[med-svn] [Git][med-team/python-biopython][master] add blastdbv4-tests-filter-archs.patch

[Étienne Mollier]

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

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View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/commit/72df12d9a5a68486fc0da0b763d2275b2ed848b4
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