diff options
Diffstat (limited to 'nixpkgs/pkgs/development/python-modules/scipy')
| -rw-r--r-- | nixpkgs/pkgs/development/python-modules/scipy/default.nix | 198 | ||||
| -rwxr-xr-x | nixpkgs/pkgs/development/python-modules/scipy/update.sh | 31 |
2 files changed, 229 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/development/python-modules/scipy/default.nix b/nixpkgs/pkgs/development/python-modules/scipy/default.nix new file mode 100644 index 000000000000..b2a58d71c0b1 --- /dev/null +++ b/nixpkgs/pkgs/development/python-modules/scipy/default.nix @@ -0,0 +1,198 @@ +{ lib +, stdenv +, fetchFromGitHub +, fetchpatch +, fetchurl +, writeText +, python +, pythonOlder +, buildPythonPackage +, cython +, gfortran +, meson-python +, pkg-config +, pythran +, wheel +, nose +, setuptools +, hypothesis +, pytestCheckHook +, 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 + # + # The update script uses sed regexes to replace them with the updated hashes. + version = "1.12.0"; + srcHash = "sha256-PuiyYTgSegDTV9Kae5N68FOXT1jyJrNv9p2aFP70Z20="; + 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 = "pyproject"; + + src = fetchFromGitHub { + owner = "scipy"; + repo = pname; + rev = "v${version}"; + hash = srcHash; + fetchSubmodules = true; + }; + + patches = [ + # Helps with cross compilation, see https://github.com/scipy/scipy/pull/18167 + (fetchpatch { + url = "https://github.com/scipy/scipy/commit/dd50ac9d98dbb70625333a23e3a90e493228e3be.patch"; + hash = "sha256-Vf6/hhwu6X5s8KWhq8bUZKtSkdVu/GtEpGtj8Olxe7s="; + excludes = [ + "doc/source/dev/contributor/meson_advanced.rst" + ]; + }) + (fetchpatch { + name = "openblas-0.3.26-compat.patch"; + url = "https://github.com/scipy/scipy/commit/8c96a1f742335bca283aae418763aaba62c03378.patch"; + hash = "sha256-SGoYDxwSAkr6D5/XEqHLerF4e4nmmI+PX+z+3taWAps="; + }) + ]; + + # Upstream complicated numpy version pinning is causing issues in the + # configurePhase, so we pass on it. + postPatch = '' + substituteInPlace pyproject.toml \ + --replace-fail 'numpy==' 'numpy>=' \ + ''; + + nativeBuildInputs = [ + cython + gfortran + meson-python + pythran + pkg-config + wheel + setuptools + ]; + + buildInputs = [ + blas + lapack + pybind11 + pooch + xsimd + ] ++ lib.optionals (pythonOlder "3.9") [ + libxcrypt + ]; + + propagatedBuildInputs = [ numpy ]; + + __darwinAllowLocalNetworking = true; + + nativeCheckInputs = [ + nose + hypothesis + pytestCheckHook + pytest-xdist + ]; + + # The following tests are broken on aarch64-darwin with newer compilers and library versions. + # See https://github.com/scipy/scipy/issues/18308 + disabledTests = lib.optionals (stdenv.isDarwin && stdenv.isAarch64) [ + "test_a_b_neg_int_after_euler_hypergeometric_transformation" + "test_dst4_definition_ortho" + "test_load_mat4_le" + "hyp2f1_test_case47" + "hyp2f1_test_case3" + "test_uint64_max" + ]; + + doCheck = !(stdenv.isx86_64 && stdenv.isDarwin); + + preConfigure = '' + # Helps parallelization a bit + export NPY_NUM_BUILD_JOBS=$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=${crossFileScipy}" + ]; + + # disable stackprotector on aarch64-darwin for now + # + # build error: + # + # /private/tmp/nix-build-python3.9-scipy-1.6.3.drv-0/ccDEsw5U.s:109:15: error: index must be an integer in range [-256, 255]. + # + # ldr x0, [x0, ___stack_chk_guard];momd + # + hardeningDisable = lib.optionals (stdenv.isAarch64 && stdenv.isDarwin) [ "stackprotector" ]; + + preCheck = '' + export OMP_NUM_THREADS=$(( $NIX_BUILD_CORES / 4 )) + cd $out + ''; + + requiredSystemFeatures = [ "big-parallel" ]; # the tests need lots of CPU time + + passthru = { + inherit blas; + updateScript = [ + ./update.sh + # Pass it this file name as argument + (builtins.unsafeGetAttrPos "pname" python.pkgs.scipy).file + ] + # Pass it the names of the datasets to update their hashes + ++ (builtins.attrNames datasetsHashes) + ; + }; + + SCIPY_USE_G77_ABI_WRAPPER = 1; + + meta = with lib; { + changelog = "https://github.com/scipy/scipy/releases/tag/v${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 = licenses.bsd3; + maintainers = with maintainers; [ fridh doronbehar ]; + }; +} 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..c6b3dca49186 --- /dev/null +++ b/nixpkgs/pkgs/development/python-modules/scipy/update.sh @@ -0,0 +1,31 @@ +#!/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 |