Re: [Jmol-developers] Tag Jmol releases

inction is still there. Nico > On Tue, Aug 30, 2016 at 10:22 AM, Nicolas Vervelle <nverve...@gmail.com> > wrote: > >> >> >> On Tue, Aug 30, 2016 at 10:16 AM, Spencer Bliven < >> spencer.bli...@gmail.com> wrote: >> >>> I would advocate that

Re: [Jmol-developers] Tag Jmol releases

On Tue, Aug 30, 2016 at 10:16 AM, Spencer Bliven wrote: > I would advocate that maven should get a new artifact whenever sourceforge > gets a new jar. For this reason I've been including the date as part of the > version number. There is no way to silently replace a

[Jmol-developers] Test

Sorry for the disturbance... Nico -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more.

Re: [Jmol-developers] Java 9 issue

Hi Bob, Apparently, this is a change that is planned for Java 9: to remove the possibility to use '_' as an identifier. See http://openjdk.java.net/jeps/213 and https://bugs.openjdk.java.net/browse/JDK-8061549 It was just a convenient way for defining translatable strings, but we can change it

Re: [Jmol-developers] SVN access problem

On Mon, Jul 27, 2015 at 1:11 PM, Michael Banck mba...@debian.org wrote: On Mon, Jul 27, 2015 at 01:02:17PM +0200, Nicolas Vervelle wrote: SVN access should have been restored this weekend by sourceforge. I heard some project lost a couple of SVN revisions because the backup did not contain

Re: [Jmol-developers] list bounces

Hi, Yes, I handle this from time to time. I'm currently traveling a lot, so not too much lately. Nico On Fri, Jan 23, 2015 at 2:55 PM, Angel Herráez angel.herr...@uah.es wrote: El 23 Jan 2015 a las 7:02, Robert Hanson escribió: Who is handling these? Anyone?

Re: [Jmol-developers] http://wiki.jmol.org/index.php/Main_Page

Bob, Page is populated through templates (the {{...}}). When you are previewing in edit mode, you can see at the bottom of the page a list of templates used on this page. Click on the one you want to modify. Nico On Tue, Jul 29, 2014 at 10:26 AM, Robert Hanson hans...@stolaf.edu wrote:

Re: [Jmol-developers] Jmol web site

Hi guys, Currently, all elements to build Jmol website are under SVN in the Jmol-web Eclipse project. As Angel said, I think it requires a lot of work to update it with the current status of Jmol. The Jmol-web project contains 2 Ant build files: - build.xml for building a local version of

Re: [Jmol-developers] [Jmol-users] last chance before Jmol 14.1.11; JJSME/JSpecView

Just forgot to answer about the .tstamp files: just ignore them, they are here to speed up compilation when nothing has changed. On Mon, Mar 10, 2014 at 2:31 PM, Nicolas Vervelle nverve...@gmail.comwrote: Hi Bob, I haven't take care of the translations for quite some time... For updating

Re: [Jmol-developers] [Jmol-users] last chance before Jmol 14.1.11; JJSME/JSpecView

Hi Bob, I haven't take care of the translations for quite some time... For updating the .pot and .po files with the texts in the Java files, if you already have gettext tools installed, you just have to set to true the two variables you have found and commit at the end. It may be better not to

Re: [Jmol-developers] Test of Jmol applet signed with a trusted certificate

On Thu, Nov 7, 2013 at 10:10 AM, Rzepa, Henry S h.rz...@imperial.ac.ukwrote: Forgot to mention that I did get this message when I attempted to run the newly signed applet Its the usual message about the JAR file manifest does not contain the Permissions attribute and will be blocked in

Re: [Jmol-developers] Test of Jmol applet signed with a trusted certificate

On Thu, Nov 7, 2013 at 10:14 AM, Nicolas Vervelle nverve...@gmail.comwrote: On Thu, Nov 7, 2013 at 10:10 AM, Rzepa, Henry S h.rz...@imperial.ac.ukwrote: Forgot to mention that I did get this message when I attempted to run the newly signed applet Its the usual message about the JAR

Re: [Jmol-developers] January 2014

Hi Bob, Hard constraints are indeed being added to Java for applets and JNLP :-( I think it will still be possible to use self signed applets locally for development by circumventing this mechanism : a trusted certificate is nothing more than a certificate issued by a root certificate authority

