[med-svn] [Git][med-team/python-pbcore][master] 2 commits: Adapt to numpy 1.14 (thanks to Graham Inggs for cherry-picking from upstream)
Andreas Tille
gitlab at salsa.debian.org
Mon Jun 25 08:24:06 BST 2018
Andreas Tille pushed to branch master at Debian Med / python-pbcore
Commits:
a5551c2f by Andreas Tille at 2018-06-25T08:19:17+02:00
Adapt to numpy 1.14 (thanks to Graham Inggs for cherry-picking from upstream)
- - - - -
9ce6ea22 by Andreas Tille at 2018-06-25T08:55:37+02:00
Relax test constraint which is rather a rounding issue
- - - - -
4 changed files:
- debian/changelog
- + debian/patches/numpy1.14.patch
- + debian/patches/relax_test_constraint.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,10 +1,17 @@
python-pbcore (1.4.2+dfsg-1) UNRELEASED; urgency=medium
+ [ Afif Elghraoui ]
* New upstream version (git f3bcf3a)
* Updated patches
* Added tests dependency on python-coverage
* d/control: use build profile declarations
+ [ Andreas Tille ]
+ * Adapt to numpy 1.14 (thanks to Graham Inggs for cherry-picking from
+ upstream)
+ Closes: #900485
+ * Relax test constraint which is rather a rounding issue
+
-- Afif Elghraoui <afif at debian.org> Sun, 07 Jan 2018 02:03:14 -0500
python-pbcore (1.2.11+dfsg-1) unstable; urgency=medium
=====================================
debian/patches/numpy1.14.patch
=====================================
--- /dev/null
+++ b/debian/patches/numpy1.14.patch
@@ -0,0 +1,80 @@
+Description: Fix FTBFS with NumPy 1.14
+Bug-Debian: https://bugs.debian.org/900485
+Origin: upstream, https://github.com/PacificBiosciences/pbcore/commit/b7ef4238b6388f984a264b8a912450b652177dbf
+Author: David Seifert <dseifert at pacificbiosciences.com>
+Last-Update: 2018-01-10
+
+--- a/tests/test_pbdataset.py
++++ b/tests/test_pbdataset.py
+@@ -1693,7 +1693,7 @@ class TestDataSet(unittest.TestCase):
+ self.assertEqual(len(readers[0].referenceInfoTable), 59)
+ obstbl = [readers[0].referenceInfo('E.faecalis.1')]
+ exptbl = [(27, 27, 'E.faecalis.1', 'E.faecalis.1', 1482,
+- 'a1a59c267ac1341e5a12bce7a7d37bcb', 0L, 0L)]
++ 'a1a59c267ac1341e5a12bce7a7d37bcb', 0, 0)]
+ self.assertListOfTuplesEqual(obstbl, exptbl)
+ # TODO: add a bam with a different referenceInfoTable to check merging
+ # and id remapping:
+@@ -2220,7 +2220,7 @@ class TestDataSet(unittest.TestCase):
+ self.assertEqual(len3, 338114)
+ obstbl = aln.referenceInfoTable
+ exptbl = [(1, 1, 'lambda_NEB3011', 'lambda_NEB3011',
+- 48502, 'a1319ff90e994c8190a4fe6569d0822a', 0L, 338113L)]
++ 48502, 'a1319ff90e994c8190a4fe6569d0822a', 0, 338113)]
+ self.assertListOfTuplesEqual(obstbl, exptbl)
+ self.assertEqual(set(aln.tId), {1})
+ # + 1, because bounds are inclusive, rather than exclusive
+@@ -2247,9 +2247,9 @@ class TestDataSet(unittest.TestCase):
+ self.assertEqual(len3, 57147)
+ obstbl = aln.referenceInfoTable
+ exptbl = [(0, 0, 'ecoliK12_pbi_March2013', 'ecoliK12_pbi_March2013',
+- 4642522, '52cd7c5fa92877152fa487906ae484c5', 0L, 57034L),
++ 4642522, '52cd7c5fa92877152fa487906ae484c5', 0, 57034),
+ (1, 1, 'lambda_NEB3011', 'lambda_NEB3011', 48502,
+- 'a1319ff90e994c8190a4fe6569d0822a', 57035L, 57146L)]
++ 'a1319ff90e994c8190a4fe6569d0822a', 57035, 57146)]
+ self.assertListOfTuplesEqual(obstbl, exptbl)
+ self.assertEqual(set(aln.tId), {0, 1})
+ # + 1, because bounds are inclusive, rather than exclusive
+@@ -2282,7 +2282,7 @@ class TestDataSet(unittest.TestCase):
+ self.assertEqual(len3, 65346)
+ obstbl = aln.referenceInfoTable
+ exptbl = [(0, 0, 'ecoliK12_pbi_March2013', 'ecoliK12_pbi_March2013',
+- 4642522, '52cd7c5fa92877152fa487906ae484c5', 0L, 0L)]
++ 4642522, '52cd7c5fa92877152fa487906ae484c5', 0, 0)]
+ self.assertListOfTuplesEqual(obstbl, exptbl)
+ self.assertEqual(set(aln.tId), {0})
+ self.assertEqual(aln.referenceInfo('ecoliK12_pbi_March2013'),
+@@ -2306,7 +2306,7 @@ class TestDataSet(unittest.TestCase):
+ self.assertEqual(len1 + len2, len3)
+ self.assertEqual(len3, 160264)
+ exptbl = [(0, 0, 'ecoliK12_pbi_March2013', 'ecoliK12_pbi_March2013',
+- 4642522, '52cd7c5fa92877152fa487906ae484c5', 0L, 0L)]
++ 4642522, '52cd7c5fa92877152fa487906ae484c5', 0, 0)]
+ obstbl = aln.referenceInfoTable
+ self.assertListOfTuplesEqual(obstbl, exptbl)
+ self.assertEqual(set(aln.tId), {0})
+@@ -2338,9 +2338,9 @@ class TestDataSet(unittest.TestCase):
+ # and endrow fields for bams someday...
