Re: Could somebody please check ncbi-tools6 (Was: [GSOC] Todo List)

[Canberk Koç]

Hello all,

I think ı use the approach which fit situation .-) Thanks for your help
really .

Best Regards



Canberk Koç
[image: https://]about.me/canberkkoc


2016-08-23 1:56 GMT+03:00 Sascha Steinbiss :

> Hi Andreas,
>
> > On Mon, Aug 22, 2016 at 02:20:08PM +0200, Sascha Steinbiss wrote:
> >> BTW you don’t need to install your test data to be used in the
> autopkgtest, as tests will always be run with an decompressed source tree
> present, including the debian directory.
> >
> > I think I have influenced Canberk here with my habit to enable users
> > using the autopkgtest as usage example at the same time.  This requires
> > to have the example data installed in a binary package as well as the
> > script that is called by debci.
>
> Ah, I see — this makes sense, thanks. In cases such as this the example
> set would need to be split up across multiple binary packages though — some
> would need to go into blast2 and some into ncbi-tools-bin (or ncbi-data,
> that would work as well…).
> Anyway, I understand the motivation now and while I’m usually more of a
> minimalist I completely respect that approach!
> Canberk, please don’t let that keep you from including examples :)
>
> Cheers
> Sascha
>

Re: Could somebody please check ncbi-tools6 (Was: [GSOC] Todo List)

[Sascha Steinbiss]

Hi Andreas,

> On Mon, Aug 22, 2016 at 02:20:08PM +0200, Sascha Steinbiss wrote:
>> BTW you don’t need to install your test data to be used in the autopkgtest, 
>> as tests will always be run with an decompressed source tree present, 
>> including the debian directory.
> 
> I think I have influenced Canberk here with my habit to enable users
> using the autopkgtest as usage example at the same time.  This requires
> to have the example data installed in a binary package as well as the
> script that is called by debci.

Ah, I see — this makes sense, thanks. In cases such as this the example set 
would need to be split up across multiple binary packages though — some would 
need to go into blast2 and some into ncbi-tools-bin (or ncbi-data, that would 
work as well…).
Anyway, I understand the motivation now and while I’m usually more of a 
minimalist I completely respect that approach!
Canberk, please don’t let that keep you from including examples :)

Cheers
Sascha


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Re: Packaging wishlist for this week's H3Africa workshop

[Andreas Tille]

On Mon, Aug 22, 2016 at 05:42:26PM +0200, Michael Crusoe wrote:
> One more: snpeff http://snpeff.sourceforge.net/download.html

I had a look some weeks ago and I also have some interest.  I'm afraid
that this is one of the harder Java packages but has quite some
popularity and seems to be an interesting target.

I'd be happy if somebody would beat me in packaging this.

Kind regards

 Andreas.

-- 
http://fam-tille.de

Re: Packaging wishlist for this week's H3Africa workshop

[Andreas Tille]

On Mon, Aug 22, 2016 at 05:36:30PM +0200, Michael Crusoe wrote:
> metagenomeSeq
> https://bioconductor.org/packages/release/bioc/html/metagenomeSeq.html

Well, that's a simple one with some R packaging experience. :-)
ITP #835135, currently uploading to new.
 
> phloseq https://github.com/joey711/phyloseq
> 
> bamstats http://bamstats.sourceforge.net/

Any takers for these?

Kind regards

 Andreas.

-- 
http://fam-tille.de

Re: [Debichem-devel] [Outreachy] pymol

[merlettaia]

Hi Michael and Andreas,

The maintainers have responded, now there is apbs-1.4.2 source archive on
SourceForge.
I'll check it tomorrow.

2016-08-22 22:38 GMT+03:00 Michael Banck :

> Hi,
>
> On Sat, Aug 20, 2016 at 01:19:03PM +0300, merlettaia wrote:
> > apbs source releases are available on github, but they contain both apbs
> > and pdb2pqr (probably because they both are developed in the same
> > repository)
> > https://github.com/Electrostatics/apbs-pdb2pqr/releases
> > On SourceForge there are 2 versions of apbs (1.4.1 and 1.4.2), but they
> > both don't have source archive. Version 1.4.0 is old.
>
> Right, so they just bundled up both in one tarball.
>
> > I asked maintainers via gitter channel to add latest apbs source package
> to
> > SourceForge, let's see if they'll do it.
>
> Thanks a lot for doing that!
>
> > But probably changing debian/watch to take releases from github might be
> > the option.
>
> I agree, provided that the maintainers are not going to reply for a
> while.
>
>
> Cheers,
>
> Michael
>



-- 
Best wishes,
Tanya.

