diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix
index b86f9d1aa0d..cea4d91151c 100644
--- a/pkgs/applications/science/math/sage/sage-src.nix
+++ b/pkgs/applications/science/math/sage/sage-src.nix
@@ -39,7 +39,17 @@ stdenv.mkDerivation rec {
     ./patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch
   ];
 
-  packageUpgradePatches = [
+  packageUpgradePatches = let
+    fetchSageCommit = { rev, ...}@args: (
+      fetchpatch ({
+        url = "https://git.sagemath.org/sage.git/patch/?h=${rev}";
+        # TODO better https://git.sagemath.org/sage.git/patch/?id=${rev} ?
+        # We don't care about sage's own build system (which builds all its dependencies).
+        # Exclude build system changes to avoid conflicts.
+        excludes = [ "build/*" ];
+      } // builtins.removeAttrs args [ "rev" ])
+    );
+  in [
     # New glpk version has new warnings, filter those out until upstream sage has found a solution
     # https://trac.sagemath.org/ticket/24824
     ./patches/pari-stackwarn.patch # not actually necessary since tha pari upgrade, but necessary for the glpk patch to apply
@@ -53,11 +63,18 @@ stdenv.mkDerivation rec {
     ./patches/numpy-1.15.1.patch
 
     # ntl upgrade
+    # https://trac.sagemath.org/ticket/25532#comment:29
     (fetchpatch {
       name = "lcalc-c++11.patch";
       url = "https://git.archlinux.org/svntogit/community.git/plain/trunk/sagemath-lcalc-c++11.patch?h=packages/sagemath&id=0e31ae526ab7c6b5c0bfacb3f8b1c4fd490035aa";
       sha256 = "0p5wnvbx65i7cp0bjyaqgp4rly8xgnk12pqwaq3dqby0j2bk6ijb";
     })
+
+    (fetchpatch {
+      name = "cython-0.29.patch";
+      url = "https://git.sagemath.org/sage.git/patch/?h=f77de1d0e7f90ee12761140500cb8cbbb789ab20";
+      sha256 = "14wrpy8jgbnpza1j8a2nx8y2r946y82pll1fv3cn6gpfmm6640l3";
+    })
   ];
 
   patches = nixPatches ++ packageUpgradePatches ++ [
diff --git a/pkgs/development/python-modules/Cython/default.nix b/pkgs/development/python-modules/Cython/default.nix
index 53e9ec270ac..d4191731973 100644
--- a/pkgs/development/python-modules/Cython/default.nix
+++ b/pkgs/development/python-modules/Cython/default.nix
@@ -13,6 +13,7 @@
 
 let
   excludedTests = []
+    ++ [ "reimport_from_subinterpreter" ]
     # cython's testsuite is not working very well with libc++
     # We are however optimistic about things outside of testsuite still working
     ++ stdenv.lib.optionals (stdenv.cc.isClang or false) [ "cpdef_extern_func" "libcpp_algo" ]
@@ -25,11 +26,11 @@ let
 
 in buildPythonPackage rec {
   pname = "Cython";
-  version = "0.28.5";
+  version = "0.29";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "b64575241f64f6ec005a4d4137339fb0ba5e156e826db2fdb5f458060d9979e0";
+    sha256 = "15zama7fgp7yyi3z39xp3z2lvwcgch8fn3ycscw2cs37vqg6v4cl";
   };
 
   nativeBuildInputs = [