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<channel>
	<title>François Michonneau</title>
	<atom:link href="http://francoismichonneau.net/feed/" rel="self" type="application/rss+xml" />
	<link>http://francoismichonneau.net</link>
	<description>Sea cucumbers, marine biodiversity and informatics</description>
	<lastBuildDate>Mon, 07 May 2012 13:31:28 +0000</lastBuildDate>
	<language>en</language>
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			<item>
		<title>Offlineimap 6.4.1 and nested labels in Gmail</title>
		<link>http://francoismichonneau.net/2011/11/offlineimap-6-4-1/</link>
		<comments>http://francoismichonneau.net/2011/11/offlineimap-6-4-1/#comments</comments>
		<pubDate>Mon, 21 Nov 2011 17:51:51 +0000</pubDate>
		<dc:creator>François</dc:creator>
				<category><![CDATA[Hacking]]></category>
		<category><![CDATA[linux]]></category>
		<category><![CDATA[offlineimap]]></category>

		<guid isPermaLink="false">http://francoismichonneau.net/?p=221</guid>
		<description><![CDATA[I just upgraded to offlineimap 6.4.1 and I was getting the following error message:
&#8220;ERROR: INFINITE FOLDER CREATION DETECTED! Folder &#8216;.foo&#8217; [...]]]></description>
			<content:encoded><![CDATA[<p>I just upgraded to <a href="http://offlineimap.org" title="Offlineimap">offlineimap</a> 6.4.1 and I was getting the following error message:<br />
&#8220;ERROR: INFINITE FOLDER CREATION DETECTED! Folder &#8216;.foo&#8217; (repository &#8216;gmailLocal&#8217;) would be created as folder &#8216;/foo&#8217; (repository &#8216;gmailRemote&#8217;). The latter becomes &#8216;..foo&#8217; in return, leading to infinite folder creation cycles. SOLUTION: 1) Do set your nametrans rules on both repositories so they lead to identical names if applied back and forth. 2) Use folderfilter settings on a repository to prevent some folders from being created on the other side.&#8221;</p>
<p>It seemed a little strange that this particular folder was throwing an error message while others did not. I realized it&#8217;s because the label &#8220;foo&#8221; itself didn&#8217;t exist in my list of labels. I only had labels nested within it. In other words I had the folders &#8220;foo/bar&#8221;, &#8220;foo/bla&#8221; but I didn&#8217;t have &#8220;foo&#8221; by itself. It was working fine before I upgraded never really thought about it much before today.</p>
<p>I created the top level labels in Gmail where needed, and now everything seems to be fine.</p>
]]></content:encoded>
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		<slash:comments>5</slash:comments>
		</item>
		<item>
		<title>Happy Halloween</title>
		<link>http://francoismichonneau.net/2011/11/happy-halloween/</link>
		<comments>http://francoismichonneau.net/2011/11/happy-halloween/#comments</comments>
		<pubDate>Tue, 01 Nov 2011 18:29:13 +0000</pubDate>
		<dc:creator>François</dc:creator>
				<category><![CDATA[Photo]]></category>
		<category><![CDATA[florida]]></category>
		<category><![CDATA[spider]]></category>

		<guid isPermaLink="false">http://francoismichonneau.net/?p=214</guid>
		<description><![CDATA[


]]></description>
			<content:encoded><![CDATA[<div align="center">
<a href="http://lh6.ggpht.com/-T_3kkUWVHzw/Tq77B-4IJII/AAAAAAAACZ4/CIdExKGQmG8/s800/IMG_7086%252520%252528Modified%252520in%252520GIMP%252520Image%252520Editor%252529.JPG" title="Spider" rel="lightbox" ><img src="http://lh6.ggpht.com/-T_3kkUWVHzw/Tq77B-4IJII/AAAAAAAACZ4/CIdExKGQmG8/w400/IMG_7086%252520%252528Modified%252520in%252520GIMP%252520Image%252520Editor%252529.JPG" alt="Spider" title="Spider" class="aligncenter" width="400" /></a>
</div>
]]></content:encoded>
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		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>New paper: the éclair sea cucumber in Okinawa</title>
		<link>http://francoismichonneau.net/2011/09/new-paper-the-eclair-sea-cucumber-in-okinawa/</link>
		<comments>http://francoismichonneau.net/2011/09/new-paper-the-eclair-sea-cucumber-in-okinawa/#comments</comments>
		<pubDate>Tue, 13 Sep 2011 20:33:13 +0000</pubDate>
		<dc:creator>François</dc:creator>
				<category><![CDATA[Cukes in the news]]></category>