Re: [Debichem-devel] [Outreachy] pymol

[Michael Banck]

Hi,

On Sat, Aug 20, 2016 at 01:19:03PM +0300, merlettaia wrote:
> apbs source releases are available on github, but they contain both apbs
> and pdb2pqr (probably because they both are developed in the same
> repository)
> https://github.com/Electrostatics/apbs-pdb2pqr/releases
> On SourceForge there are 2 versions of apbs (1.4.1 and 1.4.2), but they
> both don't have source archive. Version 1.4.0 is old.

Right, so they just bundled up both in one tarball.

> I asked maintainers via gitter channel to add latest apbs source package to
> SourceForge, let's see if they'll do it.

Thanks a lot for doing that!

> But probably changing debian/watch to take releases from github might be
> the option.

I agree, provided that the maintainers are not going to reply for a
while.


Cheers,

Michael

Re: Could somebody please check ncbi-tools6 (Was: [GSOC] Todo List)

[Andreas Tille]

Hi,

On Mon, Aug 22, 2016 at 02:20:08PM +0200, Sascha Steinbiss wrote:
> BTW you don’t need to install your test data to be used in the autopkgtest, 
> as tests will always be run with an decompressed source tree present, 
> including the debian directory.

I think I have influenced Canberk here with my habit to enable users
using the autopkgtest as usage example at the same time.  This requires
to have the example data installed in a binary package as well as the
script that is called by debci.

Kind regards

 Andreas.

-- 
http://fam-tille.de

Re: Could somebody please check ncbi-tools6 (Was: [GSOC] Todo List)

[Andreas Tille]

Hi Sascha,

On Mon, Aug 22, 2016 at 02:13:14PM +0200, Sascha Steinbiss wrote:
> Hi Andreas and Canberk,
> 
> the problem was that ncbi-tools6 is still an old-style 1.0 format package, 
> which can not contain binary files (such as the binary ASN.1 file in the test 
> data) as part of the /debian directory. Either the file would need to be 
> encoded as a text file, or (perhaps the better option) the package needs to 
> be migrated to the newer 3.0 (quilt) format.
> For now I have base64-encoded the binary file to include it in the package 
> and adjusted the test script to decode it back to binary before feeding it 
> into asn2xml. I guess that’s OK for one file, but if we’d like to keep adding 
> test data then it might be helpful to migrate.
> I will upload the package including the tests soon — thanks Canberk for 
> adding the tests!

Ahhh, thanks for solving the problem.  I'd personally probably had
converted to source format quilt 3.0 since I see no reason to keep
the old format but from a users point of view that's irrelevant and
your solution is fine as well.

Thanks a lot for your work

 Andreas.

-- 
http://fam-tille.de

Processed: retitle to RFP: prokka -- rapid annotation of prokaryotic genomes

[Debian Bug Tracking System]

Processing commands for cont...@bugs.debian.org:

> retitle 778246 RFP: prokka -- rapid annotation of prokaryotic genomes
Bug #778246 [wnpp] ITP: prokka -- rapid annotation of prokaryotic genomes
Changed Bug title to 'RFP: prokka -- rapid annotation of prokaryotic genomes' 
from 'ITP: prokka -- rapid annotation of prokaryotic genomes'.
> noowner 778246
Bug #778246 [wnpp] RFP: prokka -- rapid annotation of prokaryotic genomes
Removed annotation that Bug was owned by Debian Med team 
.
> stop
Stopping processing here.

