Re: [Jmol-users] Jmol on Maven Central

[Spencer Bliven]

I wonder if it is worth noting somewhere more prominant specifically that
Jmol does not use semantic versioning. This seems to be confusing for many
developers.

On Mon, Oct 24, 2016 at 7:52 PM, Mark Williamson  wrote:

>
>
> On 24/10/16 18:22, Robert Hanson wrote:
> > It actually is not metadata. Different releases include the extension of
> > date:
> >
> > 14.6.4_2016.10.30
> >
> > is not the same version as
> >
> > 14.6.4_2016.10.22
> >
> > Sorry if that breaks a convention.
> >
>
>
> Ah, OK. Apologies; I misunderstood. Please ignore my previous comments.
>
> Thanks,
>
> Mark
>
> 
> --
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Re: [Jmol-users] Jmol on Maven Central

[Mark Williamson]

On 24/10/16 18:22, Robert Hanson wrote:
> It actually is not metadata. Different releases include the extension of
> date:
>
> 14.6.4_2016.10.30
>
> is not the same version as
>
> 14.6.4_2016.10.22
>
> Sorry if that breaks a convention.
>


Ah, OK. Apologies; I misunderstood. Please ignore my previous comments.

Thanks,

Mark

--
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Re: [Jmol-users] Jmol on Maven Central

[Robert Hanson]

It actually is not metadata. Different releases include the extension of
date:

14.6.4_2016.10.30

is not the same version as

14.6.4_2016.10.22

Sorry if that breaks a convention.


On Mon, Oct 24, 2016 at 10:39 AM, Mark Williamson  wrote:

> On 26/08/16 13:39, Robert Hanson wrote:
> > Excellent! Thanks, Nico, Spencer, and Mark.
> >
>
> Dear Spencer, Nico and Bob,
>
> It is great to see the 14.x Jmol artefacts being deployed to Maven central:
>
>
> http://search.maven.org/#search%7Cgav%7C1%7Cg%3A%22net.
> sourceforge.jmol%22%20AND%20a%3A%22jmol%22
>
> Thank you for all your efforts here.
>
>
> I also notice now that a useful piece of metadata, i.e. the date of
> release, is being appended to the version number. I know this is minor
> point (no pun intended within this context), but would it be possible to
> adhere to:
>
>http://semver.org/spec/v2.0.0.html#spec-item-10
>
> i.e. the use of a "+" instead of a "_" to delimit the version from the
> metadata?
>
> Hence
>
>14.6.4_2016.10.21
>
> would become
>
>14.6.4+2016.10.21
>
> Many thanks,
>
> Mark
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
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>



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
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
--
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Re: [Jmol-users] Jmol on Maven Central

[Mark Williamson]

On 26/08/16 13:39, Robert Hanson wrote:
> Excellent! Thanks, Nico, Spencer, and Mark.
>

Dear Spencer, Nico and Bob,

It is great to see the 14.x Jmol artefacts being deployed to Maven central:

 
http://search.maven.org/#search%7Cgav%7C1%7Cg%3A%22net.sourceforge.jmol%22%20AND%20a%3A%22jmol%22

Thank you for all your efforts here.


I also notice now that a useful piece of metadata, i.e. the date of 
release, is being appended to the version number. I know this is minor 
point (no pun intended within this context), but would it be possible to 
adhere to:

   http://semver.org/spec/v2.0.0.html#spec-item-10

i.e. the use of a "+" instead of a "_" to delimit the version from the 
metadata?

Hence

   14.6.4_2016.10.21

would become

   14.6.4+2016.10.21

Many thanks,

Mark


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Re: [Jmol-users] Jmol on Maven Central

[Spencer Bliven]

Currently I need to do the release. Theoretically this should be doable
automatically, but ant isn't that well supported anymore and I was unable
to figure out the configuration yet.

Bob, I do think it would be a good idea for you to make a sonatype account
, if only so that
you can authorize additional maintainers if needed.

-Spencer

On Fri, Aug 26, 2016 at 2:39 PM, Robert Hanson  wrote:

> Excellent! Thanks, Nico, Spencer, and Mark.
>
> When I update Jmol to new subversions, will this somehow happen
> automatically, or does Mark or Spencer need to watch out for that and do
> something?
>
> On Fri, Aug 26, 2016 at 5:26 AM, Mark Williamson  wrote:
>
>> On 25/08/16 16:10, Spencer Bliven wrote:
>> > 14.6.1_2016.08.20 is released! At least that's what it says on OSS. It's
>> > not yet showing up in maven central, but I think it might just takes a
>> > few hours to sync.
>> >
>> > Mark, thanks so much for sharing your build notes! They were essential
>>
>> Dear Spencer,
>>
>> Apologies for the recently quietness. Thank you for completing this; it
>> is of tremendous use.
>>
>> I tested an hour ago and I was able pull the new jmol jar down from
>> Maven central via an updated pom in another project. It all works.
>>
>> Best,
>>
>> Mark
>>
>>
>>
>> 
>> --
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> 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
>
>
> 
> --
>
> ___
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> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
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Re: [Jmol-users] Jmol on Maven Central

[Robert Hanson]

Excellent! Thanks, Nico, Spencer, and Mark.

When I update Jmol to new subversions, will this somehow happen
automatically, or does Mark or Spencer need to watch out for that and do
something?

On Fri, Aug 26, 2016 at 5:26 AM, Mark Williamson  wrote:

> On 25/08/16 16:10, Spencer Bliven wrote:
> > 14.6.1_2016.08.20 is released! At least that's what it says on OSS. It's
> > not yet showing up in maven central, but I think it might just takes a
> > few hours to sync.
> >
> > Mark, thanks so much for sharing your build notes! They were essential
>
> Dear Spencer,
>
> Apologies for the recently quietness. Thank you for completing this; it
> is of tremendous use.
>
> I tested an hour ago and I was able pull the new jmol jar down from
> Maven central via an updated pom in another project. It all works.
>
> Best,
>
> Mark
>
>
>
> 
> --
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
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
--
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Re: [Jmol-users] Jmol on Maven Central

[Mark Williamson]

On 25/08/16 16:10, Spencer Bliven wrote:
> 14.6.1_2016.08.20 is released! At least that's what it says on OSS. It's
> not yet showing up in maven central, but I think it might just takes a
> few hours to sync.
>
> Mark, thanks so much for sharing your build notes! They were essential

Dear Spencer,

Apologies for the recently quietness. Thank you for completing this; it 
is of tremendous use.

I tested an hour ago and I was able pull the new jmol jar down from 
Maven central via an updated pom in another project. It all works.

Best,

Mark



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Re: [Jmol-users] Jmol on Maven Central

[Spencer Bliven]

14.6.1_2016.08.20 is released! At least that's what it says on OSS. It's
not yet showing up in maven central, but I think it might just takes a few
hours to sync.

Mark, thanks so much for sharing your build notes! They were essential to
me. I will add a few more notes for future reference:



> Preamble
> -
> 0) Start with a 64 bit install of Ubuntu 14.04.4
>
> 1) Install the following packages
>sudo apt-get install mvn libsaxon-java openjdk-7-jdk ant
>
> 2) Create ~/.jmol.build.properties file with contents
>
>

3) Add your credentials to ~/.m2/settings.xml. This should include both OSS
user/password and a GPG key. Note that GPG is used to sign the full
release, in addition to the JKS self-signature configured in
~/.jmol.build.properties




sonatype-nexus-snapshots
OSS_USERNAME
OSS_PASSWORD


sonatype-nexus-staging
OSS_USERNAME
OSS_PASSWORD


releases
OSS_USERNAME
OSS_PASSWORD




gpg

GPG_KEY
GPG_PASSWORD







Main


1) Checkout the source from SVN or switch to the correct branch

svn checkout http://svn.code.sf.net/p/jmol/code/branches/v14_6 jmol-code
cd jmol-code/Jmol



> 2) Add a required jar to enable docs to be built
>mv ./unused/saxon.jar ./jars/
>
> 3) Build jar target
>ant jar
>
>
> 4) Build dist target
>ant dist
>
>
>
Note that this succeeds for me with an SVN checkout.

You should now have a build/dist-maven directory with the pom and jar files.

