Dylan Aïssi pushed to branch master at Debian Med / python-biopython
Commits: 5cd5d8d2 by Dylan Aïssi at 2020-05-15T09:42:02+02:00 Add upstream patch to fix tests with new NCBI BLAST DB v5 (Closes: #959587) - - - - - 3 changed files: - debian/changelog - debian/patches/series - + debian/patches/update_tests_new_ncbi_blast.patch Changes: ===================================== debian/changelog ===================================== @@ -1,8 +1,13 @@ python-biopython (1.76+dfsg-2) UNRELEASED; urgency=medium * Team upload. + + [ Michael R. Crusoe ] * debian/control: mark the -doc package as Multi-Arch: foreign + [ Dylan Aïssi ] + * Add upstream patch to fix tests with new NCBI BLAST DB v5 (Closes: #959587) + -- Michael R. Crusoe <[email protected]> Fri, 17 Apr 2020 10:17:15 +0200 python-biopython (1.76+dfsg-1) unstable; urgency=medium ===================================== debian/patches/series ===================================== @@ -1,3 +1,4 @@ remove_mathml-qname.patch privacy_breach.patch exclude_docstring_tests.patch +update_tests_new_ncbi_blast.patch ===================================== debian/patches/update_tests_new_ncbi_blast.patch ===================================== @@ -0,0 +1,42 @@ +From: Peter Cock <[email protected]> +Origin: https://github.com/biopython/biopython/pull/2890 +Bug: https://github.com/biopython/biopython/issues/2863 +Bug-Debian: https://bugs.debian.org/959587 +Description: Test updates for NCBI BLAST DB v5 + +--- a/Tests/test_NCBI_BLAST_tools.py ++++ b/Tests/test_NCBI_BLAST_tools.py +@@ -210,8 +210,14 @@ + self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.phr")) + self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.pin")) + self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.pog")) +- self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.psd")) +- self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.psi")) ++ self.assertTrue( ++ os.path.isfile("GenBank/NC_005816.faa.psd") ++ or os.path.isfile("GenBank/NC_005816.faa.pnd") ++ ) ++ self.assertTrue( ++ os.path.isfile("GenBank/NC_005816.faa.psi") ++ or os.path.isfile("GenBank/NC_005816.faa.pni") ++ ) + self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.psq")) + + def test_fasta_db_nucl(self): +@@ -245,8 +251,14 @@ + self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nhr")) + self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nin")) + self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nog")) +- self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nsd")) +- self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nsi")) ++ self.assertTrue( ++ os.path.isfile("GenBank/NC_005816.fna.nsd") ++ or os.path.isfile("GenBank/NC_005816.fna.nnd") ++ ) ++ self.assertTrue( ++ os.path.isfile("GenBank/NC_005816.fna.nsi") ++ or os.path.isfile("GenBank/NC_005816.fna.nni") ++ ) + self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nsq")) + + # makeblastdb makes files in the same dir as the input, clean these up View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/commit/5cd5d8d28352dc1e9206bd2e9b891eb2bc590fd6 -- View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/commit/5cd5d8d28352dc1e9206bd2e9b891eb2bc590fd6 You're receiving this email because of your account on salsa.debian.org.
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