Please contact me if you need assistance.
-- 
778246: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=778246
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

Re: Packaging wishlist for this week's H3Africa workshop

[Ghislain Vaillant]

On 22/08/16 16:42, Michael Crusoe wrote:

One more: snpeff http://snpeff.sourceforge.net/download.html

On Mon, Aug 22, 2016 at 5:36 PM, Michael Crusoe 
mailto:michael.cru...@gmail.com>> wrote:


Hello everyone,

I'm at the H3Abionet Cloud computing hackathon this week in
Pretoria, South Africa.


http://www.h3abionet.org/training-and-education/h3abionet-courses/17-h3abionet-courses/h3abionet-courses-upcoming/266-h3abionet-cloud-computing-hackathon



The resulting CWL tools and workflow descriptions will be
contributed in real time to the community repository:
https://github.com/common-workflow-language/workflows


It would be super nice if I could get assistance making Debian
packages of the following so we don't abuse Docker as a package
manager :-)

metagenomeSeq
https://bioconductor.org/packages/release/bioc/html/metagenomeSeq.html



phloseq https://github.com/joey711/phyloseq


bamstats http://bamstats.sourceforge.net/


Cheers,

-- 
Michael R. Crusoe

Community Engineer & Co-founder
Common Workflow Language project
https://impactstory.org/u/-0002-2961-9670

michael.cru...@gmail.com 
+40 720 781 765 
+1 480 627 9108 




--
Michael R. Crusoe
Community Engineer & Co-founder
Common Workflow Language project
https://impactstory.org/u/-0002-2961-9670
michael.cru...@gmail.com 
+40 720 781 765
+1 480 627 9108


Are there ITP / RFP bugs filed for these already?

If you don't know for sure, please check.

Ghis

Re: Packaging wishlist for this week's H3Africa workshop

[Michael Crusoe]

One more: snpeff http://snpeff.sourceforge.net/download.html

On Mon, Aug 22, 2016 at 5:36 PM, Michael Crusoe 
wrote:

> Hello everyone,
>
> I'm at the H3Abionet Cloud computing hackathon this week in Pretoria,
> South Africa.
>
> http://www.h3abionet.org/training-and-education/h3abionet-courses/17-
> h3abionet-courses/h3abionet-courses-upcoming/266-
> h3abionet-cloud-computing-hackathon
>
> The resulting CWL tools and workflow descriptions will be contributed in
> real time to the community repository: https://github.
> com/common-workflow-language/workflows
>
> It would be super nice if I could get assistance making Debian packages of
> the following so we don't abuse Docker as a package manager :-)
>
> metagenomeSeq https://bioconductor.org/packages/release/bioc/html/
> metagenomeSeq.html
>
> phloseq https://github.com/joey711/phyloseq
>
> bamstats http://bamstats.sourceforge.net/
>
> Cheers,
>
> --
> Michael R. Crusoe
> Community Engineer & Co-founder
> Common Workflow Language project
> https://impactstory.org/u/-0002-2961-9670
> michael.cru...@gmail.com
> +40 720 781 765
> +1 480 627 9108
>



-- 
Michael R. Crusoe
Community Engineer & Co-founder
Common Workflow Language project
https://impactstory.org/u/-0002-2961-9670
michael.cru...@gmail.com
+40 720 781 765
+1 480 627 9108

Packaging wishlist for this week's H3Africa workshop

[Michael Crusoe]

Hello everyone,

I'm at the H3Abionet Cloud computing hackathon this week in Pretoria, South
Africa.

http://www.h3abionet.org/training-and-education/h3abionet-courses/17-h3abionet-courses/h3abionet-courses-upcoming/266-h3abionet-cloud-computing-hackathon

The resulting CWL tools and workflow descriptions will be contributed in
real time to the community repository:
https://github.com/common-workflow-language/workflows

It would be super nice if I could get assistance making Debian packages of
the following so we don't abuse Docker as a package manager :-)

metagenomeSeq
https://bioconductor.org/packages/release/bioc/html/metagenomeSeq.html

phloseq https://github.com/joey711/phyloseq

bamstats http://bamstats.sourceforge.net/

Cheers,

-- 
Michael R. Crusoe
Community Engineer & Co-founder
Common Workflow Language project
https://impactstory.org/u/-0002-2961-9670
michael.cru...@gmail.com
+40 720 781 765
+1 480 627 9108

Re: Could somebody please check ncbi-tools6 (Was: [GSOC] Todo List)

[Sascha Steinbiss]

Hi Canberk,

> Main problem is package dont provide a binary named ncbi-tools6 :) There are 
> different binaries inherited from this package like blast2 and ncbi-tools-bin 
> so my test must work on two binaries from ncbi-tools6 package. Am i clear now 
> ?

