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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/toil">Debian Med / toil</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/commit/b12301687e51976fe154e778c7690a043f34f129">b1230168</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2019-01-14T08:04:55Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add/update debian/{TODO,README.source,README.debian}
</pre>
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<strong><a href="https://salsa.debian.org/med-team/toil/commit/1b603096cf70b04784a5d6d76cf7f738c03d0875">1b603096</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2019-01-14T08:04:55Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">man: symlink _toil_worker to toil
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<h4>6 changed files:</h4>
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<li class="file-stats">
<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
debian/README.Debian
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<li class="file-stats">
<a href="#cf9802e192b48f765b1b5c8268d550d89c933053">
debian/README.source
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<li class="file-stats">
<a href="#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
<span class="new-file">
+
debian/TODO
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</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#8349ebd0c596ef9478eb284b6a482b10861b7531">
<span class="new-file">
+
debian/links
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<h4>Changes:</h4>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/toil/compare/4028fdb2d11226d478e7296db766d4bdf8e815c0...1b603096cf70b04784a5d6d76cf7f738c03d0875#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</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">@@ -3,9 +3,6 @@ toil for Debian</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">This package is still preliminary since</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * testing is not activated</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> * it is awkward to have both python2 and python3 supported, left it with python2</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * manpages are missing</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> * dependency on cgcloud https://github.com/BD2KGenomics/cgcloud not followed which ruins tests</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="LC10" class="line" lang="plaintext">-- </span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> Steffen Moeller <moeller@debian.org> Sat, 14 Jan 2017 13:43:23 +0100</span></pre>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Sun, 13 Jan 2019 23:25:16 -0800</span></pre>
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<li id="cf9802e192b48f765b1b5c8268d550d89c933053">
<a href="https://salsa.debian.org/med-team/toil/compare/4028fdb2d11226d478e7296db766d4bdf8e815c0...1b603096cf70b04784a5d6d76cf7f738c03d0875#cf9802e192b48f765b1b5c8268d550d89c933053"><strong>debian/README.source</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">toil for Debian</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"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">The current version the package was derived from what was uploaded to the</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">pypi repository. This should be changed towards the gihub repository,</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">except for a lack of tags that are not set for the latest versions</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">available on Pypi.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">This initial package does not yet run the complete test suite as the Python3</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">compatability of toil is recent.</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="LC9" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Fri, 13 Jan 2017 15:58:18 +0100</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">The bulk of the manual testing is currently focused on the toil-cwl-runner</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">using the docker.io package.</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"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Sun, 13 Jan 2019 23:25:16 -0800</span></pre>
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<a href="https://salsa.debian.org/med-team/toil/compare/4028fdb2d11226d478e7296db766d4bdf8e815c0...1b603096cf70b04784a5d6d76cf7f738c03d0875#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba"><strong>debian/TODO</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">Ship</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">rest</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">docs</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="n" style="color: #333;">Continue</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">cherry</span><span class="p">-</span><span class="n" style="color: #333;">pick</span> <span class="n" style="color: #333;">Python3</span> <span class="n" style="color: #333;">fixes</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tests</span> <span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">upstream</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"><span class="nf" style="color: #900; font-weight: 600;">Run</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tests</span> <span class="n" style="color: #333;">at</span> <span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">build</span> <span class="n" style="color: #333;">time</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"><span class="n" style="color: #333;">Adapt</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">tests</span> <span class="n" style="color: #333;">into</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">AutoPkgTest</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel"><span class="n" style="color: #333;">Figure</span> <span class="n" style="color: #333;">out</span> <span class="n" style="color: #333;">how</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">tests</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">depends</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">functioning</span> <span class="n" style="color: #333;">Docker</span> <span class="n" style="color: #333;">service</span> <span class="n" style="color: #333;">work</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"><span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">build</span> <span class="n" style="color: #333;">time</span> <span class="p">&</span> <span class="n" style="color: #333;">AutoPkgTest</span> <span class="n" style="color: #333;">time</span> <span class="p">(</span><span class="n" style="color: #333;">needs</span> <span class="n" style="color: #333;">root</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">we</span> <span class="nf" style="color: #900; font-weight: 600;">run</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">docker</span> <span class="n" style="color: #333;">daemon</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="mosel"><span class="n" style="color: #333;">ourselves</span><span class="p">?)</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="mosel"><span class="n" style="color: #333;">Same</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">above</span> <span class="n" style="color: #333;">but</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">singularity</span><span class="p">-</span><span class="n" style="color: #333;">container</span> <span class="n" style="color: #333;">instead</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">docker</span><span class="p">.</span><span class="n" style="color: #333;">io</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">mesos</span></span>
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<a href="https://salsa.debian.org/med-team/toil/compare/4028fdb2d11226d478e7296db766d4bdf8e815c0...1b603096cf70b04784a5d6d76cf7f738c03d0875#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</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">@@ -4,6 +4,8 @@ toil (3.18.0-2) unstable; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> (Closes: #919228)</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Refined the package description, added 'Provides: cwl-runner'</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Remove the partial mesos support until python3-mesos is packaged</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Suggests: docker.io | singularity-container | docker-ce</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Added debian/TODO, updated debian/README.{debian,source}</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"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Sun, 13 Jan 2019 23:25:16 -0800</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/toil/compare/4028fdb2d11226d478e7296db766d4bdf8e815c0...1b603096cf70b04784a5d6d76cf7f738c03d0875#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -33,7 +33,7 @@ Recommends:</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> python3-libcloud</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"># for mesos support, but needs python3-mesos first</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"># python3-protobuf,</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">Suggests: python3-azure, python3-azure-storage</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">Suggests: <span class="idiff left right">docker.io | singularity-container | docker-ce, </span>python3-azure, python3-azure-storage</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">#Suggests: python-toil-doc</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">Description: cross-platform workflow engine</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> Toil is a scalable, efficient, cross-platform and easy-to-use workflow</span>
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<a href="https://salsa.debian.org/med-team/toil/compare/4028fdb2d11226d478e7296db766d4bdf8e815c0...1b603096cf70b04784a5d6d76cf7f738c03d0875#8349ebd0c596ef9478eb284b6a482b10861b7531"><strong>debian/links</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">/usr/share/man/man1/toil.1.gz /usr/share/man/man1/_toil_worker.1.gz</span></pre>
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