python3.pkgs.scipy: 1.10.1 -> 1.11.1
Diff: https://github.com/scipy/scipy/compare/v1.10.1...v1.11.1 Significant changes to expression: - Use `pypaBuildHook` to build it. - Use `fetchFromGitHub` instead of `fetchPypi`. - Support cross compilation using `pypaBuildHook` and `$mesonFlags`. - Add a `passthru.updateScript` that downloads and updates hashes for datasets needed for tests. - Cleanup: * Remove unneeded anymore `setupPyBuildFlags`. * Remove unnecessary `sed` command from preConfigure that fixed a Numpy issue in `setup.py` * Use `blas` and `lapack` directly, relying on them being overriden by the user in all of Python's packages' set - see commit 213d0845b5c .
This commit is contained in:
Doron Behar
committed by
Martin Weinelt
Martin Weinelt
parent
68efe0a5a7
commit
8f4914fae6
@@ -1,9 +1,15 @@
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{ lib
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, stdenv
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, fetchPypi
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, fetchFromGitHub
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, fetchpatch
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, fetchurl
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, buildPackages
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, writeText
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, python
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, pythonOlder
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, buildPythonPackage
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, pypaBuildHook
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, pipInstallHook
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, cython
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, gfortran
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, meson-python
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@@ -17,31 +23,71 @@
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, pybind11
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, pooch
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, libxcrypt
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, xsimd
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, blas
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, lapack
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}:
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buildPythonPackage rec {
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let
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pname = "scipy";
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version = "1.10.1";
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format = "pyproject";
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src = fetchPypi {
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inherit pname version;
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hash = "sha256-LPnfuAp7RYm6TEDOdYiYbW1c68VFfK0sKID2vC1C86U=";
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# DON'T UPDATE THESE ATTRIBUTES MANUALLY - USE:
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#
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# nix-shell maintainers/scripts/update.nix --argstr package python3.pkgs.scipy
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#
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# Even if you do update these hashes manually, don't change their base
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# (base16 or base64), because the update script uses sed regexes to replace
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# them with the updated hashes.
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version = "1.11.1";
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srcHash = "sha256-bgnYXe3EhzL7+Gfriz1cXCl2eYQJ8zF+rcIwHyZR8bQ=";
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datasetsHashes = {
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ascent = "1qjp35ncrniq9rhzb14icwwykqg2208hcssznn3hz27w39615kh3";
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ecg = "1bwbjp43b7znnwha5hv6wiz3g0bhwrpqpi75s12zidxrbwvd62pj";
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face = "11i8x29h80y7hhyqhil1fg8mxag5f827g33lhnsf44qk116hp2wx";
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};
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datasets = lib.mapAttrs (
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d: hash: fetchurl {
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url = "https://raw.githubusercontent.com/scipy/dataset-${d}/main/${d}.dat";
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sha256 = hash;
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}
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) datasetsHashes;
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# Additional cross compilation related properties that scipy reads in scipy/meson.build
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crossFileScipy = writeText "cross-file-scipy.conf" ''
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[properties]
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numpy-include-dir = '${numpy}/${python.sitePackages}/numpy/core/include'
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pythran-include-dir = '${pythran}/${python.sitePackages}/pythran'
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host-python-path = '${python.interpreter}'
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host-python-version = '${python.pythonVersion}'
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'';
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in buildPythonPackage {
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inherit pname version;
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format = "other";
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src = fetchFromGitHub {
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owner = "scipy";
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repo = pname;
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rev = "v${version}";
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hash = srcHash;
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fetchSubmodules = true;
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};
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patches = [
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# These tests require internet connection, currently impossible to disable
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# them otherwise, see:
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# https://github.com/scipy/scipy/pull/17965
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./disable-datasets-tests.patch
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# Helps with cross compilation, see https://github.com/scipy/scipy/pull/18167
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(fetchpatch {
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url = "https://github.com/scipy/scipy/commit/dd50ac9d98dbb70625333a23e3a90e493228e3be.patch";
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hash = "sha256-Vf6/hhwu6X5s8KWhq8bUZKtSkdVu/GtEpGtj8Olxe7s=";
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excludes = [
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"doc/source/dev/contributor/meson_advanced.rst"
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];
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})
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];
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nativeBuildInputs = [ cython gfortran meson-python pythran pkg-config wheel ];
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nativeBuildInputs = [ pypaBuildHook pipInstallHook cython gfortran meson-python pythran pkg-config wheel ];
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buildInputs = [
