Merge pull request #59989 from timokau/sage-8.8

sage: 8.7 -> 8.8

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

@@ -130,7 +130,7 @@ let
   singular = pkgs.singular.override { inherit flint; };
 
   # https://trac.sagemath.org/ticket/26625
-  maxima-ecl = pkgs.maxima-ecl-5_41;
+  maxima-ecl = pkgs.maxima-ecl;
 
   # *not* to confuse with the python package "pynac"
   pynac = pkgs.pynac.override { inherit singular flint; };

pkgs/applications/science/math/sage/patches/do-not-test-package-manifests.patch

@@ -1,26 +0,0 @@
-diff --git a/src/sage/misc/package.py b/src/sage/misc/package.py
-index 3bca15d53b..7cf04ff8d1 100644
---- a/src/sage/misc/package.py
-+++ b/src/sage/misc/package.py
-@@ -478,16 +478,16 @@ def package_manifest(package):
- 
-     EXAMPLES::
- 
--        sage: from sage.misc.package import package_manifest
--        sage: sagetex_manifest = package_manifest('sagetex')
--        sage: sagetex_manifest['package_name'] == 'sagetex'
-+        sage: from sage.misc.package import package_manifest # optional - buildsystem
-+        sage: sagetex_manifest = package_manifest('sagetex') # optional - buildsystem
-+        sage: sagetex_manifest['package_name'] == 'sagetex' # optional - buildsystem
-         True
--        sage: 'files' in sagetex_manifest
-+        sage: 'files' in sagetex_manifest # optional - buildsystem
-         True
- 
-     Test a nonexistent package::
- 
--        sage: package_manifest('dummy-package')
-+        sage: package_manifest('dummy-package') # optional - buildsystem
-         Traceback (most recent call last):
-         ...
-         KeyError: 'dummy-package'

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

@@ -0,0 +1,57 @@
+diff --git a/src/sage_setup/docbuild/__init__.py b/src/sage_setup/docbuild/__init__.py
+index 0f2700168a..60f71357d2 100644
+--- a/src/sage_setup/docbuild/__init__.py
++++ b/src/sage_setup/docbuild/__init__.py
+@@ -86,26 +86,6 @@ def builder_helper(type):
+     """
+     Returns a function which builds the documentation for
+     output type ``type``.
+-
+-    TESTS:
+-
+-    Check that :trac:`25161` has been resolved::
+-
+-        sage: from sage_setup.docbuild import DocBuilder, setup_parser
+-        sage: DocBuilder._options = setup_parser().parse_args([])[0] # builder_helper needs _options to be set
+-
+-        sage: import sage_setup.docbuild.sphinxbuild
+-        sage: def raiseBaseException():
+-        ....:     raise BaseException("abort pool operation")
+-        sage: original_runsphinx, sage_setup.docbuild.sphinxbuild.runsphinx = sage_setup.docbuild.sphinxbuild.runsphinx, raiseBaseException
+-
+-        sage: from sage_setup.docbuild import builder_helper, build_many, build_ref_doc
+-        sage: helper = builder_helper("html")
+-        sage: try:
+-        ....:     build_many(build_ref_doc, [("docname", "en", "html", {})])
+-        ....: except Exception as E:
+-        ....:     "Non-exception during docbuild: abort pool operation" in str(E)
+-        True
+     """
+     def f(self, *args, **kwds):
+         output_dir = self._output_dir(type)
+@@ -127,10 +107,9 @@ def builder_helper(type):
+         logger.debug(build_command)
+ 
+         # Run Sphinx with Sage's special logger
+-        sys.argv = ["sphinx-build"] + build_command.split()
+-        from .sphinxbuild import runsphinx
++        args = "python -um sage_setup.docbuild.sphinxbuild -N".split() + build_command.split()
+         try:
+-            runsphinx()
++            subprocess.check_call(args)
+         except Exception:
+             if ABORT_ON_ERROR:
+                 raise
+diff --git a/src/sage_setup/docbuild/sphinxbuild.py b/src/sage_setup/docbuild/sphinxbuild.py
+index 9a2fba79bc..77c8ed3592 100644
+--- a/src/sage_setup/docbuild/sphinxbuild.py
++++ b/src/sage_setup/docbuild/sphinxbuild.py
+@@ -318,3 +318,8 @@ def runsphinx():
+         sys.stderr = saved_stderr
+         sys.stdout.flush()
+         sys.stderr.flush()
++
++if __name__ == '__main__':
++    import sys
++    sys.argv[0] = "sphinx-build"
++    runsphinx()

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

@@ -10,14 +10,14 @@
 # all get the same sources with the same patches applied.
 
 stdenv.mkDerivation rec {
-  version = "8.7";
+  version = "8.8";
   pname = "sage-src";
 
   src = fetchFromGitHub {
     owner = "sagemath";
     repo = "sage";
     rev = version;
-    sha256 = "05vvrd6syh0hlmrk6kzjrwd0hpmvxp8vr8p3mkjb0jh5p2kjdd27";
+    sha256 = "0jm7zdkz8wfgrmf6620jfr8kgvprrz3qfl8gzx6rl5z5cm734b6x";
   };
 
   # Patches needed because of particularities of nix or the way this is packaged.
@@ -45,46 +45,23 @@ stdenv.mkDerivation rec {
     # Fixes a potential race condition which can lead to transient doctest failures.
     ./patches/fix-ecl-race.patch
 
