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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/tombo">Debian Med / tombo</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/tombo/-/commit/160286781eb4373ae63afcf7b9a84a89c9700a4f">16028678</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-06-15T22:39:56+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add (Build-)Depends until mappy is really needed
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<h4>5 changed files:</h4>
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<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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<a href="#1d2a6c0c9f28e89358b99c47654277b227c6ce5b">
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+
debian/patches/no_future.patch
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+
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/tombo/-/commit/160286781eb4373ae63afcf7b9a84a89c9700a4f#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">tombo (1.5.1-1) 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"> * Initial release (Closes: #<bug>)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> TODO: python3-mappy (from minimap2)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> blocked by https://salsa.debian.org/med-team/ksw2</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"> -- Andreas Tille <tille@debian.org> Mon, 15 Jun 2020 11:13:59 +0200</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/tombo/-/commit/160286781eb4373ae63afcf7b9a84a89c9700a4f#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">@@ -3,7 +3,13 @@ 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: Andreas Tille <tille@debian.org></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 (= 13)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> python3-all-dev,</span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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="LC10" class="line" lang="plaintext"> cython3,</span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext"> python3-numpy,</span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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="LC12" class="line" lang="plaintext"> python3-tqdm</span>
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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/tombo</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/tombo.git</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">@@ -12,7 +18,13 @@ Homepage: https://github.com/nanoporetech/tombo</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Package: tombo</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Depends: ${shlibs: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="LC21" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> python3-h5py,</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> python3-numpy,</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> python3-scipy,</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> python3-mappy,</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> python3-tqdm</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Description: identification of modified nucleotides from raw nanopore sequencing data</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> Tombo is a suite of tools primarily for the identification of modified</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> nucleotides from nanopore sequencing data. Tombo also provides tools for</span>
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<li id="1d2a6c0c9f28e89358b99c47654277b227c6ce5b">
<a href="https://salsa.debian.org/med-team/tombo/-/commit/160286781eb4373ae63afcf7b9a84a89c9700a4f#1d2a6c0c9f28e89358b99c47654277b227c6ce5b"><strong>debian/patches/no_future.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -1,4 +1,3 @@</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import unicode_literals</span></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"> import os</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -58,7 +57,7 @@</span> setup(</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> version = __version__,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> packages = ["tombo"],</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> install_requires = ['h5py', 'numpy', 'scipy', 'cython',</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;">- 'setuptools >= 18.0', 'mappy >= 2.10', 'future', 'tqdm'],</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;">+ 'setuptools >= 18.0', 'mappy >= 2.10', 'tqdm'],</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> extras_require={'full':extras_require},</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> author = "Marcus Stoiber",</span></pre>
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<a href="https://salsa.debian.org/med-team/tombo/-/commit/160286781eb4373ae63afcf7b9a84a89c9700a4f#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">no_future.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/tombo/-/commit/160286781eb4373ae63afcf7b9a84a89c9700a4f#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">@@ -18,14 +18,10 @@ include /usr/share/dpkg/default.mk</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> dh $@<span class="idiff left right"> --with python3 --buildsystem=pybuild</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">#override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"># do_stuff_for_testing</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">#endif</span></pre>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">#get-orig-source:</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"># . debian/get-orig-source</span></pre>
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