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<h3>
Sascha Steinbiss pushed to branch master
at <a href="https://salsa.debian.org/med-team/hhsuite">Debian Med / hhsuite</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/hhsuite/-/commit/4596d8d1546690a8f9c00294e73e8cac3f56ee72">4596d8d1</a></strong>
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<span>by Sascha Steinbiss</span>
<i>at 2021-11-20T13:16:20+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">make sure tests do not overwrite example files
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<h4>2 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#f08eb90f999e1167db4ecd41e4ca62ae7b0ce6f2">
debian/patches/test_without_mpi
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/hhsuite/-/commit/4596d8d1546690a8f9c00294e73e8cac3f56ee72#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hhsuite (3.3.0+ds-6) 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"> * Adjust patch to not overwrite example files in tests.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> This caused a modified file to be packaged containing the build time,</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> leaving the package unreproducible (and is likely not intended here?)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Sascha Steinbiss <satta@debian.org> Sat, 20 Nov 2021 13:14:10 +0100</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">hhsuite (3.3.0+ds-5) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Fix watchfile to detect new versions on github</span>
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<li id="f08eb90f999e1167db4ecd41e4ca62ae7b0ce6f2">
<a href="https://salsa.debian.org/med-team/hhsuite/-/commit/4596d8d1546690a8f9c00294e73e8cac3f56ee72#f08eb90f999e1167db4ecd41e4ca62ae7b0ce6f2"><strong>debian/patches/test_without_mpi</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">@@ -3,17 +3,18 @@ Date: Tue, 1 Sep 2020 22:23:03 +0200</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Subject: Make test script work without MPI</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Origin: upstream, https://github.com/soedinglab/hh-suite/commit/c296b369410900b193a6b74f0554ac90ccfd7d08</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">hhsuite.orig</span>/data/test.sh</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">hhsuite</span>/data/test.sh</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -2,36 +2,<span class="idiff left right">49</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/data/test.sh</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/data/test.sh</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -2,36 +2,<span class="idiff left right">51</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> rm -f single* search_* blits_*</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> </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;">-hhalign -i query.a3m -t query.a3m</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;">+if $(command -v "ffindex_apply_mpi" >/dev/null 2>&1); then</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;">+ MPI=1</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+fi</span></span>
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<pre style="margin: 0;"> <span id="LC16" 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="LC16" class="line" lang="diff"><span class="idiff left right"> </span>hhalign -i query.a3m -t query.a3m</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;"><span class="idiff left">+</span>hhalign -i query.a3m <span class="idiff right">-o result.hhr </span>-t query.a3m</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> ffindex_build -s single.ffdata single.ffindex query.a3m</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> </span>
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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">@@ -44,7 +45,8 @@ Forwarded: not-needed</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cstranslate -i single -o single_cs219 -b -x 0.3 -c 4 -I a3m -f</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+fi</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"> hhblits -i query.a3m -d single -blasttab blits_app_res -n 1</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-hhblits -i query.a3m -d single -blasttab blits_app_res -n 1</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+hhblits -i query.a3m -o result.hhr -d single -blasttab blits_app_res -n 1</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> hhblits_omp -i single -d single -blasttab blits_omp_res -n 1</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-mpirun -np 2 hhblits_mpi -i single -d single -blasttab blits_mpi_res -n 1</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -55,7 +57,8 @@ Forwarded: not-needed</td>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ diff <(tr -d '\000' < blits_mpi_res.ffdata) blits_app_res</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+fi</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"> hhsearch -i query.a3m -d single -blasttab search_app_res</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-hhsearch -i query.a3m -d single -blasttab search_app_res</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+hhsearch -i query.a3m -o result.hhr -d single -blasttab search_app_res</span></span>
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59
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> hhsearch_omp -i single -d single -blasttab search_omp_res</span>
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60
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-mpirun -np 2 hhsearch_mpi -i single -d single -blasttab search_mpi_res</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -68,3 +71,5 @@ Forwarded: not-needed</td>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+fi</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="diff"> diff <(cut -f 1-10,12 blits_app_res) <(cut -f 1-10,12 search_app_res)</span>
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<pre style="margin: 0;">+<span id="LC74" 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="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+rm -f result.hhr</span></span></pre>
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