Re: [Jmol-developers] January 2014

complex this is going to be within an organization that requires local testing. Right? On Wed, Nov 6, 2013 at 8:08 AM, Nicolas Vervelle nverve...@gmail.comwrote: Hi Bob, Hard constraints are indeed being added to Java for applets and JNLP :-( I think it will still be possible to use self

Re: [Jmol-developers] January 2014

it when I see it. That's not one of options they mention in the blog. Seems to me that would have been the obvious solution. On Wed, Nov 6, 2013 at 8:30 AM, Nicolas Vervelle nverve...@gmail.comwrote: You misunderstood me. You will need to sign Jmol applet even to test it locally, I agree

[Jmol-developers] Test of Jmol applet signed with a trusted certificate

Hi, I've produced jars for Jmol signet applet that are signed with my own trusted certificate. The jars are also time-stamped. You can try them by downloading at http://site4145.mutu.sivit.org/Temporary/JmolAppletSigned.zip Nico

Re: [Jmol-developers] Important Java changes - January 2014

Hi Bob, For a certificate from a trusted authority, you can get one from Certum for free as an open source developer. I got one about two weeks ago, and it seems to work ok. https://www.certum.eu/certum/cert,offer_en_open_source_cs.xml Nico On Thu, Oct 31, 2013 at 11:38 PM, Robert Hanson

Re: [Jmol-developers] I've got all my machines synced to the repository Jmol as of today… when are we switching over?

Hi Bob, I'm still travelling with poor internet access. I let you do it, or it will have to wait two weeks. Cheers Nico On Sun, Mar 10, 2013 at 3:05 AM, Robert Hanson hans...@stolaf.edu wrote: I'm synced. Nico -- do you want to initiate the upgrade? I won't check anything in until I hear

Re: [Jmol-developers] Next release is..?

Hi, I'm currently travelling abroad, and so far the internet accesses I had weren't very fast. If I get a fast access at some point, I will do the release, otherwise it will have to wait a month or for someone else to make this release. Nicolas On Thu, Feb 21, 2013 at 11:17 AM, N David Brown

Re: [Jmol-developers] How to build the Maven artifact?

Hi, The Maven artifact is generated using tools/jmol-sonatype.xml. Nico On Thu, Feb 14, 2013 at 11:04 PM, N David Brown hubd...@gmail.com wrote: How do you generate the Maven artifact available in Maven Central from your Jmol SVN working directory? Running any of the build.xml variants

Re: [Jmol-developers] JMol + Naga

No idea... I don't even know what we are using Naga for (I don't see it in the project). But it's probably not very difficult to go up one release. Nico On Mon, Dec 31, 2012 at 6:06 PM, Robert Hanson hans...@stolaf.edu wrote: I'm sure we can. Nico, is this something you are familiar with? Is

Re: [Jmol-developers] lots of spam in Jmol Wiki

Hi Angel, I've started the upgrade this weekend (wiki is in read only mode for the moment). I tried to upgrade to MW 1.20, but my hosting service doesn't have the required version of PHP. I've to try with MW 1.19. Nico On Fri, Nov 23, 2012 at 9:18 PM, Nicolas Vervelle nverve...@gmail.comwrote

Re: [Jmol-developers] lots of spam in Jmol Wiki

Hi Angel, You're right, we should put something more to fight against this. ConfirmAccount extension seems now available again. I'll try to upgrade the wiki this weekend and put ConfirmAccount in service. Nico On Fri, Nov 23, 2012 at 9:15 PM, Angel Herráez angel.herr...@uah.es wrote: Hi Nico

Re: [Jmol-developers] Jmol releases in maven repository?

On Tue, May 29, 2012 at 9:43 AM, Tomas Pluskal plus...@oist.jp wrote: Do you plan to have both stable releases (12.2.x currently) and pre-releases (12.3.x currently) ? How would they be distinguished so that people wanting only stable releases will automatically get the last stable release

Re: [Jmol-developers] Jmol releases in maven repository?

Hi Tomas, Ok also for me for deploying Jmol releases into a Maven repository. I'm already using an Ant script for deploying Jmol releases into sourceforge (tools/jmol-release.xml). If you can write the scripts for the deployment, the maven deployment could be added in this script. Nico On Mon,

Re: [Jmol-developers] Optimizing Chinese Translation

Hi, I have just included the latest translations done on launchpad in Jmol trunk. They will be available in SVN in a few minutes Nico On Sat, May 19, 2012 at 5:53 AM, Gong Zhang u5094...@anu.edu.au wrote: Hi, I am trying to do Chinese translation in the launchpad service. Thanks.

