Merge pull request #122592 from collares/sage-9.3

sage: 9.3rc4 -> 9.3

pkgs/applications/science/math/gap/default.nix

@@ -1,7 +1,6 @@
 { stdenv
 , lib
 , fetchurl
-, fetchpatch
 , makeWrapper
 , readline
 , gmp
@@ -35,7 +34,7 @@ let
     "autpgrp-*"
     "alnuth-*"
     "crisp-*"
-    "ctbllib"
+    "ctbllib-*"
     "FactInt-*"
     "fga"
     "irredsol-*"
@@ -62,11 +61,11 @@ in
 stdenv.mkDerivation rec {
   pname = "gap";
   # https://www.gap-system.org/Releases/
-  version = "4.11.0";
+  version = "4.11.1";
 
   src = fetchurl {
-    url = "https://files.gap-system.org/gap-${lib.versions.major version}.${lib.versions.minor version}/tar.bz2/gap-${version}.tar.bz2";
+    url = "https://github.com/gap-system/gap/releases/download/v${version}/gap-${version}.tar.gz";
-    sha256 = "sha256-vwcKENwqxgWT/mXfD4c9ctTWdQHobrJipva9SPyGhgI=";
+    sha256 = "sha256-ZjXF2n2CdV+DOUhrnKwzdm9YcS8pfoI0+6QIGJAuowQ=";
   };
 
   # remove all non-essential packages (which take up a lot of space)
@@ -84,23 +83,6 @@ stdenv.mkDerivation rec {
     makeWrapper
   ];
 
-  patches = [
-    # Fix for locale specific tests causing issues. Already upstream.
-    # Backport of https://github.com/gap-system/gap/pull/4022
-    (fetchpatch {
-      name = "remove-locale-specific-tests.patch";
-      url = "https://github.com/gap-system/gap/commit/c18b0c4215b5212a2cc4f305e2d5b94ba716bee8.patch";
-      sha256 = "sha256-De+T9Y7ewRT6plJrj2VR8axRvD/JCTYKOBWB7Bw0oq0=";
-    })
-
-    # fixes aarch64 gc crashes: https://github.com/gap-system/gap/pull/3965
-    (fetchpatch {
-      name = "mark-genstackfuncbags-as-noinline.patch";
-      url = "https://github.com/gap-system/gap/commit/f0a8f49ff8dad0a5fa77253d45457c6f40f96778.patch";
-      sha256 = "sha256-GU9tOP1stX2vn8m8kXOBupEpxIYArA76ibKL8eLn0MY=";
-    })
-  ];
-
   # "teststandard" is a superset of testinstall. It takes ~1h instead of ~1min.
   # tests are run twice, once with all packages loaded and once without
   # checkTarget = "teststandard";

pkgs/applications/science/math/gap/mark-genstackfuncbags-as-noinline.patch

@@ -1,13 +0,0 @@
-diff --git a/src/gasman.c b/src/gasman.c
-index 417811401..314a74190 100644
---- a/src/gasman.c
-+++ b/src/gasman.c
-@@ -1861,7 +1861,7 @@ void SparcStackFuncBags( void )
- #endif
- 
- 
--void GenStackFuncBags ( void )
-+NOINLINE void GenStackFuncBags ( void )
- {
-     Bag *               top;            /* top of stack                    */
-     Bag *               p;              /* loop variable                   */

pkgs/applications/science/math/pynac/default.nix

@@ -22,23 +22,44 @@ stdenv.mkDerivation rec {
   };
 
   patches = [
-    (fetchpatch {
+    # the five patches below are included with sage 9.3. since pynac
-      name = "handle_factor.patch";
+    # is a self-described "Sage Math support library", we include them
-      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/handle_factor.patch?h=9.3.rc3";
+    # here.
-      sha256 = "sha256-U1lb5qwBqZZgklfDMhBX4K5u8bz5x42O4w7hyNy2YVw=";
-    })
 
+    # https://trac.sagemath.org/ticket/30688
     (fetchpatch {
       name = "power_inf_loop.patch";
-      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/power_inf_loop.patch?h=9.3.rc3";
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/power_inf_loop.patch?h=9.3";
       sha256 = "sha256-VYeaJl8u2wl7FQ/6xnpZv1KpdNYEmJoPhuMrBADyTRs=";
     })
 
+    # https://trac.sagemath.org/ticket/31479
+    (fetchpatch {
+      name = "disable_poly_mul_expand.patch";
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/disable_poly_mul_expand.patch?h=9.3";
+      sha256 = "sha256-gRjoltU9Tzj7fjNyE25fY+iyDxERzSTOMigzxFpUqPo=";
+    })
+
+    # https://trac.sagemath.org/ticket/31530
     (fetchpatch {
       name = "too_much_sub.patch";
-      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/too_much_sub.patch?h=9.3.rc3";
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/too_much_sub.patch?h=9.3";
       sha256 = "sha256-lw7xSQ/l+rzPu+ghWF4omYF0mKksGGPuuHJTktvbdis=";
     })
+
+    # https://trac.sagemath.org/ticket/31554
+    (fetchpatch {
+      name = "handle_factor.patch";
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/handle_factor.patch?h=9.3";
+      sha256 = "sha256-U1lb5qwBqZZgklfDMhBX4K5u8bz5x42O4w7hyNy2YVw=";
+    })
+
+    # https://trac.sagemath.org/ticket/31645
+    (fetchpatch {
+      name = "seriesbug.patch";
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/seriesbug.patch?h=9.3";
+      sha256 = "sha256-b3//oirN7JHDYqrvE+tDYcnKpSYQJ08yBzcNlII2Dts=";
+    })
   ];
 
   buildInputs = [

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

@@ -24,14 +24,14 @@ let
   );
 in
 stdenv.mkDerivation rec {
-  version = "9.3.rc4";
+  version = "9.3";
   pname = "sage-src";
 
   src = fetchFromGitHub {
     owner = "sagemath";
     repo = "sage";
     rev = version;
-    sha256 = "sha256-LDY07By2j6JagkgT9zeDJ93+m2/oXXEnDRTDzmR8ftk=";
+    sha256 = "sha256-l9DX8jcDdKA7GJ6xU+nBsmlZxrcZ9ZUAJju621ooBEo=";
   };
 
