[med-svn] [Git][med-team/python-biopython][master] 4 commits: d/rules: reduce BLASTDB_LMDB_MAP_SIZE for arm64
Étienne Mollier
gitlab at salsa.debian.org
Tue Sep 15 23:43:12 BST 2020
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 <etienne.mollier at mailoo.org> 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
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