Re: [Jmol-developers] Optimizing Chinese Translation

Hi, For changing translations, you have at least 2 ways : - Use launchpad service to translate directly there. I check regularly if new translations have been done and include them in Jmol - Translate directly the .po files, and send them either to me, Angel, the developers list, ...

Re: [Jmol-developers] Hi everyone

Welcome, Any interests in specific parts/features of Jmol ? Nico On Fri, Apr 20, 2012 at 10:21 AM, Gong Zhang u5094...@anu.edu.au wrote: Hi, I am pleasure to join the developer group of Jmol. I have check out the source code and build the project in the IDE. Firstly, I will read and

Re: [Jmol-developers] file and popup dates do not match in 12.2.16

Should be working that way for next releases. On Mon, Mar 5, 2012 at 10:00 PM, Robert Hanson hans...@stolaf.edu wrote: If we could switch that to the properties file, that would be better. On Mon, Mar 5, 2012 at 1:49 PM, Nicolas Vervelle nverve...@gmail.comwrote: Hi, The problem

Re: [Jmol-developers] Catalan translation update

Hi, Thanks for the translation, I've included it in Jmol, it will be available in the next release 12.3.x release. Nico 2012/3/23 Adrià Cereto Massagué ssorga...@gmail.com Hello, I have updated the catalan translation of JmolApplet. msgfmt gives some warnings but I see nothing wrong with

Re: [Jmol-developers] Do we need to initialize the graphics environment when Jmol is running headless?

Hi, You can check also tools like xvfb which can create a virtual display. Even without the GUI, image generation may require a display for some image operations (like fonts, ...), this is a Java limitation. I used xvfb in several projects where I needed to create images without having a real

Re: [Jmol-developers] file and popup dates do not match in 12.2.16

Hi, The problem is that the date displayed in the menu comes from the last time JmolConstants.java file was committed in SVN. (JmolConstants.java, lines 85 and 86) Nico 2012/3/1 Angel Herráez angel.herr...@uah.es El 28 Feb 2012 a las 11:23, Robert Hanson escribió: feel free! The splash is

Re: [Jmol-developers] Links to Jmol Wiki broken.

Hi, The Jmol wiki is available at http://wiki.jmol.org (without the 81 port) Apparently, we forgot to update one link when we changed the wiki configuration a long time ago (I checked other links that seems ok) Nico On Tue, Jan 17, 2012 at 4:27 PM, Aalex Gabi aalexg...@gmail.com wrote:

Re: [Jmol-developers] Links to Jmol Wiki broken.

Ok :) 2012/1/17 Angel Herráez angel.herr...@uah.es Nico, if you want I can revise all links in the website and put any fixes and commit. Then you can update the site. · Dr. Angel Herraez Dep. Bioquimica y Biologia Molecular, Universidad de Alcala E-28871 Alcala de Henares (Madrid),

Re: [Jmol-developers] Links to Jmol Wiki broken.

Thanks Angel, Jmol website should be fixed now. Nico 2012/1/17 Angel Herráez angel.herr...@uah.es Done and committed. On 17 Jan 2012 at 20:04, Nicolas Vervelle wrote: Ok :) -- Keep Your Developer Skills

Re: [Jmol-developers] Fwd: [Launchpad-translators] Release of Jmol 12.2

Hi Bob, I thought again about this translation business. What is the current status ? If I understood correctly : - There's 1 text having a [...] that should be kept in the displayed text (bad [R, G, B] color) - 1 or 2 texts having a [...] that should be removed in the displayed text

Re: [Jmol-developers] Fwd: [Launchpad-translators] Release of Jmol 12.2

or remove the [[ ]] -- we will have to check for those anyway. Yes. Bob On Fri, Oct 7, 2011 at 6:26 AM, Nicolas Vervelle nverve...@gmail.comwrote: Hi Bob, I thought again about this translation business. What is the current status ? If I understood correctly : - There's 1 text

[Jmol-developers] Fwd: [Launchpad-translators] Release of Jmol 12.2

that would only display Top) ? Nico -- Forwarded message -- From: Ilia Lilov lilo...@gmail.com Date: Tue, Oct 4, 2011 at 2:30 AM Subject: Re: [Launchpad-translators] Release of Jmol 12.2 To: Nicolas Vervelle nverve...@gmail.com Nicolas, I contributed a bit to Russian translation