-    # Parallelize docubuild using subprocesses, fixing an isolation issue. See
-    # https://groups.google.com/forum/#!topic/sage-packaging/YGOm8tkADrE
-    (fetchpatch {
-      name = "sphinx-docbuild-subprocesses.patch";
-      url = "https://salsa.debian.org/science-team/sagemath/raw/8a215b17e6f791ddfae6df8ce6d01dfb89acb434/debian/patches/df-subprocess-sphinx.patch";
-      sha256 = "07p9i0fwjgapmfvmi436yn6v60p8pvmxqjc93wsssqgh5kd8qw3n";
-      stripLen = 1;
-    })
-
-    # Part of the build system. Should become unnecessary with sage 8.8.
-    # Upstream discussion here: https://trac.sagemath.org/ticket/27124#comment:33
-    ./patches/do-not-test-package-manifests.patch
-
     # Not necessary since library location is set explicitly
     # https://trac.sagemath.org/ticket/27660#ticket
     ./patches/do-not-test-find-library.patch
 
-    # https://trac.sagemath.org/ticket/27697#ticket
-    (fetchpatch {
-      name = "pplpy-doc-location-configurable.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?h=c4d966e7cb0c7b87c55d52dc6f46518433a2a0a2";
-      sha256 = "0pqbbsx8mriwny422s9mp3z5d095cnam32sm62q4mxk8g8jb9vm9";
-    })
 
     # https://trac.sagemath.org/ticket/28007
     ./patches/threejs-offline.patch
+
+    # Parallelize docubuild using subprocesses, fixing an isolation issue. See
+    # https://groups.google.com/forum/#!topic/sage-packaging/YGOm8tkADrE
+    ./patches/sphinx-docbuild-subprocesses.patch
   ];
 
   # Since sage unfortunately does not release bugfix releases, packagers must
   # fix those bugs themselves. This is for critical bugfixes, where "critical"
   # == "causes (transient) doctest failures / somebody complained".
-  bugfixPatches = [
+  bugfixPatches = [ ];
-    # Transient doctest failure in src/sage/modular/abvar/torsion_subgroup.py
-    # https://trac.sagemath.org/ticket/27477
-    (fetchpatch {
-      name = "sig_on_in_matrix_sparce.patch";
-      url = "https://git.sagemath.org/sage.git/patch?id2=10407524b18659e14e184114b61c043fb816f3c2&id=c9b0cc9d0b8748ab85e568f8f57f316c5e8cbe54";
-      sha256 = "0wgp7yvn9sm1ynlhcr4l0hzmvr2n28llg4xc01p6k1zz4im64c17";
-    })
-  ];
 
   # Patches needed because of package updates. We could just pin the versions of
   # dependencies, but that would lead to rebuilds, confusion and the burdons of
@@ -116,35 +93,6 @@ stdenv.mkDerivation rec {
       stripLen = 1;
     })
 
-    # https://trac.sagemath.org/ticket/26451
-    (fetchSageDiff {
-      name = "sphinx-1.8.patch";
-      base = "8.7";
-      rev = "737afd8f314bd1e16feaec562bb4b5efa2effa8b";
-      sha256 = "0n56ss88ds662bp49j23z5c2i6hsn3jynxw13wv76hyl0h7l1hjh";
-    })
-
-    # https://trac.sagemath.org/ticket/27653
-    (fetchpatch {
-      name = "sympy-1.4.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?h=3277ba76d0ba7174608a31a0c6623e9210c63e3d";
-      sha256 = "09avaanwmdgqv14mmllbgw9z2scf4lc0y0kzdhlriiq8ss9j8iir";
-    })
-
-    # https://trac.sagemath.org/ticket/27094
-    (fetchpatch {
-      name = "gap-4.10.1.patch";
-      url = "https://git.sagemath.org/sage.git/patch?id=d3483110474591ea6cc8e3210cd884f3e0018b3e";
-      sha256 = "028i6h8l8npwzx5z0ax0rcywl85gc83qw1jf93zf523msdfcsk0n";
-    })
-
-    # https://trac.sagemath.org/ticket/27738
-    (fetchpatch {
-      name = "R-3.6.0.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?h=8b7dbd0805d02d0e8674a272e161ceb24a637966";
-      sha256 = "1c81f13z1w62s06yvp43gz6vkp8mxcs289n6l4gj9xj10slimzff";
-    })
-
     # https://trac.sagemath.org/ticket/26932
     (fetchSageDiff {
       name = "givaro-4.1.0_fflas-ffpack-2.4.0_linbox-1.6.0.patch";
@@ -152,13 +100,6 @@ stdenv.mkDerivation rec {
       rev = "c11d9cfa23ff9f77681a8f12742f68143eed4504";
       sha256 = "0xzra7mbgqvahk9v45bjwir2mqz73hrhhy314jq5nxrb35ysdxyi";
     })
-
-    # https://trac.sagemath.org/ticket/26718
-    (fetchpatch {
-      name = "threejs-r100.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?h=86c5bb000259e6de5d7c60afc608a4b0d010b690";
-      sha256 = "0sgqqd4df2bxsq19b6kfy7dvgyxprlpg7f3xx7g3fs8ij937m352";
-    })
   ];
 
   patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;

pkgs/top-level/all-packages.nix

@@ -22955,12 +22955,6 @@ in
     ecl-fasl = true;
     sbcl = null;
   };
-  # old version temporarily kept for sage
-  maxima-ecl-5_41 = callPackage ../applications/science/math/maxima/5.41.nix {
-    ecl = ecl_16_1_2;
-    ecl-fasl = true;
-    sbcl = null;
-  };
 
   mxnet = callPackage ../applications/science/math/mxnet {
     inherit (linuxPackages) nvidia_x11;