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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/fieldbioinformatics">Debian Med / fieldbioinformatics</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/fieldbioinformatics/-/commit/0a85c1b257a6119937875df5c7a5a9a8878d0ee9">0a85c1b2</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-06-22T14:19:15+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Step forward with some autopkgtest. Please note: The current test script is requiring downloading data which is not possible at build time. But as far as I learned it can be done in autopkgtest. But it should be tested on a local machine first
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#24c7628a3d977662c64013a82c189854e9550f8c">
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+
debian/fieldbioinformatics-examples.install
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<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="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/fieldbioinformatics/-/commit/0a85c1b257a6119937875df5c7a5a9a8878d0ee9#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" 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">@@ -3,14 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Malihe Asemani <ml.asemani@gmail.com></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (=12), python3<span class="idiff left right">-all</span>, python3-setuptools, dh-python</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (=12), python3, python3-setuptools, dh-python</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Standards-Version: 4.1.3</span>
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<td class="diff-line-num new_line" data-linenumber="8" 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">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/fieldbioinformatics</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/fieldbioinformatics.git</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Homepage: https://github.com/artic-network/fieldbioinformatics</span>
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<td class="diff-line-num old_line" data-linenumber="11" 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">
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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">Package: fieldbioinformatics</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Architecture: a<span class="idiff left right">ny</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Architecture: a<span class="idiff left right">ll</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Description: pipeline for working with virus sequencing data sequenced with nanopore</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" 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="diff-line-num unfold js-unfold new_line" data-linenumber="19" 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">@@ -19,3 +19,17 @@ Description: pipeline for working with virus sequencing data sequenced with nano</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> protocol to take the output from the sequencing protocol to consensus</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> genome sequences. Includes basecalling, de-multiplexing, mapping, polishing</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> and consensus generation.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Package: fieldbioinformatics-examples</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Enhances: fieldbioinformatics</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Description: pipeline for working with virus sequencing data sequenced with nanopore (examples)</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> This is the ARTIC bioinformatics pipeline for working with virus sequencing</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> data, sequenced with nanopore. Nanopore is a complete bioinformatics</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> protocol to take the output from the sequencing protocol to consensus</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> genome sequences. Includes basecalling, de-multiplexing, mapping, polishing</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> and consensus generation.</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> This package contains some example data.</span></pre>
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<a href="https://salsa.debian.org/med-team/fieldbioinformatics/-/commit/0a85c1b257a6119937875df5c7a5a9a8878d0ee9#24c7628a3d977662c64013a82c189854e9550f8c"><strong>debian/fieldbioinformatics-examples.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">fieldbioinformatics</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span></span></pre>
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<a href="https://salsa.debian.org/med-team/fieldbioinformatics/-/commit/0a85c1b257a6119937875df5c7a5a9a8878d0ee9#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">@@ -21,8 +21,8 @@ export PYBUILD_NAME=fieldbioinformatics</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"><span class="idiff left right">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"><span class="idiff left right">#override_dh_auto_test:</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"><span class="idiff left right">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"><span class="idiff left right"># do_stuff_for_testing</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"><span class="idiff left right">#</span>endif</span></pre>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"><span class="idiff left right">override_dh_auto_test:</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"><span class="idiff left right">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"><span class="idiff left right"> echo "Test is downloading extra data and thus can not be running here"</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"><span class="idiff left right"> # ./test-runner.sh nanopolish</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">endif</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/fieldbioinformatics/-/commit/0a85c1b257a6119937875df5c7a5a9a8878d0ee9#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#PACKAGENAME#</span></span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="idiff left right">fieldbioinformatics</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" 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="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</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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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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12
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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13
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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14
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,4 +13,6 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#do_stuff_to_test_package#</span></span></pre>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">bash ./test-runner.sh nanopolish</span></pre>
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