Re: [Jmol-developers] Fwd: [Launchpad-translators] Release of Jmol 12.2

:32 AM, Nicolas Vervelle nverve...@gmail.com wrote: I made an announcement on launchpad mailing list for the release of Jmol 12.2. Did the updated for 'Dutch' came through properly? Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet

Re: [Jmol-developers] Jmol 12.2.0 ready for release

Hi, I was sailing the last few days, so unable to check the problem. I'm answering from my mobile. AFAIR, strings are added to Jmol or JmolApplet po files depending on the package they are. Are there new packages that should on the JmolApplet? The selection of packages for JmolApplet is

Re: [Jmol-developers] Refactoring ideas for cleaner code

On Wed, Aug 3, 2011 at 11:43 PM, Robert Hanson hans...@stolaf.edu wrote: On Wed, Aug 3, 2011 at 4:31 PM, Nicolas Vervelle nverve...@gmail.comwrote: Hi Bob, I agree about putting the constants in a new package, a little preference for org.jmol.constants (we may have other things than enum

Re: [Jmol-developers] Refactoring ideas for cleaner code

it easy to find those you are interested in, without have a good idea what they are called. I think we just need to categorize them more carefully. Jonathan On Aug 2, 2011, at 1:03 PM, Nicolas Vervelle wrote: Hi, Looking at JmolConstants, I think we could refactor it to have much cleaner

Re: [Jmol-developers] Refactoring ideas for cleaner code

is essentially done, so I'll be slowing down for a week or so. Bob On Wed, Aug 3, 2011 at 1:09 PM, Nicolas Vervelle nverve...@gmail.comwrote: I have just committed a simple example of using Enum on the axes mode : - Revision 15918 in SVN - Changes http://bazaar.launchpad.net

[Jmol-developers] Refactoring ideas for cleaner code

Hi, Looking at JmolConstants, I think we could refactor it to have much cleaner code in Jmol. I think especially about the list of constants. Since we are now using Java 5 code, what do you think about using Enum ? For example, replacing all the CALLBACK_xxx constants and callbackNames[] by an

Re: [Jmol-developers] Wiki - recent proliferation of abusive newusers

Hi, The email confirmation mechanism only worked correctly for a few days :( I have decided to reinforce the access by authorizing several kinds of modifications (page creation, file uploading, ...) to users that have been registered for at least 4 days. Since then, 9 days ago, we had only one

Re: [Jmol-developers] Latest stable Jmol release and problem with popup menu language

), and the name is saved in a Hashtable, so then only one is updated. I have deleted the Edit/Select items because that's not really what we are doing -- Display/Select makes more sense. Alternatively we could leave them there and rename all the keys. Bob On Wed, Mar 23, 2011 at 1:06 PM, Nicolas

Re: [Jmol-developers] Latest stable Jmol release and problem with popup menu language

Hi Johannes, I tried running the current Jmol application, and I see the following problem : the Edit/Select menu stays in the language in which the application was started, even after changing language using the popup menu. Bob, has something been modified when switching language ? Nico On

Re: [Jmol-developers] report: users cleanup in the Wiki

Hi Angel, Thanks for the work done on the users list. It's a lot cleaner now. We have less vandalism than before, but unfortunately it's not down to zero :( And we still have a lot of new users each day, without any contributions : it's not a big problem, but the user list will probably grow

Re: [Jmol-developers] Wiki - recent proliferation of abusive new users

, Mar 5, 2011 at 10:00 PM, Nicolas Vervelle nverve...@gmail.comwrote: ReCaptcha is now up and running on Jmol wiki. I left the default configuration : I think it is just triggered on a new user account or on bad login or on adding an url link in a page. If you think we should change

Re: [Jmol-developers] Wiki - recent proliferation of abusive newusers

On Sun, Mar 6, 2011 at 1:48 PM, jaime.prilu...@weizmann.ac.il wrote: According to Nicolas Vervelle nverve...@gmail.com: It seems that ReCaptcha is not enough to prevent spamming and vandalism :( Several edits since yesterday. I have modified the wiki configuration so that email

