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python3.pkgs.{numpy: 2.3.5 -> 2.4.1, scipy: 1.16.3 -> 1.17.0} (#477443)

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This commit is contained in:
Doron Behar
2026-01-21 13:12:43 +00:00
committed by GitHub
parent 59bc97cf4b 4467948a3e
commit fbcf1ab208
4 changed files with 107 additions and 160 deletions
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pkgs/development/python-modules/numpy/1.nix
+28 -31
View File
@@ -3,7 +3,6 @@
stdenv,
fetchPypi,
python,
numpy_1,
pythonAtLeast,
buildPythonPackage,
writeTextFile,
@@ -33,37 +32,14 @@
assert (!blas.isILP64) && (!lapack.isILP64);
let
cfg = writeTextFile {
name = "site.cfg";
text = lib.generators.toINI { } {
${blas.implementation} = {
include_dirs = "${lib.getDev blas}/include:${lib.getDev lapack}/include";
library_dirs = "${blas}/lib:${lapack}/lib";
runtime_library_dirs = "${blas}/lib:${lapack}/lib";
libraries = "lapack,lapacke,blas,cblas";
};
lapack = {
include_dirs = "${lib.getDev lapack}/include";
library_dirs = "${lapack}/lib";
runtime_library_dirs = "${lapack}/lib";
};
blas = {
include_dirs = "${lib.getDev blas}/include";
library_dirs = "${blas}/lib";
runtime_library_dirs = "${blas}/lib";
};
};
};
in
buildPythonPackage rec {
buildPythonPackage (finalAttrs: {
pname = "numpy";
version = "1.26.4";
pyproject = true;
disabled = pythonAtLeast "3.13";
src = fetchPypi {
inherit pname version;
inherit (finalAttrs) pname version;
extension = "tar.gz";
hash = "sha256-KgKrqe0S5KxOs+qUIcQgMBoMZGDZgw10qd+H76SRIBA=";
};
@@ -123,7 +99,7 @@ buildPythonPackage rec {
'';
preBuild = ''
ln -s ${cfg} site.cfg
ln -s ${finalAttrs.passthru.cfg} site.cfg
'';
enableParallelBuilding = true;
@@ -180,8 +156,29 @@ buildPythonPackage rec {
# just for backwards compatibility
blas = blas.provider;
blasImplementation = blas.implementation;
inherit cfg;
coreIncludeDir = "${numpy_1}/${python.sitePackages}/numpy/core/include";
buildConfig = {
${blas.implementation} = {
include_dirs = "${lib.getDev blas}/include:${lib.getDev lapack}/include";
library_dirs = "${blas}/lib:${lapack}/lib";
runtime_library_dirs = "${blas}/lib:${lapack}/lib";
libraries = "lapack,lapacke,blas,cblas";
};
lapack = {
include_dirs = "${lib.getDev lapack}/include";
library_dirs = "${lapack}/lib";
runtime_library_dirs = "${lapack}/lib";
};
blas = {
include_dirs = "${lib.getDev blas}/include";
library_dirs = "${blas}/lib";
runtime_library_dirs = "${blas}/lib";
};
};
cfg = writeTextFile {
name = "site.cfg";
text = lib.generators.toINI { } finalAttrs.finalPackage.buildConfig;
};
coreIncludeDir = "${finalAttrs.finalPackage}/${python.sitePackages}/numpy/core/include";
tests = {
inherit sage;
};
@@ -192,10 +189,10 @@ buildPythonPackage rec {
env.NOSE_EXCLUDE = "test_large_file_support";
meta = {
changelog = "https://github.com/numpy/numpy/releases/tag/v${version}";
changelog = "https://github.com/numpy/numpy/releases/tag/v${finalAttrs.version}";
description = "Scientific tools for Python";
mainProgram = "f2py";
homepage = "https://numpy.org/";
license = lib.licenses.bsd3;
};
}
})
pkgs/development/python-modules/numpy/2.nix
+36 -53
View File
@@ -2,9 +2,7 @@
lib,
stdenv,
fetchFromGitHub,
fetchpatch2,
python,
numpy_2,
pythonAtLeast,
pythonOlder,
buildPythonPackage,
@@ -36,32 +34,9 @@
assert (!blas.isILP64) && (!lapack.isILP64);
let
cfg = writeTextFile {
name = "site.cfg";
text = lib.generators.toINI { } {
${blas.implementation} = {
include_dirs = "${lib.getDev blas}/include:${lib.getDev lapack}/include";
library_dirs = "${blas}/lib:${lapack}/lib";
runtime_library_dirs = "${blas}/lib:${lapack}/lib";
libraries = "lapack,lapacke,blas,cblas";
};
lapack = {
include_dirs = "${lib.getDev lapack}/include";
library_dirs = "${lapack}/lib";
runtime_library_dirs = "${lapack}/lib";
};
blas = {
include_dirs = "${lib.getDev blas}/include";
library_dirs = "${blas}/lib";
runtime_library_dirs = "${blas}/lib";
};
};
};
in
buildPythonPackage rec {
buildPythonPackage (finalAttrs: {
pname = "numpy";
version = "2.3.5";
version = "2.4.1";
pyproject = true;
disabled = pythonOlder "3.11";
@@ -69,30 +44,17 @@ buildPythonPackage rec {
src = fetchFromGitHub {
owner = "numpy";
repo = "numpy";
tag = "v${version}";
tag = "v${finalAttrs.version}";
fetchSubmodules = true;
hash = "sha256-CMgJmsjPLgMCWN2iJk0OzcKIlnRRcayrTAns51S4B6k=";
hash = "sha256-3UjvAQZEvsA/1s2mqFMnvi2E9MBHG27xf91FqiMGHmo=";
};
