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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/jellyfish">Debian Med / jellyfish</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/jellyfish/commit/2d410647cf509988d95efd9c319102dc64f850ce">2d410647</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-09-21T06:45:39Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop python3-dna-jellyfish package since the Python module had issues in build process
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<strong><a href="https://salsa.debian.org/med-team/jellyfish/commit/6e0840884bea5d162b9dfd75812d66c99820976b">6e084088</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-09-21T06:58:28Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
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<h4>4 changed files:</h4>
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debian/NEWS.Debian
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="cd17ac7b86c178cbc1654c388dec4bb7b211db49">
<a href="https://salsa.debian.org/med-team/jellyfish/compare/69f40959442997142e115c4634999724d71f3963...6e0840884bea5d162b9dfd75812d66c99820976b#cd17ac7b86c178cbc1654c388dec4bb7b211db49"><strong>debian/NEWS.Debian</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">jellyfish (2.2.10-1) unstable; 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"> The the binary package python3-dna-jellyfish containing the Python module</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> was dropped due to issues in the build process which is documented in this</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> mail to the developers list</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"> https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-September/065549.html</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"> I'd happily re-introduce the Python module if anybody will provide a</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> patch for a successful build.</span>
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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"> -- Andreas Tille <tille@debian.org> Mon, 03 Sep 2018 11:57:00 +0200</span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/jellyfish/compare/69f40959442997142e115c4634999724d71f3963...6e0840884bea5d162b9dfd75812d66c99820976b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">jellyfish (2.2.10-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">jellyfish (2.2.10-1) <span class="idiff left right">unstable</span>; 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"> * New upstream version</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,8 +8,10 @@ jellyfish (2.2.10-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> * Catch exceptions by reference</span>
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<td class="diff-line-num old_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> * Do not replace random '-L' strings in command line</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> Closes: #907819</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Drop python3-dna-jellyfish package since the Python module had issues in</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> build process and nobody seemed to be interested to help solving theses</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Mon, 03 Sep 2018 08:34:22</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Fri, 21 Sep 2018 08:45:53</span> +0200</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">jellyfish (2.2.8-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/jellyfish/compare/69f40959442997142e115c4634999724d71f3963...6e0840884bea5d162b9dfd75812d66c99820976b#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">@@ -92,28 +92,28 @@ Description: count k-mers in DNA sequences (development files of jellyfish)</td>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext"> This package contains the development files (static library and</span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"> header files)</span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext">Package: python3-dna-jellyfish</span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="plaintext">Section: python</span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="plaintext"> ${shlibs:Depends}</span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext">Description: count k-mers in DNA sequences (Python bindings of jellyfish)</span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext"> JELLYFISH is a tool for fast, memory-efficient counting of k-mers in</span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="plaintext"> DNA. A k-mer is a substring of length k, and counting the occurrences</span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="plaintext"> of all such substrings is a central step in many analyses of DNA</span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="plaintext"> sequence. JELLYFISH can count k-mers using an order of magnitude less</span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext"> memory and an order of magnitude faster than other k-mer counting</span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="plaintext"> packages by using an efficient encoding of a hash table and by</span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext"> exploiting the "compare-and-swap" CPU instruction to increase</span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext"> parallelism.</span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext"> .</span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext"> JELLYFISH is a command-line program that reads FASTA and multi-FASTA</span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="plaintext"> files containing DNA sequences. It outputs its k-mer counts in an</span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext"> binary format, which can be translated into a human-readable text</span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="plaintext"> format using the "jellyfish dump" command.</span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="plaintext"> .</span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="plaintext"> This package contains the Python bindings of jellyfish.