sage, sageWithDoc: 10.2 -> 10.3

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

@@ -15,7 +15,7 @@ let
     pkgs = pkgs.python3.pkgs.overrideScope (self: super: {
       # `sagelib`, i.e. all of sage except some wrappers and runtime dependencies
       sagelib = self.callPackage ./sagelib.nix {
-        inherit flint arb;
+        inherit flint3;
         inherit sage-src env-locations singular;
         inherit (maxima) lisp-compiler;
         linbox = pkgs.linbox.override { withSage = true; };
@@ -73,7 +73,7 @@ let
     sagelib = python3.pkgs.sagelib;
     sage-docbuild = python3.pkgs.sage-docbuild;
     inherit env-locations;
-    inherit python3 singular palp flint pythonEnv maxima;
+    inherit python3 singular palp flint3 pythonEnv maxima;
     pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config
   };
 
@@ -125,9 +125,7 @@ let
     ignoreCollisions = true;
   } // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible
 
-  arb = pkgs.arb.override { inherit flint; };
-
-  singular = pkgs.singular.override { inherit flint; };
+  singular = pkgs.singular.override { inherit flint3; };
 
   maxima = pkgs.maxima-ecl.override {
     lisp-compiler = pkgs.ecl.override {
@@ -149,7 +147,7 @@ let
   # openblas instead of openblasCompat. Apparently other packages somehow use flints
   # blas when it is available. Alternative would be to override flint to use
   # openblasCompat.
-  flint = pkgs.flint.override { withBlas = false; };
+  flint3 = pkgs.flint3.override { withBlas = false; };
 
   # Multiple palp dimensions need to be available and sage expects them all to be
   # in the same folder.

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

@@ -26,15 +26,13 @@ writeTextFile rec {
     export GPDOCDIR="${pari}/share/pari/doc"
     export SINGULARPATH='${singular}/share/singular'
     export SINGULAR_SO='${singular}/lib/libSingular.so'
-    export GAP_SO='${gap}/lib/libgap.so'
     export SINGULAR_EXECUTABLE='${singular}/bin/Singular'
     export MAXIMA_FAS='${maxima}/lib/maxima/${maxima.version}/binary-ecl/maxima.fas'
     export MAXIMA_PREFIX="${maxima}"
     export GRAPHS_DATA_DIR='${graphs}/share/graphs'
     export ELLCURVE_DATA_DIR='${elliptic_curves}/share/ellcurves'
     export POLYTOPE_DATA_DIR='${polytopes_db}/share/reflexive_polytopes'
-    export GAP_LIB_DIR='${gap}/lib/gap'
-    export GAP_SHARE_DIR='${gap}/share/gap'
+    export GAP_ROOT_PATHS='${gap}/lib/gap;${gap}/share/gap'
     export ECLDIR='${maxima.lisp-compiler}/lib/${maxima.lisp-compiler.pname}-${maxima.lisp-compiler.version}/'
     export COMBINATORIAL_DESIGN_DATA_DIR="${combinatorial_designs}/share/combinatorial_designs"
     export CREMONA_MINI_DATA_DIR="${elliptic_curves}/share/cremona"

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

@@ -4,6 +4,7 @@
 , jupyter-sphinx
 , sphinx
 , sphinx-copybutton
+, sphinx-inline-tabs
 }:
 
 buildPythonPackage rec {
@@ -15,6 +16,7 @@ buildPythonPackage rec {
     jupyter-sphinx
     sphinx
     sphinx-copybutton
+    sphinx-inline-tabs
   ];
 
   preBuild = ''

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

@@ -42,7 +42,7 @@
 , flintqs
 , blas
 , lapack
-, flint
+, flint3
 , gmp
 , mpfr
 , zlib
@@ -155,7 +155,7 @@ writeTextFile rec {
     # cython needs to find these libraries, otherwise will fail with `ld: cannot find -lflint` or similar
     export LDFLAGS='${
       lib.concatStringsSep " " (map (pkg: "-L${pkg}/lib") [
-        flint
+        flint3
         gap
         glpk
         gmp
@@ -174,7 +174,7 @@ writeTextFile rec {
         singular
         gmp.dev
         glpk
-        flint
+        flint3
         gap
         mpfr.dev
       ])

