diff options
Diffstat (limited to 'nixpkgs/pkgs/development/python-modules/scipy')
3 files changed, 127 insertions, 30 deletions
diff --git a/nixpkgs/pkgs/development/python-modules/scipy/default.nix b/nixpkgs/pkgs/development/python-modules/scipy/default.nix index 1090e724a7fd..d51c049589ee 100644 --- a/nixpkgs/pkgs/development/python-modules/scipy/default.nix +++ b/nixpkgs/pkgs/development/python-modules/scipy/default.nix @@ -1,9 +1,14 @@ { lib , stdenv -, fetchPypi +, fetchFromGitHub +, fetchpatch +, fetchurl +, writeText , python , pythonOlder , buildPythonPackage +, pypaBuildHook +, pipInstallHook , cython , gfortran , meson-python @@ -17,31 +22,77 @@ , pybind11 , pooch , libxcrypt +, xsimd +, blas +, lapack }: -buildPythonPackage rec { +let pname = "scipy"; - version = "1.10.1"; - format = "pyproject"; - - src = fetchPypi { - inherit pname version; - hash = "sha256-LPnfuAp7RYm6TEDOdYiYbW1c68VFfK0sKID2vC1C86U="; + # 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${version}"; + hash = srcHash; + fetchSubmodules = true; }; patches = [ - # These tests require internet connection, currently impossible to disable - # them otherwise, see: - # https://github.com/scipy/scipy/pull/17965 - ./disable-datasets-tests.patch + # Helps with cross compilation, see https://github.com/scipy/scipy/pull/18167 + (fetchpatch { + url = "https://github.com/scipy/scipy/commit/dd50ac9d98dbb70625333a23e3a90e493228e3be.patch"; + hash = "sha256-Vf6/hhwu6X5s8KWhq8bUZKtSkdVu/GtEpGtj8Olxe7s="; + excludes = [ + "doc/source/dev/contributor/meson_advanced.rst" + ]; + }) ]; - nativeBuildInputs = [ cython gfortran meson-python pythran pkg-config wheel ]; + postPatch = '' + substituteInPlace pyproject.toml \ + --replace "pybind11>=2.10.4,<2.11.0" "pybind11>=2.10.4,<2.12.0" + ''; + + nativeBuildInputs = [ pypaBuildHook pipInstallHook cython gfortran meson-python pythran pkg-config wheel ]; buildInputs = [ - numpy.blas + blas + lapack pybind11 pooch + xsimd ] ++ lib.optionals (pythonOlder "3.9") [ libxcrypt ]; @@ -53,9 +104,29 @@ buildPythonPackage rec { doCheck = !(stdenv.isx86_64 && stdenv.isDarwin); preConfigure = '' - sed -i '0,/from numpy.distutils.core/s//import setuptools;from numpy.distutils.core/' setup.py + # Relax deps a bit + substituteInPlace pyproject.toml \ + --replace 'numpy==' 'numpy>=' + # Helps parallelization a bit export NPY_NUM_BUILD_JOBS=$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=${crossFileScipy}" + ]; # disable stackprotector on aarch64-darwin for now # @@ -71,7 +142,7 @@ buildPythonPackage rec { runHook preCheck pushd "$out" export OMP_NUM_THREADS=$(( $NIX_BUILD_CORES / 4 )) - ${python.interpreter} -c "import scipy; scipy.test('fast', verbose=10, parallel=$NIX_BUILD_CORES)" + ${python.interpreter} -c "import scipy, sys; sys.exit(scipy.test('fast', verbose=10, parallel=$NIX_BUILD_CORES) != True)" popd runHook postCheck ''; @@ -79,17 +150,23 @@ buildPythonPackage rec { requiredSystemFeatures = [ "big-parallel" ]; # the tests need lots of CPU time passthru = { - blas = numpy.blas; + 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) + ; }; - setupPyBuildFlags = [ "--fcompiler='gnu95'" ]; - 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 = [ maintainers.fridh ]; + maintainers = with maintainers; [ fridh doronbehar ]; }; } diff --git a/nixpkgs/pkgs/development/python-modules/scipy/disable-datasets-tests.patch b/nixpkgs/pkgs/development/python-modules/scipy/disable-datasets-tests.patch deleted file mode 100644 index a06d0d50ddf4..000000000000 --- a/nixpkgs/pkgs/development/python-modules/scipy/disable-datasets-tests.patch +++ /dev/null @@ -1,9 +0,0 @@ -diff --git i/scipy/datasets/meson.build w/scipy/datasets/meson.build -index 101377253..eec2feea4 100644 ---- i/scipy/datasets/meson.build -+++ w/scipy/datasets/meson.build -@@ -11,4 +11,3 @@ py3.install_sources( - subdir: 'scipy/datasets' - ) - --subdir('tests') diff --git a/nixpkgs/pkgs/development/python-modules/scipy/update.sh b/nixpkgs/pkgs/development/python-modules/scipy/update.sh new file mode 100755 index 000000000000..b0d6e2da4f41 --- /dev/null +++ b/nixpkgs/pkgs/development/python-modules/scipy/update.sh @@ -0,0 +1,29 @@ +#!/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'/g' $fname + # Update srcHash + srcHash='"sha256-'$(nix-prefetch-github scipy scipy --rev v${version} --fetch-submodules | jq --raw-output .sha256)'"' + sed -i 's/srcHash = .*=";/srcHash = '$srcHash';/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 |