debian/changelog

-simpleitk (1.1.0-1) UNRELEASED; urgency=medium
+simpleitk (1.0.1-3) unstable; urgency=medium
 
   [ Dylan Aïssi ]
   * Team upload.
   * Add references to registries.
 
-  [ Andreas Tille ]
-  * New upstream version
+  [ Matthias Klose ]
+  * Backport Python 3.7 test fix from upstream to fix Python index test
+    with empty comparison
     Closes: #912583
-  * Standards-Version: 4.2.1
-  * Testsuite: autopkgtest-pkg-python
-  * Build-Depends: libgdcm-tools, libvtkgdcm2-dev, libvtkgdcm-cil,
-                   libvtkgdcm-java, python3-vtkgdcm
+  * d/watch only reports source tarballs
+  * No need for versioned Build-Depends: dpkg-dev any more
+  * Standards-Version: 4.3.0
 
- -- Andreas Tille <tille@debian.org>  Sun, 02 Dec 2018 22:34:26 +0100
+ -- Andreas Tille <tille@debian.org>  Tue, 29 Jan 2019 17:11:04 +0100
 
 simpleitk (1.0.1-2) unstable; urgency=medium
 

debian/control

@@ -2,12 +2,10 @@ Source: simpleitk
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Ghislain Antony Vaillant <ghisvail@gmail.com>
 Section: libs
-Testsuite: autopkgtest-pkg-python
 Priority: optional
 Build-Depends: cmake (>= 3.0),
                debhelper (>= 11),
                dh-python,
-               dpkg-dev (>= 1.17.14),
                googletest <!nocheck>,
                libfftw3-dev,
                libinsighttoolkit4-dev (>= 4.11),
@@ -15,13 +13,8 @@ Build-Depends: cmake (>= 3.0),
                python3-dev,
                python3-numpy,
                python3-setuptools,
-               swig (>= 3.0.12),
-               libgdcm-tools,
-               libvtkgdcm2-dev,
-               libvtkgdcm-cil,
-               libvtkgdcm-java,
-               python3-vtkgdcm
-Standards-Version: 4.2.1
+               swig (>= 3.0.12)
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/simpleitk
 Vcs-Git: https://salsa.debian.org/med-team/simpleitk.git
 Homepage: http://www.simpleitk.org/
@@ -44,7 +37,6 @@ Package: libsimpleitk1-dev
 Architecture: any
 Multi-Arch: same
 Section: libdevel
-Testsuite: autopkgtest-pkg-python
 Depends: ${misc:Depends},
          ${shlibs:Depends},
          libsimpleitk1.0 (= ${binary:Version})
@@ -60,7 +52,6 @@ Description: development files for SimpleITK
 Package: python3-simpleitk
 Architecture: any
 Section: python
-Testsuite: autopkgtest-pkg-python
 Depends: ${misc:Depends},
          ${python3:Depends},
          ${shlibs:Depends}

debian/patches/Fix-Python-index-test-with-empty-comparison.patch

+From: Bradley Lowekamp <blowekamp@mail.nih.gov>
+Date: Thu, 16 Aug 2018 09:50:39 -0400
+Bug-Debian: https://bugs.debian.org/912583
+Subject: [PATCH] Fix Python index test with empty comparison
+
+This addresses a test failure with Python 3.7 due to a change in the
+StopIteration exception handling from PEP 479.
+
+This test case has a slice index which results in an empty image. The
+iteration produces a StopIteration exception which with Python 3.7 is
+converted into a Run-time exception:
+
+Traceback (most recent call last):
+  File
+  "/home/circleci/SimpleITK/Testing/Unit/Python/ImageIndexingTest.py",
+  line 87, in test_2d
+    self.assertImageNDArrayEquals(img[-4:-1:-2,-2:-1:1],nda[-2:-1:1,-4:-1:-2])
+  File
+  "/home/circleci/SimpleITK/Testing/Unit/Python/ImageIndexingTest.py",
+  line 35, in assertImageNDArrayEquals
+    for p,n in zip(img, nda.flat):
+RuntimeError: generator raised StopIteration
+---
+ Testing/Unit/Python/ImageIndexingTest.py | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/Testing/Unit/ImageIndexingTest.py b/Testing/Unit/Python/ImageIndexingTest.py
+index 2740f6e62..c9889de7c 100644
+--- a/Testing/Unit/ImageIndexingTest.py
++++ b/Testing/Unit/ImageIndexingTest.py
+@@ -69,6 +69,7 @@ def test_2d(self):
+         self.assertEqual(len(img[:,2:1]), 0)
+         self.assertEqual(len(img[-6:0,:]), 0)
+         self.assertEqual(len(img[0:0,:]), 0)
++        self.assertEqual(len(img[-4:-1:-2,-2:-1:1]), 0)
+ 
+ 
+ 
+@@ -84,7 +85,7 @@ def test_2d(self):
+ 
+         # some negative cases
+         self.assertImageNDArrayEquals(img[-4:-1,-2:-1],nda[-2:-1,-4:-1])
+-        self.assertImageNDArrayEquals(img[-4:-1:-2,-2:-1:1],nda[-2:-1:1,-4:-1:-2])
++        self.assertImageNDArrayEquals(img[-1:-4:-2,-2:-1:1],nda[-2:-1:1,-1:-4:-2])
+         self.assertImageNDArrayEquals(img[::-1,:],nda[:,::-1])
+ 
+         # check some exceptions