5) Stage to OSS

   ant -f ./tools/jmol-sonatype.xml dist-release


(I assume that patch 33  will
be merged in before the next release

6) Go to https://oss.sonatype.org/, find the newly staged release, and
manually 'Close' and 'Release' it. This process should be automatable, but
the 'nexus' plugin referenced in the 'close-release' and 'promote-release'
ant targets is no longer available, and I wasn't able to get its
replacement, the nexus-staging-maven-plugin
, to
work right.
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Re: [Jmol-users] Jmol on Maven Central

[Spencer Bliven]

Thanks a lot, Nico!

On Wed, Aug 24, 2016 at 6:22 PM, Nicolas Vervelle 
wrote:

> Ok,
>
> I've added a comment to request access for you.
> https://issues.sonatype.org/browse/OSSRH-3633?
> focusedCommentId=369327=com.atlassian.jira.plugin.
> system.issuetabpanels:comment-tabpanel#comment-369327
>
> Nico
>
>
> On Wed, Aug 24, 2016 at 11:12 AM, Spencer Bliven  > wrote:
>
>> I volunteer to push releases to maven central. My OSS username is
>> sbliven.
>>
>> To authorize someone, I believe that it is sufficient to add a comment to
>> your OSS project ticket (https://issues.sonatype.org/browse/OSSRH-3633)
>> requesting access for the username.
>>
>> -Spencer
>>
>> On Tue, Aug 23, 2016 at 10:55 PM, Robert Hanson 
>> wrote:
>>
>>> not aware of any volunteers.
>>>
>>> On Tue, Aug 23, 2016 at 10:40 AM, Spencer Bliven <
>>> spencer.bli...@gmail.com> wrote:
>>>
 I just wanted to bump this thread. Any chance of getting a new maven
 maintainer added soon?

 Cheers,
 Spencer

 On Fri, Aug 12, 2016 at 10:19 AM, Spencer Bliven <
 spencer.bli...@gmail.com> wrote:

> So I guess the next step that needs to happen is for Nico to request
> that Mark get added to the OSS ticket. I haven't been an active Jmol
> contributor, but I'd be happy to help with maintaining the maven package 
> if
> you want to add me too (OSS user sbliven).
>
> -Spencer
>
> On Thu, Aug 11, 2016 at 11:29 PM, Robert Hanson 
> wrote:
>
>> all checked in.
>>
>> On Thu, Aug 11, 2016 at 3:09 AM, Spencer Bliven <
>> spencer.bli...@gmail.com> wrote:
>>
>>> Awesome. BioJava has good mmtf support, so if we can get the new
>>> Jmol release into maven then MMTF might be a good exchange format for
>>> passing structures to Jmol. We're currently stuck with using PDB and are
>>> hurting from the limitations (e.g. on chain identifiers & number of 
>>> atoms).
>>>
>>> -Spencer
>>>
>>> On Wed, Aug 10, 2016 at 6:41 PM, Robert Hanson 
>>> wrote:
>>>
 Thanks, Spencer. I am in the process of releasing an important
 update for BioJava, as a matter of fact -- PyMOL 1.8 dump_binary PSE 
 files
 and the new MMTF format from RCSB (which is FANTASTIC by the way...)

 Bob

 On Wed, Aug 10, 2016 at 9:25 AM, Spencer Bliven <
 spencer.bli...@gmail.com> wrote:

> Hey,
>
> I also took a crack at getting the dist-release command to
> complete, since it would be extremely nice to get BioJava using a more
> recent version of Jmol. Using the latest trunk I got all steps to 
> complete
> by modifying tools/jmol-sonatype.xml as you suggest to refer to "
> ${Jmol.properties.Jmol.___JmolVersion}" in line 30. This creates
> the build/dist-maven directory as desired.
>
> Right now only Tomas (plusik) and Nico (nicov) appear to be
> authorized to upload to maven central. It would be great if some 
> additional
> people (e.g. Mark, Bob, perhaps even myself if desired) could get 
> added to
> this. Authorization is granted by adding a user to your OSS
> project ticket (https://issues.sonatype.org/browse/OSSRH-3633).
>
> Any work towards a maven release is much appreciated. Let me know
> if I can do anything to help with this.
>
> -Spencer
>
>
>
> On Sat, Jul 30, 2016 at 4:39 AM, Robert Hanson  > wrote:
>
>> I'm not sure how ${Jmol.properties.___JmolVersion} would be  the
>> version number. In Build.xml it is:
>>
>>   > value="${Jmol.properties.Jmol.___JmolVersion}"
>> />
>>   > override = "true"
>>   input="${version}"
>> regexp='"'
>>   replace=""
>> global="true"
>>   />
>>   
>>
>>
>> So you are missing that regex process.
>>
>>
>>
>> On Mon, Jul 25, 2016 at 9:18 AM, Mark Williamson 
>> wrote:
>>
>>> On 17/05/16 23:15, Robert Hanson wrote:
>>> > Will be checking in Jmol 14.6 release as soon as I can. But
>>> it's not a
>>> Maven release. Someone else has to do that.
>>>
>>> Sorry for the delay in replying. I have been attempting to use
>>> the ant
>>> build script, tools/jmol-sonatype.xml, to build some artifacts
>>> for
>>> deployment to Maven central. Here is my protocol (apologies, I
>>> am not
>>> that familiar with ant and may have made some basic 

Re: [Jmol-users] Jmol on Maven Central

[Nicolas Vervelle]

Ok,

I've added a comment to request access for you.
https://issues.sonatype.org/browse/OSSRH-3633?focusedCommentId=369327=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-369327

Nico


On Wed, Aug 24, 2016 at 11:12 AM, Spencer Bliven 
wrote:

> I volunteer to push releases to maven central. My OSS username is
> sbliven.
>
> To authorize someone, I believe that it is sufficient to add a comment to
> your OSS project ticket (https://issues.sonatype.org/browse/OSSRH-3633)
> requesting access for the username.
>
> -Spencer
>
> On Tue, Aug 23, 2016 at 10:55 PM, Robert Hanson 
> wrote:
>
>> not aware of any volunteers.
>>
>> On Tue, Aug 23, 2016 at 10:40 AM, Spencer Bliven <
>> spencer.bli...@gmail.com> wrote:
>>
>>> I just wanted to bump this thread. Any chance of getting a new maven
>>> maintainer added soon?
>>>
>>> Cheers,
>>> Spencer
>>>
>>> On Fri, Aug 12, 2016 at 10:19 AM, Spencer Bliven <
>>> spencer.bli...@gmail.com> wrote:
>>>
 So I guess the next step that needs to happen is for Nico to request
 that Mark get added to the OSS ticket. I haven't been an active Jmol
 contributor, but I'd be happy to help with maintaining the maven package if
 you want to add me too (OSS user sbliven).

 -Spencer

 On Thu, Aug 11, 2016 at 11:29 PM, Robert Hanson 
 wrote:

> all checked in.
>
> On Thu, Aug 11, 2016 at 3:09 AM, Spencer Bliven <
> spencer.bli...@gmail.com> wrote:
>
>> Awesome. BioJava has good mmtf support, so if we can get the new Jmol
>> release into maven then MMTF might be a good exchange format for passing
>> structures to Jmol. We're currently stuck with using PDB and are hurting
>> from the limitations (e.g. on chain identifiers & number of atoms).
>>
>> -Spencer
>>
>> On Wed, Aug 10, 2016 at 6:41 PM, Robert Hanson 
>> wrote:
>>
>>> Thanks, Spencer. I am in the process of releasing an important
>>> update for BioJava, as a matter of fact -- PyMOL 1.8 dump_binary PSE 
>>> files
>>> and the new MMTF format from RCSB (which is FANTASTIC by the way...)
>>>
>>> Bob
>>>
>>> On Wed, Aug 10, 2016 at 9:25 AM, Spencer Bliven <
>>> spencer.bli...@gmail.com> wrote:
>>>
 Hey,

 I also took a crack at getting the dist-release command to
 complete, since it would be extremely nice to get BioJava using a more
 recent version of Jmol. Using the latest trunk I got all steps to 
 complete
 by modifying tools/jmol-sonatype.xml as you suggest to refer to "${
 Jmol.properties.Jmol.___JmolVersion}" in line 30. This creates the
 build/dist-maven directory as desired.

