debian/changelog

 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@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

+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@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

+Author: Andreas Tille <tille@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

@@ -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