new versions of my programs
Hi folks, I have just finished the new release of my data analysis programs: Athena 0.8.027 and Artemis 0.7.003. This release contains mostly bug fixes and feature enhancements. As you may recall, last month's release of Artemis generated a very large amount of traffic on this list due to several problems surrounding the new project file format and other file management issues. I have addressed almost all of the problems that were reported and am cautiously optimistic that this release of Artemis will be much more solid than the last. There is one significant new feature in this release -- the program Hephaestus, which will be a permanent part of future releases. Hephaestus replaces the Atoms Periodic Table and expands greatly upon its functionality. I will describe Hephaestus in more detail in a message later this morning. Source code tarballs are already available on my web site and at SourceForge. The Windows updater package will be available soon. Change logs with all the details of the new features of Athena and Artemis are on my web site. Lots of people helped out this time with excellent suggestions and bug reports. Special thanks to Mauro Ravezzi, David Barton, Peter Pfalzer, Gerrit Schmithals, Stanislav Stoupin, and Shelly Kelly. Regards, B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Hi Bruce, I installed the programs very recently, using the installer from Matt's page. Now that you released the new programs, will the installer be updated? It is so convenient to use... Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI
On Wednesday 14 April 2004 07:37 am, Stefano Ciurli wrote:
Hi Bruce, I installed the programs very recently, using the installer from Matt's page. Now that you released the new programs, will the installer be updated? It is so convenient to use...
Stefano To quote from the announcement: "Source code tarballs are already available on my web site and at SourceForge. The Windows updater package will be available soon." You need to remember that Matt and I do this software thing entirely as a volunteer effort. That is especially true for the Windows package because neither of us develops our codes on Windows, which is a secondary platform for both of us. I believe that Matt has users at his beamline this week and that has to take priority over his preparing the new Windows updater. You simply must be patient. Perhaps now is a good time for someone who relies upon the Windows version to step up and volunteer to take the maintenance of the Windows package off of our hands... B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Hi Bruce,
You need to remember that Matt and I do this software thing entirely as a volunteer effort.
and we are all very thankful!
That is especially true for the Windows package ... You simply must be patient.
OK. No problem. I will continue fiddling with the version I have and talk to the EMBL people next weekend. Btw, I am a Mac user, not Windows :-)) Ciao, Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI
Stefano: It is my understanding that Mac OSX has something called fink which works much like Debian's apt-get. I have always been curious as to whether source packages from a Debian system could be ported easily through this method? Can you tell me a bit about it? Carlo On Wed, 14 Apr 2004, Stefano Ciurli wrote:
Hi Bruce,
You need to remember that Matt and I do this software thing entirely as a volunteer effort.
and we are all very thankful!
That is especially true for the Windows package ... You simply must be patient.
OK. No problem. I will continue fiddling with the version I have and talk to the EMBL people next weekend. Btw, I am a Mac user, not Windows :-))
Ciao, Stefano
-- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre@iit.edu http://www.iit.edu/~segre
Ciao Carlo,
It is my understanding that Mac OSX has something called fink which works much like Debian's apt-get.
yes it has. But I am not a guru of linux or unix (to say the least) and as a newcomer I used the installer provided kindly by Matt. For other programs I used fink, no problem. You can go and see some interesting pages at http://chemistry.ucsc.edu/~wgscott/xtal/
I have always been curious as to whether source packages from a Debian system could be ported easily through this method? Can you tell me a bit about it?
not much. I follow the instructions given in the site I give above to install the programs I need, mostrly for crystallography and protein NMR. Ciao, Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI
I thought I would jump in here and say I have been compiling my own version of ifeffit and horae-033 (the last time the day 033 came out). I know something about programming and am very interested in getting horae and ifeffit as packages in fink. In essence the work I now do for myself for the latest horae to run could be used by every one who can type "fink update horae". Info on fink is available at http:fink.sourceforge.net. In other words once everything is set up, I would be glad to be the maintainer. Of course, the installer concept is easier, but rather wasteful of resources (all that usually needs to be recompiled is horae, e.g. ifeffit, pgplot, perl widgets etc. are all the same between releases of horae so the amount of files to be downloaded is much less (about 5 MB for 033). Now that Matt is maintaining a Mac installer, putting up a fink version still makes sense as it is quick and light meaning, since I upgrade horae for myself, I can have the updated version available very quickly (little or no repackaging is required (unlike an installer) as the fink system would download horae itself locally, I would only upload install scripts and dependency files. For Mac users there is another (slight) advantage in that the fink pgplot is aquaterm enabled (aquaterm.sourceforge.net); aquaterm is a cocoa application that displays the pgplot output instead of X11. The biggest advantage is that it buffers its input so the graphics can be resized anytime (pgplot does not buffer anything internally so this is not possible in X11 directly). It also allows direct printing and saving of any window (it would support multiple windows let's say if athena and artemis or multiple copies of either were running) as an eps or pdf file (these features are supported directly by the Mac OS so it is not pgplot doing the rerendering). Are there any mac users out there that might be interested. Stefano, I will be going to Triesete next month to do an experiment with Federico Boscherini (from Bologna as well -- physics department). Is there any chance you will be there? Paul On Apr 15, 2004, at 12:41 AM, Stefano Ciurli wrote:
Ciao Carlo,
It is my understanding that Mac OSX has something called fink which works much like Debian's apt-get.
yes it has. But I am not a guru of linux or unix (to say the least) and as a newcomer I used the installer provided kindly by Matt. For other programs I used fink, no problem. You can go and see some interesting pages at http://chemistry.ucsc.edu/~wgscott/xtal/
I have always been curious as to whether source packages from a Debian system could be ported easily through this method? Can you tell me a bit about it?
not much. I follow the instructions given in the site I give above to install the programs I need, mostrly for crystallography and protein NMR. Ciao, Stefano
-- ____________________________________________
Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203
"Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons@aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８ 茨城県つくば市東１−１−1 つくば中央第４ 近接場光応用工学センター ポール・フォンス主任研究官
Dear Paul,
I thought I would jump in here and say I have been compiling my own version of ifeffit and horae-033 (the last time the day 033 came out). I know something about programming and am very interested in getting horae and ifeffit as packages in fink.
I am currently updating my fink version to 0.7.0, the latest release. I will try to compile the latest software from Bruce on my mac. I will let you know how things went.
In essence the work I now do for myself for the latest horae to run could be used by every one who can type "fink update horae". Info on fink is available at http:fink.sourceforge.net. In other words once everything is set up, I would be glad to be the maintainer.
fantastique! It would be really convenient for me and maybe for others, even though the installer built by Matt has been for me a very nice tool, certainly complementary and alternative
For Mac users there is another (slight) advantage in that the fink pgplot is aquaterm enabled (aquaterm.sourceforge.net); aquaterm is a cocoa application that displays the pgplot output instead of X11. The biggest advantage is that it buffers its input so the graphics can be resized anytime (pgplot does not buffer anything internally so this is not possible in X11 directly). It also allows direct printing and saving of any window (it would support multiple windows let's say if athena and artemis or multiple copies of either were running) as an eps or pdf file (these features are supported directly by the Mac OS so it is not pgplot doing the rerendering). Are there any mac users out there that might be interested.
I am
Stefano, I will be going to Triesete next month to do an experiment with Federico Boscherini (from Bologna as well -- physics department). Is there any chance you will be there?
no, I will go to Hamburg this afternoon for data collection. I usually do not go to Trieste, too long to explain why. Ciao, Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI
Hi Paul, Sefano, I have a few comments on this thread about Mac OS X and Fink packages for Ifeffit. It's fine with me if you want to maintain Fink or debian packages (or RPMS or ...). In general, my preference is to make the source kits easier to use when possible, and if you have Fink, then using the source kits _should_ be possible. The current binary distribution of Ifeffit ignores (or is supposed to ignore) the Fink installation. This is so that Fink is not *required* for Ifeffit and users without Fink can install Ifeffit and run the Ifeffit Apps by double-clicking (admittedly ugly) icons. I prefer to keep the independence from Fink. For Bruce's codes, the Ifeffit installer puts a lot of stuff in the Perl directory (/Library/Perl), including Perl/Tk. That is, all of horae's dependencies are already in place from the binary installer, and ready to use. So one approach to getting updates for horae would be to make the binary installer more Fink-friendly, so that it would be possible to do ~> /Applications/Ifeffit/bin/iff_init.sh ~> horae_update from the Terminal for a system with Ifeffit installed from the binary and Fink (with g77) installed. This would then follow the 'normal unix update' and would allow a Fink-enabled Mac to update as soon as Bruce released a new version, without a separate 'package'. To get this to work will likely mean fiddling with the horae_update script and the horae Makefile.PL, and with the binary installer. I think this is non-trivial but not too hard. It might take a few iterations, but seems much more desirable than a Fink package to me. == On the Aquaterm/PGPLOT terminal: The last time I looked (many months ago), the Aquaterm device for PGPLOT did not support the cursor. That seems like a big drawback to me. The current binary install of Ifeffit uses a PGPLOT library that I built myself, with the X11 but not the Aquaterm device (of course, athena and artemis also require X11...). I'm willing to have both X11 and Aquaterm devices, but I could not get the Aquaterm device to build from source the last time I tried. If you (or anyone else) knows how to do this, that would be very helpful. Finally, I think that getting the Mac Installer and horae_update to work together is better than building a Fink package. --Matt
I, agree with Matt on this one. A good mac installer is much more useful to me than a Fink package. I, as well have stopped using Aquaterm due to the lack of a cursor. Oddly enough, this is a major omission for something that is fairly trivial to implement programatically. It may be that passing the coordinates back is the problem rather than getting them from the window. But I really haven't looked at the Aquaterm source in any depth. Jeff
== On the Aquaterm/PGPLOT terminal:
The last time I looked (many months ago), the Aquaterm device for PGPLOT did not support the cursor. That seems like a big drawback to me. The current binary install of Ifeffit uses a PGPLOT library that I built myself, with the X11 but not the Aquaterm device (of course, athena and artemis also require X11...). I'm willing to have both X11 and Aquaterm devices, but I could not get the Aquaterm device to build from source the last time I tried. If you (or anyone else) knows how to do this, that would be very helpful.
Finally, I think that getting the Mac Installer and horae_update to work together is better than building a Fink package.
--Matt
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
On Monday 19 April 2004 04:37 pm, Matt Newville wrote:
For Bruce's codes, the Ifeffit installer puts a lot of stuff in the Perl directory (/Library/Perl), including Perl/Tk. That is, all of horae's dependencies are already in place from the binary installer, and ready to use. So one approach to getting updates for horae would be to make the binary installer more Fink-friendly, so that it would be possible to do ~> /Applications/Ifeffit/bin/iff_init.sh ~> horae_update
from the Terminal for a system with Ifeffit installed from the binary and Fink (with g77) installed. This would then follow the 'normal unix update' and would allow a Fink-enabled Mac to update as soon as Bruce released a new version, without a separate 'package'.
To get this to work will likely mean fiddling with the horae_update script and the horae Makefile.PL, and with the binary installer. I think this is non-trivial but not too hard. It might take a few iterations, but seems much more desirable than a Fink package to me.
My $0.02. I would STRONGLY encourage the mac crowd here on the list to consider the approach that Matt suggests. It does mean that Mac users would have to get Fink up and running on their computers (and get G77, etc working), and that would certainly increase the height of the potential barrier for the not-so-computer-savvy Mac user. On the other hand, it means that *no one* has to maintain a binary package for the Mac since Mac users would get to use the source code package which I maintain and use myself. And, as far as I know, the horae_updater script is working well for everyone who is using it. I am, of course, open to suggestions for modifying either horae_update or the main Makefile.PL to be more Mac/Fink friendly. That just seems like the best way to go. But what do I know about the Macintosh world -- I'm just a numbskull linux user. ;-) B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Hi Bruce, Fink is a very nice package when it is working. Unfortunately, it is not always working. Fink was broken for a significant portion of time during the 10.2 to 10.3 OS upgrade. Could have been 10.1 to 10.2, lost in the fog of time. Anyway, forcing non-command line savvy mac users to synchronize fink, fortran compilers, perl versions, especially as another OS upgrade cycle is likely approaching seems problematic to me. It's also so unmac-like to force users to compile from scratch.
I would STRONGLY encourage the mac crowd here on the list to consider the approach that Matt suggests. It does mean that Mac users would have to get Fink up and running on their computers (and get G77, etc working), and that would certainly increase the height of the potential barrier for the not-so-computer-savvy Mac user.
That just seems like the best way to go. But what do I know about the Macintosh world -- I'm just a numbskull linux user. ;-)
Well, nobody's perfect ;-) Jeff
On Monday 19 April 2004 05:11 pm, Jeff Terry wrote:
It's also so unmac-like to force users to compile from scratch.
I acknowledge that this was said with tongue in cheek. Still, I cannot come up with the right language to express how extremely little being "mac-like" matters to me. That said, I think that I neglected to mention a few of the underlying assumptions of my last posting. Assumption #1: My codes have bugs. Some of them get in the way of getting work done. Assumption #2: I am constantly working on fixing the problems in my codes. That is a good thing. Assumption #3: People would prefer to avail themselves of code that fixes serious bugs in the timeliest manner possible because it is better to use code with fewer bugs than code with more bugs. I maintain the source code package continuously. Thus, the fastest way to disseminate bug fixes to end users is in the form of source code. This has the additional advantage of not requiring the additional and probably time consuming step of building and verifying a binary package. But I am not the sort to pass judgement on a culture that I am not a part of. If doing things the "Macintosh way" takes priority over doing anaylsis with code which has fewer bugs, than that is just fine with me. B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
I can see both sides. It is important to have ease of installation so that the programs can be disseminated to more users. This will help the development process. That being said, it is important to have a committed group to keep up to date with the sources so that everyone is talking about the same versions and can benefit from the latest improvements. I suspect taht once the horae software reaches an advanced version number, issues like this will become less important as stability in the basic code is reached. Carlo On Mon, 19 Apr 2004, Bruce Ravel wrote:
On Monday 19 April 2004 05:11 pm, Jeff Terry wrote:
It's also so unmac-like to force users to compile from scratch.
I acknowledge that this was said with tongue in cheek. Still, I cannot come up with the right language to express how extremely little being "mac-like" matters to me.
That said, I think that I neglected to mention a few of the underlying assumptions of my last posting.
Assumption #1: My codes have bugs. Some of them get in the way of getting work done.
Assumption #2: I am constantly working on fixing the problems in my codes. That is a good thing.
Assumption #3: People would prefer to avail themselves of code that fixes serious bugs in the timeliest manner possible because it is better to use code with fewer bugs than code with more bugs.
I maintain the source code package continuously. Thus, the fastest way to disseminate bug fixes to end users is in the form of source code. This has the additional advantage of not requiring the additional and probably time consuming step of building and verifying a binary package.
But I am not the sort to pass judgement on a culture that I am not a part of. If doing things the "Macintosh way" takes priority over doing anaylsis with code which has fewer bugs, than that is just fine with me.
B
-- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre@iit.edu http://www.iit.edu/~segre
When I mentioned fink, I was never thinking of replacing the binary installer, rather just making it easier for the people not afraid to click a compile button to have the latest version compiled from source. For instance, the latest version of aquaterm does have a cursor ... and is part of fink! The idea would be for it to be trivial for someone who has fink installed to graduate to the latest version. As I am hacking around anyway trying to get things to work in fink, I thought it would be nice if someone else could easily update their systems more easily. It is possible incidentally to do binary installs using Fink. The idea is just to make it trivial for someone to install the latest version without worrying about the details that someone else has already worried about. Actually I like the sound of what Matt was describing, but I don't grasp all of the details. One of the largest benefits of fink (and I assume Debian is the same idea) is that Fink keeps track of dependencies and can offer to upgrade the dependent packages if necessary. How would this work with the binary installer bit? I assume the basic idea is that the binary installer would install a complete working package and that fink could offer to upgrade that package. This would seem to conflict (or at least potentially conflict) with the package management feature of fink. In any case the idea would not be to replace the binary installer for those who don't want to bother with the hassle of compiling things, but for those who are willing but just don't know enough about the process to do it themselves to get the latest source code release running. I believe currently, using my installation of horae, ifeffit and friends, Bruce's script works "out of the box". I have installed horae and ifeffit on a friend's machine which works nicely using the fink installed packages (but not using fink itself for the installation yet). On my own machine, I have upgraded to the latest version of perl, etc. and things are a little more complicated (but not much). I was just curious to see if anyone else would be interested in a fink based installation (with all of its pitfalls and warts) as in principle it would be only a small amount of extra work to take what I am doing to keep my horae updated and pass it along to others. On the other hand, if there is not interest, there is no point. If there is a hybrid solution like the one Matt mentioned that would be optimal it seems to me (more thinking/discussion required). Do try the latest version of aquaterm though, it is nice to have things resize on demand! Paul On 2004/04/20, at 6:45, Carlo U. Segre wrote:
I can see both sides. It is important to have ease of installation so that the programs can be disseminated to more users. This will help the development process. That being said, it is important to have a committed group to keep up to date with the sources so that everyone is talking about the same versions and can benefit from the latest improvements.
I suspect taht once the horae software reaches an advanced version number, issues like this will become less important as stability in the basic code is reached.
Carlo
On Mon, 19 Apr 2004, Bruce Ravel wrote:
On Monday 19 April 2004 05:11 pm, Jeff Terry wrote:
It's also so unmac-like to force users to compile from scratch.
I acknowledge that this was said with tongue in cheek. Still, I cannot come up with the right language to express how extremely little being "mac-like" matters to me.
That said, I think that I neglected to mention a few of the underlying assumptions of my last posting.
Assumption #1: My codes have bugs. Some of them get in the way of getting work done.
Assumption #2: I am constantly working on fixing the problems in my codes. That is a good thing.
Assumption #3: People would prefer to avail themselves of code that fixes serious bugs in the timeliest manner possible because it is better to use code with fewer bugs than code with more bugs.
I maintain the source code package continuously. Thus, the fastest way to disseminate bug fixes to end users is in the form of source code. This has the additional advantage of not requiring the additional and probably time consuming step of building and verifying a binary package.
But I am not the sort to pass judgement on a culture that I am not a part of. If doing things the "Macintosh way" takes priority over doing anaylsis with code which has fewer bugs, than that is just fine with me.
B
-- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre@iit.edu http://www.iit.edu/~segre _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons@aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８ 茨城県つくば市東１−１−1 つくば中央第４ 近接場光応用工学センター ポール・フォンス主任研究官
Hi Paul, Just to be clear, I mean a 'Fink-friendly' installer to allow a user to run 'horae_update' if g77 works, which probably means having Fink installed. It would not use any Fink packages itself.
I believe currently, using my installation of horae, ifeffit and friends, Bruce's script works "out of the box". I have installed horae and ifeffit on a friend's machine which works nicely using the fink installed packages (but not using fink itself for the installation yet). On my own machine, I have upgraded to the latest version of perl, etc. and things are a little more complicated (but not much).
horae_update sort of works for me, but not well enough to use with the binary installer. It tries to build Ifeffit.bs, the link between perl and the ifeffit library. Currently, this gives several warnings about unneeded Framework stuff and produces a non-working Ifeffit.bs for me: This seems to be due to how ifeffit wants to link with my version of the PGPLOT library. This is solvable, but it means altering Makefile.PL (and probably re-building PGPLOT to make Makefile.PL easier). Another issue is that horae_update installs to /usr/local/bin, which means the clickable icons in /Applications/Ifeffit won't point to the updated versions. Again, that's a small Mac-specific alteration to Makefile.PL. BTW, none of this is Bruce's fault: using /Applications/Ifeffit is very Mac-specific, and horae_update expects 'normal perl on Unix' rules. Re: Aquaterm, I'd be willing to include this (I beleive I'd also need to include Aquaterm.app in the binary installer. That's OK, but Aquaterm claims to be in alpha-phase, so might not be the best idea). I have not tried building the latest Aquaterm. I should rebuild PGPLOT anyway, so I'm willing to try this. Finally, For what it's worth, my view is that building from source is ALWAYS better than using a binary. As an example, the current binary installer of Ifeffit for Mac only works on 10.3. The source code can be made to work on 10.2 as well, and will likely work on 10.4. Binary packages from Fink or debian do not adequately manage 'dependencies', no matter what they may claim. --Matt
On Wednesday 21 April 2004 01:26 pm, Matt Newville wrote:
horae_update sort of works for me, but not well enough to use with the binary installer. It tries to build Ifeffit.bs, the link between perl and the ifeffit library. Currently, this gives several warnings about unneeded Framework stuff and produces a non-working Ifeffit.bs for me: This seems to be due to how ifeffit wants to link with my version of the PGPLOT library. This is solvable, but it means altering Makefile.PL (and probably re-building PGPLOT to make Makefile.PL easier). Another issue is that horae_update installs to /usr/local/bin, which means the clickable icons in /Applications/Ifeffit won't point to the updated versions. Again, that's a small Mac-specific alteration to Makefile.PL. BTW, none of this is Bruce's fault: using /Applications/Ifeffit is very Mac-specific, and horae_update expects 'normal perl on Unix' rules.
It should be easy enough to modify horae_update and/or Makefile.PL to recognize this situation and act accordingly. For the installation location business, that is easy enough to change at "make install" time. Look at the `private_install' script to see how it is done -- it's easy. As for changes to Makefile.PL to build a working .bs file -- just let me know what needs to be done and I'll make the changes. B -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Hi Matt (Bruce), I see what you mean. Although I use fink a lot for my own purposes, I understand your philosophy and admit it is probably correct for the average feffit/horae user. Certainly the issue where things are installed can be fixed -- or at least circumvented by either overwriting the /Applications launchers or making them applescript applications that can realize that the latest binaries are now in /usr/bin/local. I believe there is an installer for the g77 as well on the net somewhere (or at least there was for 10.2) so perhaps fink may not be necessary at all. By the way the latest version of aquaterm may be alpha, but so far in its interactions with horae (I only use it with horae), I have not had a single problem with it. What would be the next logical step to make this a reality? Should I pass along my makefile changes? If you could describe your setup (or put it into a tar archive, perhaps I could download it and help with the hacking). Paul On Apr 22, 2004, at 2:26 AM, Matt Newville wrote:
Hi Paul,
Just to be clear, I mean a 'Fink-friendly' installer to allow a user to run 'horae_update' if g77 works, which probably means having Fink installed. It would not use any Fink packages itself.
I believe currently, using my installation of horae, ifeffit and friends, Bruce's script works "out of the box". I have installed horae and ifeffit on a friend's machine which works nicely using the fink installed packages (but not using fink itself for the installation yet). On my own machine, I have upgraded to the latest version of perl, etc. and things are a little more complicated (but not much).
horae_update sort of works for me, but not well enough to use with the binary installer. It tries to build Ifeffit.bs, the link between perl and the ifeffit library. Currently, this gives several warnings about unneeded Framework stuff and produces a non-working Ifeffit.bs for me: This seems to be due to how ifeffit wants to link with my version of the PGPLOT library. This is solvable, but it means altering Makefile.PL (and probably re-building PGPLOT to make Makefile.PL easier). Another issue is that horae_update installs to /usr/local/bin, which means the clickable icons in /Applications/Ifeffit won't point to the updated versions. Again, that's a small Mac-specific alteration to Makefile.PL. BTW, none of this is Bruce's fault: using /Applications/Ifeffit is very Mac-specific, and horae_update expects 'normal perl on Unix' rules.
Re: Aquaterm, I'd be willing to include this (I beleive I'd also need to include Aquaterm.app in the binary installer. That's OK, but Aquaterm claims to be in alpha-phase, so might not be the best idea). I have not tried building the latest Aquaterm. I should rebuild PGPLOT anyway, so I'm willing to try this.
Finally, For what it's worth, my view is that building from source is ALWAYS better than using a binary. As an example, the current binary installer of Ifeffit for Mac only works on 10.3. The source code can be made to work on 10.2 as well, and will likely work on 10.4. Binary packages from Fink or debian do not adequately manage 'dependencies', no matter what they may claim.
--Matt
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons@aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８ 茨城県つくば市東１−１−1 つくば中央第４ 近接場光応用工学センター ポール・フォンス主任研究官
Hi Paul, I would like to get your makefile for use with Aquaterm, if you're willing to pass it on. I really liked Aquaterm until I got tired of not having a cursor. Jeff Jeff Terry Biological, Chemical, and Physical Sciences Illinois Institute of Technology Chicago IL 60616 phone 630-252-9708 fax 630-252-0358 email: terryj@iit.edu http://mrmac.mr.aps.anl.gov/~jterry/ On Apr 21, 2004, at 6:16 PM, Paul Fons wrote:
Hi Matt (Bruce),
I see what you mean. Although I use fink a lot for my own purposes, I understand your philosophy and admit it is probably correct for the average feffit/horae user. Certainly the issue where things are installed can be fixed -- or at least circumvented by either overwriting the /Applications launchers or making them applescript applications that can realize that the latest binaries are now in /usr/bin/local. I believe there is an installer for the g77 as well on the net somewhere (or at least there was for 10.2) so perhaps fink may not be necessary at all. By the way the latest version of aquaterm may be alpha, but so far in its interactions with horae (I only use it with horae), I have not had a single problem with it. What would be the next logical step to make this a reality? Should I pass along my makefile changes? If you could describe your setup (or put it into a tar archive, perhaps I could download it and help with the hacking).
Paul
On Apr 22, 2004, at 2:26 AM, Matt Newville wrote:
Hi Paul,
Just to be clear, I mean a 'Fink-friendly' installer to allow a user to run 'horae_update' if g77 works, which probably means having Fink installed. It would not use any Fink packages itself.
I believe currently, using my installation of horae, ifeffit and friends, Bruce's script works "out of the box". I have installed horae and ifeffit on a friend's machine which works nicely using the fink installed packages (but not using fink itself for the installation yet). On my own machine, I have upgraded to the latest version of perl, etc. and things are a little more complicated (but not much).
horae_update sort of works for me, but not well enough to use with the binary installer. It tries to build Ifeffit.bs, the link between perl and the ifeffit library. Currently, this gives several warnings about unneeded Framework stuff and produces a non-working Ifeffit.bs for me: This seems to be due to how ifeffit wants to link with my version of the PGPLOT library. This is solvable, but it means altering Makefile.PL (and probably re-building PGPLOT to make Makefile.PL easier). Another issue is that horae_update installs to /usr/local/bin, which means the clickable icons in /Applications/Ifeffit won't point to the updated versions. Again, that's a small Mac-specific alteration to Makefile.PL. BTW, none of this is Bruce's fault: using /Applications/Ifeffit is very Mac-specific, and horae_update expects 'normal perl on Unix' rules.
Re: Aquaterm, I'd be willing to include this (I beleive I'd also need to include Aquaterm.app in the binary installer. That's OK, but Aquaterm claims to be in alpha-phase, so might not be the best idea). I have not tried building the latest Aquaterm. I should rebuild PGPLOT anyway, so I'm willing to try this.
Finally, For what it's worth, my view is that building from source is ALWAYS better than using a binary. As an example, the current binary installer of Ifeffit for Mac only works on 10.3. The source code can be made to work on 10.2 as well, and will likely work on 10.4. Binary packages from Fink or debian do not adequately manage 'dependencies', no matter what they may claim.
--Matt
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568
tel. +81-298-61-5636 fax. +81-298-61-2939
email: paul-fons@aist.go.jp
The lines below are in a Japanese font
〒３０５−８５６８ 茨城県つくば市東１−１−1 つくば中央第４ 近接場光応用工学センター ポール・フォンス主任研究官 _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
This is one of these things I can't really take credit for. The latest version of alpha [AquaTerm v1.0.a2 (v1.0.a2)] is included in fink as well as in sourceforge (aquaterm.sourceforge.net). I used fink to build the latest version of aquaterm and appropriately modify my pgplot build (the instructions for doing the pgplot device addition are on the aquaterm homepage) and used the flag: -laquaterm . That's it! Here is the appropriate incantation from my (modified) version of Bruce's makefile [tachyon:~/Ports/horae-033] paulfons% grep -n aquaterm Makefile 40:LDDLFLAGS = -bundle -undefined dynamic_lookup -L/usr/local/lib -L/usr/local/lib -framework Foundation -laquaterm I then just set the environment variable PGPLOT_DEV to /aqt and voila, it just works. Hope this helps, Paul On 2004/04/22, at 9:10, Jeff Terry wrote:
Hi Paul,
I would like to get your makefile for use with Aquaterm, if you're willing to pass it on. I really liked Aquaterm until I got tired of not having a cursor.
Jeff
Jeff Terry Biological, Chemical, and Physical Sciences Illinois Institute of Technology Chicago IL 60616 phone 630-252-9708 fax 630-252-0358 email: terryj@iit.edu http://mrmac.mr.aps.anl.gov/~jterry/ On Apr 21, 2004, at 6:16 PM, Paul Fons wrote:
Hi Matt (Bruce),
I see what you mean. Although I use fink a lot for my own purposes, I understand your philosophy and admit it is probably correct for the average feffit/horae user. Certainly the issue where things are installed can be fixed -- or at least circumvented by either overwriting the /Applications launchers or making them applescript applications that can realize that the latest binaries are now in /usr/bin/local. I believe there is an installer for the g77 as well on the net somewhere (or at least there was for 10.2) so perhaps fink may not be necessary at all. By the way the latest version of aquaterm may be alpha, but so far in its interactions with horae (I only use it with horae), I have not had a single problem with it. What would be the next logical step to make this a reality? Should I pass along my makefile changes? If you could describe your setup (or put it into a tar archive, perhaps I could download it and help with the hacking).
Paul
On Apr 22, 2004, at 2:26 AM, Matt Newville wrote:
Hi Paul,
Just to be clear, I mean a 'Fink-friendly' installer to allow a user to run 'horae_update' if g77 works, which probably means having Fink installed. It would not use any Fink packages itself.
I believe currently, using my installation of horae, ifeffit and friends, Bruce's script works "out of the box". I have installed horae and ifeffit on a friend's machine which works nicely using the fink installed packages (but not using fink itself for the installation yet). On my own machine, I have upgraded to the latest version of perl, etc. and things are a little more complicated (but not much).
horae_update sort of works for me, but not well enough to use with the binary installer. It tries to build Ifeffit.bs, the link between perl and the ifeffit library. Currently, this gives several warnings about unneeded Framework stuff and produces a non-working Ifeffit.bs for me: This seems to be due to how ifeffit wants to link with my version of the PGPLOT library. This is solvable, but it means altering Makefile.PL (and probably re-building PGPLOT to make Makefile.PL easier). Another issue is that horae_update installs to /usr/local/bin, which means the clickable icons in /Applications/Ifeffit won't point to the updated versions. Again, that's a small Mac-specific alteration to Makefile.PL. BTW, none of this is Bruce's fault: using /Applications/Ifeffit is very Mac-specific, and horae_update expects 'normal perl on Unix' rules.
Re: Aquaterm, I'd be willing to include this (I beleive I'd also need to include Aquaterm.app in the binary installer. That's OK, but Aquaterm claims to be in alpha-phase, so might not be the best idea). I have not tried building the latest Aquaterm. I should rebuild PGPLOT anyway, so I'm willing to try this.
Finally, For what it's worth, my view is that building from source is ALWAYS better than using a binary. As an example, the current binary installer of Ifeffit for Mac only works on 10.3. The source code can be made to work on 10.2 as well, and will likely work on 10.4. Binary packages from Fink or debian do not adequately manage 'dependencies', no matter what they may claim.
--Matt
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568
tel. +81-298-61-5636 fax. +81-298-61-2939
email: paul-fons@aist.go.jp
The lines below are in a Japanese font
〒３０５−８５６８ 茨城県つくば市東１−１−1 つくば中央第４ 近接場光応用工学センター ポール・フォンス主任研究官 _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons@aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８ 茨城県つくば市東１−１−1 つくば中央第４ 近接場光応用工学センター ポール・フォンス主任研究官
Hi Paul,
I see what you mean. Although I use fink a lot for my own purposes, I understand your philosophy and admit it is probably correct for the average feffit/horae user. Certainly the issue where things are installed can be fixed -- or at least circumvented by either overwriting the /Applications launchers or making them applescript applications that can realize that the latest binaries are now in /usr/bin/local. I believe there is an installer for the g77 as well on the net somewhere (or at least there was for 10.2) so perhaps fink may not be necessary at all. By the way the latest version of aquaterm may be alpha, but so far in its interactions with horae (I only use it with horae), I have not had a single problem with it. What would be the next logical step to make this a reality? Should I pass along my makefile changes? If you could describe your setup (or put it into a tar archive, perhaps I could download it and help with the hacking).
What's next? Well, I'm heading out of town for a few days... I'll have my powerbook with me but may not work on this until next week. I think the first thing is to build a PGPLOT library that does X, Postscript, Png, and Aquaterm, preferrably linking in png/zlib staically (so as to avoid '-lpgplot -lpng -lz' which often prefers Fink shared- verses non-Fink static libraries). A Makefile for PGPLOT/ Aquaterm would be helpful. Then I just point PGPLOT_DIR appropriately and build Ifeffit with ./configure --prefix=/Applications/Ifeffit ; sudo make install. For horae, I use horae's Makefile.PL, then move the binaries from /usr/local, but go back to ifeffit/wrapper/perl to make and install the perl module there. That's kludgy, but easy enough to do once or twice -- but would have to be fixed if 'horae_update' is to be robust.. again this is all easy enough. The binary package and installer are pretty straightforward: just taking everything from /Library/Perl and /Applications/Ifeffit and use Package Manager and Disk Utility. If there's someone who knows anything about Applescript or how Mac Icons work, the Applescript wrappers could be improved. Really, /Applications/Ifeffit/applescript is the sum total of my Applescript experience: I conquered 'do_shell_script' and not much else. An alternative route might be to figure out how to really make applets without Applescript. --Matt
participants (6)
-
Bruce Ravel -
Carlo U. Segre -
Jeff Terry -
Matt Newville -
Paul Fons -
Stefano Ciurli