 Right now only Tomas (plusik) and Nico (nicov) appear to be
 authorized to upload to maven central. It would be great if some 
 additional
 people (e.g. Mark, Bob, perhaps even myself if desired) could get 
 added to
 this. Authorization is granted by adding a user to your OSS
 project ticket (https://issues.sonatype.org/browse/OSSRH-3633).

 Any work towards a maven release is much appreciated. Let me know
 if I can do anything to help with this.

 -Spencer



 On Sat, Jul 30, 2016 at 4:39 AM, Robert Hanson 
 wrote:

> I'm not sure how ${Jmol.properties.___JmolVersion} would be  the
> version number. In Build.xml it is:
>
>    value="${Jmol.properties.Jmol.___JmolVersion}"
> />
>    override = "true"
>   input="${version}"
> regexp='"'
>   replace=""
> global="true"
>   />
>   
>
>
> So you are missing that regex process.
>
>
>
> On Mon, Jul 25, 2016 at 9:18 AM, Mark Williamson 
> wrote:
>
>> On 17/05/16 23:15, Robert Hanson wrote:
>> > Will be checking in Jmol 14.6 release as soon as I can. But
>> it's not a
>> Maven release. Someone else has to do that.
>>
>> Sorry for the delay in replying. I have been attempting to use
>> the ant
>> build script, tools/jmol-sonatype.xml, to build some artifacts for
>> deployment to Maven central. Here is my protocol (apologies, I am
>> not
>> that familiar with ant and may have made some basic errors):
>>
>>
>> Preamble
>> -
>> 0) Start with a 64 bit install of Ubuntu 14.04.4
>>
>> 1) Install the following packages
>>sudo apt-get install mvn libsaxon-java openjdk-7-jdk ant
>>
>> 

Re: [Jmol-users] Jmol on Maven Central

[Spencer Bliven]

I volunteer to push releases to maven central. My OSS username is sbliven.

To authorize someone, I believe that it is sufficient to add a comment to
your OSS project ticket (https://issues.sonatype.org/browse/OSSRH-3633)
requesting access for the username.

-Spencer

On Tue, Aug 23, 2016 at 10:55 PM, Robert Hanson  wrote:

> not aware of any volunteers.
>
> On Tue, Aug 23, 2016 at 10:40 AM, Spencer Bliven  > wrote:
>
>> I just wanted to bump this thread. Any chance of getting a new maven
>> maintainer added soon?
>>
>> Cheers,
>> Spencer
>>
>> On Fri, Aug 12, 2016 at 10:19 AM, Spencer Bliven <
>> spencer.bli...@gmail.com> wrote:
>>
>>> So I guess the next step that needs to happen is for Nico to request
>>> that Mark get added to the OSS ticket. I haven't been an active Jmol
>>> contributor, but I'd be happy to help with maintaining the maven package if
>>> you want to add me too (OSS user sbliven).
>>>
>>> -Spencer
>>>
>>> On Thu, Aug 11, 2016 at 11:29 PM, Robert Hanson 
>>> wrote:
>>>
 all checked in.

 On Thu, Aug 11, 2016 at 3:09 AM, Spencer Bliven <
 spencer.bli...@gmail.com> wrote:

> Awesome. BioJava has good mmtf support, so if we can get the new Jmol
> release into maven then MMTF might be a good exchange format for passing
> structures to Jmol. We're currently stuck with using PDB and are hurting
> from the limitations (e.g. on chain identifiers & number of atoms).
>
> -Spencer
>
> On Wed, Aug 10, 2016 at 6:41 PM, Robert Hanson 
> wrote:
>
>> Thanks, Spencer. I am in the process of releasing an important update
>> for BioJava, as a matter of fact -- PyMOL 1.8 dump_binary PSE files and 
>> the
>> new MMTF format from RCSB (which is FANTASTIC by the way...)
>>
>> Bob
>>
>> On Wed, Aug 10, 2016 at 9:25 AM, Spencer Bliven <
>> spencer.bli...@gmail.com> wrote:
>>
>>> Hey,
>>>
>>> I also took a crack at getting the dist-release command to complete,
>>> since it would be extremely nice to get BioJava using a more recent 
>>> version
>>> of Jmol. Using the latest trunk I got all steps to complete by modifying
>>> tools/jmol-sonatype.xml as you suggest to refer to "${Jmol
>>> .properties.Jmol.___JmolVersion}" in line 30. This creates the
>>> build/dist-maven directory as desired.
>>>
>>> Right now only Tomas (plusik) and Nico (nicov) appear to be
>>> authorized to upload to maven central. It would be great if some 
>>> additional
>>> people (e.g. Mark, Bob, perhaps even myself if desired) could get added 
>>> to
>>> this. Authorization is granted by adding a user to your OSS project
>>> ticket (https://issues.sonatype.org/browse/OSSRH-3633).
>>>
>>> Any work towards a maven release is much appreciated. Let me know if
>>> I can do anything to help with this.
>>>
>>> -Spencer
>>>
>>>
>>>
>>> On Sat, Jul 30, 2016 at 4:39 AM, Robert Hanson 
>>> wrote:
>>>
 I'm not sure how ${Jmol.properties.___JmolVersion} would be  the
 version number. In Build.xml it is:

   >>> value="${Jmol.properties.Jmol.___JmolVersion}"
 />
   >>> override = "true"
   input="${version}"
 regexp='"'
   replace=""
 global="true"
   />
   


 So you are missing that regex process.



 On Mon, Jul 25, 2016 at 9:18 AM, Mark Williamson 
 wrote:

> On 17/05/16 23:15, Robert Hanson wrote:
> > Will be checking in Jmol 14.6 release as soon as I can. But it's
> not a
> Maven release. Someone else has to do that.
>
> Sorry for the delay in replying. I have been attempting to use the
> ant
> build script, tools/jmol-sonatype.xml, to build some artifacts for
> deployment to Maven central. Here is my protocol (apologies, I am
> not
> that familiar with ant and may have made some basic errors):
>
>
> Preamble
> -
> 0) Start with a 64 bit install of Ubuntu 14.04.4
>
> 1) Install the following packages
>sudo apt-get install mvn libsaxon-java openjdk-7-jdk ant
>
> 2) Create ~/.jmol.build.properties file with contents
>
>
>
> Main
> 
> 1) Obtain the source code and extract
>wget
> http://heanet.dl.sourceforge.net/project/jmol/Jmol/Version%2
> 014.6/Version%2014.6.1/Jmol-14.6.1_2016.07.11-full.tar.gz
>
>tar xfvz Jmol-14.6.1_2016.07.11-full.tar.gz
>cd jmol-14.6.1_2016.07.11

Re: [Jmol-users] Jmol on Maven Central

[Robert Hanson]

not aware of any volunteers.

On Tue, Aug 23, 2016 at 10:40 AM, Spencer Bliven 
wrote:

> I just wanted to bump this thread. Any chance of getting a new maven
> maintainer added soon?
>
> Cheers,
> Spencer
>
> On Fri, Aug 12, 2016 at 10:19 AM, Spencer Bliven  > wrote:
>
>> So I guess the next step that needs to happen is for Nico to request that
>> Mark get added to the OSS ticket. I haven't been an active Jmol
>> contributor, but I'd be happy to help with maintaining the maven package if
>> you want to add me too (OSS user sbliven).
>>
>> -Spencer
>>
>> On Thu, Aug 11, 2016 at 11:29 PM, Robert Hanson 
>> wrote:
>>
>>> all checked in.
>>>
>>> On Thu, Aug 11, 2016 at 3:09 AM, Spencer Bliven <
>>> spencer.bli...@gmail.com> wrote:
>>>
 Awesome. BioJava has good mmtf support, so if we can get the new Jmol
 release into maven then MMTF might be a good exchange format for passing
 structures to Jmol. We're currently stuck with using PDB and are hurting
 from the limitations (e.g. on chain identifiers & number of atoms).

