<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">Release v0.8</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 v0.8. Screed is a database<br style>engine capable of storing and retrieving short-read sequence data and is<br style>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 contains developer documentation for contributing to the<br style>Screed project and a code of conduct for interacting with other contributors<br style>and project maintainers. Documentation is available at<br style><a href="http://screed.readthedocs.org/en/v0.8/" style="color:rgb(65,131,196);text-decoration:none;background:transparent">http://screed.readthedocs.org/en/v0.8/</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><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 release successfully installs and passes its unit tests on Ubuntu 14.04 and the latest release of Mac OS X 10 &quot;Yosemite&quot;. It also passes the khmer acceptance tests as per the <a href="https://github.com/ged-lab/literate-resting/blob/master/kp/README.txt" style="color:rgb(65,131,196);text-decoration:none;background:transparent">eelpond testing protocol.</a></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 release of screed has renamed the &#39;accuracy&#39; attribute of read records to &#39;quality;&#39; this API change will need to be adopted by all users wanting to upgrade to this version. Unlike the khmer project, Screed is not currently under semantic versioning. It will be with the 1.0 release.</p><ul class="task-list" 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 style>Screed now has automatic compression detection via magic bit sniffing for gzip and bzip2 compressed files (from <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background:transparent">@mr-c</a> in <a href="https://github.com/ged-lab/khmer/issues/432" class="issue-link" title="screed should sniff for gzip/bz2 files by magic number not by file extension" style="color:rgb(65,131,196);text-decoration:none;background:transparent">ged-lab/khmer#432</a>)</li><li style>Screed now supports streaming of uncompressed FASTA and FASTQ formatted nucleotide sequence data. bzip2 compressed FASTA and FASTQ formatted nucleotide sequence data can also be streamed but not gzip compressed FASTA and FASTQ formatted nucleotide sequence data. (from <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background:transparent">@mr-c</a>, see <a href="https://github.com/ged-lab/khmer/issues/633" class="issue-link" title="normalize-by-median.py does not accept reads on the stdin" style="color:rgb(65,131,196);text-decoration:none;background:transparent">ged-lab/khmer#633</a>)</li><li style>Screed now has a Changelog, developer documentation and a code of conduct (from <a href="https://github.com/ctb" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background:transparent">@ctb</a>,<a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background:transparent">@mr-c</a>, <a href="https://github.com/bocajnotnef" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background:transparent">@bocajnotnef</a> in <a href="https://github.com/ged-lab/khmer/issues/625" class="issue-link" title="Bring screed up to date" style="color:rgb(65,131,196);text-decoration:none;background:transparent">ged-lab/khmer#625</a>)</li><li style>Versions are now autogenerated using git tags via Versioneer (from <a href="https://github.com/bocajnotnef" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background:transparent">@bocajnotnef</a> in<a href="https://github.com/ged-lab/screed/commit/cadceb52b062f9c7fb85015f948df76c8acbc965" class="commit-link" style="color:rgb(65,131,196);text-decoration:none;background:transparent"><tt 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)">cadceb5</tt></a>)</li><li style>Documentation is now autogenerated using Doxygen (from <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background:transparent">@mr-c</a> in <a href="https://github.com/ged-lab/screed/commit/d8ed05b537f7ac0131ea1003713a8f15a611251f" class="commit-link" style="color:rgb(65,131,196);text-decoration:none;background:transparent"><tt 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)">d8ed05b</tt></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">Notable bugs fixed/issues closed:</h2><ul class="task-list" 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 style>A khmer script was not accepting reads on the stdin <a href="https://github.com/ged-lab/khmer/issues/633" class="issue-link" title="normalize-by-median.py does not accept reads on the stdin" style="color:rgb(65,131,196);text-decoration:none;background:transparent">ged-lab/khmer#633</a> by <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background:transparent">@mr-c</a></li><li style>screed returning the wrong version and breaking dev installs <a href="https://github.com/ged-lab/khmer/issues/803" class="issue-link" title="screed getting wrong version; breaking new dev installs" style="color:rgb(65,131,196);text-decoration:none;background:transparent">ged-lab/khmer#803</a> by <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background:transparent">@mr-c</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 class="task-list" 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 style>Screed records cannot be sliced requiring un-Pythonic techniques to achieve the same behavior. This will be included in a future release. This is being tracked in <a href="https://github.com/ged-lab/khmer/issues/768" class="issue-link" title="Allow slicing of screed records" style="color:rgb(65,131,196);text-decoration:none;background:transparent">ged-lab/khmer#768</a></li><li style>Screed self-tests do not use a temporary directory which causes tests run from package-based installs to fail. This is being tracked in <a href="https://github.com/ged-lab/khmer/issues/748" class="issue-link" title="[screed] tests don&#39;t use temporary directory; fail if screed/tests/ directory is read-only" style="color:rgb(65,131,196);text-decoration:none;background:transparent">ged-lab/khmer#748</a></li><li style>Screed does not support gzip file streaming. This is an issue with Python 2.x and will likely<em style>not</em> be fixed in future releases. This is being tracked in <a href="https://github.com/ged-lab/khmer/issues/700" class="issue-link" title="state of streaming I/O in khmer, mark 2" style="color:rgb(65,131,196);text-decoration:none;background:transparent">ged-lab/khmer#700</a></li><li style>Screed is overly tolerant of spaces in fast{a,q} which is against spec. This is being tracked in<a href="https://github.com/ged-lab/khmer/issues/108" class="issue-link" title="screed is too tolerant of spaces in FASTQ files" style="color:rgb(65,131,196);text-decoration:none;background:transparent">ged-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;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"><a href="https://github.com/bocajnotnef" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background:transparent">@bocajnotnef</a> <a href="https://github.com/mr-c" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background:transparent">@mr-c</a> <a href="https://github.com/brtaylor92" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background:transparent">@brtaylor92</a> <a href="https://github.com/wrightmhw" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background:transparent">@wrightmhw</a> <a href="https://github.com/kdmurray91" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background:transparent">@kdmurray91</a> <a href="https://github.com/luizirber" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background:transparent">@luizirber</a> <a href="https://github.com/ctb" class="user-mention" style="color:rgb(51,51,51);text-decoration:none;font-weight:bold;white-space:nowrap;background:transparent">@ctb</a></p></div>