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 eaafcd26553f94742a3a10139372d1db858014fe..e127a14f7066c39926379e59291b4d94ac9f3095 100644 (file)
--- 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 <jlec@gentoo.org>
+  +files/biopython-1.65-test-fix-backport.patch, biopython-1.65.ebuild:
+  Backport test fix
 
   26 Mar 2015; Justin Lecher <jlec@gentoo.org> biopython-1.65.ebuild:
   Add note for embos support, bug #543510

diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index 760815db04a06100f4ac16f6e1fea2880512f62f..3b41fbbd32cb116fa7f11e3935a82de7507daa8e 100644 (file)
--- 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 194117f335c6c7abc567f6e9365eeef8f8eec4526aac2a0af6f07b7ce026074dc4be024bc8ce1a1f40182d50eb2c241da7b0656f2a42cb19eecd3088dd9148e1
 AUX biopython-1.62-SffIO.patch 2133 SHA256 93177adc422c4bcdadde3d36b0fa92b707aa54620932fca341c9a99c59f758ad SHA512 77b9ab665d2ccd4e8ad64e96f69133764241976f100239dee475636984d3822be2ba3e0afa4a054c26dd994ebce0feff7593ee9520de854f1f81367761f587c6 WHIRLPOOL ea82687b66dc4ad31634fb7921f9046505aec8a663213eeb8741082ba0a70ce9da62cc25367a3b660e28fffb6a8538b3e839adb67fc7658f473c179f1190fafb
+AUX biopython-1.65-test-fix-backport.patch 2070 SHA256 e232b49f97f417255f62ff4cd4be70a43b7b958840d4be411e62d503e463a9aa SHA512 c5b2ed12361727bde109c98d5e2733fe7b826e6accb25279eb8c0190dcd89dc3b5e9b7328a3ace2d57ce91f0668617518c2eeb21e80f6eb97ff9010e4004f53b WHIRLPOOL dff88a361a6564732a665fb5142155f81ae10e108eac230b199fd2adaea0f0ee45e8c02b94696c968af0473481caa5d36ddd88c7438db361f8d24fd5bb773a97
 DIST biopython-1.57.tar.gz 6945024 SHA256 07c16a86127770c8d5b653a6e82fee0999159f7284a3a01c98cf66ed2f0ec4a0
 DIST biopython-1.64.tar.gz 11671170 SHA256 f79c4f4a7abc6a73b546f2177f041e5d27f68610be8685065b7180d21ec78916 SHA512 f744eee08e4eaa63836ff8fbc56be4d70659d1e36b52c5eed517001bd9d5e64b1d5f3f1c9879c1e82318ff981b3bd6b8d50942415c40b0e855df5aec41ab3dc6 WHIRLPOOL 1f2c4478109d90f73fdc7325c1d298d9f2508f6257ecaf5d3bd8a38bf51019ff596da57665fc2d480eb006b628ee123934c661a1da1746fd8ba27e9e6001dcaa
 DIST biopython-1.65.tar.gz 12641342 SHA256 463cc81db84e9bfcdfb15629511c81ed556a6c0287e670dbfe80f03c65d2a88e SHA512 2a9c6a89d0279374c243938d13bfdd6f2b124a08afbfb0c262e1e4827c48a141fb9941f4cdb960f76b523f0ac152095a8c6ea566d9b469ce9daf8a7e7993f7af WHIRLPOOL 40757938c0eb7e30c9609ef5aa2d397fa21ad92cd20c9b6300cde1b381a0e6c21e4ebb7f4d25bf02651789437d7d86341154b907ccc0007759c17939f2e29da2
 EBUILD biopython-1.57.ebuild 1423 SHA256 9096221918c30adbd01157581f42e61286cb7d20b8ad52ad52756d8c7de155df SHA512 782410b327703e9d6d612c22daf4c977e06051995e7d7a9763690ef101d0261e0689b7787a27ae0a205d26a01df09fa6b98e2d4bc6047856b35917bb87a3a262 WHIRLPOOL a58be3d9ed1aa3fee35d2fbf5ad208b82a1e0ff6067aa989a21989f9f45d5fe6020eb4ee639cdd2ab87820dbb5f52bdcb53aebe300e91c45584f000b914c41de