 -Spencer

 On Wed, Aug 10, 2016 at 6:41 PM, Robert Hanson 
 wrote:

> Thanks, Spencer. I am in the process of releasing an important update
> for BioJava, as a matter of fact -- PyMOL 1.8 dump_binary PSE files and 
> the
> new MMTF format from RCSB (which is FANTASTIC by the way...)
>
> Bob
>
> On Wed, Aug 10, 2016 at 9:25 AM, Spencer Bliven <
> spencer.bli...@gmail.com> wrote:
>
>> Hey,
>>
>> I also took a crack at getting the dist-release command to complete,
>> since it would be extremely nice to get BioJava using a more recent 
>> version
>> of Jmol. Using the latest trunk I got all steps to complete by modifying
>> tools/jmol-sonatype.xml as you suggest to refer to "${Jmol
>> .properties.Jmol.___JmolVersion}" in line 30. This creates the
>> build/dist-maven directory as desired.
>>
>> Right now only Tomas (plusik) and Nico (nicov) appear to be
>> authorized to upload to maven central. It would be great if some 
>> additional
>> people (e.g. Mark, Bob, perhaps even myself if desired) could get added 
>> to
>> this. Authorization is granted by adding a user to your OSS project
>> ticket (https://issues.sonatype.org/browse/OSSRH-3633).
>>
>> Any work towards a maven release is much appreciated. Let me know if
>> I can do anything to help with this.
>>
>> -Spencer
>>
>>
>>
>> On Sat, Jul 30, 2016 at 4:39 AM, Robert Hanson 
>> wrote:
>>
>>> I'm not sure how ${Jmol.properties.___JmolVersion} would be  the
>>> version number. In Build.xml it is:
>>>
>>>   >> value="${Jmol.properties.Jmol.___JmolVersion}"
>>> />
>>>   >> override = "true"
>>>   input="${version}"
>>> regexp='"'
>>>   replace=""
>>> global="true"
>>>   />
>>>   
>>>
>>>
>>> So you are missing that regex process.
>>>
>>>
>>>
>>> On Mon, Jul 25, 2016 at 9:18 AM, Mark Williamson 
>>> wrote:
>>>
 On 17/05/16 23:15, Robert Hanson wrote:
 > Will be checking in Jmol 14.6 release as soon as I can. But it's
 not a
 Maven release. Someone else has to do that.

 Sorry for the delay in replying. I have been attempting to use the
 ant
 build script, tools/jmol-sonatype.xml, to build some artifacts for
 deployment to Maven central. Here is my protocol (apologies, I am
 not
 that familiar with ant and may have made some basic errors):


 Preamble
 -
 0) Start with a 64 bit install of Ubuntu 14.04.4

 1) Install the following packages
sudo apt-get install mvn libsaxon-java openjdk-7-jdk ant

 2) Create ~/.jmol.build.properties file with contents



 Main
 
 1) Obtain the source code and extract
wget
 http://heanet.dl.sourceforge.net/project/jmol/Jmol/Version%2
 014.6/Version%2014.6.1/Jmol-14.6.1_2016.07.11-full.tar.gz

tar xfvz Jmol-14.6.1_2016.07.11-full.tar.gz
cd jmol-14.6.1_2016.07.11

 2) Add a required jar to enable docs to be built
cp /usr/share/java/saxon.jar ./jars/

 3) Build jar target
ant jar


 4) Build dist target
ant dist


 This fails with an error stating that “srcjsv does not exist” and
 this
 is because I do not have the source to JSpecView in the tree.
 However,
 if I should omit the line 1216 in 

Re: [Jmol-users] Jmol on Maven Central

[Spencer Bliven]

I just wanted to bump this thread. Any chance of getting a new maven
maintainer added soon?

Cheers,
Spencer

On Fri, Aug 12, 2016 at 10:19 AM, Spencer Bliven 
wrote:

> So I guess the next step that needs to happen is for Nico to request that
> Mark get added to the OSS ticket. I haven't been an active Jmol
> contributor, but I'd be happy to help with maintaining the maven package if
> you want to add me too (OSS user sbliven).
>
> -Spencer
>
> On Thu, Aug 11, 2016 at 11:29 PM, Robert Hanson 
> wrote:
>
>> all checked in.
>>
>> On Thu, Aug 11, 2016 at 3:09 AM, Spencer Bliven > > wrote:
>>
>>> Awesome. BioJava has good mmtf support, so if we can get the new Jmol
>>> release into maven then MMTF might be a good exchange format for passing
>>> structures to Jmol. We're currently stuck with using PDB and are hurting
>>> from the limitations (e.g. on chain identifiers & number of atoms).
>>>
>>> -Spencer
>>>
>>> On Wed, Aug 10, 2016 at 6:41 PM, Robert Hanson 
>>> wrote:
>>>
 Thanks, Spencer. I am in the process of releasing an important update
 for BioJava, as a matter of fact -- PyMOL 1.8 dump_binary PSE files and the
 new MMTF format from RCSB (which is FANTASTIC by the way...)

 Bob

 On Wed, Aug 10, 2016 at 9:25 AM, Spencer Bliven <
 spencer.bli...@gmail.com> wrote:

> Hey,
>
> I also took a crack at getting the dist-release command to complete,
> since it would be extremely nice to get BioJava using a more recent 
> version
> of Jmol. Using the latest trunk I got all steps to complete by modifying
> tools/jmol-sonatype.xml as you suggest to refer to "${Jmol.properties.
> Jmol.___JmolVersion}" in line 30. This creates the build/dist-maven
> directory as desired.
>
> Right now only Tomas (plusik) and Nico (nicov) appear to be authorized
> to upload to maven central. It would be great if some additional people
> (e.g. Mark, Bob, perhaps even myself if desired) could get added to this. 
> Authorization
> is granted by adding a user to your OSS project ticket (
> https://issues.sonatype.org/browse/OSSRH-3633).
>
> Any work towards a maven release is much appreciated. Let me know if I
> can do anything to help with this.
>
> -Spencer
>
>
>
> On Sat, Jul 30, 2016 at 4:39 AM, Robert Hanson 
> wrote:
>
>> I'm not sure how ${Jmol.properties.___JmolVersion} would be  the
>> version number. In Build.xml it is:
>>
>>   > />
>>   > override = "true"
>>   input="${version}"
>> regexp='"'
>>   replace=""
>> global="true"
>>   />
>>   
>>
>>
>> So you are missing that regex process.
>>
>>
>>
>> On Mon, Jul 25, 2016 at 9:18 AM, Mark Williamson 
>> wrote:
>>
>>> On 17/05/16 23:15, Robert Hanson wrote:
>>> > Will be checking in Jmol 14.6 release as soon as I can. But it's
>>> not a
>>> Maven release. Someone else has to do that.
>>>
>>> Sorry for the delay in replying. I have been attempting to use the
>>> ant
>>> build script, tools/jmol-sonatype.xml, to build some artifacts for
>>> deployment to Maven central. Here is my protocol (apologies, I am not
>>> that familiar with ant and may have made some basic errors):
>>>
>>>
>>> Preamble
>>> -
>>> 0) Start with a 64 bit install of Ubuntu 14.04.4
>>>
>>> 1) Install the following packages
>>>sudo apt-get install mvn libsaxon-java openjdk-7-jdk ant
>>>
>>> 2) Create ~/.jmol.build.properties file with contents
>>>
>>>
>>>
>>> Main
>>> 
>>> 1) Obtain the source code and extract
>>>wget
>>> http://heanet.dl.sourceforge.net/project/jmol/Jmol/Version%2
>>> 014.6/Version%2014.6.1/Jmol-14.6.1_2016.07.11-full.tar.gz
>>>
>>>tar xfvz Jmol-14.6.1_2016.07.11-full.tar.gz
>>>cd jmol-14.6.1_2016.07.11
>>>
>>> 2) Add a required jar to enable docs to be built
>>>cp /usr/share/java/saxon.jar ./jars/
>>>
>>> 3) Build jar target
>>>ant jar
>>>
>>>
>>> 4) Build dist target
>>>ant dist
>>>
>>>
>>> This fails with an error stating that “srcjsv does not exist” and
>>> this
>>> is because I do not have the source to JSpecView in the tree.
>>> However,
>>> if I should omit the line 1216 in build.xml, for the sake of reaching
>>> the next step:
>>>
>>>   
>>>
>>> And proceed to this:
>>>
>>>ant -f ./tools/jmol-sonatype.xml dist-release
>>>
>>> Then, the following error is seen:
>>> BUILD FAILED
>>> /home/mw529/code/jmol/dev/jmol-14.6.1_2016.07.11/tools/jmol-
>>> 

Re: [Jmol-users] Jmol on Maven Central

[Spencer Bliven]

So I guess the next step that needs to happen is for Nico to request that
Mark get added to the OSS ticket. I haven't been an active Jmol
contributor, but I'd be happy to help with maintaining the maven package if
you want to add me too (OSS user sbliven).

