i8x29h80y7hhyqhil1fg8mxag5f827g33lhnsf44qk116hp2wx";
  };
  datasets = lib.mapAttrs (
    d: hash:
    fetchurl {
      url = "https://raw.githubusercontent.com/scipy/dataset-${d}/main/${d}.dat";
      sha256 = hash;
    }
  ) datasetsHashes;
  # Additional cross compilation related properties that scipy reads in scipy/meson.build
  crossFileScipy = writeText "cross-file-scipy.conf" ''
    [properties]
    numpy-include-dir = '${numpy.coreIncludeDir}'
    pythran-include-dir = '${pythran}/${python.sitePackages}/pythran'
    host-python-path = '${python.interpreter}'
    host-python-version = '${python.pythonVersion}'
  '';
in
buildPythonPackage {
  inherit pname version;
  pyproject = true;

  src = fetchFromGitHub {
    owner = "scipy";
    repo = "scipy";
    tag = "v${version}";
    hash = srcHash;
    fetchSubmodules = true;
  };

  patches = [
    # Helps with cross compilation, see https://github.com/scipy/scipy/pull/18167
    (fetchpatch {
      url = "https://github.com/scipy/scipy/commit/dd50ac9d98dbb70625333a23e3a90e493228e3be.patch";
      hash = "sha256-Vf6/hhwu6X5s8KWhq8bUZKtSkdVu/GtEpGtj8Olxe7s=";
      excludes = [ "doc/source/dev/contributor/meson_advanced.rst" ];
    })
  ];
  # A NOTE regarding the Numpy version relaxing: Both Numpy versions 1.x &
  # 2.x are supported. However upstream wants to always build with Numpy 2,
  # and with it to still be able to run with a Numpy 1 or 2. We insist to
  # perform this substitution even though python3.pkgs.numpy is of version 2
  # nowadays, because our ecosystem unfortunately doesn't allow easily
  # separating runtime and build-system dependencies. See also:
  #
  # https://discourse.nixos.org/t/several-comments-about-priorities-and-new-policies-in-the-python-ecosystem/51790
  #
  # Being able to build (& run) with Numpy 1 helps for python environments
  # that override globally the `numpy` attribute to point to `numpy_1`.
  postPatch = ''
    substituteInPlace pyproject.toml \
      --replace-fail "numpy>=2.0.0,<2.6" numpy
  '';

  build-system = [
    cython
    gfortran
    meson-python
    nukeReferences
    pythran
    pkg-config
    setuptools
  ]
  ++ lib.optionals stdenv.hostPlatform.isDarwin [
    # Minimal version required according to:
    # https://github.com/scipy/scipy/blob/v1.16.0/scipy/meson.build#L238-L244
    (xcbuild.override {
      sdkVer = "13.3";
    })
  ];

  buildInputs = [
    blas
    lapack
    pybind11
    pooch
    xsimd
  ];

  dependencies = [ numpy ];

  __darwinAllowLocalNetworking = true;

  nativeCheckInputs = [
    hypothesis
    pytestCheckHook
    pytest-xdist
  ];

  disabledTests =
    lib.optionals (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isAarch64) [
      # The following tests are broken on aarch64-darwin with newer compilers and library versions.
      # See https://github.com/scipy/scipy/issues/18308
      "test_a_b_neg_int_after_euler_hypergeometric_transformation"
      "test_dst4_definition_ortho"
      "test_load_mat4_le"
      "hyp2f1_test_case47"
      "hyp2f1_test_case3"
      "test_uint64_max"
      "test_large_m4" # https://github.com/scipy/scipy/issues/22466
    ]
    ++ lib.optionals (python.isPy311) [
      # https://github.com/scipy/scipy/issues/22789 Observed only with Python 3.11
      "test_funcs"
    ];

  doCheck = !(stdenv.hostPlatform.isx86_64 && stdenv.hostPlatform.isDarwin);

  preConfigure = ''
    # Helps parallelization a bit
    export NPY_NUM_BUILD_JOBS=$NIX_BUILD_CORES
    # We download manually the datasets and this variable tells the pooch
    # library where these files are cached. See also:
    # https://github.com/scipy/scipy/pull/18518#issuecomment-1562350648 And at:
    # https://github.com/scipy/scipy/pull/17965#issuecomment-1560759962
    export XDG_CACHE_HOME=$PWD; export HOME=$(mktemp -d); mkdir scipy-data
  ''
  + (lib.concatStringsSep "\n" (
    lib.mapAttrsToList (
      d: dpath:
      # Actually copy the datasets
      "cp ${dpath} scipy-data/${d}.dat"
    ) datasets
  ));

  mesonFlags = [
    "-Dblas=${blas.pname}"
    "-Dlapack=${lapack.pname}"
    # We always run what's necessary for cross compilation, which is passing to
    # meson the proper cross compilation related arguments. See also:
    # https://docs.scipy.org/doc/scipy/building/cross_compilation.html
    "--cross-file=${crossFileScipy}"
  ];

  # disable stackprotector on aarch64-darwin for now
  #
  # build error:
  #
  # /private/tmp/nix-build-python3.9-scipy-1.6.3.drv-0/ccDEsw5U.s:109:15: error: index must be an integer in range [-256, 255].
  #
  #         ldr     x0, [x0, ___stack_chk_guard];momd
  #
  hardeningDisable = lib.optionals (stdenv.hostPlatform.isAarch64 && stdenv.hostPlatform.isDarwin) [
    "stackprotector"
  ];

  # remove references to dev dependencies
  postInstall = ''
    nuke-refs $out/${python.sitePackages}/scipy/__config__.py
    rm $out/${python.sitePackages}/scipy/__pycache__/__config__.*.opt-1.pyc
  '';

  preCheck = ''
    export OMP_NUM_THREADS=$(( $NIX_BUILD_CORES / 4 ))
    cd $out
  '';

  requiredSystemFeatures = [ "big-parallel" ]; # the tests need lots of CPU time

  passthru = {
    inherit blas;
    updateScript = [
      ./update.sh
      # Pass it this file name as argument
      (builtins.unsafeGetAttrPos "pname" python.pkgs.scipy).file
    ]
    # Pass it the names of the datasets to update their hashes
    ++ (builtins.attrNames datasetsHashes);
    tests = {
      inherit sage;
    };
  };

  SCIPY_USE_G77_ABI_WRAPPER = 1;

  meta = {
    changelog = "https://github.com/scipy/scipy/releases/tag/v${version}";
    description = "SciPy (pronounced 'Sigh Pie') is open-source software for mathematics, science, and engineering";
    downloadPage = "https://github.com/scipy/scipy";
    homepage = "https://www.scipy.org/";
    license = lib.licenses.bsd3;
    maintainers = with lib.maintainers; [ doronbehar ];
  };
}