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 <hans...@stolaf.edu> 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 <hans...@stolaf.edu>
>> 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 <hans...@stolaf.edu>
>>>> wrote:
>>>>
>>>>> I'm not sure how ${Jmol.properties.___JmolVersion} would be the
>>>>> version number. In Build.xml it is:
>>>>>
>>>>> <property name="version" value="${Jmol.properties.Jmol.___JmolVersion}"
>>>>> />
>>>>> <propertyregex property="version"
>>>>> override = "true"
>>>>> input="${version}"
>>>>> regexp='"'
>>>>> replace=""
>>>>> global="true"
>>>>> />
>>>>> <echo message="version=${version}" />
>>>>>
>>>>>
>>>>> So you are missing that regex process.
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Jul 25, 2016 at 9:18 AM, Mark Williamson <m...@mjw.name> 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
>>>>>> <property name="keystore.name" value="selfSignedCertificate" />
>>>>>>
>>>>>>
>>>>>> 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
>>>>>> <input ~/.jmol.build.properties as the private property file >
>>>>>>
>>>>>> 4) Build dist target
>>>>>> ant dist
>>>>>> <input ~/.jmol.build.properties as the private property file >
>>>>>>
>>>>>> 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:
>>>>>>
>>>>>> <!-- <fileset dir="srcjsv" />-->
>>>>>>
>>>>>> 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. 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
>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> 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
>>>
>>>
>>
>> ------------------------------------------------------------
>> ------------------
>> 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
>
>
> ------------------------------------------------------------
> ------------------
> 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
>
>
------------------------------------------------------------------------------
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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