I see. I have always found it easiest in such cases to make a single test for 
all binary packages in the whole source package, especially if they are 
thematically related. This is absolutely fine as long as you require both 
binary packages (or ‘@‘) in your d/tests/control file. BTW you don’t need to 
install your test data to be used in the autopkgtest, as tests will always be 
run with an decompressed source tree present, including the debian directory. 
Your new ncbi-tools6.examples file wouldn’t have been used anyway since there 
is no binary package ‘ncbi-tools6’.

BTW, I have also made a few adjustments to the test, see git repo.

Cheers
Sascha

> 
> Best Regards
> 
> 
> Canberk Koç
> about.me/canberkkoc
> 
> 
> 2016-08-22 13:49 GMT+03:00 Sascha Steinbiss :
> Hi Andreas,
> 
> I’ll take a look.
> 
> Cheers
> Sascha
> 
> > On 22 Aug 2016, at 11:29, Andreas Tille  wrote:
> >
> > Hi,
> >
> > On Sat, Aug 20, 2016 at 10:16:14AM +0300, Canberk Koç wrote:
> >> I'll commit a test for tools6 but there is a problem ncbi-tools6 not come
> >> from apt-get install so test broke . There is 2 package i have blast2 and
> >> tools-bin i made tests for them but i cannot make it work can you look at
> >> it .
> >
> > For me the current Git archive does not build using gbp.  I get:
> >
> > ...
> > dpkg-source -i.git -I.git -b ncbi-tools6-6.1.20120620
> > dpkg-source: warning: no source format specified in debian/source/format, 
> > see dpkg-source(1)
> > dpkg-source: info: using source format '1.0'
> > dpkg-source: info: building ncbi-tools6 using existing 
> > ncbi-tools6_6.1.20120620.orig.tar.gz
> > dpkg-source: info: building ncbi-tools6 in 
> > ncbi-tools6_6.1.20120620-12.diff.gz
> > dpkg-source: error: cannot represent change to 
> > debian/ncbi-tools6.tests/nc0615.aso: binary file contents changed
> > dpkg-source: warning: the diff modifies the following upstream files:
> > api/alignmgr2.c
> > api/aliread.c
> > api/pgppop.c
> > api/txalign.c
> > corelib/ncbienv.c
> > ...
> >
> >
> > Since I'm currently busy with some real life things it would be great if
> > somebody could have a look and check the tests Canberk has created.
> > Sponsering of the package would be welcome.
> >
> > Kind regards
> >
> > Andreas.
> >
> > --
> > http://fam-tille.de
> >
> 
> 



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Re: Could somebody please check ncbi-tools6 (Was: [GSOC] Todo List)

[Sascha Steinbiss]

Hi Andreas and Canberk,

the problem was that ncbi-tools6 is still an old-style 1.0 format package, 
which can not contain binary files (such as the binary ASN.1 file in the test 
data) as part of the /debian directory. Either the file would need to be 
encoded as a text file, or (perhaps the better option) the package needs to be 
migrated to the newer 3.0 (quilt) format.
For now I have base64-encoded the binary file to include it in the package and 
adjusted the test script to decode it back to binary before feeding it into 
asn2xml. I guess that’s OK for one file, but if we’d like to keep adding test 
data then it might be helpful to migrate.
I will upload the package including the tests soon — thanks Canberk for adding 
the tests!