		<guid isPermaLink="false">http://francoismichonneau.net/?p=206</guid>
		<description><![CDATA[A new paper with our Japanese colleagues was recently published in the Biological Magazine of Okinawa. It&#8217;s the first records [...]]]></description>
			<content:encoded><![CDATA[<p>A new paper with our Japanese colleagues was recently published in the Biological Magazine of Okinawa. It&#8217;s the first records of <em>Holothuria nigralutea</em> after its original description from Western Australia. In this paper we also report that it lives on the Great Barrier Reef in Australia. It seems to me that these observations suggest that this species is much more widespread than we think. In most places, it probably lives too deep to be noticed by SCUBA divers though&#8230;</p>
<p>You can download the paper <a href="http://francoismichonneau.net/articles/Uyeno+2011.pdf" title="Uyeno et al 2011. Holothuria nigralutea in Okinawa">here</a>.</p>
<p>This paper is also the occasion to give the species its common Japanese name: the éclair sea cucumber. Look for the figure in the paper <img src='http://francoismichonneau.net/wp-includes/images/smilies/icon_smile.gif' alt=':)' class='wp-smiley' /> .</p>
<p>I also wrote a <a href="http://spinelessscience.blogspot.com/2011/05/trip-to-okinawa-1-how-do-you-tell.html">couple</a> of <a href="http://spinelessscience.blogspot.com/2011/06/trip-to-okinawa-2-how-do-you-tell.html">posts</a> a few months ago concerning this species and why we are studying it in more details.</p>
<p><a href="http://lh5.ggpht.com/-pKkcFKlghzk/TeDcIfKDOTI/AAAAAAAACRM/k53Fs02i4vU/w800/Holothuria_nigralutea_dGUOK10-6042.JPG" title="Holothuria nigralutea. Okinawa. 45m. Dorsal side." rel="lightbox" ><img src="http://lh5.ggpht.com/-pKkcFKlghzk/TeDcIfKDOTI/AAAAAAAACRM/k53Fs02i4vU/w400/Holothuria_nigralutea_dGUOK10-6042.JPG" alt="Holothuria_nigralutea_dGUOK10-6042.JPG" title="Holothuria nigralutea. Okinawa. 45m. Dorsal side." class="centered" width="400" /></a></p>
<p style="text-align: center; font-size:.8em"><i>Holothuria nigralutea</i>. Okinawa. 45m. Dorsal side.</p>
]]></content:encoded>
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		</item>
		<item>
		<title>Evolution 3 and offlineimap</title>
		<link>http://francoismichonneau.net/2011/06/evolution-3-and-offlineimap/</link>
		<comments>http://francoismichonneau.net/2011/06/evolution-3-and-offlineimap/#comments</comments>
		<pubDate>Sat, 11 Jun 2011 19:01:59 +0000</pubDate>
		<dc:creator>François</dc:creator>
				<category><![CDATA[Hacking]]></category>
		<category><![CDATA[evolution]]></category>
		<category><![CDATA[linux]]></category>
		<category><![CDATA[ubuntu]]></category>

