From 5caa76705bd839fb6733f64740dec95d7b2fefc5 Mon Sep 17 00:00:00 2001
From: Ben Darwin <bcdarwin@gmail.com>
Date: Mon, 27 Apr 2020 15:04:43 -0400
Subject: [PATCH] elastix: update for ITK 5.1.0

- fetch patches to build elastix 5.0 with ITK 5.1
- update 'platforms': builds on Darwin, fails on aarch64
---
 .../science/biology/elastix/default.nix       | 20 ++++++++++++++++---
 1 file changed, 17 insertions(+), 3 deletions(-)

diff --git a/pkgs/development/libraries/science/biology/elastix/default.nix b/pkgs/development/libraries/science/biology/elastix/default.nix
index e5565aae29b..4d98b12928f 100644
--- a/pkgs/development/libraries/science/biology/elastix/default.nix
+++ b/pkgs/development/libraries/science/biology/elastix/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, cmake, itk, python3 }:
+{ stdenv, fetchFromGitHub, fetchpatch, cmake, itk, python3 }:
 
 stdenv.mkDerivation rec {
   pname    = "elastix";
@@ -11,10 +11,24 @@ stdenv.mkDerivation rec {
     sha256 = "1zrl7rz4lwsx88b2shnl985f3a97lmp4ksbd437h9y0hfjq8l0lj";
   };
 
+  patches = [
+    (fetchpatch {
+      name = "itk-5.1-compat.patch";
+      url = "https://github.com/SuperElastix/elastix/commit/402e9a26f22f805b8f2db00c00e59f75fa1783ad.patch";
+      sha256 = "1il6gc1lgy78i0w6gkkppr61nh6g0yjspbfk19hcz20778m5jhz9";
+    })
+    (fetchpatch {
+      name = "fix-osx-build.patch";
+      url = "https://github.com/SuperElastix/elastix/commit/52e1dc3928046f9fbb85d4b2ecd0d5175fa9695d.patch";
+      sha256 = "1hf7kgx1jv497pf0x5wj79sy1wncxcvhrkix9w086lcr8zwxvn9q";
+    })
+  ];
+
+
   nativeBuildInputs = [ cmake python3 ];
   buildInputs = [ itk ];
 
-  doCheck = true;
+  doCheck = !stdenv.isDarwin;  # usual dynamic linker issues
 
   preCheck = "
     export LD_LIBRARY_PATH=$(pwd)/bin
@@ -24,7 +38,7 @@ stdenv.mkDerivation rec {
     homepage = "http://elastix.isi.uu.nl/";
     description = "Image registration toolkit based on ITK";
     maintainers = with maintainers; [ bcdarwin ];
-    platforms = platforms.linux;
+    platforms = platforms.x86_64;  # libitkpng linker issues with ITK 5.1
     license = licenses.asl20;
   };
 }