From justin at ukans.edu Thu Oct 7 03:39:22 1999 From: justin at ukans.edu (Justin Bradford) Date: Mon Feb 6 02:00:19 2006 Subject: [pyorbit] move to autoconf Message-ID: I have a local copy of PyORBit building with autoconf/automake (making use of James' automake modifications in gnome-python). Unfortunately, I'm not able to commit at the moment (permission denied messages). Once I figure that out, I'll commit my changes and make a 0.0.2 release. Justin From bizzaro at bc.edu Thu Oct 7 12:40:27 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Mon Feb 6 02:00:22 2006 Subject: [pyorbit] move to autoconf References: Message-ID: <37FCCCFB.54F9A9E@bc.edu> Justin Bradford wrote: > > I have a local copy of PyORBit building with autoconf/automake (making use > of James' automake modifications in gnome-python). Unfortunately, I'm not > able to commit at the moment (permission denied messages). Once I figure > that out, I'll commit my changes and make a 0.0.2 release. You should be able to commit now. The problem we have is when someone creates a new file, the group is set to the user's default group, which is not 'cvs'. Does anyone know how to get around this problem? Cheers. Jeff -- +----------------------------+ | J.W. Bizzaro | | jeff@theopenlab.uml.edu | | | | THE OPEN LAB | | Open Source Bioinformatics | | | | http://theopenlab.uml.edu/ | +----------------------------+ From hortiz at neurobio.upr.clu.edu Thu Oct 7 12:34:18 1999 From: hortiz at neurobio.upr.clu.edu (Humberto Ortiz Zuazaga) Date: Mon Feb 6 02:00:22 2006 Subject: [pyorbit] move to autoconf In-Reply-To: Your message of "Thu, 07 Oct 1999 16:40:27 GMT." <37FCCCFB.54F9A9E@bc.edu> Message-ID: <199910071634.MAA09443@chimbo.neurobio.upr.clu.edu> > when someone creates a > new file, the group is set to the user's default group, which is not 'cvs'. > Does anyone know how to get around this problem? Make the directories setgid cvs? -- Humberto Ortiz Zuazaga Bioinformatics Specialist Institute of Neurobiology hortiz@neurobio.upr.clu.edu From bizzaro at bc.edu Thu Oct 7 13:22:07 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Mon Feb 6 02:00:22 2006 Subject: [pyorbit] move to autoconf References: <37FCCCFB.54F9A9E@bc.edu> Message-ID: <37FCD6BF.545A9F6B@bc.edu> "J.W. Bizzaro" wrote: > > The problem we have is when someone creates a > new file, the group is set to the user's default group, which is not 'cvs'. I don't think this is a problem afterall. Providing the directory /home/cvs belongs to the group cvs, we should be able to commit. I just did a checkout, added a blank line to README and commited the module, and I got no error. :-P Jeff -- +----------------------------+ | J.W. Bizzaro | | jeff@theopenlab.uml.edu | | | | THE OPEN LAB | | Open Source Bioinformatics | | | | http://theopenlab.uml.edu/ | +----------------------------+ From bizzaro at bc.edu Thu Oct 7 13:47:47 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Mon Feb 6 02:00:23 2006 Subject: [pyorbit] move to autoconf References: <37FCCCFB.54F9A9E@bc.edu> <37FCD6BF.545A9F6B@bc.edu> Message-ID: <37FCDCC3.CE38775D@bc.edu> "J.W. Bizzaro" wrote: > > I just did a checkout, added a blank line to README and commited the module, and > I got no error. I tried making changes to loci-core under different usernames, and I don't get any errors there either. Jeff -- +----------------------------+ | J.W. Bizzaro | | jeff@theopenlab.uml.edu | | | | THE OPEN LAB | | Open Source Bioinformatics | | | | http://theopenlab.uml.edu/ | +----------------------------+ From james at daa.com.au Fri Oct 8 04:14:51 1999 From: james at daa.com.au (James Henstridge) Date: Mon Feb 6 02:00:23 2006 Subject: [pyorbit] move to autoconf In-Reply-To: <37FCDCC3.CE38775D@bc.edu> Message-ID: I still get errors when try to cvs update my tree (I get the Permission Denied messages). It can do an initial checkout correctly, so it is not an authentication failure. I