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{ lib
, stdenv
, fetchFromGitHub
, fetchpatch
, fetchurl
, writeText
, python
, pythonOlder
, buildPythonPackage
, pypaBuildHook
, pipInstallHook
, cython
, gfortran
, meson-python
, pkg-config
, pythran
, wheel
, nose
, pytest
, pytest-xdist
, numpy
, pybind11
, pooch
, libxcrypt
, xsimd
, blas
, lapack
}:
let
pname = "scipy";
# DON'T UPDATE THESE ATTRIBUTES MANUALLY - USE:
#
# nix-shell maintainers/scripts/update.nix --argstr package python3.pkgs.scipy
#
# Even if you do update these hashes manually, don't change their base
# (base16 or base64), because the update script uses sed regexes to replace
# them with the updated hashes.
version = "1.11.1";
srcHash = "sha256-bgnYXe3EhzL7+Gfriz1cXCl2eYQJ8zF+rcIwHyZR8bQ=";
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 = '${numpy}/${python.sitePackages}/numpy/core/include'
pythran-include-dir = '${pythran}/${python.sitePackages}/pythran'
host-python-path = '${python.interpreter}'
host-python-version = '${python.pythonVersion}'
'';
in buildPythonPackage {
inherit pname version;
format = "other";
src = fetchFromGitHub {
owner = "scipy";
repo = pname;
rev = "v${version}";
hash = srcHash;
fetchSubmodules = true;
};
patches = [
# Helps with cross compilation, see https://github.com/scipy/scipy/pull/18167
(fetchpatch {
url = "https://github.com/scipy/scipy/commit/dd50ac9d98dbb70625333a23e3a90e493228e3be.patch";
hash = "sha256-Vf6/hhwu6X5s8KWhq8bUZKtSkdVu/GtEpGtj8Olxe7s=";
excludes = [
"doc/source/dev/contributor/meson_advanced.rst"
];
})
];
postPatch = ''
substituteInPlace pyproject.toml \
--replace "pybind11>=2.10.4,<2.11.0" "pybind11>=2.10.4,<2.12.0"
'';
nativeBuildInputs = [ pypaBuildHook pipInstallHook cython gfortran meson-python pythran pkg-config wheel ];
buildInputs = [
blas
lapack
pybind11
pooch
xsimd
] ++ lib.optionals (pythonOlder "3.9") [
libxcrypt
];
propagatedBuildInputs = [ numpy ];
nativeCheckInputs = [ nose pytest pytest-xdist ];
doCheck = !(stdenv.isx86_64 && stdenv.isDarwin);
preConfigure = ''
# Relax deps a bit
substituteInPlace pyproject.toml \
--replace 'numpy==' 'numpy>='
# Helps parallelization a bit
export NPY_NUM_BUILD_JOBS=$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=${crossFileScipy}"
];
# disable stackprotector on aarch64-darwin for now
#
# build error:
#
# /private/tmp/nix-build-python3.9-scipy-1.6.3.drv-0/ccDEsw5U.s:109:15: error: index must be an integer in range [-256, 255].
#
# ldr x0, [x0, ___stack_chk_guard];momd
#
hardeningDisable = lib.optionals (stdenv.isAarch64 && stdenv.isDarwin) [ "stackprotector" ];
checkPhase = ''
runHook preCheck
pushd "$out"
export OMP_NUM_THREADS=$(( $NIX_BUILD_CORES / 4 ))
${python.interpreter} -c "import scipy, sys; sys.exit(scipy.test('fast', verbose=10, parallel=$NIX_BUILD_CORES) != True)"
popd
runHook postCheck
'';
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)
;
};
SCIPY_USE_G77_ABI_WRAPPER = 1;
meta = with lib; {
description = "SciPy (pronounced 'Sigh Pie') is open-source software for mathematics, science, and engineering";
homepage = "https://www.scipy.org/";
license = licenses.bsd3;
maintainers = with maintainers; [ fridh doronbehar ];
};
}
|