		<guid isPermaLink="false">http://francoismichonneau.net/?p=183</guid>
		<description><![CDATA[I use offlineimap to fetch my emails from my Gmail account. I use labels as folders, some are nested, and [...]]]></description>
			<content:encoded><![CDATA[<p>I use <a href="https://github.com/nicolas33/offlineimap">offlineimap</a> to fetch my emails from my Gmail account. I use labels as folders, some are nested, and some contains a dot in their names. I have about 120 of them. They contain my about 30000 messages and weight about 6 Gb.</p>
<p>After migrating to <a href="https://launchpad.net/~danilo/+archive/evolution">Evolution 3</a>, new mails that go directly in folders stopped showing up in Evolution. Further, some of my emails starting to get their labels removed on my Gmail account.</p>
<p>As Evolution 3 stores messages in the maildir format, when you point it out to the folder where offlineimap synchronizes your emails, it starts by creating hidden folders with the same names and moves the current messages in them. So, if you start with a folder called let&#8217;s say &#8220;Alerts&#8221;, evolution will create a folder called &#8220;.Alerts&#8221;. Your current (&#8220;cur&#8221;) folder under &#8220;Alerts&#8221; will be emptied and moved in the &#8220;cur&#8221; folder under &#8220;.Alerts&#8221;. The issue with this is that offlineimap interprets that you just removed the &#8220;Alerts&#8221; label to all your messages.</p>
<p>For the labels that are nested, Evolution actually now follows the maildir standard and use the dot as a separator. For instance, a Gmail labeled called &#8220;Alerts/Comments&#8221; will become in your maildir folder &#8220;.Alerts.Comments&#8221;.</p>
<p>Furthermore, if you had a dot in the name of your label, let&#8217;s say &#8220;2010.Archives&#8221;, during the renaming folder process, Evolution 3 will convert this to &#8220;.2010_Archives&#8221;.</p>
<p>How to fix this and make it work again?</p>
<ol>
<li>First, stop offlineimap to check for your account (cancel the cron job if it&#8217;s how you tell offlineimap to check your account).</li>
<li>Second delete your <code>~/.offlineimap</code> folder so that modifications to your maildir folder are not interpreted as labels being removed.</li>
<li>Start Evolution 3 and let it do all the renaming and moving around of your messages</li>
<li>Close Evolution, delete all the cmeta, index and data files created by Evolution in the maildir directory</li>
<li>Delete all the folders that used to contain your messages (after making sure that they&#8217;re all empty)</li>
<li>Edit your <code>.offlinemaprc</code> file:
<ol>
<li>change <code>sep=/</code> to <code>sep=.</code></li>
<li>change your nametrans line to: <code>nametrans = lambda folder: re.sub('\s+', '', re.sub('(.+)(\\.)(.+)', '\\1_\\3', re.sub('(^.{1})', '.\\1', re.sub('.*Trash$', 'Trash', re.sub('.*Drafts$', 'Drafts', re.sub('.*Sent Mail$', 'Sent', re.sub('.*Starred$', 'Starred', re.sub('.*All Mail$', 'Archive', re.sub('^(INBOX)', ' ', folder)))))))))</code></li>
<li>This series of regular expressions does the following:
<ol>
<li>Every folder gets a dot appended in the front. <code>'(^.{1})', '.\\1'</code></li>
<li>Dots inside your labels are replaced with underscores (you&#8217;ll need to change it if you have more than one dot in your labels): <code>'(.+)(\\.)(.+)', '\\1_\\3'</code></li>
<li>All the Gmail special folders are moved to the root (i.e., &#8220;[Gmail]/Trash&#8221; becomes &#8220;Trash&#8221;)</li>
<li>The Inbox folder is moved to the root of your directory. This is done in three steps, first &#8220;INBOX&#8221; is replaced by a space <code>'^(INBOX)', ' '</code>, then a dot is appended in front (like all the other folders) and the extra trailing space is then deleted <code>'\s+', ''</code>.</li>
</ol>
</ol>
</li>
<li>Restart offlineimap and make sure that everything is working the way it&#8217;s supposed to.</li>
</ol>
<p>The process was a little bumpy but I can now read my emails in Evolution again.</p>
<p>Here you can download the full version of the <a href="http://francoismichonneau.net/wp-uploads/2011/06/exampleOfflineimaprc.txt"><code>.offlineimaprc</code></a> file.</p>
]]></content:encoded>
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		</item>
		<item>
		<title>Photos: Heron &amp; Egret</title>
		<link>http://francoismichonneau.net/2010/11/photos-heron-egret/</link>
		<comments>http://francoismichonneau.net/2010/11/photos-heron-egret/#comments</comments>
		<pubDate>Sun, 28 Nov 2010 16:07:53 +0000</pubDate>
		<dc:creator>François</dc:creator>
				<category><![CDATA[Photo]]></category>
		<category><![CDATA[birds]]></category>
		<category><![CDATA[florida]]></category>

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		<description><![CDATA[

Great Egret (Ardea alba) and Great Blue Heron (Ardea herodius).

