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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-biopython">Debian Med / python-biopython</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/509814769e051f5e76a713a61fa1853f9fe387fa">50981476</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-16T00:10:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">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.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/6507098c97a520e0187a9e3957ce8e049f9e5dfb">6507098c</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-16T00:12:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">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.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/ae007ca1bab58f7d3cf619112ec14b60cd1f9c99">ae007ca1</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-16T00:15:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove blastdbv4-tests-filter-archs.patch
This should be unneeded, now that most issues around makeblastdb are
identified and corrected.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/6d43a7339ec9e5055d1ce04ba103e5cba72adf53">6d43a733</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-09-16T00:18:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/rules: reduce BLASTDB_LMDB_MAP_SIZE for arm64
for real this time, with drop for arm64, not amd64. >_<
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#7da704709b4a6546301e4eb1a49247877bac9a6c">
<span class="deleted-file">
−
debian/patches/blastdbv4-tests-filter-archs.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/f2babc28481c3a29407222251743c51ad0701664...6d43a7339ec9e5055d1ce04ba103e5cba72adf53#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">biopython</span> <span class="p">(</span><span class="m" style="color: #099;">1.78</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">UNRELEASED</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Added</span> <span class="n" style="color: #333;">DEP3</span> <span class="n" style="color: #333;">description</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">blastdbv4</span><span class="p">-</span><span class="n" style="color: #333;">tests</span><span class="p">-</span><span class="n" style="color: #333;">filter</span><span class="p">-</span><span class="n" style="color: #333;">archs</span><span class="p">.</span><span class="n" style="color: #333;">patch</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Removed</span><span class="p">,</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">last</span><span class="p">,</span> <span class="n" style="color: #333;">patch</span> <span class="n" style="color: #333;">working</span> <span class="n" style="color: #333;">around</span> <span class="n" style="color: #333;">makeblastd</span> <span class="n" style="color: #333;">bug</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">v5</span><span class="p">.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="mosel"> <span class="p">--</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">É</span><span class="n" style="color: #333;">tienne</span> <span class="n" style="color: #333;">Mollier</span> <span class="p"><</span><span class="n" style="color: #333;">etienne</span><span class="p">.</span><span class="n" style="color: #333;">mollier</span><span class="p">@</span><span class="n" style="color: #333;">mailoo</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span> <span class="n" style="color: #333;">Mon</span><span class="p">,</span> <span class="m" style="color: #099;">14</span> <span class="n" style="color: #333;">Sep</span> <span class="m" style="color: #099;">2020</span> <span class="m" style="color: #099;">21</span><span class="p">:</span><span class="m" style="color: #099;">28</span><span class="p">:</span><span class="m" style="color: #099;">54</span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="mosel"></span>
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<li id="7da704709b4a6546301e4eb1a49247877bac9a6c">
<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/f2babc28481c3a29407222251743c51ad0701664...6d43a7339ec9e5055d1ce04ba103e5cba72adf53#7da704709b4a6546301e4eb1a49247877bac9a6c"><strong>debian/patches/blastdbv4-tests-filter-archs.patch</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: fall back makeblastdb wrapper test to v4 on unsupported archs</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"> While makeblastdb -blastdb_version 5 is gaining stable support, under some</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"> architectures, it is still necessary to fall back to -blastdb_version 4 to be</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> able to run the test. This patch implements a way to select a list of</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> architectures to run with a blastdb v4.</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> Note: it is expected that Biopython 1.79 might test both blastdb v4 and v5.</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">Author: Étienne Mollier</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/969608</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="p">Last-Update: 2020-09-13 18:18:22 +0200</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-biopython.orig/Tests/test_NCBI_BLAST_tools.py</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-biopython/Tests/test_NCBI_BLAST_tools.py</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="p">@@ -16,6 +16,12 @@</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> import unittest</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> import re</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# makeblastdb v5 is buggy on some architectures for the moment</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+dbver = 5</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+arch_version_fallback = ["aarch64-linux-gnu"]</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if sys.implementation._multiarch in arch_version_fallback:</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ dbver = 4</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> from Bio.Application import _escape_filename</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> from Bio import MissingExternalDependencyError</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> from Bio.Blast import Applications</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="p">@@ -217,6 +224,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> global exe_names</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> cline = Applications.NcbimakeblastdbCommandline(</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> exe_names["makeblastdb"],</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ blastdb_version=dbver,</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> input_file="GenBank/NC_005816.faa",</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> dbtype="prot",</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> hash_index=True,</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="p">@@ -228,6 +236,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"> self.assertEqual(</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"> str(cline),</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"> _escape_filename(exe_names["makeblastdb"])</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ + " -blastdb_version " + str(dbver)</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"> + " -dbtype prot -in GenBank/NC_005816.faa"</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> " -parse_seqids -hash_index -max_file_sz 20MB"</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"> " -taxid 10",</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="p">@@ -263,6 +272,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"> global exe_names</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"> cline = Applications.NcbimakeblastdbCommandline(</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"> exe_names["makeblastdb"],</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ blastdb_version=dbver,</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"> input_file="GenBank/NC_005816.fna",</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"> dbtype="nucl",</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"> hash_index=True,</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"><span class="p">@@ -274,6 +284,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"> self.assertEqual(</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"> str(cline),</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"> _escape_filename(exe_names["makeblastdb"])</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ + " -blastdb_version " + str(dbver)</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"> + " -dbtype nucl -in GenBank/NC_005816.fna"</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"> " -parse_seqids -hash_index -max_file_sz 20MB"</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"> " -taxid 10",</span></pre>
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<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/f2babc28481c3a29407222251743c51ad0701664...6d43a7339ec9e5055d1ce04ba103e5cba72adf53#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,6 @@ remove_mathml-qname.patch</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">privacy_breach.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">privacy_breach_ie9.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">blastdbv4-impl.patch</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">blastdbv4-tests-filter-archs.patch</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">fix-use-of-unversioned-python.patch</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">stabilize-phyml-test.patch</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">spelling-error-in-binaries.patch</span>
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<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/f2babc28481c3a29407222251743c51ad0701664...6d43a7339ec9e5055d1ce04ba103e5cba72adf53#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,6 +34,15 @@ else</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> EXCLUDEARCHamd64=raxml_tool</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"># arm64 virtualized environment, esp. with schroot, may be too constrained for</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"># the memory allocation required by the test_NCBI_BLAST_tools. See #969608</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"># following for more details:</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"># https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=969608#40</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">ifeq ($(BUILDARCH),arm64)</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> export BLASTDB_LMDB_MAP_SIZE=20000000000</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"># avoid tests requiring data base connections if no server is running while we are doing the build</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"># This would not trigger a failure but bloats the build log with irrelevant noise</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">EXCLUDEDATABASE=BioSQL_MySQLdb BioSQL_psycopg2</span>
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<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/f2babc28481c3a29407222251743c51ad0701664...6d43a7339ec9e5055d1ce04ba103e5cba72adf53#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,6 +27,15 @@ if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" != "amd64" ]; then</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> test_BWA_tool.py</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># arm64 virtualized environment, esp. with schroot, may be too constrained for</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># the memory allocation required by the test_NCBI_BLAST_tools. See #969608</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># following for more details:</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=969608#40</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>dpkg-architecture <span class="nt" style="color: #000080;">-qDEB_BUILD_ARCH</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">"arm64"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">BLASTDB_LMDB_MAP_SIZE</span><span class="o" style="font-weight: 600;">=</span>20000000000</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">export </span>BLASTDB_LMDB_MAP_SIZE</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># execute tests</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">################################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># in the Debian package dialign it is not needed to set DIALIGN2_DIR but the</span></span>
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