On Mon, Mar 10, 2014 at 11:50 AM, Spencer Bliven <[email protected]> wrote:
> Bob,
>
> This should indeed be done by whoever maintains the maven port. I had
> originally assumed that this would be you, but I see I'm incorrect. Perhaps
> that person watches this list and would benefit from the following info.
>
> It appears that no one is distributing a Naga maven artifact. So that
> would have to be included in the jar (or separately maintained), as would
> JSpecView and SparshUI. The maintainer is currently including vecmath as
> well, which should ship with java but has an undependable API. There are a
> couple maven repos with more stable versions. Maven central has 1.3.1, and
> http://maven.geotoolkit.org distributes 1.5.2.
>
>
vecmath is long gone. No dependency there.
JSpecView is really part of this project.
SparshUI code is also used - with modification.
> While adding commons-cli and vecmath as dependencies rather than including
> them in the jar is more in line with the maven philosophy, I did manage to
> work around this problem for my own project:
>
> 1) Put jMol last in the pom's dependency list, so that tools like eclipse
> load position it last when they construct a classpath
> 2) Exclude the conflicting classes manually when building distribution
> jars. I'm using the maven shade plugin, so this looks like
>
> <plugin>
> <artifactId>maven-shade-plugin</artifactId>
> ...
> <executions><execution>
> ...
> <configuration><filters>
> <filter>
> <artifact>net.sourceforge.jmol:jmol</artifact>
> <excludes>
> <exclude>org/apache/commons/cli/**</exclude>
> <exclude>javax/vecmath/**</exclude>
> </excludes>
> </filter>
> </filters></configuration>
> </execution></executions>
> </plugin>
>
>
So you are OK with how we have it now? -- no vecmath necessary; just cli, I
think.
>
> -Spencer
>
>
>
> On Thu, Mar 6, 2014 at 2:20 PM, Robert Hanson <[email protected]> wrote:
>
>> OK, so I removed Obrador (unused JPEG encoder) and what we are left with
>> is:
>>
>> <srcfiles dir="${lib.dir}" includes="${naga.jar}"/>
>> <srcfiles dir="${lib.dir}" includes="${commons-cli.jar}"/>
>> <srcfiles dir="${lib.dir}" includes="JSpecView.jar"/>
>>
>> and also, in code, SparshUI.
>>
>> JSpecView is part of Jmol, so that's fine. Does Naga have a maven piece?
>>
>> Is there any reason why someone doing the Maven port can't just take
>> these out themselves?
>>
>> Bob
>>
>>
>>
>> On Thu, Mar 6, 2014 at 7:00 AM, Robert Hanson <[email protected]> wrote:
>>
>>> Yes, good point. SparshUI is very specialized -- I doubt there is any
>>> Maven artifact for that -- it is only used for one particular (old)
>>> multi-touch application. No need for the obrador package at all; also no
>>> need for netscape for the application as it doesn't have the applet files
>>> anyway, or needn't.
>>>
>>> So the Maven idea is that you create pieces that by themselves do not
>>> run?
>>>
>>> Bob
>>>
>>>
>>> On Thu, Mar 6, 2014 at 5:04 AM, Spencer Bliven <[email protected]> wrote:
>>>
>>>> If they're unused they could just be removed from the jar file. However
>>>> commons-cli is still a problem, since it's a fairly common package. I still
>>>> think it would be nice to provide a maven artifact without any of the
>>>> dependency classes included.
>>>>
>>>>
>>>> On Wed, Mar 5, 2014 at 6:20 PM, Robert Hanson <[email protected]>wrote:
>>>>
>>>>> That's a good point, for sure.
>>>>>
>>>>> Really there are almost no dependencies. Here's the whole list:
>>>>>
>>>>> commons-cli-1.0.jar -- Command Line Interface -- Application only
>>>>> naga.jar -- very specialized MolecularPlayground/application only
>>>>> netscape.jar -- JSObject / Java applet only
>>>>>
>>>>> Anything else in the jars folder is not used.
>>>>>
>>>>> Since we have gone to JavaScript none of these dependencies are
>>>>> accessed by the applet. The application uses a command line interface, and
>>>>> it allows socket communication using naga. The Java applet uses the
>>>>> absolute minimum of just JSObject and JSException.
>>>>>
>>>>> So what do you suggest, Spencer?
>>>>>
>>>>> Bob
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Wed, Mar 5, 2014 at 9:39 AM, Spencer Bliven <[email protected]>wrote:
>>>>>
>>>>>> Maybe this has been addressed, but I couldn't find it in the list
>>>>>> archives. I noticed that since 12.2.0, jmol has not listed any
>>>>>> dependencies
>>>>>> in the maven pom file, but instead it includes them directly in the jar
>>>>>> file. This has the effect of breaking maven's dependency resolution for
>>>>>> project which include both jmol and its dependencies. I found that out
>>>>>> the
>>>>>> hard way through some very odd classpath errors in a project that
>>>>>> declared
>>>>>> a commons-cli:1.2 dependency but which was actually loading the 1.0
>>>>>> classes
>>>>>> from the jmol jar.
>>>>>>
>>>>>> I assume the reason that the dependencies were bundled together was
>>>>>> to allow a stand-alone jar to be distributed. This can be supported by
>>>>>> building two profiles: a standard jar which does not include dependencies
>>>>>> and that gets uploaded to the maven repo; and a distribution jar which
>>>>>> gets
>>>>>> built using the maven-shade-plugin in order to include all dependencies,
>>>>>> and which gets distributed via the website.
>>>>>>
>>>>>> -Spencer
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Subversion Kills Productivity. Get off Subversion & Make the Move to
>>>>>> Perforce.
>>>>>> With Perforce, you get hassle-free workflows. Merge that actually
>>>>>> works.
>>>>>> Faster operations. Version large binaries. Built-in WAN optimization
>>>>>> and the
>>>>>> freedom to use Git, Perforce or both. Make the move to Perforce.
>>>>>>
>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
>>>>>> _______________________________________________
>>>>>> Jmol-users mailing list
>>>>>> [email protected]
>>>>>> 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
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Subversion Kills Productivity. Get off Subversion & Make the Move to
>>>>> Perforce.
>>>>> With Perforce, you get hassle-free workflows. Merge that actually
>>>>> works.
>>>>> Faster operations. Version large binaries. Built-in WAN optimization
>>>>> and the
>>>>> freedom to use Git, Perforce or both. Make the move to Perforce.
>>>>>
>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
>>>>> _______________________________________________
>>>>> Jmol-users mailing list
>>>>> [email protected]
>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>>
>>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Subversion Kills Productivity. Get off Subversion & Make the Move to
>>>> Perforce.
>>>> With Perforce, you get hassle-free workflows. Merge that actually works.
>>>> Faster operations. Version large binaries. Built-in WAN optimization
>>>> and the
>>>> freedom to use Git, Perforce or both. Make the move to Perforce.
>>>>
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
>>>> _______________________________________________
>>>> Jmol-users mailing list
>>>> [email protected]
>>>> 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
>>>
>>>
>>
>>
>> --
>> 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
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Subversion Kills Productivity. Get off Subversion & Make the Move to
>> Perforce.
>> With Perforce, you get hassle-free workflows. Merge that actually works.
>> Faster operations. Version large binaries. Built-in WAN optimization and
>> the
>> freedom to use Git, Perforce or both. Make the move to Perforce.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
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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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"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
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