]]></description>
			<content:encoded><![CDATA[<div class="center">
<a href="http://lh3.ggpht.com/_DiOeIryp5ac/TPJ9Rw75iMI/AAAAAAAACLA/g_exTFWqQzU/s800/IMG_8397.jpg" title="IMG_8397.jpg" rel="lightbox" ><img src="http://lh3.ggpht.com/_DiOeIryp5ac/TPJ9Rw75iMI/AAAAAAAACLA/g_exTFWqQzU/w400/IMG_8397.jpg" alt="IMG_8397.jpg" title="IMG_8397.jpg" class="aligncenter" width="400" /></a><br />
Great Egret (<em>Ardea alba</em>) and Great Blue Heron (<em>Ardea herodius</em>).
</div>
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		<item>
		<title>Photos: Thanksgiving birding</title>
		<link>http://francoismichonneau.net/2010/11/photos-thanksgiving-birding/</link>
		<comments>http://francoismichonneau.net/2010/11/photos-thanksgiving-birding/#comments</comments>
		<pubDate>Thu, 25 Nov 2010 17:03:17 +0000</pubDate>
		<dc:creator>François</dc:creator>
				<category><![CDATA[Photo]]></category>
		<category><![CDATA[birds]]></category>

		<guid isPermaLink="false">http://francoismichonneau.net/?p=152</guid>
		<description><![CDATA[A few shots from Payne&#8217;s prairie in the morning light.


Little blue heron (Egretta caerula)

Little blue heron (Egretta caerula)