can't cvs update a fresh checkout either. There may be some problem with the CVS setup on the server end. James. -- Email: james@daa.com.au WWW: http://www.daa.com.au/~james/ On Thu, 7 Oct 1999, J.W. Bizzaro wrote: > "J.W. Bizzaro" wrote: > > > > I just did a checkout, added a blank line to README and commited the module, and > > I got no error. > > I tried making changes to loci-core under different usernames, and I don't get > any errors there either. > > > Jeff > -- > +----------------------------+ > | J.W. Bizzaro | > | jeff@theopenlab.uml.edu | > | | > | THE OPEN LAB | > | Open Source Bioinformatics | > | | > | http://theopenlab.uml.edu/ | > +----------------------------+ > > _______________________________________________ > pyorbit maillist - pyorbit@theopenlab.uml.edu > http://theopenlab.uml.edu/mailman/listinfo/pyorbit > From bizzaro at bc.edu Fri Oct 8 10:27:53 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Mon Feb 6 02:00:23 2006 Subject: [pyorbit] move to autoconf References: Message-ID: <37FDFF69.45B61F29@bc.edu> James Henstridge wrote: > > I still get errors when try to cvs update my tree (I get the Permission > Denied messages). It can do an initial checkout correctly, so it is not > an authentication failure. I can't cvs update a fresh checkout either. > > There may be some problem with the CVS setup on the server end. I found out that when I upgraded the OS to Red Hat 6, CVS was unintentionally upgraded too. That _may_ have been the problem. I just reinstalled the original version of CVS. Please give it another try. I'm sorry for the inconvenience. Cheers. Jeff -- +----------------------------+ | J.W. Bizzaro | | jeff@theopenlab.uml.edu | | | | THE OPEN LAB | | Open Source Bioinformatics | | | | http://theopenlab.uml.edu/ | +----------------------------+ From justin at ukans.edu Fri Oct 8 18:54:33 1999 From: justin at ukans.edu (Justin Bradford) Date: Mon Feb 6 02:00:23 2006 Subject: [pyorbit] autoconf version committed Message-ID: Thanks to Jeff's changes to the CVS server, I was able to commit my autoconf changes. I'm having some trouble getting the spec file right to automatically make distributions (won't include the samples and misc directories). Once I figure that out, I'll put version 0.0.2 on the website. Then, I can start working on new functionality. Justin From bizzaro at bc.edu Sat Oct 9 20:56:30 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Mon Feb 6 02:00:23 2006 Subject: [pyorbit] preview new web page design Message-ID: <37FFE43E.3E2CB8CE@bc.edu> Greetings. The PyORBit Web page has been redesigned, complements of Gary Van Domselaar. Check out this preview (THIS IS A TEMPORARY URL; THE PAGE WILL REMAIN AT THEOPENLAB): http://gvd.v-wave.com/pyorbit/ Hit 'Reload' on your browser for special treat. Cheers. Jeff -- +----------------------------+ | J.W. Bizzaro | | jeff@theopenlab.uml.edu | | | | THE OPEN LAB | | Open Source Bioinformatics | | | | http://theopenlab.uml.edu/ | +----------------------------+ From robinson at netrinsics.com Sat Oct 9 23:24:13 1999 From: robinson at netrinsics.com (Michael Robinson) Date: Mon Feb 6 02:00:23 2006 Subject: [pyorbit] preview new web page design In-Reply-To: <37FFE43E.3E2CB8CE@bc.edu> Message-ID: <199910100324.LAA00672@netrinsics.com> >The PyORBit Web page has been redesigned, complements of Gary Van Domselaar. >Check out this preview (THIS IS A TEMPORARY URL; THE PAGE WILL REMAIN AT >THEOPENLAB): > > http://gvd.v-wave.com/pyorbit/ > >Hit 'Reload' on your browser for special treat. Totally cool. Totally illegible. Perhaps the text could be put into a table cell, or a color could be selected which contrasted sufficiently with the all the background tiles in the pool. -Michael Robinson From bizzaro at bc.edu Sat Oct 9 23:52:35 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Mon Feb 6 02:00:23 2006 Subject: [pyorbit] preview new web page design References: <199910100324.LAA00672@netrinsics.com> Message-ID: <38000D83.FC5EDFFB@bc.edu> Michael Robinson wrote: > > Totally illegible. You're not seeing the off-white table cell behind the text? What browser are you using? It works with Navigator 4.6, but I just noticed the table cell is transparent with the latest Mozilla. Jeff -- +----------------------------+ | J.W. Bizzaro | | jeff@theopenlab.uml.edu | | | | THE OPEN LAB | | Open Source Bioinformatics | | | | http://theopenlab.uml.edu/ | +----------------------------+ From robinson at netrinsics.com Sun Oct 10 01:05:38 1999 From: robinson at netrinsics.com (Michael Robinson) Date: Mon Feb 6 02:00:24 2006 Subject: [pyorbit] preview new web page design In-Reply-To: <38000D83.FC5EDFFB@bc.edu> Message-ID: <199910100505.NAA00902@netrinsics.com> >You're not seeing the off-white table cell behind the text? What browser are >you using? It works with Navigator 4.6, but I just noticed the table cell is >transparent with the latest Mozilla. Navigator Gold 3.04, FreeBSD -Michael Robinson From justin at ukans.edu Sun Oct 10 13:26:42 1999 From: justin at ukans.edu (Justin Bradford) Date: Mon Feb 6 02:00:24 2006 Subject: [pyorbit] new tarball on the website Message-ID: I have a tarball for 0.0.2 on the website. I tried to send an announcement on freshmeat, but I don't seem to have access to it. Jeff, could you do it then? Justin From bizzaro at bc.edu Sun Oct 10 14:20:04 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Mon Feb 6 02:00:24 2006 Subject: [pyorbit] new tarball on the website References: Message-ID: <3800D8D4.8E60D2DF@bc.edu> Justin Bradford wrote: > > I have a tarball for 0.0.2 on the website. > I tried to send an announcement on freshmeat, but I don't seem to have > access to it. Jeff, could you do it then? Sure. I'll also put it on the Gnome software map. Cheers. Jeff -- +----------------------------+ | J.W. Bizzaro | | jeff@theopenlab.uml.edu | | | | THE OPEN LAB | | Open Source Bioinformatics | | | | http://theopenlab.uml.edu/ | +----------------------------+ From Johannes.Hoelzl at t-online.de Mon Oct 11 12:19:01 1999 From: Johannes.Hoelzl at t-online.de (Johannes =?iso-8859-1?Q?H=F6lzl?=) Date: Mon Feb 6 02:00:24 2006 Subject: [pyorbit] new tarball on the website References: Message-ID: <38020DF5.F015773A@t-online.de> Justin Bradford wrote: > > I have a tarball for 0.0.2 on the website. > I tried to send an announcement on freshmeat, but I don't seem to have > access to it. Jeff, could you do it then? > > Justin > I tried to get this package but i've got a "404 Not Found". Whats wrong ?? Johannes From justin at ukans.edu Mon Oct 11 12:29:35 1999 From: justin at ukans.edu (Justin Bradford) Date: Mon Feb 6 02:00:24 2006 Subject: [pyorbit] new tarball on the website In-Reply-To: <38020DF5.F015773A@t-online.de> Message-ID: > I tried to get this package but i've got a "404 Not Found". > Whats wrong ?? I seem to have lost access to the website, and the new page design has an old link. However, the person who changed this left the old version backed up here (where you can download the new package): http://theopenlab.uml.edu/pyorbitgvd/ Justin From justin at ukans.edu Mon Oct 11 12:32:55 1999 From: justin at ukans.edu (Justin Bradford) Date: Mon Feb 6 02:00:25 2006 Subject: [pyorbit] new tarball on the website In-Reply-To: <3800D8D4.8E60D2DF@bc.edu> Message-ID: When the new web page went up for pyorbit, I lost access to the files and directory. The new page has a link to 0.0.1 (rather than the current 0.0.2) and I can't edit it. Also, the tarballs were removed from the directory. It would probably be a better idea to put tarballs on the ftp side, too. I noticed you had anonymous ftp setup. Anyway I could get a pyorbit directory under pub? Justin From bizzaro at bc.edu Mon Oct 11 13:13:57 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Mon Feb 6 02:00:25 2006 Subject: [pyorbit] new tarball on the