+ obstbl = aln.referenceInfoTable
+ exptbl = [(0, 0, 'ecoliK12_pbi_March2013', 'ecoliK12_pbi_March2013',
+- 4642522, '52cd7c5fa92877152fa487906ae484c5', 0L, 0L),
++ 4642522, '52cd7c5fa92877152fa487906ae484c5', 0, 0),
+ (1, 1, 'lambda_NEB3011', 'lambda_NEB3011', 48502,
+- 'a1319ff90e994c8190a4fe6569d0822a', 0L, 0L)]
++ 'a1319ff90e994c8190a4fe6569d0822a', 0, 0)]
+ self.assertListOfTuplesEqual(obstbl, exptbl)
+ self.assertEqual(set(aln.tId), {0, 1})
+ self.assertEqual(aln.referenceInfo('ecoliK12_pbi_March2013'),
+@@ -2372,9 +2372,9 @@ class TestDataSet(unittest.TestCase):
+ self.assertEqual(len4, 160376)
+ obstbl = aln.referenceInfoTable
+ exptbl = [(0, 0, 'ecoliK12_pbi_March2013', 'ecoliK12_pbi_March2013',
+- 4642522, '52cd7c5fa92877152fa487906ae484c5', 0L, 0L),
++ 4642522, '52cd7c5fa92877152fa487906ae484c5', 0, 0),
+ (1, 1, 'lambda_NEB3011', 'lambda_NEB3011', 48502,
+- 'a1319ff90e994c8190a4fe6569d0822a', 0L, 0L)]
++ 'a1319ff90e994c8190a4fe6569d0822a', 0, 0)]
+ self.assertListOfTuplesEqual(obstbl, exptbl)
+ self.assertEqual(set(aln.tId), {0, 1})
+ self.assertEqual(aln.referenceInfo('ecoliK12_pbi_March2013'),
=====================================
debian/patches/relax_test_constraint.patch
=====================================
--- /dev/null
+++ b/debian/patches/relax_test_constraint.patch
@@ -0,0 +1,19 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 25 Jun 2018 08:54:11 +0200
+Description: Relax test constraint which is rather a rounding issue
+ Traceback (most recent call last):
+ File "/build/python-pbcore-1.4.2+dfsg/tests/test_pbdataset.py", line 2125, in test_stats_metadata
+ 2322.16060475)
+ AssertionError: 2322.1606047549185 != 2322.16060475
+
+--- a/tests/test_pbdataset.py
++++ b/tests/test_pbdataset.py
+@@ -2121,7 +2121,7 @@ class TestDataSet(unittest.TestCase):
+ 2322.805559802698)
+ self.assertEqual(ds2.metadata.summaryStats.readLenDist.sampleStd,
+ 2322.805559802698)
+- self.assertEqual(ds3.metadata.summaryStats.readLenDist.sampleStd,
++ self.assertAlmostEqual(ds3.metadata.summaryStats.readLenDist.sampleStd,
+ 2322.16060475)
+ # uses the bins, not the previous values for mean, std, etc.:
+ self.assertEqual(ds3.metadata.summaryStats.readLenDist.sampleMed, 45)
=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,5 @@ doc-theme.patch
enable-build-time-testing.patch
remove-unnecessary-cython-dep.patch
ignore-pyxb.patch
+numpy1.14.patch
+relax_test_constraint.patch
View it on GitLab: https://salsa.debian.org/med-team/python-pbcore/compare/a60fd5be18191d305e1e3f04b855d63bd2481999...9ce6ea2263880559e9778e7c824f5ec7dd35f8e2
--
View it on GitLab: https://salsa.debian.org/med-team/python-pbcore/compare/a60fd5be18191d305e1e3f04b855d63bd2481999...9ce6ea2263880559e9778e7c824f5ec7dd35f8e2
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