Re: [Jmol-developers] Wiki - recent proliferation of abusive new users

are still allowing users to create their own accounts, but no more spam since. Andreas 2011/3/4 Angel Herráez angel.herr...@uah.es: El 4 Mar 2011 a las 18:29, Nicolas Vervelle escribió: Do you think we should installUser_Merge_and_Deleteto merge the spammers account and reduce the list

Re: [Jmol-developers] Wiki - recent proliferation of abusive new users

ReCaptcha is now up and running on Jmol wiki. I left the default configuration : I think it is just triggered on a new user account or on bad login or on adding an url link in a page. If you think we should change the configuration, tell me. Nico On Sat, Mar 5, 2011 at 9:46 PM, Nicolas Vervelle

Re: [Jmol-developers] Wiki - recent proliferation of abusive new users

Forgot to answer to the list also... On Fri, Mar 4, 2011 at 6:21 PM, Nicolas Vervelle nverve...@gmail.comwrote: Hi again, We should first try installing ConfirmEdithttp://www.mediawiki.org/wiki/Extension:ConfirmEdit and ReCAPTCHA http://www.mediawiki.org/wiki/Extension:ReCAPTCHA to see

Re: [Jmol-developers] Wiki - recent proliferation of abusive new users

2011/3/4 Angel Herráez angel.herr...@uah.es El 4 Mar 2011 a las 18:29, Nicolas Vervelle escribió: Do you think we should installUser_Merge_and_Deleteto merge the spammers account and reduce the list of such accounts ? It sounds the reasonable thing, but what I read on the web

[Jmol-developers] Changes for Jmol in Launchpad

Hi everyone, Just for information. The translations for Jmol are managed with Launchpad at https://translations.launchpad.net/jmol I have done some configuration changes recently that should make the translations management easier : - The code under SVN in sourceforge is now replicated

Re: [Jmol-developers] Finnish translations for Jmol

Hi Johannes, Thanks for the translations ! I have finished including them in Jmol. It will be in the next version (12.1.30) that will be released. The translation is now available in launchpad https://translations.launchpad.net/jmol/trunk/+lang/fi Nico 2011/1/3 Angel Herráez

Re: [Jmol-developers] [Jmol-users] Language about Jmol Web Page Maker

Hi Angel, For the problem compiling Jmol with the new language menu, I only modified build.xml to tell the Java compiler that the source files were encoded in UTF8 (otherwise, it was deciding alone what the encoding was). I believe Java Strings are quite agnostic about the encoding. It's only

Re: [Jmol-developers] [Jmol-users] Language about Jmol Web Page Maker

it might be that we lose the encoding when passing strings at some point. Jonathan On Dec 20, 2010, at 12:05 PM, Nicolas Vervelle wrote: Hi Angel, For the problem compiling Jmol with the new language menu, I only modified build.xml to tell the Java compiler that the source files were

Re: [Jmol-developers] localizations available from popup

Hi Angel, Building works fine on my computer. The problems seems to come from the encoding used by Java when you compile (I had to change GT.java encoding to UTF8). I've just committed a modification to force using UTF8 when building. Tell me if it works better. Nico 2010/12/17 Angel Herráez

Re: [Jmol-developers] localizations available from popup

Angel, The menu is broken on my computer with the last fix. It only shows 4 lines : null - Català, ..., null - Deutsch. Nico 2010/12/17 Angel Herráez angel.herr...@uah.es Works great, Nico! No complains building now. All languages display well in the menu (I see blocks for those whose

Re: [Jmol-developers] localizations available from popup

Bob, It's fixed, the problem was only that there was no encoding specified for the build, so the encoding used was depending on the computer used to build. I changed the build to force UTF8 encoding. Nico On Fri, Dec 17, 2010 at 11:44 PM, Robert Hanson hans...@stolaf.edu wrote: I see --

[Jmol-developers] Errors in unit tests

Hi Bob, Several errors in unit tests. ** junit.framework.AssertionFailedError: Error returned for ..\Jmol-datafiles\mol\f_socl2b.mol: Error reading file at line 9: 1 2 1 null for file f_socl2b.mol type Mol ** junit.framework.AssertionFailedError: Error returned for

Re: [Jmol-developers] Errors in unit tests

/alanine.2D.v3000 On Fri, Dec 17, 2010 at 4:49 PM, Nicolas Vervelle nverve...@gmail.comwrote: Hi Bob, Several errors in unit tests. ** junit.framework.AssertionFailedError: Error returned for ..\Jmol-datafiles\mol\f_socl2b.mol: Error reading file at line 9: 1 2 1 null for file

