From 5880c449dde5eafe8d8412694312e11d34f73912 Mon Sep 17 00:00:00 2001
From: Timo Kaufmann <timokau@zoho.com>
Date: Thu, 4 Apr 2019 14:48:49 +0200
Subject: [PATCH 1/3] nauty: small refactoring

---
 pkgs/applications/science/math/nauty/default.nix | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/pkgs/applications/science/math/nauty/default.nix b/pkgs/applications/science/math/nauty/default.nix
index 5b431f419261..b16ea82a7af3 100644
--- a/pkgs/applications/science/math/nauty/default.nix
+++ b/pkgs/applications/science/math/nauty/default.nix
@@ -1,4 +1,7 @@
-{stdenv, fetchurl}:
+{ stdenv
+, lib
+, fetchurl
+}:
 stdenv.mkDerivation rec {
   name = "nauty-${version}";
   version = "26r11";
@@ -14,18 +17,18 @@ stdenv.mkDerivation rec {
     find . -type f -perm -111 \! -name '*.*' \! -name configure -exec cp '{}' "$out/bin" \;
     cp [Rr][Ee][Aa][Dd]* COPYRIGHT This* [Cc]hange* "$out/share/doc/nauty"
 
-    cp *.h $dev/include/nauty
+    cp *.h "$dev/include/nauty"
     for i in *.a; do
       cp "$i" "$dev/lib/lib$i";
     done
   '';
   checkTarget = "checks";
-  meta = {
+  meta = with lib; {
     inherit version;
     description = ''Programs for computing automorphism groups of graphs and digraphs'';
-    license = stdenv.lib.licenses.asl20;
-    maintainers = [stdenv.lib.maintainers.raskin];
-    platforms = stdenv.lib.platforms.linux;
+    license = licenses.asl20;
+    maintainers = with maintainers; [ raskin ];
+    platforms = platforms.linux;
     homepage = http://pallini.di.uniroma1.it/;
   };
 }

From 15045e6233838c32847cbd60d267070f078e0262 Mon Sep 17 00:00:00 2001
From: Timo Kaufmann <timokau@zoho.com>
Date: Thu, 4 Apr 2019 14:54:31 +0200
Subject: [PATCH 2/3] nauty: add timokau as a maintainer

I'm interested in this package as a sage dependency.
---
 pkgs/applications/science/math/nauty/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/applications/science/math/nauty/default.nix b/pkgs/applications/science/math/nauty/default.nix
index b16ea82a7af3..35c4fdb829b3 100644
--- a/pkgs/applications/science/math/nauty/default.nix
+++ b/pkgs/applications/science/math/nauty/default.nix
@@ -27,7 +27,7 @@ stdenv.mkDerivation rec {
     inherit version;
     description = ''Programs for computing automorphism groups of graphs and digraphs'';
     license = licenses.asl20;
-    maintainers = with maintainers; [ raskin ];
+    maintainers = with maintainers; [ raskin timokau ];
     platforms = platforms.linux;
     homepage = http://pallini.di.uniroma1.it/;
   };

From 7f22a4297638c6d0ea5cfcbe3b83a011d1286c23 Mon Sep 17 00:00:00 2001
From: Timo Kaufmann <timokau@zoho.com>
Date: Thu, 4 Apr 2019 14:50:38 +0200
Subject: [PATCH 3/3] nauty: disable cpu feature detection

---
 pkgs/applications/science/math/nauty/default.nix | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/pkgs/applications/science/math/nauty/default.nix b/pkgs/applications/science/math/nauty/default.nix
index 35c4fdb829b3..7351de53cfce 100644
--- a/pkgs/applications/science/math/nauty/default.nix
+++ b/pkgs/applications/science/math/nauty/default.nix
@@ -1,6 +1,7 @@
 { stdenv
 , lib
 , fetchurl
+, optimize ? false # impure
 }:
 stdenv.mkDerivation rec {
   name = "nauty-${version}";
@@ -10,6 +11,13 @@ stdenv.mkDerivation rec {
     sha256 = "05z6mk7c31j70md83396cdjmvzzip1hqb88pfszzc6k4gy8h3m2y";
   };
   outputs = [ "out" "dev" ];
+  configureFlags = lib.optionals (!optimize) [
+    # Prevent nauty from sniffing some cpu features. While those are very
+    # widely available, it can lead to nasty bugs when they are not available:
+    # https://groups.google.com/forum/#!topic/sage-packaging/Pe4SRDNYlhA
+    "--disable-popcnt"
+    "--disable-clz"
+  ];
   buildInputs = [];
   installPhase = ''
     mkdir -p "$out"/{bin,share/doc/nauty} "$dev"/{lib,include/nauty}