patches =
lib.optionals python.hasDistutilsCxxPatch [
# We patch cpython/distutils to fix https://bugs.python.org/issue1222585
# Patching of numpy.distutils is needed to prevent it from undoing the
# patch to distutils.
./numpy-distutils-C++.patch
]
++
lib.optionals
(pythonAtLeast "3.14" && stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isAarch64)
[
# don't assert RecursionError in monster dtype test
# see https://github.com/numpy/numpy/pull/30375
(fetchpatch2 {
url = "https://github.com/numpy/numpy/commit/eeaf04662e07cc8e2041f3e25bbd3698949a0c02.patch?full_index=1";
excludes = [ ".github/workflows/macos.yml" ];
hash = "sha256-bLPLExlKnX18MXhbZxzCHniaAE0yTSyK9WuQyFyYHOI=";
})
];
patches = lib.optionals python.hasDistutilsCxxPatch [
# We patch cpython/distutils to fix https://bugs.python.org/issue1222585
# Patching of numpy.distutils is needed to prevent it from undoing the
# patch to distutils.
./numpy-distutils-C++.patch
];
postPatch = ''
# remove needless reference to full Python path stored in built wheel
@@ -127,7 +89,7 @@ buildPythonPackage rec {
];
preBuild = ''
ln -s ${cfg} site.cfg
ln -s ${finalAttrs.finalPackage.passthru.cfg} site.cfg
'';
enableParallelBuilding = true;
@@ -193,18 +155,39 @@ buildPythonPackage rec {
# just for backwards compatibility
blas = blas.provider;
blasImplementation = blas.implementation;
inherit cfg;
coreIncludeDir = "${numpy_2}/${python.sitePackages}/numpy/_core/include";
buildConfig = {
${blas.implementation} = {
include_dirs = "${lib.getDev blas}/include:${lib.getDev lapack}/include";
library_dirs = "${blas}/lib:${lapack}/lib";
runtime_library_dirs = "${blas}/lib:${lapack}/lib";
libraries = "lapack,lapacke,blas,cblas";
};
lapack = {
include_dirs = "${lib.getDev lapack}/include";
library_dirs = "${lapack}/lib";
runtime_library_dirs = "${lapack}/lib";
};
blas = {
include_dirs = "${lib.getDev blas}/include";
library_dirs = "${blas}/lib";
runtime_library_dirs = "${blas}/lib";
};
};
cfg = writeTextFile {
name = "site.cfg";
text = lib.generators.toINI { } finalAttrs.finalPackage.buildConfig;
};
coreIncludeDir = "${finalAttrs.finalPackage}/${python.sitePackages}/numpy/_core/include";
tests = {
inherit sage;
};
};
meta = {
changelog = "https://github.com/numpy/numpy/releases/tag/${src.tag}";
changelog = "https://github.com/numpy/numpy/releases/tag/${finalAttrs.src.tag}";
description = "Scientific tools for Python";
homepage = "https://numpy.org/";
license = lib.licenses.bsd3;
maintainers = with lib.maintainers; [ doronbehar ];
};
}
})
pkgs/development/python-modules/scipy/default.nix
+43 -45
View File
@@ -2,7 +2,7 @@
lib,
stdenv,
fetchurl,
writeText,
writeTextFile,
python,
buildPythonPackage,
fetchFromGitHub,
@@ -43,45 +43,16 @@
sage,
}:
let
buildPythonPackage (finalAttrs: {
pname = "scipy";