-Spencer

On Thu, Aug 11, 2016 at 11:29 PM, Robert Hanson  wrote:

> all checked in.
>
> On Thu, Aug 11, 2016 at 3:09 AM, Spencer Bliven 
> wrote:
>
>> Awesome. BioJava has good mmtf support, so if we can get the new Jmol
>> release into maven then MMTF might be a good exchange format for passing
>> structures to Jmol. We're currently stuck with using PDB and are hurting
>> from the limitations (e.g. on chain identifiers & number of atoms).
>>
>> -Spencer
>>
>> On Wed, Aug 10, 2016 at 6:41 PM, Robert Hanson 
>> wrote:
>>
>>> Thanks, Spencer. I am in the process of releasing an important update
>>> for BioJava, as a matter of fact -- PyMOL 1.8 dump_binary PSE files and the
>>> new MMTF format from RCSB (which is FANTASTIC by the way...)
>>>
>>> Bob
>>>
>>> On Wed, Aug 10, 2016 at 9:25 AM, Spencer Bliven <
>>> spencer.bli...@gmail.com> wrote:
>>>
 Hey,

 I also took a crack at getting the dist-release command to complete,
 since it would be extremely nice to get BioJava using a more recent version
 of Jmol. Using the latest trunk I got all steps to complete by modifying
 tools/jmol-sonatype.xml as you suggest to refer to "${Jmol.properties.
 Jmol.___JmolVersion}" in line 30. This creates the build/dist-maven
 directory as desired.

 Right now only Tomas (plusik) and Nico (nicov) appear to be authorized
 to upload to maven central. It would be great if some additional people
 (e.g. Mark, Bob, perhaps even myself if desired) could get added to this. 
 Authorization
 is granted by adding a user to your OSS project ticket (
 https://issues.sonatype.org/browse/OSSRH-3633).

 Any work towards a maven release is much appreciated. Let me know if I
 can do anything to help with this.

 -Spencer



 On Sat, Jul 30, 2016 at 4:39 AM, Robert Hanson 
 wrote:

> I'm not sure how ${Jmol.properties.___JmolVersion} would be  the
> version number. In Build.xml it is:
>
>    />
>    override = "true"
>   input="${version}"
> regexp='"'
>   replace=""
> global="true"
>   />
>   
>
>
> So you are missing that regex process.
>
>
>
> On Mon, Jul 25, 2016 at 9:18 AM, Mark Williamson  wrote:
>
>> On 17/05/16 23:15, Robert Hanson wrote:
>> > Will be checking in Jmol 14.6 release as soon as I can. But it's
>> not a
>> Maven release. Someone else has to do that.
>>
>> Sorry for the delay in replying. I have been attempting to use the ant
>> build script, tools/jmol-sonatype.xml, to build some artifacts for
>> deployment to Maven central. Here is my protocol (apologies, I am not
>> that familiar with ant and may have made some basic errors):
>>
>>
>> Preamble
>> -
>> 0) Start with a 64 bit install of Ubuntu 14.04.4
>>
>> 1) Install the following packages
>>sudo apt-get install mvn libsaxon-java openjdk-7-jdk ant
>>
>> 2) Create ~/.jmol.build.properties file with contents
>>
>>
>>
>> Main
>> 
>> 1) Obtain the source code and extract
>>wget
>> http://heanet.dl.sourceforge.net/project/jmol/Jmol/Version%2
>> 014.6/Version%2014.6.1/Jmol-14.6.1_2016.07.11-full.tar.gz
>>
>>tar xfvz Jmol-14.6.1_2016.07.11-full.tar.gz
>>cd jmol-14.6.1_2016.07.11
>>
>> 2) Add a required jar to enable docs to be built
>>cp /usr/share/java/saxon.jar ./jars/
>>
>> 3) Build jar target
>>ant jar
>>
>>
>> 4) Build dist target
>>ant dist
>>
>>
>> This fails with an error stating that “srcjsv does not exist” and this
>> is because I do not have the source to JSpecView in the tree. However,
>> if I should omit the line 1216 in build.xml, for the sake of reaching
>> the next step:
>>
>>   
>>
>> And proceed to this:
>>
>>ant -f ./tools/jmol-sonatype.xml dist-release
>>
>> Then, the following error is seen:
>> BUILD FAILED
>> /home/mw529/code/jmol/dev/jmol-14.6.1_2016.07.11/tools/jmol-
>> sonatype.xml:91:
>> Warning: Could not find file
>> /home/mw529/code/jmol/dev/jmol-14.6.1_2016.07.11/build/dist/
>> jmol-${Jmol.properties.___JmolVersion}-javadoc.jar
>> to copy.
>>
>>
>> I am guessing that this seems to be some form of mis-parsing of the
>> Jmol.properties.___JmolVersion in the build/dist directory?
>>
>> Do you have any 

Re: [Jmol-users] Jmol on Maven Central

[Robert Hanson]

all checked in.

On Thu, Aug 11, 2016 at 3:09 AM, Spencer Bliven 
wrote:

> Awesome. BioJava has good mmtf support, so if we can get the new Jmol
> release into maven then MMTF might be a good exchange format for passing
> structures to Jmol. We're currently stuck with using PDB and are hurting
> from the limitations (e.g. on chain identifiers & number of atoms).
>
> -Spencer
>
> On Wed, Aug 10, 2016 at 6:41 PM, Robert Hanson  wrote:
>
>> Thanks, Spencer. I am in the process of releasing an important update for
>> BioJava, as a matter of fact -- PyMOL 1.8 dump_binary PSE files and the new
>> MMTF format from RCSB (which is FANTASTIC by the way...)
>>
>> Bob
>>
>> On Wed, Aug 10, 2016 at 9:25 AM, Spencer Bliven > > wrote:
>>
>>> Hey,
>>>
>>> I also took a crack at getting the dist-release command to complete,
>>> since it would be extremely nice to get BioJava using a more recent version
>>> of Jmol. Using the latest trunk I got all steps to complete by modifying
>>> tools/jmol-sonatype.xml as you suggest to refer to "${Jmol.properties.
>>> Jmol.___JmolVersion}" in line 30. This creates the build/dist-maven
>>> directory as desired.
>>>
>>> Right now only Tomas (plusik) and Nico (nicov) appear to be authorized
>>> to upload to maven central. It would be great if some additional people
>>> (e.g. Mark, Bob, perhaps even myself if desired) could get added to this. 
>>> Authorization
>>> is granted by adding a user to your OSS project ticket (
>>> https://issues.sonatype.org/browse/OSSRH-3633).
>>>
>>> Any work towards a maven release is much appreciated. Let me know if I
>>> can do anything to help with this.
>>>
>>> -Spencer
>>>
>>>
>>>
>>> On Sat, Jul 30, 2016 at 4:39 AM, Robert Hanson 
>>> wrote:
>>>
 I'm not sure how ${Jmol.properties.___JmolVersion} would be  the
 version number. In Build.xml it is:

   >>> />
   >>> override = "true"
   input="${version}"
 regexp='"'
   replace=""
 global="true"
   />
   


 So you are missing that regex process.



