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
