<div dir="ltr"><h1 style="font-size:2.25em;margin-right:0px;margin-bottom:16px;margin-left:0px;line-height:1.2;padding-bottom:0.3em;border-bottom-width:1px;border-bottom-style:solid;border-bottom-color:rgb(238,238,238);color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;margin-top:0px!important">Screed Release v0.9</h1><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">We are pleased to announce the release of Screed v0.9. Screed is a database<br>engine capable of storing and retrieving short-read sequence data and is<br>designed to be fast and adaptable to different sequence file formats.</p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">This version of Screed features Python 3 syntax with compatibility with Python 2. Additional changes have broken backwards compatibility in several small ways in preparation for our 1.0 release and adoption of strict semantic versioning from there on out.</p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">It is also the first release since our move to the University of Davis, California and also under our new name, the Lab for Data Intensive Biology.</p><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">Documentation is available at <a href="http://screed.readthedocs.org/en/v0.9/" style="color:rgb(64,120,192);text-decoration:none;background-color:transparent" target="_blank">http://screed.readthedocs.org/en/v0.9/</a></p><h2 style="margin-top:1em;margin-bottom:16px;line-height:1.225;font-size:1.75em;padding-bottom:0.3em;border-bottom-width:1px;border-bottom-style:solid;border-bottom-color:rgb(238,238,238);color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif">New items of note:</h2><ul style="padding:0px 0px 0px 2em;margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px"><li><p style="margin-top:16px;margin-bottom:16px">Now a primarily Python 3 codebase with Python 2 compatibility. <a href="https://github.com/dib-lab/screed/pull/41" title="Add missing close method to screed.open" style="color:rgb(64,120,192);text-decoration:none;background-color:transparent" target="_blank">#41</a> <a href="https://github.com/luizirber" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent" target="_blank">@luizirber</a> &amp; <a href="https://github.com/mr-c" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent" target="_blank">@mr-c</a></p></li><li><p style="margin-top:16px;margin-bottom:16px">Tests now correctly run using temporary directories and the test data is now shipped allowing the tests to be run after installation. <a href="https://github.com/dib-lab/screed/pull/30" title="Make screed tests use tmpdirs where applicable, addresses khmer/748" style="color:rgb(64,120,192);text-decoration:none;background-color:transparent" target="_blank">#30</a> <a href="https://github.com/bocajnotnef" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent" target="_blank">@bocajnotnef</a> <a href="https://github.com/dib-lab/screed/pull/40" title="ship relocated test data &amp; unbreak Record rename" style="color:rgb(64,120,192);text-decoration:none;background-color:transparent" target="_blank">#40</a> <a href="https://github.com/mr-c" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent" target="_blank">@mr-c</a></p></li><li>The private method <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">screed/screedRecord._screed_record_dict()</code> has been renamed to <code style="font-family:Consolas,&#39;Liberation Mono&#39;,Menlo,Courier,monospace;font-size:13.6000003814697px;padding:0.2em 0px;margin:0px;border-radius:3px;background-color:rgba(0,0,0,0.0392157)">screed.screedRecord.Record()</code>. This is <strong>not</strong> a backwards compatible change. <a href="https://github.com/dib-lab/screed/pull/35" title="renamed _screed_record_dict()" style="color:rgb(64,120,1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rthomas</a></li></ul><h2 style="margin-top:1em;margin-bottom:16px;line-height:1.225;font-size:1.75em;padding-bottom:0.3em;border-bottom-width:1px;border-bottom-style:solid;border-bottom-color:rgb(238,238,238);color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif">Known Issues</h2><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px">These are all pre-existing</p><ul style="padding:0px 0px 0px 2em;margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px"><li>Screed does not support gzip file streaming. This is an issue with Python 2.x and will likely<em>not</em> be fixed in future releases. This is being tracked in <a href="https://github.com/dib-lab/khmer/issues/700" title="state of streaming I/O in khmer, mark 2" style="color:rgb(64,120,192);text-decoration:none;background-color:transparent" target="_blank">dib-lab/khmer#700</a></li><li>Screed is overly tolerant of spaces in fast{a,q} which is against spec. This is being tracked in<a href="https://github.com/dib-lab/khmer/issues/108" title="screed is too tolerant of spaces in FASTQ files" style="color:rgb(64,120,192);text-decoration:none;background-color:transparent" target="_blank">dib-lab/khmer#108</a></li></ul><h2 style="margin-top:1em;margin-bottom:16px;line-height:1.225;font-size:1.75em;padding-bottom:0.3em;border-bottom-width:1px;border-bottom-style:solid;border-bottom-color:rgb(238,238,238);color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif">Contributors</h2><p style="margin-top:0px;margin-bottom:16px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px"><a href="https://github.com/luizirber" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent" target="_blank">@luizirber</a> <a href="https://github.com/mr-c" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent" target="_blank">@mr-c</a> <a href="https://github.com/bocajnotnef" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent" target="_blank">@bocajnotnef</a> <a href="https://github.com/ctb" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent" target="_blank">@ctb</a> *<a href="https://github.com/proteasome" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent" target="_blank">@proteasome</a> *<a href="https://github.com/anotherthomas" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent" target="_blank">@anotherthomas</a> *<a href="https://github.com/sguermond" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background-color:transparent" target="_blank">@sguermond</a></p><p style="margin-top:0px;color:rgb(51,51,51);font-family:&#39;Helvetica Neue&#39;,Helvetica,&#39;Segoe UI&#39;,Arial,freesans,sans-serif;font-size:16px;line-height:25.6000003814697px;margin-bottom:0px!important">* Indicates new contributors</p><br clear="all"><div><br></div>-- <br><div><div dir="ltr"><font face="courier new, monospace"><span style="font-size:small">Michael R. Crusoe: Programmer &amp; Bioinformatician </span><a href="mailto:mcrusoe@msu.edu" style="color:rgb(17,85,204);font-size:small" target="_blank">crusoe@ucdavis.edu</a><br style="font-size:small"><span style="font-size:small">The lab for Data Intensive Biology; University of California, Davis</span><br style="font-size:small"><a href="https://impactstory.org/MichaelRCrusoe" style="color:rgb(17,85,204);font-size:small" target="_blank">https://impactstory.org/MichaelRCrusoe</a><font size="2"> <a href="http://twitter.com/biocrusoe" target="_blank">http://twitter.com/biocrusoe</a></font></font><br></div></div></div>