jlec 15/03/26 12:17:18 Added: biopython-1.65-test-fix-backport.patch Log: Backport test fix (Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)
Revision Changes Path 1.1 sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch?rev=1.1&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch?rev=1.1&content-type=text/plain Index: biopython-1.65-test-fix-backport.patch =================================================================== >From 08c72f8778a87701586a03dffcce33c7589bc6d7 Mon Sep 17 00:00:00 2001 From: Peter Cock <[email protected]> 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:
