1 files changed, 67 insertions, 63 deletions

diff --git a/pkgs/development/python-modules/scipy/default.nix b/pkgs/development/python-modules/scipy/default.nix
index 64e261c374039..1bd02b708089e 100644
--- a/pkgs/development/python-modules/scipy/default.nix
+++ b/pkgs/development/python-modules/scipy/default.nix
@@ -1,30 +1,34 @@
-{ lib
-, stdenv
-, fetchFromGitHub
-, fetchpatch
-, fetchurl
-, writeText
-, python
-, pythonOlder
-, buildPythonPackage
-, cython
-, gfortran
-, meson-python
-, nukeReferences
-, pkg-config
-, pythran
-, wheel
-, setuptools
-, hypothesis
-, pytest7CheckHook
-, pytest-xdist
-, numpy
-, pybind11
-, pooch
-, libxcrypt
-, xsimd
-, blas
-, lapack
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  fetchpatch,
+  fetchurl,
+  writeText,
+  python,
+  pythonOlder,
+  buildPythonPackage,
+  cython,
+  gfortran,
+  meson-python,
+  nukeReferences,
+  pkg-config,
+  pythran,
+  wheel,
+  setuptools,
+  hypothesis,
+  pytest7CheckHook,
+  pytest-xdist,
+  numpy,
+  pybind11,
+  pooch,
+  libxcrypt,
+  xsimd,
+  blas,
+  lapack,
+
+  # Reverse dependency
+  sage,
 }:
 
 let
@@ -34,15 +38,16 @@ let
   #     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 = "1.13.0";
-  srcHash = "sha256-HaYk92hOREHMOXppK+Bs9DrBu9KUVUsZ0KV+isTofUo=";
+  version = "1.13.1";
+  srcHash = "sha256-KpTvBJhiJ/IBjIFQhvS+NhRP3tbyXU5gQnAiFv47sKU=";
   datasetsHashes = {
     ascent = "1qjp35ncrniq9rhzb14icwwykqg2208hcssznn3hz27w39615kh3";
     ecg = "1bwbjp43b7znnwha5hv6wiz3g0bhwrpqpi75s12zidxrbwvd62pj";
     face = "11i8x29h80y7hhyqhil1fg8mxag5f827g33lhnsf44qk116hp2wx";
   };
   datasets = lib.mapAttrs (
-    d: hash: fetchurl {
+    d: hash:
+    fetchurl {
       url = "https://raw.githubusercontent.com/scipy/dataset-${d}/main/${d}.dat";
       sha256 = hash;
     }
@@ -55,7 +60,8 @@ let
     host-python-path = '${python.interpreter}'
     host-python-version = '${python.pythonVersion}'
   '';
-in buildPythonPackage {
+in
+buildPythonPackage {
   inherit pname version;
   format = "pyproject";
 
@@ -72,16 +78,8 @@ in buildPythonPackage {
     (fetchpatch {
       url = "https://github.com/scipy/scipy/commit/dd50ac9d98dbb70625333a23e3a90e493228e3be.patch";
       hash = "sha256-Vf6/hhwu6X5s8KWhq8bUZKtSkdVu/GtEpGtj8Olxe7s=";
-      excludes = [
-        "doc/source/dev/contributor/meson_advanced.rst"
-      ];
+      excludes = [ "doc/source/dev/contributor/meson_advanced.rst" ];
     })
-    # Fix for https://github.com/scipy/scipy/issues/20300 until 1.13.1 is
-    # released. Patch is based upon:
-    # https://github.com/scipy/pocketfft/commit/9367142748fcc9696a1c9e5a99b76ed9897c9daa
-    # Couldn't use fetchpatch because it is a submodule of scipy, and
-    # extraPrefix doesn't fit this purpose.
-    ./pocketfft-aligned_alloc.patch
   ];
 
   # Upstream says in a comment in their pyproject.toml that building against
@@ -110,9 +108,7 @@ in buildPythonPackage {
     pybind11
     pooch
     xsimd
-  ] ++ lib.optionals (pythonOlder "3.9") [
-    libxcrypt
-  ];
+  ] ++ lib.optionals (pythonOlder "3.9") [ libxcrypt ];
 
   propagatedBuildInputs = [ numpy ];
 
@@ -138,18 +134,23 @@ in buildPythonPackage {
 
   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));
+  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}"
@@ -185,14 +186,17 @@ in 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)
-    ;
+    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;
+    };
   };
 
   SCIPY_USE_G77_ABI_WRAPPER = 1;