 On Mon, Jul 25, 2016 at 9:18 AM, Mark Williamson  wrote:

> On 17/05/16 23:15, Robert Hanson wrote:
> > Will be checking in Jmol 14.6 release as soon as I can. But it's not
> a
> Maven release. Someone else has to do that.
>
> Sorry for the delay in replying. I have been attempting to use the ant
> build script, tools/jmol-sonatype.xml, to build some artifacts for
> deployment to Maven central. Here is my protocol (apologies, I am not
> that familiar with ant and may have made some basic errors):
>
>
> Preamble
> -
> 0) Start with a 64 bit install of Ubuntu 14.04.4
>
> 1) Install the following packages
>sudo apt-get install mvn libsaxon-java openjdk-7-jdk ant
>
> 2) Create ~/.jmol.build.properties file with contents
>
>
>
> Main
> 
> 1) Obtain the source code and extract
>wget
> http://heanet.dl.sourceforge.net/project/jmol/Jmol/Version%2
> 014.6/Version%2014.6.1/Jmol-14.6.1_2016.07.11-full.tar.gz
>
>tar xfvz Jmol-14.6.1_2016.07.11-full.tar.gz
>cd jmol-14.6.1_2016.07.11
>
> 2) Add a required jar to enable docs to be built
>cp /usr/share/java/saxon.jar ./jars/
>
> 3) Build jar target
>ant jar
>
>
> 4) Build dist target
>ant dist
>
>
> This fails with an error stating that “srcjsv does not exist” and this
> is because I do not have the source to JSpecView in the tree. However,
> if I should omit the line 1216 in build.xml, for the sake of reaching
> the next step:
>
>   
>
> And proceed to this:
>
>ant -f ./tools/jmol-sonatype.xml dist-release
>
> Then, the following error is seen:
> BUILD FAILED
> /home/mw529/code/jmol/dev/jmol-14.6.1_2016.07.11/tools/jmol-
> sonatype.xml:91:
> Warning: Could not find file
> /home/mw529/code/jmol/dev/jmol-14.6.1_2016.07.11/build/dist/
> jmol-${Jmol.properties.___JmolVersion}-javadoc.jar
> to copy.
>
>
> I am guessing that this seems to be some form of mis-parsing of the
> Jmol.properties.___JmolVersion in the build/dist directory?
>
> Do you have any suggestions on how to resolve this?
>
> Thanks,
>
> Mark
>
>
>
> 
> --
> What NetFlow Analyzer can do for you? Monitors network bandwidth and
> traffic
> patterns at an interface-level. Reveals which users, apps, and
> protocols are
> consuming the most bandwidth. Provides multi-vendor support for
> NetFlow,
> J-Flow, sFlow and other flows. Make informed 

Re: [Jmol-users] Jmol on Maven Central

[Spencer Bliven]

Awesome. BioJava has good mmtf support, so if we can get the new Jmol
release into maven then MMTF might be a good exchange format for passing
structures to Jmol. We're currently stuck with using PDB and are hurting
from the limitations (e.g. on chain identifiers & number of atoms).

-Spencer

On Wed, Aug 10, 2016 at 6:41 PM, Robert Hanson  wrote:

> Thanks, Spencer. I am in the process of releasing an important update for
> BioJava, as a matter of fact -- PyMOL 1.8 dump_binary PSE files and the new
> MMTF format from RCSB (which is FANTASTIC by the way...)
>
> Bob
>
> On Wed, Aug 10, 2016 at 9:25 AM, Spencer Bliven 
> wrote:
>
>> Hey,
>>
>> I also took a crack at getting the dist-release command to complete,
>> since it would be extremely nice to get BioJava using a more recent version
>> of Jmol. Using the latest trunk I got all steps to complete by modifying
>> tools/jmol-sonatype.xml as you suggest to refer to "${Jmol.properties.
>> Jmol.___JmolVersion}" in line 30. This creates the build/dist-maven
>> directory as desired.
>>
>> Right now only Tomas (plusik) and Nico (nicov) appear to be authorized to
>> upload to maven central. It would be great if some additional people (e.g.
>> Mark, Bob, perhaps even myself if desired) could get added to this. 
>> Authorization
>> is granted by adding a user to your OSS project ticket (
>> https://issues.sonatype.org/browse/OSSRH-3633).
>>
>> Any work towards a maven release is much appreciated. Let me know if I
>> can do anything to help with this.
>>
>> -Spencer
>>
>>
>>
>> On Sat, Jul 30, 2016 at 4:39 AM, Robert Hanson 
>> wrote:
>>
>>> I'm not sure how ${Jmol.properties.___JmolVersion} would be  the
>>> version number. In Build.xml it is:
>>>
>>>   >> />
>>>   >> override = "true"
>>>   input="${version}"
>>> regexp='"'
>>>   replace=""
>>> global="true"
>>>   />
>>>   
>>>
>>>
>>> So you are missing that regex process.
>>>
>>>
>>>
>>> On Mon, Jul 25, 2016 at 9:18 AM, Mark Williamson  wrote:
>>>
 On 17/05/16 23:15, Robert Hanson wrote:
 > Will be checking in Jmol 14.6 release as soon as I can. But it's not a
 Maven release. Someone else has to do that.

 Sorry for the delay in replying. I have been attempting to use the ant
 build script, tools/jmol-sonatype.xml, to build some artifacts for
 deployment to Maven central. Here is my protocol (apologies, I am not
 that familiar with ant and may have made some basic errors):


 Preamble
 -
 0) Start with a 64 bit install of Ubuntu 14.04.4

 1) Install the following packages
sudo apt-get install mvn libsaxon-java openjdk-7-jdk ant

 2) Create ~/.jmol.build.properties file with contents



 Main
 
 1) Obtain the source code and extract
wget
 http://heanet.dl.sourceforge.net/project/jmol/Jmol/Version%2
 014.6/Version%2014.6.1/Jmol-14.6.1_2016.07.11-full.tar.gz

tar xfvz Jmol-14.6.1_2016.07.11-full.tar.gz
cd jmol-14.6.1_2016.07.11

 2) Add a required jar to enable docs to be built
cp /usr/share/java/saxon.jar ./jars/

 3) Build jar target
ant jar


 4) Build dist target
ant dist


 This fails with an error stating that “srcjsv does not exist” and this
 is because I do not have the source to JSpecView in the tree. However,
 if I should omit the line 1216 in build.xml, for the sake of reaching
 the next step:

   

 And proceed to this:

ant -f ./tools/jmol-sonatype.xml dist-release

 Then, the following error is seen:
 BUILD FAILED
 /home/mw529/code/jmol/dev/jmol-14.6.1_2016.07.11/tools/jmol-
 sonatype.xml:91:
 Warning: Could not find file
 /home/mw529/code/jmol/dev/jmol-14.6.1_2016.07.11/build/dist/
 jmol-${Jmol.properties.___JmolVersion}-javadoc.jar
 to copy.


 I am guessing that this seems to be some form of mis-parsing of the
 Jmol.properties.___JmolVersion in the build/dist directory?

 Do you have any suggestions on how to resolve this?

 Thanks,

 Mark



 
 --
 What NetFlow Analyzer can do for you? Monitors network bandwidth and
 traffic
 patterns at an interface-level. Reveals which users, apps, and
 protocols are
 consuming the most bandwidth. Provides multi-vendor support for NetFlow,
 J-Flow, sFlow and other flows. Make informed decisions using capacity
 planning
 reports.http://sdm.link/zohodev2dev
 ___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol on Maven Central

[Spencer Bliven]

Hey,

I also took a crack at getting the dist-release command to complete, since
it would be extremely nice to get BioJava using a more recent version of
Jmol. Using the latest trunk I got all steps to complete by modifying tools/
jmol-sonatype.xml as you suggest to refer to
"${Jmol.properties.Jmol.___JmolVersion}"
in line 30. This creates the build/dist-maven directory as desired.

Right now only Tomas (plusik) and Nico (nicov) appear to be authorized to
upload to maven central. It would be great if some additional people (e.g.
Mark, Bob, perhaps even myself if desired) could get added to this.
Authorization
is granted by adding a user to your OSS project ticket (
https://issues.sonatype.org/browse/OSSRH-3633).

Any work towards a maven release is much appreciated. Let me know if I can
do anything to help with this.

