[Backport release-24.11] sage: 10.4 -> 10.5.rc0 (#357544)

pkgs/by-name/ga/gap/package.nix

@@ -1,6 +1,5 @@
 { stdenv
 , lib
-, fetchpatch
 , fetchurl
 , makeWrapper
 , readline
@@ -67,20 +66,13 @@ in
 stdenv.mkDerivation rec {
   pname = "gap";
   # https://www.gap-system.org/Releases/
-  version = "4.12.2";
+  version = "4.13.1";
 
   src = fetchurl {
     url = "https://github.com/gap-system/gap/releases/download/v${version}/gap-${version}.tar.gz";
-    sha256 = "sha256-ZyMIdF63iiIklO6N1nhu3VvDMUVvzGRWrAZL2yjVh6g=";
+    sha256 = "sha256-l5Tb26b7mY4KLQqoziH8iEitPT+cyZk7C44gvn4dvro=";
   };
 
-  patches = [
-    (fetchpatch {
-      url = "https://github.com/gap-system/gap/commit/c786e229413a44b7462196716b99ae9bb0071f4c.patch";
-      hash = "sha256-g3jrEMSavHAUKlHoPqWmOw49hWHU+29SA788Klnr0Uw=";
-    })
-  ];
-
   # remove all non-essential packages (which take up a lot of space)
   preConfigure = lib.optionalString (!keepAll) (removeNonWhitelistedPkgs packagesToKeep) + ''
     patchShebangs .

pkgs/by-name/sa/sage/patches/sphinx-docbuild-subprocesses.patch

@@ -1,5 +1,5 @@
 diff --git a/src/sage_docbuild/builders.py b/src/sage_docbuild/builders.py
-index 871cc4705a2..4b718136b91 100644
+index ab39d93c280..e6501c083d5 100644
 --- a/src/sage_docbuild/builders.py
 +++ b/src/sage_docbuild/builders.py
 @@ -106,31 +106,6 @@ def builder_helper(type):
@@ -48,13 +48,13 @@ index 871cc4705a2..4b718136b91 100644
              if build_options.ABORT_ON_ERROR:
                  raise
 diff --git a/src/sage_docbuild/sphinxbuild.py b/src/sage_docbuild/sphinxbuild.py
-index 5621fe9e456..b1b91ce7b2c 100644
+index 62b2d3cb112..aa7dc07741b 100644
 --- a/src/sage_docbuild/sphinxbuild.py
 +++ b/src/sage_docbuild/sphinxbuild.py
-@@ -323,3 +323,8 @@ def runsphinx():
-         sys.stderr = saved_stderr
-         sys.stdout.flush()
-         sys.stderr.flush()
+@@ -331,3 +331,8 @@ def runsphinx():
+ 
+     if not sys.warnoptions:
+         warnings.filters = original_filters[:]
 +
 +if __name__ == '__main__':
 +    import sys

pkgs/by-name/sa/sage/sage-src.nix

@@ -11,14 +11,14 @@
 # all get the same sources with the same patches applied.
 
 stdenv.mkDerivation rec {
-  version = "10.4";
+  version = "10.5.rc0";
   pname = "sage-src";
 
   src = fetchFromGitHub {
     owner = "sagemath";
     repo = "sage";
     rev = version;
-    hash = "sha256-BDO00ZSm5lnjEuA56VsY/FZyAhoG1hkFxdIlTtBZVBA=";
+    hash = "sha256-qjgEgyPOpT/g7D8YNhkqO1EHGNftZnuR5ucLNZBa9Sg=";
   };
 
   # contains essential files (e.g., setup.cfg) generated by the bootstrap script.
@@ -26,8 +26,8 @@ stdenv.mkDerivation rec {
   configure-src = fetchurl {
     # the hash below is the tagged commit's _parent_. it can also be found by looking for
     # the "configure" asset at https://github.com/sagemath/sage/releases/tag/${version}
-    url = "mirror://sageupstream/configure/configure-3c279ec5712e0fa35c5733e03e010970727d7189.tar.gz";
-    hash = "sha256-3bRlgIUSIq9tDzvI+ZfEd5LMy1qHXdItEwu1say4cx4=";
+    url = "mirror://sageupstream/configure/configure-d9c38a7c581e6ed54fbe420122b8bba488b16074.tar.gz";
+    hash = "sha256-y1EpsuYK9wloptjeiTew+TZaIUZ2K/NKCbSteojFa4s=";
   };
 
   # Patches needed because of particularities of nix or the way this is packaged.
@@ -54,20 +54,6 @@ stdenv.mkDerivation rec {
   # fix those bugs themselves. This is for critical bugfixes, where "critical"
   # == "causes (transient) doctest failures / somebody complained".
   bugfixPatches = [
-    # https://github.com/sagemath/sage/pull/38628, landed in 10.5.beta4
-    (fetchpatch {
-      name = "pari-stack-cysignals-exception.patch";
-      url = "https://github.com/sagemath/sage/commit/4a9c985b769b1209902c970ade1892f18ab48c10.diff";
-      hash = "sha256-S6NdonB7needJlQdx52Huk34Q8/vG3nyGicA5JpsdWc=";
-    })
-
-    # https://github.com/sagemath/sage/pull/38851, landed in 10.5.beta8
-    (fetchpatch {
-      name = "glpk-aarch64-hang-workaround.patch";
-      url = "https://github.com/sagemath/sage/commit/ce4a78dcb4178f85273619cea076c97345977ee1.diff";
-      hash = "sha256-TibTx5llkXjkEZB/MDy4hfGwKBmwtitEpWP6K/ykke0=";
-    })
-
     # compile libs/gap/element.pyx with -O1
     # a more conservative version of https://github.com/sagemath/sage/pull/37951
     ./patches/gap-element-crash.patch
@@ -80,26 +66,6 @@ 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/38500, landed in 10.5.beta3
-    (fetchpatch {
-      name = "cython-3.0.11-upgrade.patch";
-      url = "https://patch-diff.githubusercontent.com/raw/sagemath/sage/pull/38500.diff";
-      hash = "sha256-ePfH3Gy1T0UfpoVd3EZowCfy88CbE+yE2MV2itWthsA=";
-    })
-
-    # https://github.com/sagemath/sage/pull/36641, landed in 10.5.beta3
-    (fetchpatch {
-      name = "sympy-1.13.2-update.patch";
-      url = "https://github.com/sagemath/sage/commit/100189fa62f9a40e7aa0d856615366ea99b87aff.diff";
-      sha256 = "sha256-uWr3I15WByQYGVxbJFqG4zUJ7c7+4rjkcgwkAT85O7w=";
-    })
-
-    # https://github.com/sagemath/sage/pull/38250, landed in 10.5.beta0
-    (fetchpatch {
-      name = "numpy-2.0-compat.patch";
-      url = "https://github.com/sagemath/sage/commit/0962e0bcb159d342e7c7d83557a71e7b670fff47.diff";
-      sha256 = "sha256-4SBhgPgT9VsBxcBH8+T5uYtWzYP5tZi9+iKOG55hWgI=";
-    })
   ];
 
   patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;