Étienne Mollier pushed to branch master at Debian Med / python-biopython
Commits: 50981476 by Étienne Mollier at 2020-09-16T00:10:41+02:00 d/rules: reduce BLASTDB_LMDB_MAP_SIZE for arm64 This should allow build time testings to pass, even on constrained configurations involved by schroot environments. - - - - - 6507098c by Étienne Mollier at 2020-09-16T00:12:26+02:00 d/t/run-unit-test: reduce BLASTDB_LMDB_MAP_SIZE For arm64 virtualised environments, maybe more, this change should allow autopkgtest to run with makeblastdb database version 5 without having to fall back to version 4. - - - - - ae007ca1 by Étienne Mollier at 2020-09-16T00:15:31+02:00 remove blastdbv4-tests-filter-archs.patch This should be unneeded, now that most issues around makeblastdb are identified and corrected. - - - - - 6d43a733 by Étienne Mollier at 2020-09-16T00:18:32+02:00 d/rules: reduce BLASTDB_LMDB_MAP_SIZE for arm64 for real this time, with drop for arm64, not amd64. >_< - - - - - 5 changed files: - debian/changelog - − debian/patches/blastdbv4-tests-filter-archs.patch - debian/patches/series - debian/rules - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,6 +1,7 @@ python-biopython (1.78+dfsg-2) UNRELEASED; urgency=medium * Added DEP3 description to blastdbv4-tests-filter-archs.patch. + * Removed, at last, patch working around makeblastd bug in v5. -- Étienne Mollier <[email protected]> Mon, 14 Sep 2020 21:28:54 +0200 ===================================== debian/patches/blastdbv4-tests-filter-archs.patch deleted ===================================== @@ -1,58 +0,0 @@ -Description: fall back makeblastdb wrapper test to v4 on unsupported archs - While makeblastdb -blastdb_version 5 is gaining stable support, under some - architectures, it is still necessary to fall back to -blastdb_version 4 to be - able to run the test. This patch implements a way to select a list of - architectures to run with a blastdb v4. - . - Note: it is expected that Biopython 1.79 might test both blastdb v4 and v5. -Author: Étienne Mollier -Bug-Debian: https://bugs.debian.org/969608 -Forwarded: no -Last-Update: 2020-09-13 18:18:22 +0200 ---- 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 ===================================== @@ -2,7 +2,6 @@ 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 ===================================== debian/rules ===================================== @@ -34,6 +34,15 @@ else EXCLUDEARCHamd64=raxml_tool endif +# arm64 virtualized environment, esp. with schroot, may be too constrained for +# the memory allocation required by the test_NCBI_BLAST_tools. See #969608 +# following for more details: +# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=969608#40 +ifeq ($(BUILDARCH),arm64) + export BLASTDB_LMDB_MAP_SIZE=20000000000 +endif + + # avoid tests requiring data base connections if no server is running while we are doing the build # This would not trigger a failure but bloats the build log with irrelevant noise EXCLUDEDATABASE=BioSQL_MySQLdb BioSQL_psycopg2 ===================================== debian/tests/run-unit-test ===================================== @@ -27,6 +27,15 @@ if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" != "amd64" ]; then rm -f test_BWA_tool.py fi +# arm64 virtualized environment, esp. with schroot, may be too constrained for +# the memory allocation required by the test_NCBI_BLAST_tools. See #969608 +# following for more details: +# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=969608#40 +if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" != "arm64" ]; then + BLASTDB_LMDB_MAP_SIZE=20000000000 + export BLASTDB_LMDB_MAP_SIZE +fi + # execute tests ################################################################################ # in the Debian package dialign it is not needed to set DIALIGN2_DIR but the View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/f2babc28481c3a29407222251743c51ad0701664...6d43a7339ec9e5055d1ce04ba103e5cba72adf53 -- View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/f2babc28481c3a29407222251743c51ad0701664...6d43a7339ec9e5055d1ce04ba103e5cba72adf53 You're receiving this email because of your account on salsa.debian.org.
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