-Spencer



On Sat, Jul 30, 2016 at 4:39 AM, Robert Hanson  wrote:

> I'm not sure how ${Jmol.properties.___JmolVersion} would be  the version
> number. In Build.xml it is:
>
>/>
>override = "true"
>   input="${version}"
> regexp='"'
>   replace=""
> global="true"
>   />
>   
>
>
> So you are missing that regex process.
>
>
>
> On Mon, Jul 25, 2016 at 9:18 AM, Mark Williamson  wrote:
>
>> On 17/05/16 23:15, Robert Hanson wrote:
>> > Will be checking in Jmol 14.6 release as soon as I can. But it's not a
>> Maven release. Someone else has to do that.
>>
>> Sorry for the delay in replying. I have been attempting to use the ant
>> build script, tools/jmol-sonatype.xml, to build some artifacts for
>> deployment to Maven central. Here is my protocol (apologies, I am not
>> that familiar with ant and may have made some basic errors):
>>
>>
>> Preamble
>> -
>> 0) Start with a 64 bit install of Ubuntu 14.04.4
>>
>> 1) Install the following packages
>>sudo apt-get install mvn libsaxon-java openjdk-7-jdk ant
>>
>> 2) Create ~/.jmol.build.properties file with contents
>>
>>
>>
>> Main
>> 
>> 1) Obtain the source code and extract
>>wget
>> http://heanet.dl.sourceforge.net/project/jmol/Jmol/Version%2
>> 014.6/Version%2014.6.1/Jmol-14.6.1_2016.07.11-full.tar.gz
>>
>>tar xfvz Jmol-14.6.1_2016.07.11-full.tar.gz
>>cd jmol-14.6.1_2016.07.11
>>
>> 2) Add a required jar to enable docs to be built
>>cp /usr/share/java/saxon.jar ./jars/
>>
>> 3) Build jar target
>>ant jar
>>
>>
>> 4) Build dist target
>>ant dist
>>
>>
>> This fails with an error stating that “srcjsv does not exist” and this
>> is because I do not have the source to JSpecView in the tree. However,
>> if I should omit the line 1216 in build.xml, for the sake of reaching
>> the next step:
>>
>>   
>>
>> And proceed to this:
>>
>>ant -f ./tools/jmol-sonatype.xml dist-release
>>
>> Then, the following error is seen:
>> BUILD FAILED
>> /home/mw529/code/jmol/dev/jmol-14.6.1_2016.07.11/tools/jmol-
>> sonatype.xml:91:
>> Warning: Could not find file
>> /home/mw529/code/jmol/dev/jmol-14.6.1_2016.07.11/build/dist/
>> jmol-${Jmol.properties.___JmolVersion}-javadoc.jar
>> to copy.
>>
>>
>> I am guessing that this seems to be some form of mis-parsing of the
>> Jmol.properties.___JmolVersion in the build/dist directory?
>>
>> Do you have any suggestions on how to resolve this?
>>
>> Thanks,
>>
>> Mark
>>
>>
>>
>> 
>> --
>> What NetFlow Analyzer can do for you? Monitors network bandwidth and
>> traffic
>> patterns at an interface-level. Reveals which users, apps, and protocols
>> are
>> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
>> J-Flow, sFlow and other flows. Make informed decisions using capacity
>> planning
>> reports.http://sdm.link/zohodev2dev
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> 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
>
>
> 
> --
>
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. 

Re: [Jmol-users] Jmol on Maven Central

[Robert Hanson]

I'm not sure how ${Jmol.properties.___JmolVersion} would be  the version
number. In Build.xml it is:

  
  
  


So you are missing that regex process.



On Mon, Jul 25, 2016 at 9:18 AM, Mark Williamson  wrote:

> On 17/05/16 23:15, Robert Hanson wrote:
> > Will be checking in Jmol 14.6 release as soon as I can. But it's not a
> Maven release. Someone else has to do that.
>
> Sorry for the delay in replying. I have been attempting to use the ant
> build script, tools/jmol-sonatype.xml, to build some artifacts for
> deployment to Maven central. Here is my protocol (apologies, I am not
> that familiar with ant and may have made some basic errors):
>
>
> Preamble
> -
> 0) Start with a 64 bit install of Ubuntu 14.04.4
>
> 1) Install the following packages
>sudo apt-get install mvn libsaxon-java openjdk-7-jdk ant
>
> 2) Create ~/.jmol.build.properties file with contents
>
>
>
> Main
> 
> 1) Obtain the source code and extract
>wget
>
> http://heanet.dl.sourceforge.net/project/jmol/Jmol/Version%2014.6/Version%2014.6.1/Jmol-14.6.1_2016.07.11-full.tar.gz
>
>tar xfvz Jmol-14.6.1_2016.07.11-full.tar.gz
>cd jmol-14.6.1_2016.07.11
>
> 2) Add a required jar to enable docs to be built
>cp /usr/share/java/saxon.jar ./jars/
>
> 3) Build jar target
>ant jar
>
>
> 4) Build dist target
>ant dist
>
>
> This fails with an error stating that “srcjsv does not exist” and this
> is because I do not have the source to JSpecView in the tree. However,
> if I should omit the line 1216 in build.xml, for the sake of reaching
> the next step:
>
>   
>
> And proceed to this:
>
>ant -f ./tools/jmol-sonatype.xml dist-release
>
> Then, the following error is seen:
> BUILD FAILED
>
> /home/mw529/code/jmol/dev/jmol-14.6.1_2016.07.11/tools/jmol-sonatype.xml:91:
> Warning: Could not find file
>
> /home/mw529/code/jmol/dev/jmol-14.6.1_2016.07.11/build/dist/jmol-${Jmol.properties.___JmolVersion}-javadoc.jar
> to copy.
>
>
> I am guessing that this seems to be some form of mis-parsing of the
> Jmol.properties.___JmolVersion in the build/dist directory?
>
> Do you have any suggestions on how to resolve this?
>
> Thanks,
>
> Mark
>
>
>
>
> --
> What NetFlow Analyzer can do for you? Monitors network bandwidth and
> traffic
> patterns at an interface-level. Reveals which users, apps, and protocols
> are
> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using capacity
> planning
> reports.http://sdm.link/zohodev2dev
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
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
--
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Re: [Jmol-users] Jmol on Maven Central

[Mark Williamson]

On 17/05/16 23:15, Robert Hanson wrote:
> Will be checking in Jmol 14.6 release as soon as I can. But it's not a
Maven release. Someone else has to do that.

Sorry for the delay in replying. I have been attempting to use the ant 
build script, tools/jmol-sonatype.xml, to build some artifacts for 
deployment to Maven central. Here is my protocol (apologies, I am not 
that familiar with ant and may have made some basic errors):


Preamble
-
0) Start with a 64 bit install of Ubuntu 14.04.4

1) Install the following packages
   sudo apt-get install mvn libsaxon-java openjdk-7-jdk ant

2) Create ~/.jmol.build.properties file with contents
   


Main

1) Obtain the source code and extract
   wget 
http://heanet.dl.sourceforge.net/project/jmol/Jmol/Version%2014.6/Version%2014.6.1/Jmol-14.6.1_2016.07.11-full.tar.gz

   tar xfvz Jmol-14.6.1_2016.07.11-full.tar.gz
   cd jmol-14.6.1_2016.07.11

2) Add a required jar to enable docs to be built
   cp /usr/share/java/saxon.jar ./jars/

3) Build jar target
   ant jar
   

4) Build dist target
   ant dist
   

This fails with an error stating that “srcjsv does not exist” and this 
is because I do not have the source to JSpecView in the tree. However, 
if I should omit the line 1216 in build.xml, for the sake of reaching 
the next step:

  

And proceed to this:

   ant -f ./tools/jmol-sonatype.xml dist-release

Then, the following error is seen:
BUILD FAILED
/home/mw529/code/jmol/dev/jmol-14.6.1_2016.07.11/tools/jmol-sonatype.xml:91: 
Warning: Could not find file 
/home/mw529/code/jmol/dev/jmol-14.6.1_2016.07.11/build/dist/jmol-${Jmol.properties.___JmolVersion}-javadoc.jar
 
to copy.


I am guessing that this seems to be some form of mis-parsing of the 
Jmol.properties.___JmolVersion in the build/dist directory?

Do you have any suggestions on how to resolve this?

Thanks,

Mark



--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
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Re: [Jmol-users] Jmol on Maven Central

[Robert Hanson]

Will be checking in Jmol 14.6 release as soon as I can. But it's not a
Maven release. Someone else has to do that.

