From 90bc5ce04ddc5dfda7d29486061ebf980424f161 Mon Sep 17 00:00:00 2001
From: Timo Kaufmann <timokau@zoho.com>
Date: Mon, 10 Dec 2018 19:36:24 +0100
Subject: [PATCH] sage: 8.5.beta5 -> 8.5.beta6

---
 .../math/sage/patches/dont-test-guess-gaproot.patch | 13 +++++++++++++
 pkgs/applications/science/math/sage/sage-src.nix    | 11 +++--------
 2 files changed, 16 insertions(+), 8 deletions(-)
 create mode 100644 pkgs/applications/science/math/sage/patches/dont-test-guess-gaproot.patch

diff --git a/pkgs/applications/science/math/sage/patches/dont-test-guess-gaproot.patch b/pkgs/applications/science/math/sage/patches/dont-test-guess-gaproot.patch
new file mode 100644
index 000000000000..32b877428d51
--- /dev/null
+++ b/pkgs/applications/science/math/sage/patches/dont-test-guess-gaproot.patch
@@ -0,0 +1,13 @@
+diff --git a/src/sage/libs/gap/util.pyx b/src/sage/libs/gap/util.pyx
+index 5ff67107c1..1318df86fd 100644
+--- a/src/sage/libs/gap/util.pyx
++++ b/src/sage/libs/gap/util.pyx
+@@ -165,7 +165,7 @@ def _guess_gap_root():
+     EXAMPLES::
+ 
+         sage: from sage.libs.gap.util import _guess_gap_root
+-        sage: _guess_gap_root()
++        sage: _guess_gap_root() # not tested (not necessary on nixos)
+         The gap-4.5.5.spkg (or later) seems to be not installed!
+         ...
+     """
diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix
index 81386533a39c..4685ee61957d 100644
--- a/pkgs/applications/science/math/sage/sage-src.nix
+++ b/pkgs/applications/science/math/sage/sage-src.nix
@@ -9,14 +9,14 @@
 # all get the same sources with the same patches applied.
 
 stdenv.mkDerivation rec {
-  version = "8.5.beta5";
+  version = "8.5.beta6";
   name = "sage-src-${version}";
 
   src = fetchFromGitHub {
     owner = "sagemath";
     repo = "sage";
     rev = version;
-    sha256 = "1jnlk4y7njkg095kd3rhsi5929k6q90lzgyb7pshsjz251866nyv";
+    sha256 = "0b3f7m1mxqh2sjb8q2bci7202gw8qi1kin13fzsmvfd3caxvxzcy";
   };
 
   # Patches needed because of particularities of nix or the way this is packaged.
@@ -47,7 +47,7 @@ stdenv.mkDerivation rec {
     # https://trac.sagemath.org/ticket/26110 for an upstream discussion.
     ./patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch
 
-    ./patches/no-invalid-gap-test.patch
+    ./patches/dont-test-guess-gaproot.patch
   ];
 
   # Patches needed because of package updates. We could just pin the versions of
@@ -79,11 +79,6 @@ stdenv.mkDerivation rec {
       stripLen = 1;
     })
 
-    (fetchpatch {
-      name = "cython-0.29.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?h=f77de1d0e7f90ee12761140500cb8cbbb789ab20";
-      sha256 = "14wrpy8jgbnpza1j8a2nx8y2r946y82pll1fv3cn6gpfmm6640l3";
-    })
     # https://trac.sagemath.org/ticket/26360
     (fetchpatch {
       name = "arb-2.15.1.patch";