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numpy.blas
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blas
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lapack
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pybind11
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pooch
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xsimd
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] ++ lib.optionals (pythonOlder "3.9") [
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libxcrypt
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];
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@@ -53,9 +99,29 @@ buildPythonPackage rec {
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doCheck = !(stdenv.isx86_64 && stdenv.isDarwin);
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preConfigure = ''
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sed -i '0,/from numpy.distutils.core/s//import setuptools;from numpy.distutils.core/' setup.py
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# Relax deps a bit
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substituteInPlace pyproject.toml \
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--replace 'numpy==' 'numpy>='
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# Helps parallelization a bit
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export NPY_NUM_BUILD_JOBS=$NIX_BUILD_CORES
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'';
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# We download manually the datasets and this variable tells the pooch
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# library where these files are cached. See also:
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# https://github.com/scipy/scipy/pull/18518#issuecomment-1562350648 And at:
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# https://github.com/scipy/scipy/pull/17965#issuecomment-1560759962
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export XDG_CACHE_HOME=$PWD; mkdir scipy-data
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'' + (lib.concatStringsSep "\n" (lib.mapAttrsToList (d: dpath:
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# Actually copy the datasets
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"cp ${dpath} scipy-data/${d}.dat"
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) datasets));
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mesonFlags = [
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"-Dblas=${blas.pname}"
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"-Dlapack=${lapack.pname}"
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# We always run what's necessary for cross compilation, which is passing to
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# meson the proper cross compilation related arguments. See also:
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# https://docs.scipy.org/doc/scipy/building/cross_compilation.html
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"--cross-file=${crossFileScipy}"
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];
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# disable stackprotector on aarch64-darwin for now
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#
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@@ -79,11 +145,17 @@ buildPythonPackage rec {
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requiredSystemFeatures = [ "big-parallel" ]; # the tests need lots of CPU time
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passthru = {
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blas = numpy.blas;
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inherit blas;
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updateScript = [
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./update.sh
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# Pass it this file name as argument
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(builtins.unsafeGetAttrPos "pname" python.pkgs.scipy).file
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]
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# Pass it the names of the datasets to update their hashes
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++ (builtins.attrNames datasetsHashes)
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;
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};
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setupPyBuildFlags = [ "--fcompiler='gnu95'" ];
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SCIPY_USE_G77_ABI_WRAPPER = 1;
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meta = with lib; {
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@@ -1,9 +0,0 @@
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diff --git i/scipy/datasets/meson.build w/scipy/datasets/meson.build
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index 101377253..eec2feea4 100644
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--- i/scipy/datasets/meson.build
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+++ w/scipy/datasets/meson.build
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@@ -11,4 +11,3 @@ py3.install_sources(
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subdir: 'scipy/datasets'
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)
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-subdir('tests')
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+29
@@ -0,0 +1,29 @@
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#!/usr/bin/env nix-shell
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#!nix-shell -i bash -p jq nix-prefetch-github
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set -euo pipefail
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echoerr() { echo "$@" 1>&2; }
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fname="$1"
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echoerr got fname $fname
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shift
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datasets="$@"
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echoerr datasets are: "$@"
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latest_release=$(curl --silent https://api.github.com/repos/scipy/scipy/releases/latest)
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version=$(jq -r '.tag_name' <<<"$latest_release" | cut -c2-)
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# Update version, if needed
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if grep -q 'version = "'$version $fname; then
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echo "Current version $version is the latest available, will update only datasets' hashes (don't take long)"
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else
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echoerr got version $version
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sed -i -E 's/(version = ).*=/\1'$version'/g' $fname
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# Update srcHash
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srcHash='"sha256-'$(nix-prefetch-github scipy scipy --rev v${version} --fetch-submodules | jq --raw-output .sha256)'"'
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sed -i 's/srcHash = .*=";/srcHash = '$srcHash';/g' $fname
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fi
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for d in $datasets; do
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datasetHash=$(nix-prefetch-url "https://raw.githubusercontent.com/scipy/dataset-${d}/main/${d}.dat")
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sed -i 's/'$d' = "[0-9a-z]\+/'$d' = "'$datasetHash'/g' $fname
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echoerr updated hash for dataset "'$d'"
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done
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