   # Patches needed because of particularities of nix or the way this is packaged.

pkgs/applications/science/math/singular/default.nix

@@ -31,11 +31,9 @@ stdenv.mkDerivation rec {
     owner = "Singular";
     repo = "Singular";
 
-    # 4.2.0p2 is not tagged, but the tarball matches commit
+    # 4.2.0p2 is not tagged, but the tarball matches the commit below.
-    # 6f68939ddf612d96e3caaaaa8275f77613ac1da8. the commit below has
+    rev = "6f68939ddf612d96e3caaaaa8275f77613ac1da8";
-    # two extra fixes.
+    sha256 = "sha256-BJNzYylzDqD/5YjzjxPRb/c96tYiuGy9Y+A7qf3ZSG8=";
-    rev = "3cda50c00a849455efa2502e56596955491a353a";
-    sha256 = "sha256-OizPhGE6L2LTOrKfeDdDB6BSdvYkDVXvbbYjV14hnHM=";
 
     # if a release is tagged it will be in the format below.
     # rev = "Release${lib.replaceStrings ["."] ["-"] version}";
@@ -60,6 +58,13 @@ stdenv.mkDerivation rec {
     # https://github.com/alsa-project/alsa-firmware/issues/3 for a
     # related issue.
     ./use-older-ax-prog-cc-for-build.patch
+
+    # https://github.com/Singular/Singular/issues/1086
+    (fetchpatch {
+      name = "schubert-lib-fails-with-too-many-cpus.patch";
+      url = "https://github.com/Singular/Singular/commit/3cda50c00a849455efa2502e56596955491a353a.patch";
+      sha256 = "sha256-fgYd+2vT32w5Ki8kKx6PfZn2e4QSJcYWOwEFXtc+lSA=";
+    })
   ] ++ lib.optionals enableDocs [
     # singular supports building without 4ti2, bertini, normaliz or
     # topcom just fine, but the docbuilding does not skip manual pages
@@ -67,6 +72,13 @@ stdenv.mkDerivation rec {
     # doc2tex.pl::HandleLib, since it seems to ignore "-exclude"
     # argumens). skip them manually.
     ./disable-docs-for-optional-unpackaged-deps.patch
+
+    # fix some non-ascii characters in doc/decodegb.doc
+    (fetchpatch {
+      name = "decodegb-ascii.patch";
+      url = "https://github.com/Singular/Singular/commit/36966d9009de572ee4dbc487f3e5744098fe91be.patch";
+      sha256 = "sha256-9WcEov/oOQRC584ag6WVHFwY2aCjbM75HWyvZoEwppw=";
+    })
   ];
 
   configureFlags = [
@@ -83,9 +95,6 @@ stdenv.mkDerivation rec {
     substituteInPlace Tst/regress.cmd --replace 'mysystem_catch("hostname")' 'nix_test_runner'
 
     patchShebangs .
-  '' + lib.optionalString enableDocs ''
-    # work around encoding problem
-    sed -i -e 's/\xb7/@cdot{}/g' doc/decodegb.doc
   '';
 
   # For reference (last checked on commit 75f460d):
@@ -149,7 +158,7 @@ stdenv.mkDerivation rec {
 
   # singular tests are a bit complicated, see
   # https://github.com/Singular/Singular/tree/spielwiese/Tst
-  # https://www.singular.uni-kl.de/forum/viewtopic.php&t=2773
+  # https://www.singular.uni-kl.de/forum/viewtopic.php?f=10&t=2773
   testsToRun = [
     "Old/universal.lst"
     "Buch/buch.lst"
@@ -181,7 +190,7 @@ stdenv.mkDerivation rec {
       2>"$TMPDIR/out-err.log"
 
     # unfortunately regress.cmd always returns exit code 0, so check stderr
-    # https://www.singular.uni-kl.de/forum/viewtopic.php&t=2773
+    # https://www.singular.uni-kl.de/forum/viewtopic.php?f=10&t=2773
     if [[ -s "$TMPDIR/out-err.log" ]]; then
       cat "$TMPDIR/out-err.log"
       exit 1

pkgs/data/misc/graphs/default.nix

@@ -7,9 +7,7 @@ stdenv.mkDerivation rec {
   version = "20210214";
 
   src = fetchurl {
-    url = "https://mirrors.mit.edu/sage/spkg/upstream/${pname}/${pname}-${version}.tar.bz2";
+    url = "mirror://sageupstream/${pname}/${pname}-${version}.tar.bz2";
-    # TODO: switch to the url below once Sage 9.3 is released
-    # url = "mirror://sageupstream/${pname}/${pname}-${version}.tar.bz2";
     sha256 = "sha256-ByN8DZhTYRUFw4n9e7klAMh0P1YxurtND0Xf2DMvN0E=";
   };