website References: Message-ID: <38021AD5.B7D159EB@bc.edu> Justin Bradford wrote: > > When the new web page went up for pyorbit, I lost access to the files and > directory. The new page has a link to 0.0.1 (rather than the current > 0.0.2) and I can't edit it. > Also, the tarballs were removed from the directory. We'll have to blame it on Gary ;-) I changed the permissions to the new pyorbit directory so you (those in the web group) have access. The tarballs and README were copied over from the old directory and I added the block about the 0.0.2 release to the Web page. We're using PHP3 so, (I think) you edit the index.php3 file. So, have at it! > It would probably be a better idea to put tarballs on the ftp side, too. > I noticed you had anonymous ftp setup. Anyway I could get a pyorbit > directory under pub? We _could_. But we should talk about the security of anonymous FTP on the tol-admin list. I was thinking about making a central TOL repository on the Web side at http://theopenlab.uml.edu/resources/download/ Cheers. Jeff -- +----------------------------+ | J.W. Bizzaro | | jeff@theopenlab.uml.edu | | | | THE OPEN LAB | | Open Source Bioinformatics | | | | http://theopenlab.uml.edu/ | +----------------------------+ From gvd at redpoll.pharmacy.ualberta.ca Tue Oct 12 03:26:34 1999 From: gvd at redpoll.pharmacy.ualberta.ca (Gary Van Domselaar) Date: Mon Feb 6 02:00:25 2006 Subject: [pyorbit] new tarball on website Message-ID: <3802E2AA.A095F9FF@redpoll.pharmacy.ualberta.ca> > I tried to get this package but i've got a "404 Not Found". > Whats wrong ?? I seem to have lost access to the website, and the new page design has an old link. Jeez guys, I'm not sure what all this fuss is about. I checked the link and it worked fine for me. Justin: I looked at the permissions for the pyorbit site and they look fine for you-- you should be able to edit them no problem. Sorry for all the bother. I hope these wrinkles get worked out soon. --gary =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Gary Van Domselaar gvd@redpoll.pharmacy.ualberta.ca Faculty of Pharmacy Phone: (780) 492-4493 University of Alberta FAX: (780) 492-5305 Edmonton, Alberta, Canada http://redpoll.pharmacy.ualberta.ca/~gvd From bizzaro at bc.edu Tue Oct 12 17:54:22 1999 From: bizzaro at bc.edu (J.W. Bizzaro) Date: Mon Feb 6 02:00:25 2006 Subject: [pyorbit] new tarball on website References: <3802E2AA.A095F9FF@redpoll.pharmacy.ualberta.ca> Message-ID: <3803AE0E.6E389D0C@bc.edu> Gary Van Domselaar wrote: > > Jeez guys, I'm not sure what all this fuss is about. I checked the link > and it worked fine for me. Justin: I looked at the permissions for the > pyorbit site and they look fine for you-- you should be able to edit > them no problem. I beat you to it, Gary, but neglected to tell you :-P There really was a problem, honest :-) Jeff -- +----------------------------+ | J.W. Bizzaro | | jeff@theopenlab.uml.edu | | | | THE OPEN LAB | | Open Source Bioinformatics | | | | http://theopenlab.uml.edu/ | +----------------------------+ From adustman at comstar.net Fri Oct 22 16:01:21 1999 From: adustman at comstar.net (Andy Dustman) Date: Mon Feb 6 02:00:26 2006 Subject: [pyorbit] libIDL Message-ID: My libIDL doesn't link against the ORBit IDL library. I'm guessing this is a Makefile problem. I manually adjusted the makefile (added -lIDL to the link flags) and it now works. I'm thinking, this really ought to be called IDLmodule instead of libIDLmodule. For snicks, I wrote a teeny program to parse and dump the IDL parse tree. #!/usr/bin/python import libIDL def dump_tree(tree, indent=0): from types import TupleType, ListType t = tree.get_type() v = tree.get_value() print " "*indent, t, v if type(v) not in (TupleType, ListType): v = (v,) for subtree in v: if type(subtree) is type(tree): dump_tree(subtree, indent=indent+2) if __name__ == "__main__": import sys dump_tree(libIDL.parse_filename(sys.argv[1])) Works on the Typesmodule/Types.idl. Is anyone actively working on using this for marshalling/demarshalling, as opposed to using C stubs/skeletons? I would assume that's part of the point of this module... My impression so far is that pyorbit and ORBit are quite fast. -- andy dustman | programmer/analyst | comstar.net, inc. telephone: 770.485.6025 / 706.549.7689 | icq: 32922760 | pgp: 0xc72f3f1d From bizzaro at geoserve.net Wed Oct 27 13:48:44 1999 From: bizzaro at geoserve.net (J.W. Bizzaro) Date: Mon Feb 6 02:00:26 2006 Subject: [pyorbit] The Open Lab (was Re: Tkinter) Message-ID: <38173AFB.10953FAD@geoserve.net> Jeffrey Chang wrote: > > We could use Tkinter to create a GUI for biopython. Is this worth > > exploring? > Also, I should mention that there are some open source projects working on > GUI's for bioinformatics. The Open Lab (http://theopenlab.uml.edu/) has > some work going on developing GUI's with Python. We (The Open Lab) have a strong preference for Python, but we are not excluding any projects based on language. Our criterion for bioinformatics development projects is that the _license_ be compatible with the GNU GPL. As for software, we hope to be the Free Software Foundation (GNU) of bioinformatics. We also have research and information projects. > Another intriguing possibility would be to work through the CORBA > interface that Ewan's been working out. That way, bioperl and biopython > could share a GUI. But I'm getting ahead of myself... Along this line, The Open Lab is developing The Loci Project, which is a CORBA-based, Python-implemented graphical programming language for distributed data processing (bioinformatics in particular): http://theopenlab.uml.edu/loci/ We (Justin Bradford et al.) are developing Python bindings to ORBit (GNU's CORBA system): http://theopenlab.uml.edu/pyorbit/ This is the only free and open-source CORBA implementation for Python. I am curious about what Ewan is up to regarding Python and CORBA. Regarding the cross-platform capabilities of GTK (versus Tkinter), The Open Lab is hosting the only port of the PyGTK (GTK/Python bindings) widget set to the Windows OS: http://theopenlab.uml.edu/pygtkwin/ We have mailing lists for all of our projects and we hope that more Python developers for bioinformatics will join in on the fun, as your own Jeff Chang has already contributed to the Python Phylogenetics project: http://theopenlab.uml.edu/pyphy/ It's true that we have great interests in GUI development, and the BioPython project addresses infrastructure programming, which we have not so far. I think The Open Lab and BioPython as well as BioPerl all complement each other in that respect. Congratulations on starting this project, and I hope that we can work closely on some projects. Cheers. The other Jeff -- +----------------------------+ | J.W. Bizzaro | | jeff@theopenlab.uml.edu | | | | THE OPEN LAB | | Open Source Bioinformatics | | | | http://theopenlab.uml.edu/ | +----------------------------+ From glowstars at gmx.de Thu Oct 28 03:10:48 1999 From: glowstars at gmx.de (glowstars@gmx.de) Date: Mon Feb 6 02:00:26 2006 Subject: [pyorbit] The Open Lab (was Re: Tkinter) References: <38173AFB.10953FAD@geoserve.net> Message-ID: <25511.941094648@www12.gmx.net> > We (Justin Bradford et al.) are developing Python bindings to ORBit > (GNU's CORBA system): > > http://theopenlab.uml.edu/pyorbit/ > > This is the only free and open-source CORBA implementation for Python. > I am curious about what Ewan is up to regarding Python and CORBA. FYI omniORB which has been released under GPL/LGPL recently will have Python bindings in the very near future. A first pre-release is expected for next week. http://www.uk.research.att.com/omniORB/omniORB.html Search the mailing list archives for more information. Cheers, Thorsten Roskowetz (glowstars@gmx.de) -- Sent through Global Message Exchange - http://www.gmx.net