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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/simka">Debian Med / simka</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/simka/-/commit/d246e494090f0dca12f57f847f9796c02903a849">d246e494</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-04-07T22:58:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">initialize changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/simka/-/commit/397541bf6466449671b2ad3a7aac29c6dfd075a7">397541bf</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-04-07T22:58:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/t/run-unit-test: remove argument from py script
The python script does not take arguments, so its use in the d/t/r
script is misleading. However the bash test script takes it properly
into account.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/simka/-/commit/ce9d02613f0687d8604f8f0a64b162e7a91ed9bc">ce9d0261</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-04-07T23:02:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add high_cores_count.patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/simka/-/commit/44be76b17010021e4f3eb343dab94b68430fe6e9">44be76b1</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-04-07T23:08:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">high_cores_count.patch dep3 header
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/simka/-/commit/f83093f768e596efc2cdf57bd593f7a977eed375">f83093f7</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-04-07T23:12:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update changelog
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#7fec5adc24a416382ded8a7faa621b345c6c7ffa">
<span class="new-file">
+
debian/patches/high_cores_count.patch
</span>
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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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/simka/-/compare/80cc29378d7f4275d7804dcb8133b2e7ab7ea826...f83093f768e596efc2cdf57bd593f7a977eed375#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">simka (1.5.3-4) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * debian/tests/run-unit-test: remove misleading argument from Python script.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Add high_cores_count.patch to fix deadlock with Python test script.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> (Closes: #986256)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Étienne Mollier <etienne.mollier@mailoo.org> Wed, 07 Apr 2021 23:08:57 +0200</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">simka (1.5.3-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Team upload.</span>
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<li id="7fec5adc24a416382ded8a7faa621b345c6c7ffa">
<a href="https://salsa.debian.org/med-team/simka/-/compare/80cc29378d7f4275d7804dcb8133b2e7ab7ea826...f83093f768e596efc2cdf57bd593f7a977eed375#7fec5adc24a416382ded8a7faa621b345c6c7ffa"><strong>debian/patches/high_cores_count.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: run tests on a single core</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> On very high cores count machines, simka may deadlock if left to using as many</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> threads as there are cores available. Parallel runs are kept for tests which</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> explicitly test the parallel aspect of the program.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> Additional flush=True are for better readability of the autopkgtest output.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Author: Étienne Mollier <etienne.mollier@mailoo.org></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Bug: https://github.com/GATB/simka/issues/20</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/cgi-bin/bugreport.cgi?bug=986256</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">Last-Update: 2021-04-07</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">---</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- simka.orig/tests/simple_test.py</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ simka/tests/simple_test.py</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -90,39 +90,39 @@</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> #test k=31 t=0</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> clear()</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print("TESTING k=31 t=0")</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-command = "simka -in simka_input.txt -out ./__results__/results_k31_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 0 -verbose 0"</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print(command)</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print("TESTING k=31 t=0", flush=True)</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+command = "simka -in simka_input.txt -out ./__results__/results_k31_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 0 -verbose 0 -nb-cores 1"</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print(command, flush=True)</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> os.system(command + suffix)</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> test_dists("results_k31_t0")</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> #test k=21 t=0</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> clear()</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print("TESTING k=21 t=0")</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-command = "simka -in simka_input.txt -out ./__results__/results_k21_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -verbose 0"</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print(command)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print("TESTING k=21 t=0", flush=True)</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+command = "simka -in simka_input.txt -out ./__results__/results_k21_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -verbose 0 -nb-cores 1"</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print(command, flush=True)</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> os.system(command + suffix)</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> test_dists("results_k21_t0")</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> #test k=31 t=2</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> clear()</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print("TESTING k=31 t=2")</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-command = "simka -in simka_input.txt -out ./__results__/results_k31_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 2 -verbose 0"</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print(command)</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print("TESTING k=31 t=2", flush=True)</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+command = "simka -in simka_input.txt -out ./__results__/results_k31_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 2 -verbose 0 -nb-cores 1"</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print(command, flush=True)</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> os.system(command + suffix)</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> test_dists("results_k31_t2")</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> #test k=21 t=2</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> clear()</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print("TESTING k=21 t=2")</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-command = "simka -in simka_input.txt -out ./__results__/results_k21_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 2 -verbose 0"</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print(command)</span></span>
</pre>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print("TESTING k=21 t=2", flush=True)</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+command = "simka -in simka_input.txt -out ./__results__/results_k21_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 2 -verbose 0 -nb-cores 1"</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="57" 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">
57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print(command, flush=True)</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> os.system(command + suffix)</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> test_dists("results_k21_t2")</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> #test resources 1</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> clear()</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print("TESTING parallelization")</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print("TESTING parallelization", flush=True)</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> command = "simka -in simka_input.txt -out ./__results__/results_resources1 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -nb-cores 20 -max-memory 4000 -verbose 0"</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> os.system(command + suffix)</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> command = "simka -in simka_input.txt -out ./__results__/results_resources2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -nb-cores 2 -max-memory 2000 -verbose 0"</span></pre>
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<a href="https://salsa.debian.org/med-team/simka/-/compare/80cc29378d7f4275d7804dcb8133b2e7ab7ea826...f83093f768e596efc2cdf57bd593f7a977eed375#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">@@ -4,3 +4,4 @@ fix_binary_path.patch</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">fix_test_path.patch</span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">2to3.patch</span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">use_debian_packaged_libraries.patch</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">high_cores_count.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/simka/-/compare/80cc29378d7f4275d7804dcb8133b2e7ab7ea826...f83093f768e596efc2cdf57bd593f7a977eed375#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">@@ -28,7 +28,7 @@ then</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"> <span class="nv" style="color: #008080;">NR_CPUS</span><span class="o" style="font-weight: 600;">=</span>8</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell">bash simple_test.sh <span class="nt" style="color: #000080;">-nb-cores</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NR_CPUS</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell">python3 simple_test.py<span class="idiff left"> </span><span class="nt" style="color: #000080;"><span class="idiff">-nb-cores</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$NR_CPUS</span></span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell">python3 simple_test.py</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"FIXME: Testing simkaMin does not work - needs more investigation"</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"FIXME: The test suite slows dramatically down when exceeding 8 cores."</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># python3 simkaMin/test_simkaMin.py</span></span></pre>
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