 EBUILD biopython-1.64.ebuild 1326 SHA256 0683b026831015249844c3acc0f9e35eead01e0ae1061f7d88ab29d76c9fef2e SHA512 a07fed11f1f1a4d16b4837e58698302fecd6b2552bf74e65d1d5f0bc485bfc7d10c59a58a42546f3783b229e3677cea291ca329e6cc1fafbe51d57347e2be86a WHIRLPOOL 40ede10189505c6565ece5a5bca156c3b74ad366e0cadb3622b2ba7085428b54f3ab66210b0a96ab682ee3a6a5784ce77b52ccc6656fdb0831207237937cbc21
-EBUILD biopython-1.65.ebuild 1612 SHA256 3b14c91b89314d4474ea95c258b45e76bba6842ff6a840e6b0a80c9db95b6eea SHA512 7cfa6e843ca0b1aedc1fef905aa0318d769ff76dc10b3a79d2cb2313be991463c918761568b052c1bd8dc42bcc8038a7531b875b53f69fb282df828c0df5f67c WHIRLPOOL 077cc500c1ef81e59ea66853f2b955a26fa7190ff17392c9ba503b8ecfb4faa7034b4c3650b222c2d22fbfb66fcc33ee93433a3979e1c8ccdc47628c45034545
-MISC ChangeLog 12497 SHA256 482a561e41f89e01c5a51ee9d6b13e46523839310452997cdb261e530ba9a7d8 SHA512 3972132f0aee9eef490cecea77365ac0d8436bad2cffa5f6091bcfbec4e7c6b7f379445f2b6bc6de8af9a130930279892e890e4b8423b1543385e9771c4b0d1e WHIRLPOOL 140e8ee71729a2694f53fe6dd2b0b7a2923624a629a937c29c4be554b80d33cebf3f30627ce20cef400f13783bbf40a151b3a17b9faabd99206ba75435b280c3
+EBUILD biopython-1.65.ebuild 1668 SHA256 4ba14363d8d7b7d8aa16bf60624d94b86eba389fdb97006e37a0918b017ef986 SHA512 919dafb3e2bbbbd82b01c66bc5f723f4c5fac20e14c4ba22c527625b3fd6b5a1f59de95f99ab1f9d1b95ddc18cc3c4ef765e3aa89974879476c06fa1672f5946 WHIRLPOOL 6bf9812ea3a593ea243a8605dd2222870d7203c7f99c5cfe53495b6cab2ed63f270f5c03b0040f91293cc4cbf7c863f1818c2abedf8c6c0f14b53234c7e891bb
+MISC ChangeLog 12637 SHA256 64e9e3e34c31b41c79322cb1f7c655c915b1ff7c7f27271ac24988e36317b7e8 SHA512 3db9567dfdf94d8aa0d6d459238e423b1f182664fd87fefdead5cc631ddee9651395b04bf323046aece894441390808c291fb7659503890d7ebbf000ad122ce7 WHIRLPOOL bfda2df306d3948d111df8b4726e90b9125ea130747b0383d07f58bcedf2ef5b0eb68158cf470e01c9d7f08562704dfdbbcdbbe19aea6c9abf4bcd4e174f638b
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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diff --git a/sci-biology/biopython/biopython-1.65.ebuild b/sci-biology/biopython/biopython-1.65.ebuild
index b79d71c82e764fe2bc695fffd2e1b618edf1379f..e6a0eb48a2b0c1ceb5a9c882f122deb399dd502a 100644 (file)
--- a/sci-biology/biopython/biopython-1.65.ebuild
+++ b/sci-biology/biopython/biopython-1.65.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.65.ebuild,v 1.2 2015/03/26 07:11:28 jlec Exp $
+# $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 (file)
index 0000000..2efdef9
--- /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 <p.j.a.cock@googlemail.com>
+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: