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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/community/2020-covid19-hackathon">Debian Med / community / 2020-covid19-hackathon</a>
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Commits:
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<strong><a href="https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/commit/d0dd9e830a6fa817f9218e1fae9bb9dd03bc8373">d0dd9e83</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-06-04T15:26:47+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Preparation for announcement mail of second Debian Med hackathon
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<h4>1 changed file:</h4>
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202006_Debian-Med_hackathon.md
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<h4>Changes:</h4>
<li id="1f877f6f9f0b5b2d56683e830e0aee4412164ff9">
<a href="https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/commit/d0dd9e830a6fa817f9218e1fae9bb9dd03bc8373#1f877f6f9f0b5b2d56683e830e0aee4412164ff9"><strong>202006_Debian-Med_hackathon.md</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Second Debian Med COVID-19 hackathon</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown">Planning the second Debian-Med COVID-19 hackathon</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown">Dear Debian Community,</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown">Debian Med joined the virtual (online) <span class="p">[</span><span class="nv" style="color: #008080;">COVID-19 Biohackathon from April 5-11</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/virtual-biohackathons/covid-19-bh20</span><span class="p">)</span>,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p">2020.</span> We considered the outcome a great success in terms of</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown">the approached tasks, the new members we gained and the support</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown">of Debian infrastructure teams (namely the ftpmaster team).</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown">COVID-19 is not over and the Debian Med team wants to do another</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown">week of hackathon to continue with this great success. We want</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown">to do this from June 15th to June 21th 2020.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown">As in the first sprint most tasks do not require any knowledge of biology or medicine, and all</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown">types of contributions are welcome: bug triage, testing, documentation,</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown">CI, translations, packaging, and code contributions.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="p">1.</span> <span class="p">[</span><span class="nv" style="color: #008080;">Debian related bugs</span><span class="p">](</span><span class="sx" style="color: #d14;">https://blends.debian.org/med/bugs/covid-19.html</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="p">2.</span> <span class="p">[</span><span class="nv" style="color: #008080;">Software awaiting packaging</span><span class="p">](</span><span class="sx" style="color: #d14;">https://blends.debian.org/med/tasks/covid-19</span><span class="p">)</span>, please</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown">respond to the RFP with your intent so we don't duplicate work</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="p">3.</span> You can also contribute directly to the upstream packages, linked</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown">from the <span class="p">[</span><span class="nv" style="color: #008080;">Debian Med COVID-19 task page</span><span class="p">](</span><span class="sx" style="color: #d14;">https://blends.debian.org/med/tasks/covid-19</span><span class="p">)</span>. Note:</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown">many biomedical software packages are quite resource limited, even</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown">compared to a typical FOSS project. Please be kind to the upstream</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown">author/maintainers and realize that they may have limited resources to</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown">review your contribution. Triaging open issues and opening pull requests</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown">to fix problems is likely to be more useful than nitpicking their coding</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown">style.</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"><span class="p">4.</span> Architectures/porting: Please focus on amd64, as it is the primary</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown">architecture for biomedical software. A secondary tier would be arm64 /</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown">ppc64el / s390x (but beware the endian-related issues on s390x). From a</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown">free/open hardware perspective it would be great to see more riscv64</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown">support, but that is not a priority right now</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"><span class="p">5.</span> The Debian Med team is also trying to <span class="p">[</span><span class="nv" style="color: #008080;">improve the availability of</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"><span class="nv" style="color: #008080;">automated biomedical pipelines/workflows</span><span class="p">](</span><span class="sx" style="color: #d14;">https://doi.org/10.1007/s41019-017-0050-4</span><span class="p">)</span> using the</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown">Common Workflow Language open standard. The reference implementation of</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown">CWL is written in Python and there are many <span class="p">[</span><span class="nv" style="color: #008080;">open issues ready for work</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"><span class="nv" style="color: #008080;">that don't require any biomedical background</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/common-workflow-language/cwltool/issues</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"><span class="p">6.</span> It is very easy to contribute to Debian Med team. We have a lowNMU</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown">policy for all our packages. Merge requests on Salsa are usually</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown">processed quickly (but please ping some of the latest Uploaders of the</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown">package to make sure it will be noticed). Even better if you ask for</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown">membership to the team and push directly to the salsa repository.</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="p">7.</span> The <span class="p">[</span><span class="nv" style="color: #008080;">debian-med-team-policy</span><span class="p">](</span><span class="sx" style="color: #d14;">https://med-team.pages.debian.net/policy/</span><span class="p">)</span> should answer all questions how to</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown">contribute.</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"><span class="p">8.</span> There is a <span class="p">[</span><span class="nv" style="color: #008080;">work-needed wiki</span><span class="p">](</span><span class="sx" style="color: #d14;">https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/COVID-19-Hackathon-packages-needing-work</span><span class="p">)</span> that will help keep track of who is working on which projects.</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown"><span class="p">9.</span> There is also a <span class="p">[</span><span class="nv" style="color: #008080;">NEW requests wiki</span><span class="p">](</span><span class="sx" style="color: #d14;">https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/NEW-Requests</span><span class="p">)</span> where we can request expedited NEW processing to support this effort.</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown">During the hackathon we will coordinate ourselves via the the Salsa coordination page, Debian Med mailing list and IRC:</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"><span class="p">*</span> https://salsa.debian.org/med-team/community/2020-covid19-hackathon/-/wikis/Covid-19-hackathon</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"><span class="p">*</span> https://lists.debian.org/debian-med/</span>
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<td class="diff-line-num new new_line" data-linenumber="63" 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="LC63" class="line" lang="markdown"><span class="p">*</span> https://wiki.debian.org/IRC</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown"><span class="p">*</span> irc://irc.debian.org/debian-med</span>
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<td class="diff-line-num new new_line" data-linenumber="65" 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="LC65" class="line" lang="markdown"><span class="p">*</span> https://jitsi.debian.social/DebianMedCovid19</span></pre>
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