Cheers
Sascha

> On 22 Aug 2016, at 12:49, Sascha Steinbiss  wrote:
> 
> Hi Andreas,
> 
> I’ll take a look.
> 
> Cheers
> Sascha
> 
>> On 22 Aug 2016, at 11:29, Andreas Tille  wrote:
>> 
>> Hi,
>> 
>> On Sat, Aug 20, 2016 at 10:16:14AM +0300, Canberk Koç wrote:
>>> I'll commit a test for tools6 but there is a problem ncbi-tools6 not come
>>> from apt-get install so test broke . There is 2 package i have blast2 and
>>> tools-bin i made tests for them but i cannot make it work can you look at
>>> it .
>> 
>> For me the current Git archive does not build using gbp.  I get:
>> 
>> ...
>> dpkg-source -i.git -I.git -b ncbi-tools6-6.1.20120620
>> dpkg-source: warning: no source format specified in debian/source/format, 
>> see dpkg-source(1)
>> dpkg-source: info: using source format '1.0'
>> dpkg-source: info: building ncbi-tools6 using existing 
>> ncbi-tools6_6.1.20120620.orig.tar.gz
>> dpkg-source: info: building ncbi-tools6 in 
>> ncbi-tools6_6.1.20120620-12.diff.gz
>> dpkg-source: error: cannot represent change to 
>> debian/ncbi-tools6.tests/nc0615.aso: binary file contents changed
>> dpkg-source: warning: the diff modifies the following upstream files:
>> api/alignmgr2.c
>> api/aliread.c
>> api/pgppop.c
>> api/txalign.c
>> corelib/ncbienv.c
>> ...
>> 
>> 
>> Since I'm currently busy with some real life things it would be great if
>> somebody could have a look and check the tests Canberk has created.
>> Sponsering of the package would be welcome.
>> 
>> Kind regards
>> 
>>Andreas.
>> 
>> --
>> http://fam-tille.de
>> 
> 



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Re: Could somebody please check ncbi-tools6 (Was: [GSOC] Todo List)

[Canberk Koç]

Hello ,

Main problem is package dont provide a binary named ncbi-tools6 :) There
are different binaries inherited from this package like blast2 and
ncbi-tools-bin so my test must work on two binaries from ncbi-tools6
package . Am i clear now ?

Best Regards



Canberk Koç
[image: https://]about.me/canberkkoc


2016-08-22 13:49 GMT+03:00 Sascha Steinbiss :

> Hi Andreas,
>
> I’ll take a look.
>
> Cheers
> Sascha
>
> > On 22 Aug 2016, at 11:29, Andreas Tille  wrote:
> >
> > Hi,
> >
> > On Sat, Aug 20, 2016 at 10:16:14AM +0300, Canberk Koç wrote:
> >> I'll commit a test for tools6 but there is a problem ncbi-tools6 not
> come
> >> from apt-get install so test broke . There is 2 package i have blast2
> and
> >> tools-bin i made tests for them but i cannot make it work can you look
> at
> >> it .
> >
> > For me the current Git archive does not build using gbp.  I get:
> >
> > ...
> > dpkg-source -i.git -I.git -b ncbi-tools6-6.1.20120620
> > dpkg-source: warning: no source format specified in
> debian/source/format, see dpkg-source(1)
> > dpkg-source: info: using source format '1.0'
> > dpkg-source: info: building ncbi-tools6 using existing
> ncbi-tools6_6.1.20120620.orig.tar.gz
> > dpkg-source: info: building ncbi-tools6 in ncbi-tools6_6.1.20120620-12.
> diff.gz
> > dpkg-source: error: cannot represent change to 
> > debian/ncbi-tools6.tests/nc0615.aso:
> binary file contents changed
> > dpkg-source: warning: the diff modifies the following upstream files:
> > api/alignmgr2.c
> > api/aliread.c
> > api/pgppop.c
> > api/txalign.c
> > corelib/ncbienv.c
> > ...
> >
> >
> > Since I'm currently busy with some real life things it would be great if
> > somebody could have a look and check the tests Canberk has created.
> > Sponsering of the package would be welcome.
> >
> > Kind regards
> >
> > Andreas.
> >
> > --
> > http://fam-tille.de
> >
>
>

Re: Could somebody please check ncbi-tools6 (Was: [GSOC] Todo List)

[Sascha Steinbiss]

Hi Andreas,

I’ll take a look.