</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"><span class="idiff left right">#</span>Package: python3-dna-jellyfish</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"><span class="idiff left right">#</span>Architecture: any</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"><span class="idiff left right">#</span>Section: python</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"><span class="idiff left right">#</span>Depends: ${python3:Depends},</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"><span class="idiff left right">#</span> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"><span class="idiff left right">#</span> ${shlibs:Depends}</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"><span class="idiff left right">#</span>Description: count k-mers in DNA sequences (Python bindings of jellyfish)</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"><span class="idiff left right">#</span> JELLYFISH is a tool for fast, memory-efficient counting of k-mers in</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"><span class="idiff left right">#</span> DNA. A k-mer is a substring of length k, and counting the occurrences</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"><span class="idiff left right">#</span> of all such substrings is a central step in many analyses of DNA</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"><span class="idiff left right">#</span> sequence. JELLYFISH can count k-mers using an order of magnitude less</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"><span class="idiff left right">#</span> memory and an order of magnitude faster than other k-mer counting</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"><span class="idiff left right">#</span> packages by using an efficient encoding of a hash table and by</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"><span class="idiff left right">#</span> exploiting the "compare-and-swap" CPU instruction to increase</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"><span class="idiff left right">#</span> parallelism.</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"><span class="idiff left right">#</span> .</span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"><span class="idiff left right">#</span> JELLYFISH is a command-line program that reads FASTA and multi-FASTA</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"><span class="idiff left right">#</span> files containing DNA sequences. It outputs its k-mer counts in an</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"><span class="idiff left right">#</span> binary format, which can be translated into a human-readable text</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"><span class="idiff left right">#</span> format using the "jellyfish dump" command.</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"><span class="idiff left right">#</span> .</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"><span class="idiff left right">#</span> This package contains the Python bindings of jellyfish.</span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="plaintext">Package: libjellyfish-perl</span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext">Architecture: any</span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/jellyfish/compare/69f40959442997142e115c4634999724d71f3963...6e0840884bea5d162b9dfd75812d66c99820976b#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">@@ -14,22 +14,22 @@ export PERL_MM_OPT=INSTALLDIRS=vendor</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">export PYBUILD_BUILD_ARGS=build_ext --rpath "${CURDIR}/debian/tmp/usr/lib/${DEB_HOST_MULTIARCH}"</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> dh $@ --with python3</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> dh $@ <span class="idiff left right"># </span>--with python3</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">override_dh_auto_install:</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> dh_auto_install -- install-data</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> # dh_install -X*.a -X*.la -Xpkgconfig</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> dh_install -ppython3-dna-jellyfish</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> pybuild -d swig/python --name dna-jellyfish</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"># pybuild -d swig/python --name dna-jellyfish --disable test/python3</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"># pybuild -d swig/python --name dna-jellyfish --test --test-args "${CURDIR}/swig/python/ test_string_mers.py"</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"># pybuild -d swig/python --name dna-jellyfish --test --test-args "${CURDIR}/swig/python/ test_hash_counter.py"</span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> chrpath --delete debian/*/usr/lib/python*/dist-packages/_dna_jellyfish*.so</span>
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<td class="diff-line-num new new_line" data-linenumber="24" 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">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"><span class="idiff left right">#</span> dh_install -ppython3-dna-jellyfish</span>
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<td class="diff-line-num new new_line" data-linenumber="25" 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">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"><span class="idiff left right">#</span> pybuild -d swig/python --name dna-jellyfish</span>
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<td class="diff-line-num new new_line" data-linenumber="26" 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">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">#<span class="idiff left right">#</span> pybuild -d swig/python --name dna-jellyfish --disable test/python3</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">#<span class="idiff left right">#</span> pybuild -d swig/python --name dna-jellyfish --test --test-args "${CURDIR}/swig/python/ test_string_mers.py"</span>
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<td class="diff-line-num new new_line" data-linenumber="28" 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">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">#<span class="idiff left right">#</span> pybuild -d swig/python --name dna-jellyfish --test --test-args "${CURDIR}/swig/python/ test_hash_counter.py"</span>
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<td class="diff-line-num new new_line" data-linenumber="29" 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">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"><span class="idiff left right">#</span> chrpath --delete debian/*/usr/lib/python*/dist-packages/_dna_jellyfish*.so</span>
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> </span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> dh_auto_configure --sourcedirectory=swig/perl5</span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"># dh_auto_configure --sourcedirectory=swig/python</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">#<span class="idiff left right">#</span> dh_auto_configure --sourcedirectory=swig/python</span>
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> dh_auto_build --sourcedirectory=swig/perl5</span>
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<td class="diff-line-num old_line" data-linenumber="34" 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">
34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> dh_auto_install --sourcedirectory=swig/perl5</span>
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> chrpath --delete debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so</span>
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