From: Justin Lecher Date: Thu, 26 Mar 2015 12:17:19 +0000 (+0000) Subject: Backport test fix X-Git-Url: http://git.tremily.us/gitweb.cgi?a=commitdiff_plain;h=10960295252ebf57f90e419d4782fa37511ce80c;p=gentoo.git Backport test fix Package-Manager: portage-2.2.18/cvs/Linux x86_64 Manifest-Sign-Key: 0xB9D4F231BD1558AB! --- diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog index eaafcd26553f..e127a14f7066 100644 --- a/sci-biology/biopython/ChangeLog +++ b/sci-biology/biopython/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/biopython # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.79 2015/03/26 07:11:28 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.80 2015/03/26 12:17:18 jlec Exp $ + + 26 Mar 2015; Justin Lecher + +files/biopython-1.65-test-fix-backport.patch, biopython-1.65.ebuild: + Backport test fix 26 Mar 2015; Justin Lecher biopython-1.65.ebuild: Add note for embos support, bug #543510 diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest index 760815db04a0..3b41fbbd32cb 100644 --- a/sci-biology/biopython/Manifest +++ b/sci-biology/biopython/Manifest @@ -5,30 +5,31 @@ AUX SffIO_broken_padding.patch 1294 SHA256 2dece94f54f58a46ec87108d39ecfee4d0da7 AUX SffIO_error_in_check_eof.patch 511 SHA256 49492906fcab2a7694c9adc12fdb5f636cda49d181027a1e43956209f0093864 SHA512 9e05702cdeb38ec3322d797f777f08a9a4375d8b7c9194124f2d405bab46305cea4eb5eb31e1f67ee6a974ba7c5a4b8d3ce70a18b2883765147d5588cb9a7366 WHIRLPOOL 146996380d469cf6f802e8135009a363d3ee2208bcc74a5cf0e934eaacd8902be94ab948ea38cb27bba28467a5993460fc0ae10b0f481542749e57689c657f60 AUX biopython-1.51-flex.patch 782 SHA256 ad957b435fc70b218a7a65eb492b0eae5f82b7c6371d2f1451c9dd714fa056dc SHA512 4d7adf0716d8de840e0c7ef3415d16056a933ec457451e17fd83029e70bcb7c18db8aaf1c9c101a64205eea6f79cd68b78331c6a5a4133bf755ea7c1d5301e83 WHIRLPOOL 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$ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.65.ebuild,v 1.3 2015/03/26 12:17:18 jlec Exp $ EAPI=5 @@ -31,6 +31,8 @@ DEPEND="${RDEPEND} DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) +PATCHES=( "${FILESDIR}"/${P}-test-fix-backport.patch ) + python_test() { [[ ${EPYTHON} == pypy ]] && return cd Tests || die diff --git a/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch b/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch new file mode 100644 index 000000000000..2efdef97d799 --- /dev/null +++ b/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch @@ -0,0 +1,40 @@ +From 08c72f8778a87701586a03dffcce33c7589bc6d7 Mon Sep 17 00:00:00 2001 +From: Peter Cock +Date: Sun, 18 Jan 2015 02:07:54 +0000 +Subject: [PATCH] Clearer error message; update failing test. + +One of the orchid examples now returns different enough +results that the test was failing. The new error message +makes it much easier to pick another positive example to +add to the the white-list. +--- + Tests/test_NCBI_qblast.py | 9 +++++---- + 1 file changed, 5 insertions(+), 4 deletions(-) + +diff --git a/Tests/test_NCBI_qblast.py b/Tests/test_NCBI_qblast.py +index 88bfe61..19f7b35 100644 +--- a/Tests/test_NCBI_qblast.py ++++ b/Tests/test_NCBI_qblast.py +@@ -66,7 +66,7 @@ def test_orchid_est(self): + AGCCATGGATTTCTCAGAAGAAAATGATTATACTTCTTAATCAGGCAACTGATATTATCAATTTATGGCA + GCAGAGTGGTGGCTCCTTGTCCCAGCAGCAGTAATTACTTTTTTTTCTCTTTTTGTTTCCAAATTAAGAA + ACATTAGTATCATATGGCTATTTGCTCAATTGCAGATTTCTTTCTTTTGTGAATG""", +- 0.0000001, None, ["21554275", "18409071", "296087288"]) ++ 0.0000001, None, ["21554275", "18409071", "296087288", "566183510"]) + + def run_qblast(self, program, database, query, e_value, entrez_filter, expected_hits): + try: +@@ -120,9 +120,10 @@ def run_qblast(self, program, database, query, e_value, entrez_filter, expected_ + print("Update this test to have some redundancy...") + for alignment in record.alignments: + print(alignment.hit_id) +- assert found_result, "Missing all of %s in alignments" \ +- % ", ".join(expected_hits) +- self.assertTrue(found_result) ++ self.assertTrue(found_result, ++ "Missing all expected hits (%s), instead have: %s" ++ % (", ".join(expected_hits), ++ ", ".join(a.hit_id for a in record.alignments))) + + # Check the expected result(s) are found in the descriptions + if expected_hits is None: