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From: Robert H. <ha...@st...> - 2023-11-16 17:59:25
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Jmol Developers, Not sure if you are on this list you still have any interest in Jmol, but I hope some of you do. Well, it's done. The JSmol sourceforge project at https://sourceforge.net/p/jsmol is now no longer needed. I've placed all the files that were in that project into the /unused/ folder there. This is so that we still can track the histories of the files if we need to. But probably that will not be necessary. This past week I totally overhauled the way the transpiler works. For the past 10 years, the transpiler that was being used for Jmol only worked in a very old version of Eclipse "Juno" from (I think) 2013. This has been an enormous pain. For at least eight years I have avoided doing anything with this old transpiler. I finally took the step to revisit the prototype "java2script 4.2" code from 2013, and I realized that it was not so bad and that would be possible to add that code to the SwingJS transpiler plugin as an alternative transpiler option. That has worked perfectly. The new plugin is j2s.core_5.0.1.jar, at https://github.com/BobHanson/java2script/tree/master/sources/net.sf.j2s.core And, as a bonus, we now can adapt the legacy 4.2 transpiler, which is only ever to be used with Jmol anyway, to future needs. The first thing I did was move it up to Java 8 (Though it still only recognizes Java 6 syntax.) One of the things I did was to give it a way to deliver JavaScript code ready for running directly into the site/ directory. This was huge, because previously there were a series of ANT tasks that had to be run to do all sorts of minor tweaking of that output before one could test in JavaScript. But now, it's very clean and simple. You modify Java code for Jmol, save the .java file, and open your browser to see how it runs in JavaScript. Your changes are instantly there. Full integration. The way it should be. Hooray! And then I realized that we didn't need the JSmol project at all. Originally, the idea was to do all the transpiling in this separate project, just using the code that relates to the applet. But now this is not necessary. Once I got the transpiler doing what the ANT tasks were doing (and I was able to fix the various bugs in the 4.2 transpiler that were causing these problems in the first place), I realized that the only thing the JSmol project was doing (yesterday) was to add some more files. So I figured I would just put those files in the Jmol project (into site-resources/ and site-resources-zip). That's all checked in now. Happy to report that that went smoothly, and I was able to fix a few more bugs while at it. So, in short, the Jmol project is alive and well at SourceForge, now using the same transpiler plugin as SwingJS. Just the two projects - Jmol, on SourceForge, and java2script on GitHub. (OK, there's also the Jmol-SwingJS GitHub project, that's true.) No old versions of Eclipse are necessary. So long, Luna!! There's just the one plugin. And my life is way easier. Retirement (from teaching) is just terrific. The bicycling season is just about over here; looks like I will hit 4000 km this year. Drop me a line and tell me how you are doing. Bob -- Robert M. Hanson Professor of Chemistry, Emeritus St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place.* |
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From: Mark P. <pe...@so...> - 2023-11-16 22:00:37
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That's great! I did once try to compile Jmol, but I ran into those issues (Eclipse version, Java 6, etc). This should make it easier for others to contribute. Thanks, Mark On Thu, Nov 16, 2023 at 9:59 AM Robert Hanson via Jmol-developers < jmo...@li...> wrote: > Jmol Developers, > > Not sure if you are on this list you still have any interest in Jmol, but > I hope some of you do. > > Well, it's done. The JSmol sourceforge project at > https://sourceforge.net/p/jsmol is now no longer needed. I've placed all > the files that were in that project into the /unused/ folder there. This is > so that we still can track the histories of the files if we need to. But > probably that will not be necessary. > > This past week I totally overhauled the way the transpiler works. For the > past 10 years, the transpiler that was being used for Jmol only worked in a > very old version of Eclipse "Juno" from (I think) 2013. This has been an > enormous pain. For at least eight years I have avoided doing anything with > this old transpiler. > > I finally took the step to revisit the prototype "java2script 4.2" code > from 2013, and I realized that it was not so bad and that would be possible > to add that code to the SwingJS transpiler plugin as an alternative > transpiler option. > > That has worked perfectly. The new plugin is j2s.core_5.0.1.jar, at > https://github.com/BobHanson/java2script/tree/master/sources/net.sf.j2s.core > > And, as a bonus, we now can adapt the legacy 4.2 transpiler, which is only > ever to be used with Jmol anyway, to future needs. The first thing I did > was move it up to Java 8 (Though it still only recognizes Java 6 syntax.) > One of the things I did was to give it a way to deliver JavaScript code > ready for running directly into the site/ directory. This was huge, because > previously there were a series of ANT tasks that had to be run to do all > sorts of minor tweaking of that output before one could test in JavaScript. > > But now, it's very clean and simple. You modify Java code for Jmol, save > the .java file, and open your browser to see how it runs in JavaScript. > Your changes are instantly there. Full integration. The way it should be. > Hooray! > > And then I realized that we didn't need the JSmol project at all. > Originally, the idea was to do all the transpiling in this separate > project, just using the code that relates to the applet. But now this is > not necessary. Once I got the transpiler doing what the ANT tasks were > doing (and I was able to fix the various bugs in the 4.2 transpiler that > were causing these problems in the first place), I realized that the only > thing the JSmol project was doing (yesterday) was to add some more files. > So I figured I would just put those files in the Jmol project (into > site-resources/ and site-resources-zip). That's all checked in now. > > Happy to report that that went smoothly, and I was able to fix a few more > bugs while at it. > > So, in short, the Jmol project is alive and well at SourceForge, now using > the same transpiler plugin as SwingJS. Just the two projects - Jmol, on > SourceForge, and java2script on GitHub. (OK, there's also the Jmol-SwingJS > GitHub project, that's true.) No old versions of Eclipse are necessary. So > long, Luna!! There's just the one plugin. > > And my life is way easier. Retirement (from teaching) is just terrific. > The bicycling season is just about over here; looks like I will hit 4000 km > this year. > > Drop me a line and tell me how you are doing. > > Bob > > -- > Robert M. Hanson > Professor of Chemistry, Emeritus > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We > honor with gratitude the people who have stewarded the land throughout the > generations and their ongoing contributions to this region. We acknowledge > the ongoing injustices that we have committed against the Dakota Nation, > and we wish to interrupt this legacy, beginning with acts of healing and > honest storytelling about this place.* > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > |
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From: Robert H. <ha...@st...> - 2023-11-16 23:04:43
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That's certainly the idea! On Thu, Nov 16, 2023 at 4:00 PM Mark Perri <pe...@so...> wrote: > That's great! I did once try to compile Jmol, but I ran into those issues > (Eclipse version, Java 6, etc). This should make it easier for others to > contribute. > > Thanks, > Mark > > On Thu, Nov 16, 2023 at 9:59 AM Robert Hanson via Jmol-developers < > jmo...@li...> wrote: > >> Jmol Developers, >> >> Not sure if you are on this list you still have any interest in Jmol, but >> I hope some of you do. >> >> Well, it's done. The JSmol sourceforge project at >> https://sourceforge.net/p/jsmol is now no longer needed. I've placed all >> the files that were in that project into the /unused/ folder there. This is >> so that we still can track the histories of the files if we need to. But >> probably that will not be necessary. >> >> This past week I totally overhauled the way the transpiler works. For the >> past 10 years, the transpiler that was being used for Jmol only worked in a >> very old version of Eclipse "Juno" from (I think) 2013. This has been an >> enormous pain. For at least eight years I have avoided doing anything with >> this old transpiler. >> >> I finally took the step to revisit the prototype "java2script 4.2" code >> from 2013, and I realized that it was not so bad and that would be possible >> to add that code to the SwingJS transpiler plugin as an alternative >> transpiler option. >> >> That has worked perfectly. The new plugin is j2s.core_5.0.1.jar, at >> https://github.com/BobHanson/java2script/tree/master/sources/net.sf.j2s.core >> >> And, as a bonus, we now can adapt the legacy 4.2 transpiler, which is >> only ever to be used with Jmol anyway, to future needs. The first thing I >> did was move it up to Java 8 (Though it still only recognizes Java 6 >> syntax.) One of the things I did was to give it a way to deliver JavaScript >> code ready for running directly into the site/ directory. This was huge, >> because previously there were a series of ANT tasks that had to be run to >> do all sorts of minor tweaking of that output before one could test in >> JavaScript. >> >> But now, it's very clean and simple. You modify Java code for Jmol, save >> the .java file, and open your browser to see how it runs in JavaScript. >> Your changes are instantly there. Full integration. The way it should be. >> Hooray! >> >> And then I realized that we didn't need the JSmol project at all. >> Originally, the idea was to do all the transpiling in this separate >> project, just using the code that relates to the applet. But now this is >> not necessary. Once I got the transpiler doing what the ANT tasks were >> doing (and I was able to fix the various bugs in the 4.2 transpiler that >> were causing these problems in the first place), I realized that the only >> thing the JSmol project was doing (yesterday) was to add some more files. >> So I figured I would just put those files in the Jmol project (into >> site-resources/ and site-resources-zip). That's all checked in now. >> >> Happy to report that that went smoothly, and I was able to fix a few more >> bugs while at it. >> >> So, in short, the Jmol project is alive and well at SourceForge, now >> using the same transpiler plugin as SwingJS. Just the two projects - Jmol, >> on SourceForge, and java2script on GitHub. (OK, there's also the >> Jmol-SwingJS GitHub project, that's true.) No old versions of Eclipse are >> necessary. So long, Luna!! There's just the one plugin. >> >> And my life is way easier. Retirement (from teaching) is just terrific. >> The bicycling season is just about over here; looks like I will hit 4000 km >> this year. >> >> Drop me a line and tell me how you are doing. >> >> Bob >> >> -- >> Robert M. Hanson >> Professor of Chemistry, Emeritus >> St. Olaf College >> Northfield, MN >> http://www.stolaf.edu/people/hansonr >> >> >> If nature does not answer first what we want, >> it is better to take what answer we get. >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> >> *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We >> honor with gratitude the people who have stewarded the land throughout the >> generations and their ongoing contributions to this region. We acknowledge >> the ongoing injustices that we have committed against the Dakota Nation, >> and we wish to interrupt this legacy, beginning with acts of healing and >> honest storytelling about this place.* >> _______________________________________________ >> Jmol-developers mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-developers >> > -- Robert M. Hanson Professor of Chemistry, Emeritus St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place.* |
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From: Jonathan G. <gu...@uw...> - 2023-11-17 00:15:49
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Bob, This sounds great. I don’t have time currently to do anything with Jmol, but I hope to be able to take advantage of these changes in the future. Also thanks for rubbing it in…:) I’m a few years yet from retirement. My biking season ended many weeks ago because I could not get home before sunset…I’m way behind on miles. I’m jealous. Jonathan Dr. Jonathan Gutow Halsey Science Room 412 Chemistry Department UW Oshkosh web: https://cms.gutow.uwosh.edu/Gutow e-mail: gu...@uw... Ph: 920-424-1326 On Nov 16, 2023, at 11:59 AM, Robert Hanson via Jmol-developers <jmo...@li...> wrote: CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. Jmol Developers, Not sure if you are on this list you still have any interest in Jmol, but I hope some of you do. Well, it's done. The JSmol sourceforge project at https://sourceforge.net/p/jsmol is now no longer needed. I've placed all the files that were in that project into the /unused/ folder there. This is so that we still can track the histories of the files if we need to. But probably that will not be necessary. This past week I totally overhauled the way the transpiler works. For the past 10 years, the transpiler that was being used for Jmol only worked in a very old version of Eclipse "Juno" from (I think) 2013. This has been an enormous pain. For at least eight years I have avoided doing anything with this old transpiler. I finally took the step to revisit the prototype "java2script 4.2" code from 2013, and I realized that it was not so bad and that would be possible to add that code to the SwingJS transpiler plugin as an alternative transpiler option. That has worked perfectly. The new plugin is j2s.core_5.0.1.jar, at https://github.com/BobHanson/java2script/tree/master/sources/net.sf.j2s.core And, as a bonus, we now can adapt the legacy 4.2 transpiler, which is only ever to be used with Jmol anyway, to future needs. The first thing I did was move it up to Java 8 (Though it still only recognizes Java 6 syntax.) One of the things I did was to give it a way to deliver JavaScript code ready for running directly into the site/ directory. This was huge, because previously there were a series of ANT tasks that had to be run to do all sorts of minor tweaking of that output before one could test in JavaScript. But now, it's very clean and simple. You modify Java code for Jmol, save the .java file, and open your browser to see how it runs in JavaScript. Your changes are instantly there. Full integration. The way it should be. Hooray! And then I realized that we didn't need the JSmol project at all. Originally, the idea was to do all the transpiling in this separate project, just using the code that relates to the applet. But now this is not necessary. Once I got the transpiler doing what the ANT tasks were doing (and I was able to fix the various bugs in the 4.2 transpiler that were causing these problems in the first place), I realized that the only thing the JSmol project was doing (yesterday) was to add some more files. So I figured I would just put those files in the Jmol project (into site-resources/ and site-resources-zip). That's all checked in now. Happy to report that that went smoothly, and I was able to fix a few more bugs while at it. So, in short, the Jmol project is alive and well at SourceForge, now using the same transpiler plugin as SwingJS. Just the two projects - Jmol, on SourceForge, and java2script on GitHub. (OK, there's also the Jmol-SwingJS GitHub project, that's true.) No old versions of Eclipse are necessary. So long, Luna!! There's just the one plugin. And my life is way easier. Retirement (from teaching) is just terrific. The bicycling season is just about over here; looks like I will hit 4000 km this year. Drop me a line and tell me how you are doing. Bob -- Robert M. Hanson Professor of Chemistry, Emeritus St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place. _______________________________________________ Jmol-developers mailing list Jmo...@li... https://lists.sourceforge.net/lists/listinfo/jmol-developers |
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From: Angel H. <ang...@ua...> - 2023-11-17 11:50:03
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Hi Bob Congratulations, as that sounds as a big progress and success. I will nonetheless need a lot of spirits to digest the explanations ;-) All good here. Now starting a relatively easy period without teaching, till February. Best, · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28805 Alcalá de Henares (Madrid), Spain https://biomodel.uah.es/ El 16/11/2023 a las 18:59, Robert Hanson via Jmol-developers escribió: > *ATENCIÓN*: Este correo electrónico se envió desde fuera de la UAH. No > haga clic en enlaces ni abra archivos adjuntos a menos que reconozca > al remitente y sepa que el contenido es seguro. > Jmol Developers, > > Not sure if you are on this list you still have any interest in Jmol, > but I hope some of you do. > > Well, it's done. The JSmol sourceforge project at > https://sourceforge.net/p/jsmol > <https://sourceforge.net/p/jsmol> > is now no longer needed. I've placed all the files that were in that > project into the /unused/ folder there. This is so that we still can > track the histories of the files if we need to. But probably that will > not be necessary. > > This past week I totally overhauled the way the transpiler works. For > the past 10 years, the transpiler that was being used for Jmol only > worked in a very old version of Eclipse "Juno" from (I think) 2013. > This has been an enormous pain. For at least eight years I have > avoided doing anything with this old transpiler. > > I finally took the step to revisit the prototype "java2script 4.2" > code from 2013, and I realized that it was not so bad and that would > be possible to add that code to the SwingJS transpiler plugin as an > alternative transpiler option. > > That has worked perfectly. The new plugin is j2s.core_5.0.1.jar, at > https://github.com/BobHanson/java2script/tree/master/sources/net.sf.j2s.core > <https://github.com/BobHanson/java2script/tree/master/sources/net.sf.j2s.core> > > And, as a bonus, we now can adapt the legacy 4.2 transpiler, which is > only ever to be used with Jmol anyway, to future needs. The first > thing I did was move it up to Java 8 (Though it still only recognizes > Java 6 syntax.) One of the things I did was to give it a way to > deliver JavaScript code ready for running directly into the site/ > directory. This was huge, because previously there were a series of > ANT tasks that had to be run to do all sorts of minor tweaking of that > output before one could test in JavaScript. > > But now, it's very clean and simple. You modify Java code for Jmol, > save the .java file, and open your browser to see how it runs in > JavaScript. Your changes are instantly there. Full integration. The > way it should be. Hooray! > > And then I realized that we didn't need the JSmol project at all. > Originally, the idea was to do all the transpiling in this separate > project, just using the code that relates to the applet. But now this > is not necessary. Once I got the transpiler doing what the ANT tasks > were doing (and I was able to fix the various bugs in the 4.2 > transpiler that were causing these problems in the first place), I > realized that the only thing the JSmol project was doing (yesterday) > was to add some more files. So I figured I would just put those files > in the Jmol project (into site-resources/ and site-resources-zip). > That's all checked in now. > > Happy to report that that went smoothly, and I was able to fix a few > more bugs while at it. > > So, in short, the Jmol project is alive and well at SourceForge, now > using the same transpiler plugin as SwingJS. Just the two projects - > Jmol, on SourceForge, and java2script on GitHub. (OK, there's also the > Jmol-SwingJS GitHub project, that's true.) No old versions of Eclipse > are necessary. So long, Luna!! There's just the one plugin. > > And my life is way easier. Retirement (from teaching) is just > terrific. The bicycling season is just about over here; looks like I > will hit 4000 km this year. > > Drop me a line and tell me how you are doing. > > Bob > > -- > Robert M. Hanson > Professor of Chemistry, Emeritus > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > <http://www.stolaf.edu/people/hansonr> > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > /We stand on the homelands of the Wahpekute Band of the Dakota Nation. > We honor with gratitude the people who have stewarded the land > throughout the generations and their ongoing contributions to this > region. We acknowledge the ongoing injustices that we have committed > against the Dakota Nation, and we wish to interrupt this legacy, > beginning with acts of healing and honest storytelling about this place./ > > > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers |
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