sageWithDoc: 10.3 -> 10.4 (#339194)

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

@@ -97,6 +97,7 @@ let
   # Running the tests should take something in the order of 1h.
   sage-tests = callPackage ./sage-tests.nix {
     inherit sage-with-env;
+    pytest = python3.pkgs.pytest;
   };
 
   sage-src = callPackage ./sage-src.nix {};

pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch

@@ -1,15 +1,15 @@
 diff --git a/src/sage_docbuild/builders.py b/src/sage_docbuild/builders.py
-index c5be38600a..e1d15f62d3 100644
+index 871cc4705a2..4b718136b91 100644
 --- a/src/sage_docbuild/builders.py
 +++ b/src/sage_docbuild/builders.py
-@@ -105,31 +105,6 @@ def builder_helper(type):
+@@ -106,31 +106,6 @@ def builder_helper(type):
      """
      Return a function which builds the documentation for
      output type ``type``.
 -
 -    TESTS:
 -
--    Check that :trac:`25161` has been resolved::
+-    Check that :issue:`25161` has been resolved::
 -
 -        sage: from sage_docbuild.builders import DocBuilder
 -        sage: from sage_docbuild.__main__ import setup_parser
@@ -48,10 +48,10 @@ index c5be38600a..e1d15f62d3 100644
              if build_options.ABORT_ON_ERROR:
                  raise
 diff --git a/src/sage_docbuild/sphinxbuild.py b/src/sage_docbuild/sphinxbuild.py
-index 07c584de55..b83283a9ee 100644
+index 5621fe9e456..b1b91ce7b2c 100644
 --- a/src/sage_docbuild/sphinxbuild.py
 +++ b/src/sage_docbuild/sphinxbuild.py
-@@ -331,3 +331,8 @@ def runsphinx():
+@@ -323,3 +323,8 @@ def runsphinx():
          sys.stderr = saved_stderr
          sys.stdout.flush()
          sys.stderr.flush()

pkgs/applications/science/math/sage/python-modules/sage-docbuild.nix

@@ -1,6 +1,7 @@
 { lib
 , buildPythonPackage
 , sage-src
+, furo
 , jupyter-sphinx
 , sphinx
 , sphinx-copybutton
@@ -13,6 +14,7 @@ buildPythonPackage rec {
   src = sage-src;
 
   propagatedBuildInputs = [
+    furo
     jupyter-sphinx
     sphinx
     sphinx-copybutton

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

@@ -11,14 +11,14 @@
 # all get the same sources with the same patches applied.
 
 stdenv.mkDerivation rec {
-  version = "10.3";
+  version = "10.4";
   pname = "sage-src";
 
   src = fetchFromGitHub {
     owner = "sagemath";
     repo = "sage";
     rev = version;
-    hash = "sha256-OHtMv8t0RrP6R8XIREU+C1vpazeQLWa75wx9Mv6BN1U=";
+    hash = "sha256-BDO00ZSm5lnjEuA56VsY/FZyAhoG1hkFxdIlTtBZVBA=";
   };
 
   # 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-ab1a517b64b02bf15bbcb8d7c2d4d643bd5eff9b.tar.gz";
+    url = "mirror://sageupstream/configure/configure-3c279ec5712e0fa35c5733e03e010970727d7189.tar.gz";
-    hash = "sha256-pe9AxTM+gFSR4/eVfUzay+4bwjoubbYeDPc+avKjlaw=";
+    hash = "sha256-3bRlgIUSIq9tDzvI+ZfEd5LMy1qHXdItEwu1say4cx4=";
   };
 
   # Patches needed because of particularities of nix or the way this is packaged.
@@ -62,23 +62,9 @@ stdenv.mkDerivation rec {
     # https://github.com/sagemath/sage/issues/34575
     ./patches/disable-slow-glpk-test.patch
 
