python3Modules.mahotas: 1.4.10 -> 1.4.11

also updates tests from nose to pytest

pkgs/development/python-modules/mahotas/default.nix

@@ -1,26 +1,36 @@
-{ buildPythonPackage, fetchFromGitHub, nose, pillow, scipy, numpy, imread, lib, stdenv }:
+{ buildPythonPackage, fetchFromGitHub, pillow, scipy, numpy, pytestCheckHook, imread, freeimage, lib, stdenv }:
 
 buildPythonPackage rec {
   pname = "mahotas";
-  version = "1.4.10";
+  version = "1.4.11";
 
   src = fetchFromGitHub {
     owner = "luispedro";
     repo = "mahotas";
     rev = "v${version}";
-    sha256 = "0fjiyl82wj1a6xzr9mss2y2rydl4zchl2cbdbg0jm0fcrs99q4hw";
+    sha256 = "029gvy1fb855pvxvy8zwj44k4s7qpqi0161bg5wldfiprrysn1kw";
   };
 
-  # remove this as soon as https://github.com/luispedro/mahotas/issues/97 is fixed
-  patches = [ ./disable-impure-tests.patch ];
+  propagatedBuildInputs = [ numpy imread pillow scipy freeimage ];
+  checkInputs = [ pytestCheckHook ];
 
-  propagatedBuildInputs = [ numpy imread pillow scipy ];
-  checkInputs = [ nose ];
-
-  checkPhase= ''
-    python setup.py test
+  postPatch = ''
+    substituteInPlace mahotas/io/freeimage.py --replace "/opt/local/lib" "${freeimage}/lib"
   '';
 
+  # tests must be run in the build directory
+  preCheck = ''
+    cd build/lib*
+  '';
+
+  # re-enable as soon as https://github.com/luispedro/mahotas/issues/97 is fixed
+  disabledTests = [
+    "test_colors"
+    "test_ellipse_axes"
+    "test_normalize"
+    "test_haralick3d"
+  ];
+
   disabled = stdenv.isi686; # Failing tests
 
   meta = with lib; {

pkgs/development/python-modules/mahotas/disable-impure-tests.patch

@@ -1,76 +0,0 @@
-diff --git a/mahotas/tests/test_colors.py b/mahotas/tests/test_colors.py
-index 8a8183b..0d34c9f 100644
---- a/mahotas/tests/test_colors.py
-+++ b/mahotas/tests/test_colors.py
-@@ -2,7 +2,9 @@ import mahotas
- import numpy as np
- from mahotas.tests.utils import luispedro_jpg
- from mahotas.colors import rgb2xyz, rgb2lab, xyz2rgb, rgb2grey, rgb2sepia
-+from nose.tools import nottest
- 
-+@nottest
- def test_colors():
-     f = luispedro_jpg()
-     lab = rgb2lab(f)
-diff --git a/mahotas/tests/test_features_shape.py b/mahotas/tests/test_features_shape.py
-index 462f467..2381793 100644
---- a/mahotas/tests/test_features_shape.py
-+++ b/mahotas/tests/test_features_shape.py
-@@ -2,6 +2,7 @@ import mahotas.features.shape
- import numpy as np
- import mahotas as mh
- from mahotas.features.shape import roundness, eccentricity
-+from nose.tools import nottest
- 
- def test_eccentricity():
-     D = mh.disk(32, 2)
-@@ -29,6 +30,7 @@ def test_zeros():
-     I[8:4:12] = 1
-     assert eccentricity(I) == 0
- 
-+@nottest
- def test_ellipse_axes():
-     Y,X = np.mgrid[:1024,:1024]
-     Y = Y/1024.
-diff --git a/mahotas/tests/test_moments.py b/mahotas/tests/test_moments.py
-index 686c7c3..ba3487b 100644
---- a/mahotas/tests/test_moments.py
-+++ b/mahotas/tests/test_moments.py
-@@ -1,6 +1,7 @@
- import numpy as np
- import mahotas as mh
- from mahotas.features.moments import moments
-+from nose.tools import nottest
- 
- def _slow(A, p0, p1, cm):
-     c0,c1 = cm
-@@ -28,7 +29,7 @@ def test_against_slow():
-     yield perform, 1, 2, (0, 0), A
-     yield perform, 1, 0, (0, 0), A
- 
--
-+@nottest
- def test_normalize():
-     A,B = np.meshgrid(np.arange(128),np.arange(128))
-     for p0,p1 in [(1,1), (1,2), (2,1), (2,2)]:
-diff --git a/mahotas/tests/test_texture.py b/mahotas/tests/test_texture.py
-index 7e101ba..af1305d 100644
---- a/mahotas/tests/test_texture.py
-+++ b/mahotas/tests/test_texture.py
-@@ -2,7 +2,7 @@ import numpy as np
- from mahotas.features import texture
- import mahotas as mh
- import mahotas.features._texture
--from nose.tools import raises
-+from nose.tools import raises, nottest
- 
- def test__cooccurence():
-     cooccurence = mahotas.features._texture.cooccurence
-@@ -149,6 +149,7 @@ def test_float_haralick():
-     A[2,2]=12
-     texture.haralick(A)
- 
-+@nottest
- def test_haralick3d():
-     np.random.seed(22)
-     img = mahotas.stretch(255*np.random.rand(20,20,4))