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 <[email protected]> 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 <[email protected]> +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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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