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 1OOF8D-0006ug-PT for garchives@archives.gentoo.org; Mon, 14 Jun 2010 19:15:38 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 4F4BCE0AB0; Mon, 14 Jun 2010 19:15:10 +0000 (UTC) Received: from mx0.d.umn.edu (mx0.d.umn.edu [131.212.109.42]) by pigeon.gentoo.org (Postfix) with ESMTP id 2B01AE0AB0 for ; Mon, 14 Jun 2010 19:15:10 +0000 (UTC) Received: from mxr1.d.umn.edu (mxr1.d.umn.edu [131.212.109.92]) by mx0.d.umn.edu (8.13.8/8.13.8) with ESMTP id o5EJEMP8029541 for ; Mon, 14 Jun 2010 14:14:22 -0500 (CDT) Received: from mxv2.d.umn.edu (mxv2.d.umn.edu [131.212.109.136]) by mxr1.d.umn.edu (8.13.8/8.13.8) with ESMTP id o5EJEM7E003007 for ; Mon, 14 Jun 2010 14:14:22 -0500 (CDT) Received: from smtp.d.umn.edu (mx3.d.umn.edu [131.212.109.40]) by mxv2.d.umn.edu (8.13.8/8.13.8) with ESMTP id o5EJELDL016084 for ; Mon, 14 Jun 2010 14:14:21 -0500 (CDT) Received: from ledaig (ledaig.d.umn.edu [131.212.64.12]) (authenticated bits=0) by smtp.d.umn.edu (8.13.8/8.13.8) with ESMTP id o5EJDtKw022353 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NO) for ; Mon, 14 Jun 2010 14:13:56 -0500 (CDT) Date: Mon, 14 Jun 2010 14:13:48 -0500 From: Steven Trogdon Subject: [gentoo-science] sage-notebook & jmol To: gentoo-science X-Mailer: Balsa 2.4.7 Message-Id: <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: multipart/signed; protocol="application/pgp-signature"; micalg=PGP-SHA1; boundary="=-5U+k1Mt+6RZtZWnfRUBE" X-Virus-Scanned: clamav-milter 0.95.3 at mxv2.d.umn.edu X-Virus-Status: Clean X-Archives-Salt: 0670c610-5a76-4ee7-b963-3a601edddaf0 X-Archives-Hash: 89d1d448a0b2dd12e50914d6479c04c4 --=-5U+k1Mt+6RZtZWnfRUBE Content-Type: text/plain; charset=us-ascii; DelSp=Yes; Format=Flowed Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Hello, I believe Jmol is the default Sage 3D viewer. However, it seems to be =20 broken from the notebook. A sphere() from the sage prompt works as expected but not so from the notebook. =20 Here I get that the problem is in locating the JmolApplet class. It =20 appears that sagenb is coded to look in the data directory under sagenb =20 for package data, i.e. relative to the python tree in =20 site-packages/sagenb/data. After opening the notebook the contents of =20 the directory can be viewed by pointing one's browser to http://localhost:8000/java/ In particular the notebook seems to look in =20 site-packages/sagenb/data/jmol for the JmolApplet class data which was =20 removed with the advent of the sage-on-gentoo package, =20 sci-chemistry/jmol. Now here I'm able to get Jmol to work from the =20 notebook if I create either of the symlinks, site-packages/sagenb/data/jmol -> =20 /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 =20 get the sagenb package to access external data other than through a =20 symlink. If the first of the above is done then a version bump of jmol =20 will require a new sage-notebook install! There is also an "appletweb" =20 directory that's present under sagenb/data/jmol and I was curious as to =20 whether it's needed? Is it perhaps a carry-over from the older =20 Sage-provided jmol stuff? Steve --=-5U+k1Mt+6RZtZWnfRUBE Content-Type: application/pgp-signature -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.15 (GNU/Linux) iEYEABECAAYFAkwWf3MACgkQSh5h5U6haiGepgCcDFWaa0ZEmiWBROo+rZmM3PYa orgAniBo42G1ELfu7rLJc1lusmEEFZVg =VJqS -----END PGP SIGNATURE----- --=-5U+k1Mt+6RZtZWnfRUBE--