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 = "10.2";
+  version = "10.3";
   pname = "sage-src";
 
   src = fetchFromGitHub {
     owner = "sagemath";
     repo = "sage";
     rev = version;
-    sha256 = "sha256-VXnPdJhtw5Y/anecrVpevJDCyBVfnjksyuuZslNipm4=";
+    hash = "sha256-OHtMv8t0RrP6R8XIREU+C1vpazeQLWa75wx9Mv6BN1U=";
   };
 
   # contains essential files (e.g., setup.cfg) generated by the bootstrap script.
@@ -25,8 +25,8 @@ 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-b2813506039143e6f0abe859ab67a343abf72c2e.tar.gz";
-    sha256 = "sha256-a1v0XyoKI+zO6Sjm8DzEwItRHbIgRDbpj4UfwVH+/hw=";
+    url = "mirror://sageupstream/configure/configure-ab1a517b64b02bf15bbcb8d7c2d4d643bd5eff9b.tar.gz";
+    hash = "sha256-pe9AxTM+gFSR4/eVfUzay+4bwjoubbYeDPc+avKjlaw=";
   };
 
   # Patches needed because of particularities of nix or the way this is packaged.
@@ -62,11 +62,11 @@ 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/37123, to land in 10.3.beta7
+    # https://github.com/sagemath/sage/pull/37492
     (fetchpatch {
-      name = "scipy-1.12-upgrade.patch";
-      url = "https://github.com/sagemath/sage/commit/54eec464e9fdf18b411d9148aecb918178e95909.diff";
-      sha256 = "sha256-9wyNrcSfF6mYFTIV4ev2OdD7igb0AeyZZYWSc/+JrIU=";
+      name = "singular-4.3.2p14-upgrade.patch";
+      url = "https://github.com/sagemath/sage/commit/a0c56816b051e97da44ac0a4e4d4f6915cf7fa0f.diff";
+      sha256 = "sha256-WGMmPeBoj2LUC+2qxWuaJL89QUuGt6axGvxWkpM9LYg=";
     })
   ];
 

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

@@ -10,7 +10,6 @@
 , iml
 , libpng
 , readline
-, arb
 , blas
 , boost
 , brial
@@ -18,7 +17,7 @@
 , eclib
 , ecm
 , fflas-ffpack
-, flint
+, flint3
 , gap
 , giac
 , givaro
@@ -45,6 +44,7 @@
 , singular
 , sqlite
 , symmetrica
+, conway-polynomials
 , cvxopt
 , cypari2
 , cysignals
@@ -92,6 +92,7 @@ buildPythonPackage rec {
   version = src.version;
   pname = "sagelib";
   src = sage-src;
+  pyproject = true;
 
   nativeBuildInputs = [
     iml
@@ -112,7 +113,6 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [
     # native dependencies (TODO: determine which ones need to be propagated)
-    arb
     blas
     boost
     brial
@@ -120,7 +120,7 @@ buildPythonPackage rec {
     eclib
     ecm
     fflas-ffpack
-    flint
+    flint3
     gap
     giac
     givaro
@@ -149,6 +149,7 @@ buildPythonPackage rec {
     symmetrica
 
     # from src/sage/setup.cfg and requirements.txt
+    conway-polynomials
     cvxopt
     cypari2
     cysignals
@@ -202,11 +203,7 @@ buildPythonPackage rec {
     mkdir -p "$SAGE_SHARE/sage/ext/notebook-ipython"
     mkdir -p "var/lib/sage/installed"
 
-    # version lower bounds are useful, but upper bounds are a hassle because
-    # Sage tests already catch any relevant API breakage.
-    # according to the discussion at https://trac.sagemath.org/ticket/33520,
-    # upper bounds will be less noisy starting from Sage 9.6.
-    sed -i 's/, <[^, ]*//' build/pkgs/*/install-requires.txt
+    sed -i "/sage-conf/d" src/{setup.cfg,pyproject.toml,requirements.txt}
 
     cd build/pkgs/sagelib/src
   '';