Re: [Jmol-developers] localizations available from popup

Hi, It's available under SVN. Nico On Wed, Dec 15, 2010 at 1:16 PM, Nicolas Vervelle nverve...@gmail.comwrote: 2010/12/14 Angel Herráez angel.herr...@uah.es I would rather see 3 things in the menu : the language code, the language name in English, the language name in its own language

Re: [Jmol-developers] localizations available from popup

2010/12/14 Angel Herráez angel.herr...@uah.es I would rather see 3 things in the menu : the language code, the language name in English, the language name in its own language. That sounds great. After thinking again about it, I changed my mind. We should display 3 things in the menu :

Re: [Jmol-developers] localizations available from popup

Hi Angel, There may be an easy way to add a language in the popup menu if is choosen by the used. When switching language, I think GT.getTranslation() is called, which may result in a call to addBundle(). In addBundle(), we could parse the language list array, and if needed change the false to a

Re: [Jmol-developers] localizations available from popup

Yes, It would be better to add the language in the popup menu if it's used. I don't know if it's complex to implement. Nico 2010/12/13 Angel Herráez angel.herr...@uah.es I realize that certain localizations are still in an immature state, but if the JmolApplet0_i18n_pl.jar file is included

Re: [Jmol-developers] jmol for mediawiki 1.16

Hi, On Mon, Nov 22, 2010 at 1:08 AM, Alexander Schröter accou...@computational-chemistry.org wrote: Wonderful :) I just got the new files. Do you have some bug reporting where I can give you some feedback. For starters here is what I got [Mon Nov 22 00:45:47 2010] [error] [client

Re: [Jmol-developers] Ideas for Jmol extension for MediaWiki

cactus.nci.nih.gov) or a PDB code (other than www.rcsb.org) ? That way, the syntax will still be the same in Jmol script (load $SMILES or load =PDB) but the call will go through the wiki server. Nico On Sun, Nov 28, 2010 at 11:39 PM, Nicolas Vervelle nverve...@gmail.comwrote: Hi, The Jmol extension

Re: [Jmol-developers] Ideas for Jmol extension for MediaWiki

, Nicolas Vervelle wrote: Hi, I have started working again on the extension to include Jmol in Wikipedia. The current extension is not as simple as some Wikipedia people would like (see this bugzilla report). One idea there is that a Media handler for molecular files should be developed

Re: [Jmol-developers] Help with Installation 1.16 Mediawiki

the possibility to include Jmol applets in MediaWiki. Nicolas Vervelle, Angel Herraez und Jmol Development Team FCKeditor (Version fckeditor/mw-extension $Rev$ 2008) FCKeditor extension for editing wiki pages (WYSIWYG editor) FCKeditor.net und Wikia Google Analytics Integration (Version

[Jmol-developers] Ideas for Jmol extension for MediaWiki

Hi, I have started working again on the extension to include Jmol in Wikipedia. The current extension is not as simple as some Wikipedia people would like (see this bugzilla reporthttps://bugzilla.wikimedia.org/show_bug.cgi?id=16491 ). One idea there is that a Media handler for molecular files

Re: [Jmol-developers] jmol for mediawiki 1.16

Hello Angel, Yes, StubManager is no longer needed, happy to get rid of it. Help is welcome if you want to update the documentation :) I had the impression yesterday that the popup window wasn't working. I also had a look at the OggHandler extension, which apparently can display useful things

Re: [Jmol-developers] jmol for mediawiki 1.16

On Mon, Nov 22, 2010 at 1:08 AM, Alexander Schröter accou...@computational-chemistry.org wrote: Wonderful :) I just got the new files. Do you have some bug reporting where I can give you some feedback. For starters here is what I got [Mon Nov 22 00:45:47 2010] [error] [client

Re: [Jmol-developers] jmol for mediawiki 1.16

Hi Angel and others, On Mon, Nov 22, 2010 at 12:31 PM, Nicolas Vervelle nverve...@gmail.comwrote: I also had a look at the OggHandler extension, which apparently can display useful things for files in ogg format (same kind with PdfHandler). I think that would be nice to have the same kind

Re: [Jmol-developers] jmol for mediawiki 1.16

Hi Angel, No problem if it has to wait, I am also quite loaded, it took me more than a month to look at the extension not working under MW 1.16.0... I already have some work to do to understand how it can be done (the hook to display more informations on the File:... page) and don't know when I

Re: [Jmol-developers] Wiki is down and has been since this weekend...Can someone fix?