# DON'T UPDATE THESE ATTRIBUTES MANUALLY - USE:
#
# nix-shell maintainers/scripts/update.nix --argstr package python3.pkgs.scipy
#
# The update script uses sed regexes to replace them with the updated hashes.
version = "1.16.3";
srcHash = "sha256-2NVmsJqsUjWSD7oEJhRkRjbKvqwikBJenAhBio/+IuU=";
datasetsHashes = {
ascent = "1qjp35ncrniq9rhzb14icwwykqg2208hcssznn3hz27w39615kh3";
ecg = "1bwbjp43b7znnwha5hv6wiz3g0bhwrpqpi75s12zidxrbwvd62pj";
face = "11i8x29h80y7hhyqhil1fg8mxag5f827g33lhnsf44qk116hp2wx";
};
datasets = lib.mapAttrs (
d: hash:
fetchurl {
url = "https://raw.githubusercontent.com/scipy/dataset-${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;
version = "1.17.0";
pyproject = true;
src = fetchFromGitHub {
owner = "scipy";
repo = "scipy";
tag = "v${version}";
hash = srcHash;
tag = "v${finalAttrs.version}";
hash = "sha256-bDcM/RGfce/ZTYpTBNpKmX/7rXDqQs7rYkAmeXtzkZk=";
fetchSubmodules = true;
};
@@ -189,7 +160,7 @@ buildPythonPackage {
d: dpath:
# Actually copy the datasets
"cp ${dpath} scipy-data/${d}.dat"
) datasets
) finalAttrs.finalPackage.passthru.datasets
));
mesonFlags = [
@@ -198,7 +169,7 @@ buildPythonPackage {
# 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=${crossFileScipy}"
"--cross-file=${finalAttrs.finalPackage.passthru.crossFile}"
"-Duse-system-libraries=all"
];
@@ -229,26 +200,53 @@ buildPythonPackage {
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;
};
# NOTE: Every once in a while, these hashes might need an update. Use:
#
# nix build -Lf. --rebuild python3.pkgs.scipy.passthru.datasets
#
# To verify the hashes are correct.
datasetsHashes = {
ascent = "sha256-A84STBr8iA+HtV9rBhEQ4uHpOWeRhPVhTjjazGwZV+I=";
ecg = "sha256-8grTNl+5t/hF0OXEi2/mcIE3fuRmw6Igt/afNciVi68=";
face = "sha256-nYsLTQgTE+K0hXSMdwRy5ale0XOBRog9hMcDBJPoKIY=";
};
datasets = lib.mapAttrs (
d: hash:
fetchurl {
url = "https://raw.githubusercontent.com/scipy/dataset-${d}/main/${d}.dat";
inherit hash;
}
) finalAttrs.finalPackage.passthru.datasetsHashes;
# Additional cross compilation related properties that scipy reads in scipy/meson.build
buildConfig = {
properties = {
numpy-include-dir = numpy.coreIncludeDir;
pythran-include-dir = "${pythran}/${python.sitePackages}/pythran";
host-python-path = python.interpreter;
host-python-version = python.pythonVersion;
};
};
crossFile = writeTextFile {
name = "cross-file-scipy.conf";
text = lib.generators.toINI {
mkKeyValue = lib.generators.mkKeyValueDefault {
mkValueString = v: "'${v}'";
} " = ";
} finalAttrs.finalPackage.passthru.buildConfig;
};
};
SCIPY_USE_G77_ABI_WRAPPER = 1;
meta = {
changelog = "https://github.com/scipy/scipy/releases/tag/v${version}";
changelog = "https://github.com/scipy/scipy/releases/tag/v${finalAttrs.version}";
description = "SciPy (pronounced 'Sigh Pie') is open-source software for mathematics, science, and engineering";
downloadPage = "https://github.com/scipy/scipy";
homepage = "https://www.scipy.org/";
license = lib.licenses.bsd3;
maintainers = with lib.maintainers; [ doronbehar ];
};
}
})
pkgs/development/python-modules/scipy/update.sh
-31
View File
@@ -1,31 +0,0 @@
#!/usr/bin/env nix-shell
#!nix-shell -i bash -p jq nix-prefetch-github
set -euo pipefail
echoerr() { echo "$@" 1>&2; }
fname="$1"
echoerr got fname $fname
shift
datasets="$@"
echoerr datasets are: "$@"
latest_release=$(curl --silent https://api.github.com/repos/scipy/scipy/releases/latest)
version=$(jq -r '.tag_name' <<<"$latest_release" | cut -c2-)
# Update version, if needed
if grep -q 'version = "'$version $fname; then
echo "Current version $version is the latest available, will update only datasets' hashes (don't take long)"
else
echoerr got version $version
sed -i -E 's/(version = ").*(";)/\1'$version'\2/g' $fname
# Verify the sed command above did not fail
grep -q $version $fname
# Update srcHash
srcHash="$(nix-prefetch-github scipy scipy --rev v${version} --fetch-submodules | jq --raw-output .hash)"
sed -i -E 's#(srcHash = ").*(";)#\1'$srcHash'\2#g' $fname
fi
for d in $datasets; do
datasetHash=$(nix-prefetch-url "https://raw.githubusercontent.com/scipy/dataset-${d}/main/${d}.dat")
sed -i 's/'$d' = "[0-9a-z]\+/'$d' = "'$datasetHash'/g' $fname
echoerr updated hash for dataset "'$d'"
done