debian/patches/Fix-path-created-for-output-of-4D-images-in-test.patch

+From: Bradley Lowekamp <blowekamp@mail.nih.gov>
+Date: Thu, 18 May 2017 13:20:56 -0400
+Subject: Fix path created for output of 4D images in test
+
+There was missing a directory separator.
+---
+ Testing/Unit/sitkImage4DTests.cxx | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/Testing/Unit/sitkImage4DTests.cxx b/Testing/Unit/sitkImage4DTests.cxx
+index af6c16a..1dcd45c 100644
+--- a/Testing/Unit/sitkImage4DTests.cxx
++++ b/Testing/Unit/sitkImage4DTests.cxx
+@@ -491,11 +491,11 @@ TEST( IO, Image4D )
+   EXPECT_EQ( 1u, image.GetNumberOfComponentsPerPixel() );
+ 
+   sitk::ImageFileWriter imageWriter;
+-  imageWriter.SetFileName( dataFinder.GetOutputDirectory()+"image4d.nii" );
++  imageWriter.SetFileName( dataFinder.GetOutputDirectory()+"/image4d.nii" );
+   ASSERT_NO_THROW( imageWriter.Execute( image ) );
+ 
+   sitk::ImageFileReader imageReader;
+-  imageReader.SetFileName( dataFinder.GetOutputDirectory()+"image4d.nii" );
++  imageReader.SetFileName( dataFinder.GetOutputDirectory()+"/image4d.nii" );
+   ASSERT_NO_THROW( imageRead = imageReader.Execute() );
+   EXPECT_EQ ( sitk::Hash( image ), sitk::Hash( imageRead ) );
+ 
+@@ -509,12 +509,12 @@ TEST( IO, Image4D )
+   EXPECT_EQ( 21u, imageRead2.GetDepth() );
+   EXPECT_EQ( 4u, imageRead2.GetSize()[3] );
+ 
+-  imageWriter.SetFileName( dataFinder.GetOutputDirectory()+"image4d2.nii" );
++  imageWriter.SetFileName( dataFinder.GetOutputDirectory()+"/image4d2.nii" );
+   ASSERT_NO_THROW( imageWriter.Execute( imageRead2 ) );
+ 
+   sitk::Image imageRead3;
+   ASSERT_NO_THROW( imageRead3 = imageReader.Execute() );
+-  imageReader.SetFileName( dataFinder.GetOutputDirectory()+"image4d2.nii" );
++  imageReader.SetFileName( dataFinder.GetOutputDirectory()+"/image4d2.nii" );
+   EXPECT_EQ ( "9e81d4b3cdf10a4da5d54c8cd7c4954449d76d5d", sitk::Hash( imageRead3 ) );
+ 
+   // VectorImage

debian/patches/Relax-the-short-image-testing-tolerance.patch

+From: Bradley Lowekamp <blowekamp@mail.nih.gov>
+Date: Thu, 8 Mar 2018 09:14:49 -0500
+Subject: Relax the "short" image testing tolerance for discrete Gaussian
+
+
+On the i386 Debian build, it has been reported that the
+BasicFilters.DiscreteGaussianImageFilter_short test is failing with a
+RMS difference of 0.513965. This tolerance has already been relaxed
+once, and further relaxing seems reasonable due to intermediate image
+of float being converted to short without proper rounding.
+
+While this is an indication the internal ITK algorithm could be
+improved for portability and accuracy in ITK, it is not an indication
+of a problem with the SimpleITK build.
+---
+ Code/BasicFilters/json/DiscreteGaussianImageFilter.json | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/Code/BasicFilters/json/DiscreteGaussianImageFilter.json b/Code/BasicFilters/json/DiscreteGaussianImageFilter.json
+index ee9f677..3c23348 100644
+--- a/Code/BasicFilters/json/DiscreteGaussianImageFilter.json
++++ b/Code/BasicFilters/json/DiscreteGaussianImageFilter.json
+@@ -57,7 +57,7 @@
+       "tag" : "short",
+       "description" : "Simply run with a short image with default settings",
+       "settings" : [],
+-      "tolerance" : "0.5",
++      "tolerance" : "0.6",
+       "inputs" : [
+         "Input/RA-Slice-Short.nrrd"
+       ]

debian/patches/series

 Fix-build-with-ITKV3_COMPATIBILITY-enabled.patch
+Fix-path-created-for-output-of-4D-images-in-test.patch
+Relax-the-short-image-testing-tolerance.patch
+Fix-Python-index-test-with-empty-comparison.patch

debian/watch

 version=4
 opts=uversionmangle=s/(rc|a|b|c)/~$1/
     https://github.com/SimpleITK/SimpleITK/releases \
-    .*/SimpleITK@ANY_VERSION@@ARCHIVE_EXT@ debian
+    .*/SimpleITK-(\d[.\d]+)\.tar\.xz debian
 opts=component=data,uversionmangle=s/(rc|a|b|c)/~$1/ \
     https://github.com/SimpleITK/SimpleITK/releases \
-    .*/SimpleITKData@ANY_VERSION@@ARCHIVE_EXT@ same
+    .*/SimpleITKData-(\d[.\d]+)\.tar\.xz same