Wiki is up again, the migration to 1.16.0 seems to have solved the problem. I still have a lot of work to do to reapply the configuration, add all the extensions, ... and check for potential problems. On Wed, Nov 17, 2010 at 2:04 PM, Nicolas Vervelle nverve...@gmail.comwrote: On Wed, Nov 17

Re: [Jmol-developers] Wiki is down and has been since this weekend...Can someone fix?

I had problems with all the files (images, molecular files, ...) I had to delete all the images and upload them again manually. Please, check if there are mistakes. I still have to take care of the molecular files. Nico On Sun, Nov 21, 2010 at 10:58 AM, Nicolas Vervelle nverve

Re: [Jmol-developers] jmol for mediawiki 1.16

to work, but there are probably a lot of problems to be found when testing. Nico On Tue, Nov 2, 2010 at 3:47 PM, Alexander Schröter accou...@computational-chemistry.org wrote: On Tuesday 02 November 2010 15:38:24 Nicolas Vervelle wrote: Hi, I just came back this weekend, but with my being

Re: [Jmol-developers] Wiki is down and has been since this weekend...Can someone fix?

On Wed, Nov 17, 2010 at 1:53 PM, Alexander Schröter accou...@computational-chemistry.org wrote: Am Mittwoch, 17. November 2010, um 00:05:01 schrieb Jonathan Gutow: I was thinking of trying to upgrade to latest MediaWiki (1.16.0), but I need some free time to do this. If you update to

Re: [Jmol-developers] Wiki is down and has been since this weekend...Can someone fix?

Hi, I tried to change the configuration this weekend (allowing uploading pdb files), but something went wrong (I don't know what). I have changed LocalSettings.php and includes/DefaultSettings.php. I tried to go back to the original configuration, but without any useful result. I don't have much

Re: [Jmol-developers] jmol for mediawiki 1.16

... Nico should be back by now, right? Am Mittwoch, den 20.10.2010, 16:32 +0200 schrieb Nicolas Vervelle nverve...@gmail.com: 2010/10/19 Angel Herráez Has Nico taken a look at this? Nico is travelling and cannot check the wiki config for some weeks. Hi Alexander, I am currently

Re: [Jmol-developers] jmol for mediawiki 1.16

2010/10/19 Angel Herráez angel.herr...@uah.es Has Nico taken a look at this? Nico is travelling and cannot check the wiki config for some weeks. Hi Alexander, I am currently travelling for my company. I have a lot of work and a very loosy internet connection in my hotel, so I can't do much

Re: [Jmol-developers] [Jmol-users] jmolScriptWait causes exception in 12.1 branch

an iterator -- get the keys as an array and run through them. I'll work on it tonight. On Tue, Sep 7, 2010 at 12:58 PM, Nicolas Vervelle nverve...@gmail.comwrote: Hi Bob, I have just looked into the code involved, and I believe it's not a multithread problem. It's simply that we're

Re: [Jmol-developers] Getting rid of 'dead code' warnings ?

? If the statements really are the syntax you are suggesting they make little sense. Jonathan On Aug 17, 2010, at 12:12 PM, Nicolas Vervelle wrote: Hi, Could we get rid of the 'dead code' warnings ? Most of them are due to code like : if (true || xxx) ... which makes xxx a dead code. If it's

[Jmol-developers] Getting rid of 'dead code' warnings ?

Hi, Could we get rid of the 'dead code' warnings ? Most of them are due to code like : if (true || xxx) ... which makes xxx a dead code. If it's intended, I see 2 ways of removing the warning : - Removing the dead code (if the true is definitive, it will clear it definitely) -

Re: [Jmol-developers] status?

Fully compilable (only ~3000 warnings), and hopefully working correctly. On Wed, Aug 4, 2010 at 3:48 PM, Robert Hanson hans...@stolaf.edu wrote: Nico, what's the status of 12.1? All working? Is it compilable? I'm checking it out now. I did check in a couple of files (SmarterJmolAdapter and

Re: [Jmol-developers] status?

