Étienne Mollier pushed to branch master at Debian Med / python-biopython
Commits: 72df12d9 by Étienne Mollier at 2020-09-13T18:22:44+02:00 add blastdbv4-tests-filter-archs.patch This patch is a rewrap of the previous blastdbv4-test.patch. This time we test makeblastdb to create v5 databases, but fall back on v4 on architectures on which regressions are yet to be fixed. - - - - - 3 changed files: - debian/changelog - + debian/patches/blastdbv4-tests-filter-archs.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,7 +1,8 @@ python-biopython (1.78+dfsg-1) UNRELEASED; urgency=medium * Bumped build requirement on ncbi-blast+ 2.10.0-3 and greater, - * Removed patch against tests to work makeblastdb bug around on 32 bit archs. + * Reworked the patch working around makeblastd bug in v5 to fall back in v4 + only on architectures on which corrections are yet to be implemented.. * Removed patches applied upstream. * New upstream version * debhelper-compat 13 (routine-update) ===================================== debian/patches/blastdbv4-tests-filter-archs.patch ===================================== @@ -0,0 +1,47 @@ +--- python-biopython.orig/Tests/test_NCBI_BLAST_tools.py ++++ python-biopython/Tests/test_NCBI_BLAST_tools.py +@@ -16,6 +16,12 @@ + import unittest + import re + ++# makeblastdb v5 is buggy on some architectures for the moment ++dbver = 5 ++arch_version_fallback = ["aarch64-linux-gnu"] ++if sys.implementation._multiarch in arch_version_fallback: ++ dbver = 4 ++ + from Bio.Application import _escape_filename + from Bio import MissingExternalDependencyError + from Bio.Blast import Applications +@@ -217,6 +224,7 @@ + global exe_names + cline = Applications.NcbimakeblastdbCommandline( + exe_names["makeblastdb"], ++ blastdb_version=dbver, + input_file="GenBank/NC_005816.faa", + dbtype="prot", + hash_index=True, +@@ -228,6 +236,7 @@ + self.assertEqual( + str(cline), + _escape_filename(exe_names["makeblastdb"]) ++ + " -blastdb_version " + str(dbver) + + " -dbtype prot -in GenBank/NC_005816.faa" + " -parse_seqids -hash_index -max_file_sz 20MB" + " -taxid 10", +@@ -263,6 +272,7 @@ + global exe_names + cline = Applications.NcbimakeblastdbCommandline( + exe_names["makeblastdb"], ++ blastdb_version=dbver, + input_file="GenBank/NC_005816.fna", + dbtype="nucl", + hash_index=True, +@@ -274,6 +284,7 @@ + self.assertEqual( + str(cline), + _escape_filename(exe_names["makeblastdb"]) ++ + " -blastdb_version " + str(dbver) + + " -dbtype nucl -in GenBank/NC_005816.fna" + " -parse_seqids -hash_index -max_file_sz 20MB" + " -taxid 10", ===================================== debian/patches/series ===================================== @@ -2,6 +2,7 @@ remove_mathml-qname.patch privacy_breach.patch privacy_breach_ie9.patch blastdbv4-impl.patch +blastdbv4-tests-filter-archs.patch fix-use-of-unversioned-python.patch stabilize-phyml-test.patch spelling-error-in-binaries.patch View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/commit/72df12d9a5a68486fc0da0b763d2275b2ed848b4 -- View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/commit/72df12d9a5a68486fc0da0b763d2275b2ed848b4 You're receiving this email because of your account on salsa.debian.org.
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