On Tue, May 17, 2016 at 5:57 AM, Spencer Bliven 
wrote:

> We at Biojava are quite interested in getting a more recent version of
> Jmol on maven, so I thought I would bump this thread and offer some
> suggestions.
>
> Authorization is granted by adding a user to your OSS project ticket:
> https://issues.sonatype.org/browse/OSSRH-3633
>
> Right now only Tomas (plusik) and Nico (nicov) appear to be authorized.
>
> I could also help out with this if needed. My username is sbliven.
>
> -Spencer
>
>
> On Sat, Jan 23, 2016 at 5:19 PM, Nicolas Vervelle 
> wrote:
>
>> Hi Mark,
>>
>> On Fri, Jan 22, 2016 at 6:30 PM, Mark Williamson  wrote:
>>
>>> On 31/12/15 13:46, Nicolas Vervelle wrote:
>>> > Hi Mark,
>>> >
>>> > I'm probably the one who deployed the old version a long time ago (or
>>> > Bob, not sure).
>>> > I'm currently way too busy on various matters to keep doing releases
>>> for
>>> > Jmol.
>>> >
>>> > I think having a volunteer to deal with releases on Maven central would
>>> > be very helpful. Anyone interested ?
>>> > There are some ant scripts in Jmol source code to deploy there, but
>>> they
>>> > haven't been used in a very long time.
>>> > So, first thing would be to check if they still work correctly
>>> (probably
>>> > by testing snapshots releases), and then try to find which SVN revision
>>> > should be deployed as a given version.
>>> >
>>> > Nico
>>> >
>>>
>>> Dear Nico,
>>>
>>> Apologies for the delay in responding. Thank you for the reply and
>>> useful information. Egon (offlist) mentioned a script at:
>>>
>>>
>>>
>>> https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/tools/jmol-sonatype.xml
>>>
>>> which I assume is the one that you refer to.
>>>
>>
>> Yes, this is the script that I used to deploy Jmol on Maven central.
>>
>>
>>
>>> I have had experience deploying Maven projects to maven
>>> central(http://search.maven.org/#search|ga|1|oscar4  and
>>> http://search.maven.org/#search|ga|1|fortranformat ), however I think I
>>> can probably grok how the script above works within an ant context.
>>>
>>> I'm happy to try to deploy this, but there is an issue. In order to
>>> deploy to Maven central with GroupId net.sourceforge.jmol, I will
>>> probably need some authorisation from the Maven central admin peeps.
>>> IIRC the person who originally deployed these will receive an email
>>> asking if this is OK.
>>>
>>
>> Yes, no problem for me, I don't remember who has the rights to grant
>> authorisation.
>> If it's me, I will do it when I receive the email.
>>
>>
>>
>>> Secondly, from the tags on the project
>>> (http://sourceforge.net/p/jmol/code/HEAD/tree/tags/) I cannot ascertain
>>> which one I should deploy.
>>>
>>
>> I suggest first trying with snapshots with the current trunk, to check
>> that everything is working correctly.
>>
>> For the version to really deploy, I think you need to see with Bob
>> Hanson, he's the one doing almost all the development on Jmol lately and
>> the one making the releases on sourceforge.
>>
>> Nico
>>
>>
>>
>> --
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311=/4140
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
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
--
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Re: [Jmol-users] Jmol on Maven Central

[Nicolas Vervelle]

Hi Mark,

On Fri, Jan 22, 2016 at 6:30 PM, Mark Williamson  wrote:

> On 31/12/15 13:46, Nicolas Vervelle wrote:
> > Hi Mark,
> >
> > I'm probably the one who deployed the old version a long time ago (or
> > Bob, not sure).
> > I'm currently way too busy on various matters to keep doing releases for
> > Jmol.
> >
> > I think having a volunteer to deal with releases on Maven central would
> > be very helpful. Anyone interested ?
> > There are some ant scripts in Jmol source code to deploy there, but they
> > haven't been used in a very long time.
> > So, first thing would be to check if they still work correctly (probably
> > by testing snapshots releases), and then try to find which SVN revision
> > should be deployed as a given version.
> >
> > Nico
> >
>
> Dear Nico,
>
> Apologies for the delay in responding. Thank you for the reply and
> useful information. Egon (offlist) mentioned a script at:
>
>
>
> https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/tools/jmol-sonatype.xml
>
> which I assume is the one that you refer to.
>

Yes, this is the script that I used to deploy Jmol on Maven central.



> I have had experience deploying Maven projects to maven
> central(http://search.maven.org/#search|ga|1|oscar4  and
> http://search.maven.org/#search|ga|1|fortranformat ), however I think I
> can probably grok how the script above works within an ant context.
>
> I'm happy to try to deploy this, but there is an issue. In order to
> deploy to Maven central with GroupId net.sourceforge.jmol, I will
> probably need some authorisation from the Maven central admin peeps.
> IIRC the person who originally deployed these will receive an email
> asking if this is OK.
>

Yes, no problem for me, I don't remember who has the rights to grant
authorisation.
If it's me, I will do it when I receive the email.



> Secondly, from the tags on the project
> (http://sourceforge.net/p/jmol/code/HEAD/tree/tags/) I cannot ascertain
> which one I should deploy.
>

I suggest first trying with snapshots with the current trunk, to check that
everything is working correctly.

For the version to really deploy, I think you need to see with Bob Hanson,
he's the one doing almost all the development on Jmol lately and the one
making the releases on sourceforge.

Nico
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Re: [Jmol-users] Jmol on Maven Central

[Mark Williamson]

On 31/12/15 13:46, Nicolas Vervelle wrote:
> Hi Mark,
>
> I'm probably the one who deployed the old version a long time ago (or
> Bob, not sure).
> I'm currently way too busy on various matters to keep doing releases for
> Jmol.
>
> I think having a volunteer to deal with releases on Maven central would
> be very helpful. Anyone interested ?
> There are some ant scripts in Jmol source code to deploy there, but they
> haven't been used in a very long time.
> So, first thing would be to check if they still work correctly (probably
> by testing snapshots releases), and then try to find which SVN revision
> should be deployed as a given version.
>
> Nico
>

Dear Nico,

Apologies for the delay in responding. Thank you for the reply and 
useful information. Egon (offlist) mentioned a script at:

 
https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/tools/jmol-sonatype.xml

which I assume is the one that you refer to.

I have had experience deploying Maven projects to maven 
central(http://search.maven.org/#search|ga|1|oscar4  and 
http://search.maven.org/#search|ga|1|fortranformat ), however I think I 
can probably grok how the script above works within an ant context.

I'm happy to try to deploy this, but there is an issue. In order to 
deploy to Maven central with GroupId net.sourceforge.jmol, I will 
probably need some authorisation from the Maven central admin peeps. 
IIRC the person who originally deployed these will receive an email 
asking if this is OK.

Secondly, from the tags on the project 
(http://sourceforge.net/p/jmol/code/HEAD/tree/tags/) I cannot ascertain 
which one I should deploy.

Thanks,

Mark

--
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Re: [Jmol-users] Jmol on Maven Central

[Nicolas Vervelle]

Hi Mark,

I'm probably the one who deployed the old version a long time ago (or Bob,
not sure).
I'm currently way too busy on various matters to keep doing releases for
Jmol.

I think having a volunteer to deal with releases on Maven central would be
very helpful. Anyone interested ?
There are some ant scripts in Jmol source code to deploy there, but they
haven't been used in a very long time.
So, first thing would be to check if they still work correctly (probably by
testing snapshots releases), and then try to find which SVN revision should
be deployed as a given version.

Nico



On Wed, Dec 30, 2015 at 5:06 PM, Mark Williamson  wrote:

> Dear Jmol users,
>
> I see that there is a version of Jmol on Maven central:
>
> http://search.maven.org/#search|ga|1|jmol
>
> However the latest version here is around 13. I was wondering if the
> person who deployed this is on this list and if it would be possible for
> that person to deploy a more recent (say 14) version of Jmol?
>
> Thanks,
>
> Mark
>
>
> --
> ___
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>
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[Jmol-users] Jmol on Maven Central

[Mark Williamson]

Dear Jmol users,

I see that there is a version of Jmol on Maven central:

http://search.maven.org/#search|ga|1|jmol

However the latest version here is around 13. I was wondering if the 
person who deployed this is on this list and if it would be possible for 
that person to deploy a more recent (say 14) version of Jmol?

Thanks,

Mark

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