openslide: Convert to new overlay system

pkgs/all-packages.nix

@@ -7,4 +7,8 @@ self: pkgs: with pkgs; {
   meraculous = callPackage ./meraculous.nix { };
 
   openfoam = callPackage ./openfoam.nix { };
+
+  openslide = callPackage ./openslide { };
+  openslide-python = callPackage ./openslide/python.nix { };
 }
+

pkgs/openslide/default.nix

@@ -0,0 +1,39 @@
+{ stdenv, autoreconfHook, pkgconfig, fetchFromGitHub
+, zlib, openjpeg, libtiff, cairo, libpng, gdk_pixbuf, libxml2, sqlite }:
+
+stdenv.mkDerivation rec {
+  version = "3.4.1";
+  name = "openslide-${version}";
+
+  src = fetchFromGitHub {
+    owner = "openslide";
+    repo = "openslide";
+    rev = "v${version}";
+    sha256 = "1g4hhjr4cbx754cwi9wl84k33bkg232w8ajic7aqhzm8x182hszp";
+  };
+
+  buildInputs = [
+    autoreconfHook
+    pkgconfig
+    zlib
+    openjpeg
+    libtiff
+    cairo
+    libpng
+    gdk_pixbuf
+    libxml2
+    sqlite
+  ];
+
+  # Not sure why this Windows test isn't failing under Linux
+  postPatch = ''
+    sed -i -e 's|AM_CONDITIONAL(\[WINDOWS_RESOURCES\], \[test x$RC != x\])|AM_CONDITIONAL([WINDOWS_RESOURCES], [false])|' configure.ac
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = http://openslide.org;
+    description = "A C library that provides a simple interface to read whole-slide images.";
+    platforms = platforms.all;
+    license = licenses.lgpl2;
+  };
+}

pkgs/openslide/python.nix

@@ -0,0 +1,34 @@
+{ lib, fetchFromGitHub
+, python27Packages, openslide }:
+
+python27Packages.buildPythonPackage rec {
+  version = "1.1.1";
+  name = "openslide-python-${version}";
+
+  src = fetchFromGitHub {
+    owner = "openslide";
+    repo = "openslide-python";
+    rev = "v${version}";
+    sha256 = "1is8g8vy8s1xgfw8q76gdx8ygwvj56cl0vxfd3lx0iys15wzs7a4";
+  };
+
+  patches = [ ./zero-size-test-skip.patch ];
+
+  postPatch = ''
+    sed -i 's|LoadLibrary('\'''libopenslide.so.0'\''')|LoadLibrary('\'''${openslide}/lib/libopenslide.so.0'\''')|' openslide/lowlevel.py
+  '';
+
+  buildInputs = [
+    openslide
+  ];
+
+  propagatedBuildInputs = [
+    python27Packages.pillow
+  ];
+
+  meta = with lib; {
+    homepage = "http://openslide.org";
+    description = "Python bindings for OpenSlide.";
+    license = licenses.lgpl2;
+  };
+}

pkgs/openslide/zero-size-test-skip.patch

@@ -0,0 +1,82 @@
+From 4ea9211e10e9fc58d04bac909d73a2448c4a44ff Mon Sep 17 00:00:00 2001
+From: Benjamin Gilbert <bgilbert@cs.cmu.edu>
+Date: Tue, 24 Jan 2017 23:32:36 -0800
+Subject: [PATCH] tests: Avoid spurious failures with Pillow 3.4.0 - 3.4.2
+
+---
+ tests/__init__.py        | 10 ++++++++++
+ tests/test_imageslide.py |  3 ++-
+ tests/test_openslide.py  |  4 +++-
+ 3 files changed, 15 insertions(+), 2 deletions(-)
+
+diff --git a/tests/__init__.py b/tests/__init__.py
+index cc2b217..d2158b3 100644
+--- a/tests/__init__.py
++++ b/tests/__init__.py
+@@ -19,6 +19,7 @@
+ 
+ from functools import wraps
+ import os
++from PIL import Image
+ import unittest
+ 
+ try:
+@@ -28,6 +29,15 @@
+     have_optimizations = False
+ 
+ 
++# PIL.Image cannot have zero width or height on Pillow 3.4.0 - 3.4.2
++# https://github.com/python-pillow/Pillow/issues/2259
++try:
++    Image.new('RGBA', (1, 0))
++    image_dimensions_cannot_be_zero = False
++except ValueError:
++    image_dimensions_cannot_be_zero = True
++
++
+ def file_path(name):
+     return os.path.join(os.path.dirname(__file__), name)
+ 
+diff --git a/tests/test_imageslide.py b/tests/test_imageslide.py
+index bbde9ec..de2a734 100644
+--- a/tests/test_imageslide.py
++++ b/tests/test_imageslide.py
+@@ -22,7 +22,7 @@
+ from PIL import Image
+ import unittest
+ 
+-from . import file_path
++from . import file_path, image_dimensions_cannot_be_zero, skip_if
+ 
+ # Tests should be written to be compatible with Python 2.6 unittest.
+ 
+@@ -104,6 +104,7 @@ def test_read_region(self):
+         self.assertEqual(self.osr.read_region((-10, -10), 0, (400, 400)).size,
+                 (400, 400))
+ 
++    @skip_if(image_dimensions_cannot_be_zero, 'Pillow issue #2259')
+     def test_read_region_size_dimension_zero(self):
+         self.assertEqual(self.osr.read_region((0, 0), 0, (400, 0)).size,
+                 (400, 0))
+diff --git a/tests/test_openslide.py b/tests/test_openslide.py
+index 3350c76..b80e2f5 100644
+--- a/tests/test_openslide.py
++++ b/tests/test_openslide.py
+@@ -25,7 +25,8 @@
+ import sys
+ import unittest
+ 
+-from . import file_path, have_optimizations, skip_if
++from . import (file_path, have_optimizations, image_dimensions_cannot_be_zero,
++        skip_if)
+ 
+ # Tests should be written to be compatible with Python 2.6 unittest.
+ 
+@@ -110,6 +111,7 @@ def test_read_region(self):
+         self.assertEqual(self.osr.read_region((-10, -10), 1, (400, 400)).size,
+                 (400, 400))
+ 
++    @skip_if(image_dimensions_cannot_be_zero, 'Pillow issue #2259')
+     def test_read_region_size_dimension_zero(self):
+         self.assertEqual(self.osr.read_region((0, 0), 1, (400, 0)).size,
+                 (400, 0))