Great blue heron [...]]]></description>
			<content:encoded><![CDATA[<p>A few shots from Payne&#8217;s prairie in the morning light.</p>
<div class="center">
<a href="http://lh6.ggpht.com/_DiOeIryp5ac/TO6Qxn6l4uI/AAAAAAAACJQ/P8Y32Da4r0k/s800/IMG_8574.jpg" title="IMG_8574.jpg" rel="lightbox" ><img src="http://lh6.ggpht.com/_DiOeIryp5ac/TO6Qxn6l4uI/AAAAAAAACJQ/P8Y32Da4r0k/s800/IMG_8574.jpg" alt="IMG_8574.jpg" title="IMG_8574.jpg" class="centered" width="400" /></a><br />
Little blue heron (<em>Egretta caerula</em>)</p>
<p><a href="http://lh4.ggpht.com/_DiOeIryp5ac/TO6QyhnzvhI/AAAAAAAACJU/f_vvAj7m70U/s800/IMG_8580.jpg" title="IMG_8580.jpg" rel="lightbox" ><img src="http://lh4.ggpht.com/_DiOeIryp5ac/TO6QyhnzvhI/AAAAAAAACJU/f_vvAj7m70U/s800/IMG_8580.jpg" alt="IMG_8580.jpg" title="IMG_8580.jpg" class="aligncenter" width="400" /></a><br />
Little blue heron (<em>Egretta caerula</em>)</p>
<p><a href="http://lh4.ggpht.com/_DiOeIryp5ac/TO6Q0DG5gqI/AAAAAAAACJY/BQ3CJERkCAs/s800/IMG_8589.jpg" title="IMG_8589.jpg" rel="lightbox" ><img src="http://lh4.ggpht.com/_DiOeIryp5ac/TO6Q0DG5gqI/AAAAAAAACJY/BQ3CJERkCAs/s800/IMG_8589.jpg" alt="IMG_8589.jpg" title="IMG_8589.jpg" class="aligncenter" width="400" /></a><br />
Great blue heron (<em>Ardea herodius</em>)</p>
<p><a href="http://lh3.ggpht.com/_DiOeIryp5ac/TO6Q1e-_WvI/AAAAAAAACJc/zmQR8FURd8U/s800/IMG_8647.jpg" title="IMG_8647.jpg" rel="lightbox" ><img src="http://lh3.ggpht.com/_DiOeIryp5ac/TO6Q1e-_WvI/AAAAAAAACJc/zmQR8FURd8U/s800/IMG_8647.jpg" alt="IMG_8647.jpg" title="IMG_8647.jpg" class="aligncenter" width="400" /></a><br />
Red-Shouldered Hawk (<em>Buteo lineatus</em>)</p>
<p><a href="http://lh3.ggpht.com/_DiOeIryp5ac/TO6Q5zCF1BI/AAAAAAAACJg/Q21DbnC-BZc/s800/IMG_8679.jpg" title="IMG_8679.jpg" rel="lightbox" ><img src="http://lh3.ggpht.com/_DiOeIryp5ac/TO6Q5zCF1BI/AAAAAAAACJg/Q21DbnC-BZc/s800/IMG_8679.jpg" alt="IMG_8679.jpg" title="IMG_8679.jpg" class="aligncenter" width="400" /></a><br />
Young deer playing with Sandhill cranes (<em>Grus canadensis</em>)</p>
<p><a href="http://lh5.ggpht.com/_DiOeIryp5ac/TO6Q7BkiC8I/AAAAAAAACJk/ws8juVqXkSs/s800/IMG_8702.jpg" title="IMG_8702.jpg" rel="lightbox" ><img src="http://lh5.ggpht.com/_DiOeIryp5ac/TO6Q7BkiC8I/AAAAAAAACJk/ws8juVqXkSs/s800/IMG_8702.jpg" alt="IMG_8702.jpg" title="IMG_8702.jpg" class="aligncenter" width="400" /></a><br />
Red-Shouldered Hawk (<em>Buteo lineatus</em>)</p>
<p><a href="http://lh6.ggpht.com/_DiOeIryp5ac/TO6Q8LtH8KI/AAAAAAAACJo/R2eWhVMIG7M/s800/IMG_8705.jpg" title="IMG_8705.jpg" rel="lightbox" ><img src="http://lh6.ggpht.com/_DiOeIryp5ac/TO6Q8LtH8KI/AAAAAAAACJo/R2eWhVMIG7M/s800/IMG_8705.jpg" alt="IMG_8705.jpg" title="IMG_8705.jpg" class="aligncenter" width="400" /></a><br />
Savannah Sparrow (<em>Passerculus sandwichensis</em>)
</div>
]]></content:encoded>
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		</item>
		<item>
		<title>Photos: Millipedes</title>
		<link>http://francoismichonneau.net/2010/11/millipedes/</link>
		<comments>http://francoismichonneau.net/2010/11/millipedes/#comments</comments>
		<pubDate>Thu, 25 Nov 2010 01:35:52 +0000</pubDate>
		<dc:creator>François</dc:creator>
				<category><![CDATA[Photo]]></category>
		<category><![CDATA[macro]]></category>
		<category><![CDATA[terrestrial arthropod]]></category>
		<category><![CDATA[white box]]></category>

		<guid isPermaLink="false">http://francoismichonneau.net/?p=139</guid>
		<description><![CDATA[Millipede from the backyard
 
