Re: [Jmol-users] Jmol on Maven Central
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 build.xml, for the sake of
reaching
the next step:
And proceed to this:
>
Re: [Jmol-users] Jmol on Maven Central
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-
>>> sonatype.xml:91:
>>> Warning: Could not find file
>>> /home/mw529/code/jmol/dev/jmol-14.6.1_2016.07.11/build/dist/
>>> jmol-${Jmo
[Jmol-users] database of Gaussian or other
Someone remind me where the database of common compounds is that has wavefunctions -- Spartan, Gaussian, anything Jmol can read. If it doesn't exist, can someone make that? Bob -- 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
