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{
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,
boost188,
qhull,
# 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 = "1.16.3";
srcHash = "sha256-2NVmsJqsUjWSD7oEJhRkRjbKvqwikBJenAhBio/+IuU=";
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 "Cython>=3.0.8,<3.2.0" "Cython>=3.0.8" \
--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
boost188
qhull
];
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 (stdenv.hostPlatform.isPower64 && stdenv.hostPlatform.isBigEndian) [
# https://github.com/scipy/scipy/issues/24090
"test_cython_api"
"test_distance_transform_cdt05"
"test_eval_chebyt_gh20129"
"test_hyp0f1"
"test_hyp0f1_gh5764"
"test_simple_det_shapes_real_complex"
]
++ 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}"
"-Duse-system-libraries=all"
];
# 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 ];
};
}
|