Hanson hans...@stolaf.edu wrote: OK, I reverted my changes to those files and resent them. Did you end up changing any actual object types, like Hashtable to Hashmap? On Wed, Aug 4, 2010 at 8:57 AM, Nicolas Vervelle nverve...@gmail.comwrote: Fully compilable (only ~3000 warnings

Re: [Jmol-developers] status?

encountered a few strange things doing this, so I have let some unchanged. Among the 3500 initial warnings, there are only 1000 left. Nico On Wed, Aug 4, 2010 at 4:15 PM, Nicolas Vervelle nverve...@gmail.comwrote: For Hashtable, I only made some changes to use Generics : HashtableK, V I changed

Re: [Jmol-developers] Java 1.5 ?

comments - ... Nico On Tue, Jul 27, 2010 at 10:39 AM, Nicolas Vervelle nverve...@gmail.comwrote: Yes, That's part of the optimizations that could be made. For going to real Java 1.5 code, I suggest waiting until the 12.0 branch is created, and I will start doing some modifications

Re: [Jmol-developers] Java 1.5 ?

, Nico. I'll plan on NOT doing coding at the BCCE this next week, I think, or perhaps the 6-hour time difference will keep us on different schedules. Anyway, this week end it's all yours! Bob On Sat, Jul 31, 2010 at 4:45 AM, Nicolas Vervelle nverve...@gmail.comwrote: Hi, I have started

Re: [Jmol-developers] Java 1.5 ?

:29 PM, Egon Willighagen egon.willigha...@gmail.com wrote: On Sat, Jul 24, 2010 at 8:17 PM, Nicolas Vervelle nverve...@gmail.com wrote: In fact, that would already be the case with Java 1.5. Generics are in Java 1.5 (VectorString and so on...) More importantly... Replace Vector

[Jmol-developers] Java 1.5 ?

Hi everyone, We are currently building Jmol for at least Java 1.5. What about modifying Jmol code to take more advantages of Java 1.5 features (annotations, generics, ...) ? On the other side, it won't be possible to compile Jmol with older versions of Java. Nico

Re: [Jmol-developers] Java 1.5 ?

...@uwosh.edu wrote: On Jul 24, 2010, at 6:00 AM, Nicolas Vervelle wrote: On the other side, it won't be possible to compile Jmol with older versions of Java. I don't think this is much of an issue as 1.4 is no longer supported. Jonathan Even 1.5 is no longer supported. Egon -- Post-doc

Re: [Jmol-developers] packaging jmol, was Re: I want to contribute

Hi, These files are under SVN, so they could also be released in the source distribution. The only thing is that this certificate is simply a self signed one, so without any real security. If someone wants to really use the signed applet, I suggest resigning the official applet with a correct

Re: [Jmol-developers] Is is time to update the vecmath library we use?

Hi Miguel, Nice to see you around :) I think javax.vecmath is still part of the Java 3D API, see https://java3d.dev.java.net/ and not included in the standard libraries. Nico On Tue, Jul 13, 2010 at 9:40 PM, Miguel Howard mig...@jmol.org wrote: On Tue, Jul 13, 2010 at 1:23 AM, Robert Hanson

Re: [Jmol-developers] Is is time to update the vecmath library we use?

I just tested quickly what the result would be with vecmath 1.5.2 instead of our current version 1.2-1.14. Basically, the size of JmolApplet0.jar and JmolApplet.jar increases by around 25k. Nico On Mon, Jul 12, 2010 at 10:53 AM, Nicolas Vervelle nverve...@gmail.comwrote: If I find the time, I

Re: [Jmol-developers] Is is time to update the vecmath library we use?

If I find the time, I will try it to see if the size of the applet is modified or not. On Wed, Jul 7, 2010 at 5:42 PM, Robert Hanson hans...@stolaf.edu wrote: don't think so. Probably just make it bigger, not better. On Mon, Jul 5, 2010 at 9:44 AM, Jonathan Gutow gu...@uwosh.edu wrote: I

[Jmol-developers] Smiles test error

Hi Bob, One of the test for the smiles matcher (Chapter7_17) provoke an error : org.jmol.smiles.InvalidSmilesException: Invalid stereochemistry descriptor at org.jmol.smiles.SmilesParser.checkChirality(SmilesParser.java:817) at org.jmol.smiles.SmilesParser.parseAtom(SmilesParser.java:540)

[Jmol-developers] Crystal reader crash

Hi, When running the unit tests, I have several exceptions for the crystal reader : java.lang.StringIndexOutOfBoundsException: String index out of range: 28 at java.lang.String.substring(String.java:1935) at

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