 
]]></description>
			<content:encoded><![CDATA[<p>Millipede from the backyard</p>
<p><a href="http://lh5.ggpht.com/_DiOeIryp5ac/TO2zyXreZeI/AAAAAAAACIU/jYCq67x8ZXc/s800/IMG_8547.jpg" title="IMG_8547.jpg" rel="lightbox" ><img src="http://lh5.ggpht.com/_DiOeIryp5ac/TO2zyXreZeI/AAAAAAAACIU/jYCq67x8ZXc/w400/IMG_8547.jpg" alt="IMG_8547.jpg" title="IMG_8547.jpg" class="aligncenter" width="400" /></a> </p>
<p><a href="http://lh5.ggpht.com/_DiOeIryp5ac/TO20huwZZhI/AAAAAAAACIs/sBJ-zvEarq4/s800/IMG_8525.jpg" title="IMG_8525.jpg" rel="lightbox" ><img src="http://lh5.ggpht.com/_DiOeIryp5ac/TO20huwZZhI/AAAAAAAACIs/sBJ-zvEarq4/w400/IMG_8525.jpg" alt="IMG_8525.jpg" title="IMG_8525.jpg" class="aligncenter" width="400" /></a> </p>
]]></content:encoded>
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		<item>
		<title>Molecular Evolution workshop</title>
		<link>http://francoismichonneau.net/2010/07/molecular-evolution-workshop/</link>
		<comments>http://francoismichonneau.net/2010/07/molecular-evolution-workshop/#comments</comments>
		<pubDate>Sat, 31 Jul 2010 18:27:00 +0000</pubDate>
		<dc:creator>François</dc:creator>
				<category><![CDATA[News]]></category>

		<guid isPermaLink="false">http://francoismichonneau.net/?p=116</guid>
		<description><![CDATA[I&#8217;m at Woods Hole, MA for the Molecular Evolution Workshop.
]]></description>
			<content:encoded><![CDATA[<p>I&#8217;m at Woods Hole, MA for the <a href="http://www.molecularevolution.org">Molecular Evolution Workshop</a>.</p>
]]></content:encoded>
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		</item>
		<item>
		<title>Sea cucumber workshop</title>
		<link>http://francoismichonneau.net/2010/06/sea-cucumber-workshop/</link>
		<comments>http://francoismichonneau.net/2010/06/sea-cucumber-workshop/#comments</comments>
		<pubDate>Fri, 04 Jun 2010 23:27:55 +0000</pubDate>
		<dc:creator>François</dc:creator>
				<category><![CDATA[News]]></category>

		<guid isPermaLink="false">http://francoismichonneau.net/?p=111</guid>
		<description><![CDATA[I&#8217;m in Guam for the sea cucumber workshop. We are gathering experts and students to share the latest knowledge on [...]]]></description>
			<content:encoded><![CDATA[<p>I&#8217;m in Guam for the sea cucumber workshop. We are gathering experts and students to share the latest knowledge on the biology, ecology and taxonomic status of our favorite animals.</p>
<p>You can have a look at the <a href="http://cukeworkshop.wordpress.com">sea cucumber workshop website</a> for more information.</p>
]]></content:encoded>
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		</item>
		<item>
		<title>Ubuntu color palette for OpenOffice</title>
		<link>http://francoismichonneau.net/2010/02/ubuntu-color-openoffice/</link>
		<comments>http://francoismichonneau.net/2010/02/ubuntu-color-openoffice/#comments</comments>
		<pubDate>Sun, 28 Feb 2010 17:20:03 +0000</pubDate>
		<dc:creator>François</dc:creator>
				<category><![CDATA[Hacking]]></category>
		<category><![CDATA[linux]]></category>

		<guid isPermaLink="false">http://francoismichonneau.net/?p=104</guid>
		<description><![CDATA[I like the colors chosen by Ubuntu and I tend to use them for my presentations and posters. So, I [...]]]></description>
			<content:encoded><![CDATA[<p>I like the <a href="https://wiki.ubuntu.com/Artwork/Official">colors</a> chosen by Ubuntu and I tend to use them for my presentations and posters. So, I created a <a href="http://bit.ly/9i8kyl">palette</a> that can be imported in <a href="http://openoffice.org">OpenOffice</a>. How to use it?</p>
<ol>
<li>Download the <a href="http://bit.ly/9i8kyl">palette</a></li>
<li>In OpenOffice, go in Format > Area for instance</li>
<li>Click on the &#8220;Colors&#8221; tab</li>
<li>Click on the folder icon (&#8220;Load Color list&#8221;)</li>
<li>Browse for the file you downloaded</li>
<li>Enjoy, Ubuntu colors within OpenOffice</li>
</ol>
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