Unverified Commit 2a20f493 authored by George Huebner's avatar George Huebner
Browse files

sage: fixes for LLVM stdenv 

Also backport a fix that silences `xcode-select: not found` warnings
parent a9f96508

pkgs/applications/science/math/sage/patches/silence-linker.patch

0 → 100644
+27 −0
Original line number Diff line number Diff line 
From 06d3bb5d8ef007bbcd71ee157fd97cd69557383b Mon Sep 17 00:00:00 2001

From: George Huebner <george@feyor.sh>

Date: Sat, 20 Jul 2024 18:46:04 -0500

Subject: [PATCH] sage.cython: silence linker



(Nix+LLVM specific issue) "ld: warning: directory not found" causes

any cython doctest to fail and is annoying, so I told ld to shut up.

---

 src/sage/misc/cython.py | 2 +-

 1 file changed, 1 insertion(+), 1 deletion(-)



diff --git a/src/sage/misc/cython.py b/src/sage/misc/cython.py

index 545e1227b0..c5f4b69221 100644

--- a/src/sage/misc/cython.py

+++ b/src/sage/misc/cython.py

@@ -339,7 +339,7 @@ def cython(filename, verbose=0, compile_message=False,

     Cython.Compiler.Options.pre_import = "sage.all" if sage_namespace else None

 

     extra_compile_args = ['-w']  # no warnings

-    extra_link_args = []

+    extra_link_args = ['-w']

 

     ext = Extension(name,

                     sources=[pyxfile],

-- 

2.44.1

pkgs/applications/science/math/sage/sage-env.nix

+3 −1
Original line number Diff line number Diff line
@@ -10,6 +10,7 @@ 
, coreutils

, gnused

, gnugrep

, gawk

, binutils

, pythonEnv

, python3
@@ -70,6 +71,7 @@ let 
    coreutils

    gnused

    gnugrep

    gawk

    binutils.bintools

    pkg-config

    pari
@@ -186,7 +188,7 @@ writeTextFile rec { 
    export SAGE_EXTCODE='${sagelib.src}/src/sage/ext_data'



  # for find_library

    export DYLD_LIBRARY_PATH="${lib.makeLibraryPath [stdenv.cc.libc singular giac]}''${DYLD_LIBRARY_PATH:+:}$DYLD_LIBRARY_PATH"

    export DYLD_LIBRARY_PATH="${lib.makeLibraryPath [stdenv.cc.libc singular giac gap]}''${DYLD_LIBRARY_PATH:+:}$DYLD_LIBRARY_PATH"

  '';

} // { # equivalent of `passthru`, which `writeTextFile` doesn't support

  lib = sagelib;

pkgs/applications/science/math/sage/sage-src.nix

+18 −0
Original line number Diff line number Diff line 
{ stdenv

, lib

, fetchFromGitHub

, fetchpatch

, fetchurl
@@ -40,6 +41,10 @@ stdenv.mkDerivation rec { 
    # we can now set the cache dir to be within the .sage directory. This is

    # not strictly necessary, but keeps us from littering in the user's HOME.

    ./patches/sympow-cache.patch

  ] ++ lib.optionals (stdenv.cc.isClang) [

    # https://github.com/NixOS/nixpkgs/pull/264126

    # Dead links in python sysconfig cause LLVM linker warnings, leading to cython doctest failures.

    ./patches/silence-linker.patch

  ];



  # Since sage unfortunately does not release bugfix releases, packagers must
@@ -64,6 +69,13 @@ stdenv.mkDerivation rec { 
    # compile libs/gap/element.pyx with -O1

    # a more conservative version of https://github.com/sagemath/sage/pull/37951

    ./patches/gap-element-crash.patch



    # https://github.com/sagemath/sage/pull/37886, landed in 10.4.beta7

    (fetchpatch {

      name = "remove-xcode.patch";

      url = "https://github.com/sagemath/sage/commit/8e72038b4ab24fb63c06b28f6eb43097b9ab24d6.patch";

      sha256 = "sha256-hufDJFUBa/Trn1xsVNvzb2c1wE9iyhqewj3RMjVtENA=";

    })

  ];



  # Patches needed because of package updates. We could just pin the versions of
@@ -73,6 +85,12 @@ stdenv.mkDerivation rec { 
  # should come from or be proposed to upstream. This list will probably never

  # be empty since dependencies update all the time.

  packageUpgradePatches = [

    # https://github.com/sagemath/sage/pull/37646, landed in 10.4.beta1

    (fetchpatch {

      name = "cpp-17.patch";

      url = "https://github.com/sagemath/sage/commit/9b0a40d6cd17706db31d5ff8cdd78910409ba1c8.patch";

      sha256 = "sha256-2pJ9eH+o9O76Tsmklc/frzDOFkvPjvs2JQWCSqA+tMs=";

    })

    # https://github.com/sagemath/sage/pull/37763, landed in 10.4.beta2

    (fetchpatch {

      name = "scipy-fault-tolerance.patch";