[med-svn] [Git][med-team/simpleitk][master] 6 commits: d/watch only reports source tarballs
Andreas Tille
gitlab at salsa.debian.org
Mon Feb 4 14:02:17 GMT 2019
Andreas Tille pushed to branch master at Debian Med / simpleitk
Commits:
17ba98f7 by Andreas Tille at 2019-01-29T15:47:58Z
d/watch only reports source tarballs
- - - - -
73b6d71e by Andreas Tille at 2019-01-29T16:04:05Z
Restore state before importing 1.1.0 which seems to require ITK 1.13 which is not packaged
- - - - -
4ac93bb4 by Andreas Tille at 2019-01-29T16:05:15Z
d/watch only reports source tarballs
- - - - -
83c3249f by Andreas Tille at 2019-01-29T16:06:23Z
No need for versioned Build-Depends: dpkg-dev any more
- - - - -
b228e810 by Andreas Tille at 2019-01-29T16:10:56Z
Standards-Version: 4.3.0
- - - - -
c8cd6de3 by Andreas Tille at 2019-02-04T14:01:58Z
Upload to unstable
- - - - -
7 changed files:
- debian/changelog
- debian/control
- + debian/patches/Fix-Python-index-test-with-empty-comparison.patch
- + debian/patches/Fix-path-created-for-output-of-4D-images-in-test.patch
- + debian/patches/Relax-the-short-image-testing-tolerance.patch
- debian/patches/series
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,18 +1,18 @@
-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 at debian.org> Sun, 02 Dec 2018 22:34:26 +0100
+ -- Andreas Tille <tille at 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 at lists.alioth.debian.org>
Uploaders: Ghislain Antony Vaillant <ghisvail at 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
=====================================
@@ -0,0 +1,47 @@
+From: Bradley Lowekamp <blowekamp at 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
=====================================
@@ -0,0 +1,42 @@
+From: Bradley Lowekamp <blowekamp at 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
=====================================
@@ -0,0 +1,31 @@
+From: Bradley Lowekamp <blowekamp at 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
=====================================
@@ -1 +1,4 @@
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
=====================================
@@ -1,7 +1,7 @@
version=4
opts=uversionmangle=s/(rc|a|b|c)/~$1/
https://github.com/SimpleITK/SimpleITK/releases \
- .*/SimpleITK at 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 at ANY_VERSION@@ARCHIVE_EXT@ same
+ .*/SimpleITKData-(\d[.\d]+)\.tar\.xz same
View it on GitLab: https://salsa.debian.org/med-team/simpleitk/compare/d74c3b91fca01851d0237ffa5a3c02fb71615132...c8cd6de35fe994ab9be2be1cff3a6554c0e02ea3
--
View it on GitLab: https://salsa.debian.org/med-team/simpleitk/compare/d74c3b91fca01851d0237ffa5a3c02fb71615132...c8cd6de35fe994ab9be2be1cff3a6554c0e02ea3
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