-    # https://github.com/sagemath/sage/pull/37489, landed in 10.4.beta1
-    (fetchpatch {
-      name = "quaternionalgebra-random-failure.patch";
-      url = "https://github.com/sagemath/sage/commit/1c3f991b9d3c5778e409e5414c6cfcd456113f19.diff";
-      hash = "sha256-uCXchYx26DdxTjR1k2748KCEHPnekKS2fAM7SpyhNvM=";
-    })
-
     # 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
@@ -88,45 +74,11 @@ 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
+    # https://github.com/sagemath/sage/pull/38500, positively reviewed, to land in 10.5.beta3
     (fetchpatch {
-      name = "cpp-17.patch";
+      name = "cython-3.0.11-upgrade.patch";
-      url = "https://github.com/sagemath/sage/commit/9b0a40d6cd17706db31d5ff8cdd78910409ba1c8.patch";
+      url = "https://patch-diff.githubusercontent.com/raw/sagemath/sage/pull/38500.diff";
-      sha256 = "sha256-2pJ9eH+o9O76Tsmklc/frzDOFkvPjvs2JQWCSqA+tMs=";
+      hash = "sha256-ePfH3Gy1T0UfpoVd3EZowCfy88CbE+yE2MV2itWthsA=";
-    })
-    # https://github.com/sagemath/sage/pull/37763, landed in 10.4.beta2
-    (fetchpatch {
-      name = "scipy-fault-tolerance.patch";
-      url = "https://github.com/sagemath/sage/commit/551139c09f26a5da96b1187c3f0dd17b8d80ef84.diff";
-      hash = "sha256-PR4przrZ3ieHaW2nSY7l7VhNfrUupu9yCIrXpeyoAgg=";
-    })
-
-    # https://github.com/sagemath/sage/pull/37492, landed in 10.4.beta5
-    (fetchpatch {
-      name = "singular-4.3.2p14-upgrade.patch";
-      url = "https://github.com/sagemath/sage/commit/a0c56816b051e97da44ac0a4e4d4f6915cf7fa0f.diff";
-      sha256 = "sha256-WGMmPeBoj2LUC+2qxWuaJL89QUuGt6axGvxWkpM9LYg=";
-    })
-
-    # https://github.com/sagemath/sage/pull/37949, landed in 10.4.beta6
-    (fetchpatch {
-      name = "conway-polynomials-new-len.patch";
-      url = "https://github.com/sagemath/sage/commit/c9f5b45179e92ea0de1e0dbe0f47464010902851.diff";
-      hash = "sha256-DwN2UIX8dxfxjIiqVvMdGbIxJ7CR/Ag2XUmS5vUKFTs=";
-    })
-
-    # https://github.com/sagemath/sage/pull/37967, landed in 10.4.beta6
-    (fetchpatch {
-      name = "conway-polynomials-ell-point.patch";
-      url = "https://github.com/sagemath/sage/commit/4e0bbaf90262a42f8ea14d5bcfed65f9d1787f54.diff";
-      hash = "sha256-9gXydi1A+n7+K8YpH0PB8l/OMexhgO2F5NccU0cK+ls=";
-    })
-
-    # https://github.com/sagemath/sage/pull/38100, landed in 10.4.beta8
-    (fetchpatch {
-      name = "sphinx-7.3-update.patch";
-      url = "https://github.com/sagemath/sage/commit/e1b22690db42885423be5049246eb71ff52bdfef.diff";
-      hash = "sha256-04KAyz8+0pJbRV8Ld0bNX1OoEx/35gIh3Nff+6n8QUU=";
     })
   ];
 
@@ -151,7 +103,7 @@ stdenv.mkDerivation rec {
 
   installPhase = ''
     cp -r . "$out"
-    tar xkzf ${configure-src} -C "$out"
+    tar xzf ${configure-src} -C "$out"
     rm "$out/configure"
   '';
 }

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

@@ -1,5 +1,6 @@
 { stdenv
 , lib
+, pytest
 , sage-with-env
 , makeWrapper
 , files ? null # "null" means run all tests
@@ -30,6 +31,7 @@ stdenv.mkDerivation {
 
   nativeBuildInputs = [ makeWrapper ];
   buildInputs = [
+    pytest
     sage-with-env
   ];