From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1OOGeK-0006iK-AN for garchives@archives.gentoo.org; Mon, 14 Jun 2010 20:52:53 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 19F25E0950; Mon, 14 Jun 2010 20:52:39 +0000 (UTC) Received: from mxi2.callplus.net.nz (mx194.callplus.net.nz [202.180.66.194]) by pigeon.gentoo.org (Postfix) with ESMTP id 65797E0950 for ; Mon, 14 Jun 2010 20:52:39 +0000 (UTC) X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AvsEAMYzFkx8xQFN/2dsb2JhbACea3LAYYUaBA Received: from 124-197-1-77.callplus.net.nz (HELO vrooom.localnet) ([124.197.1.77]) by ismtp02.callplus.net.nz with ESMTP; 15 Jun 2010 08:52:37 +1200 From: =?iso-8859-1?q?Fran=E7ois_Bissey?= To: gentoo-science@lists.gentoo.org Subject: Re: [gentoo-science] sage-notebook & jmol Date: Tue, 15 Jun 2010 08:52:36 +1200 User-Agent: KMail/1.13.3 (Linux/2.6.32-gentoo-r7; KDE/4.4.4; i686; ; ) References: <1276542835.6175.0@ledaig> In-Reply-To: <1276542835.6175.0@ledaig> Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-science@lists.gentoo.org Reply-to: gentoo-science@lists.gentoo.org MIME-Version: 1.0 Content-Type: Text/Plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Message-Id: <201006150852.36329.f.r.bissey@massey.ac.nz> X-Archives-Salt: 6d5b85cf-87de-45de-866c-598b424cf7b6 X-Archives-Hash: 0240581b3addf3ebb924021fba04cb4b > Hello, > > I believe Jmol is the default Sage 3D viewer. However, it seems to be > broken from the notebook. A > > sphere() > > from the sage prompt works as expected but not so from the notebook. > Here I get that the problem is in locating the JmolApplet class. It > appears that sagenb is coded to look in the data directory under sagenb > for package data, i.e. relative to the python tree in > site-packages/sagenb/data. After opening the notebook the contents of > the directory can be viewed by pointing one's browser to > > http://localhost:8000/java/ > > In particular the notebook seems to look in > site-packages/sagenb/data/jmol for the JmolApplet class data which was > removed with the advent of the sage-on-gentoo package, > sci-chemistry/jmol. Now here I'm able to get Jmol to work from the > notebook if I create either of the symlinks, > > site-packages/sagenb/data/jmol -> > /usr/share/webapps/jmol/11.6.16/htdocs > or > site-packages/sagenb/data/jmol -> /var/www/localhost/htdocs/jmol > > There should be a better way to do this but I'm unable to find a way to > get the sagenb package to access external data other than through a > symlink. If the first of the above is done then a version bump of jmol > will require a new sage-notebook install! There is also an "appletweb" > directory that's present under sagenb/data/jmol and I was curious as to > whether it's needed? Is it perhaps a carry-over from the older > Sage-provided jmol stuff? > Hi, My fault completely. We noticed about a month ago that jmol was broken and I started to work on fixing it. I had troubles and hadn't find a good solution at the time. Then I more or less forgot. You are putting it back on the top of my priorities here. Francois