Cheers
Sascha

> On 22 Aug 2016, at 11:29, Andreas Tille  wrote:
> 
> Hi,
> 
> On Sat, Aug 20, 2016 at 10:16:14AM +0300, Canberk Koç wrote:
>> I'll commit a test for tools6 but there is a problem ncbi-tools6 not come
>> from apt-get install so test broke . There is 2 package i have blast2 and
>> tools-bin i made tests for them but i cannot make it work can you look at
>> it .
> 
> For me the current Git archive does not build using gbp.  I get:
> 
> ...
> dpkg-source -i.git -I.git -b ncbi-tools6-6.1.20120620
> dpkg-source: warning: no source format specified in debian/source/format, see 
> dpkg-source(1)
> dpkg-source: info: using source format '1.0'
> dpkg-source: info: building ncbi-tools6 using existing 
> ncbi-tools6_6.1.20120620.orig.tar.gz
> dpkg-source: info: building ncbi-tools6 in ncbi-tools6_6.1.20120620-12.diff.gz
> dpkg-source: error: cannot represent change to 
> debian/ncbi-tools6.tests/nc0615.aso: binary file contents changed
> dpkg-source: warning: the diff modifies the following upstream files:
> api/alignmgr2.c
> api/aliread.c
> api/pgppop.c
> api/txalign.c
> corelib/ncbienv.c
> ...
> 
> 
> Since I'm currently busy with some real life things it would be great if
> somebody could have a look and check the tests Canberk has created.
> Sponsering of the package would be welcome.
> 
> Kind regards
> 
> Andreas.
> 
> --
> http://fam-tille.de
> 



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Could somebody please check ncbi-tools6 (Was: [GSOC] Todo List)

[Andreas Tille]

Hi,

On Sat, Aug 20, 2016 at 10:16:14AM +0300, Canberk Koç wrote:
> I'll commit a test for tools6 but there is a problem ncbi-tools6 not come
> from apt-get install so test broke . There is 2 package i have blast2 and
> tools-bin i made tests for them but i cannot make it work can you look at
> it .

For me the current Git archive does not build using gbp.  I get:

...
 dpkg-source -i.git -I.git -b ncbi-tools6-6.1.20120620
dpkg-source: warning: no source format specified in debian/source/format, see 
dpkg-source(1)
dpkg-source: info: using source format '1.0'
dpkg-source: info: building ncbi-tools6 using existing 
ncbi-tools6_6.1.20120620.orig.tar.gz
dpkg-source: info: building ncbi-tools6 in ncbi-tools6_6.1.20120620-12.diff.gz
dpkg-source: error: cannot represent change to 
debian/ncbi-tools6.tests/nc0615.aso: binary file contents changed
dpkg-source: warning: the diff modifies the following upstream files: 
 api/alignmgr2.c
 api/aliread.c
 api/pgppop.c
 api/txalign.c
 corelib/ncbienv.c
...


Since I'm currently busy with some real life things it would be great if
somebody could have a look and check the tests Canberk has created.
Sponsering of the package would be welcome.

Kind regards

 Andreas.

-- 
http://fam-tille.de

Re: [GSOC] Todo List

[Andreas Tille]

Hi Canberk,

On Sat, Aug 20, 2016 at 10:53:00AM +0300, Canberk Koç wrote:
> I make testsuite for maq but package in SVN can you please move it to git .

Maq moved to Git.

I'm not sure whether I understand your mail about ncbi-tools6 but I'll
checkout and have a look.  Please excuse my slow response time in the
next couple of days.  I'm not as frequently online as usual.

Kind regards

   Andreas.


>  >   ncbi-tools6
>  >   njplot
>  >   picard-tools
>  >   maq
>  >   filo

-- 
http://fam-tille.de

Re: [Outreachy] pymol

[Andreas Tille]

Ahh, seems to be ready - so I'll go on for the sponsoring build and upload.

On Sun, Aug 21, 2016 at 01:09:31PM +0300, merlettaia wrote:
> Hi Andreas,
> I've added copyright information to debian/copyright (for UIUC and various
> font files from upstream's layer1/).
> Can you check it? I've kept UIUC license since it differs in 1st paragraph
> from BSD-3-clause mentioned at d/copyright.
> Also layer1/FontTTF.h has complex license, I copied it as it is.
> I've checked everything with cme fix dpkg-copyright.
> 
> 2016-08-20 13:19 GMT+03:00 merlettaia :
> 
> > Hi Andreas,
> > I've made testsuite for apbs (I took its own tests "(cd tests; python
> > apbs_tester.py -c test_cases.cfg)", installed them to usr/share/apbs, and
> > made sure that they work when installed).
> > Regarding python interface, which is used by pdb2pqr, it is not present in
> > source archive.
> > apbs source releases are available on github, but they contain both apbs
> > and pdb2pqr (probably because they both are developed in the same
> > repository)
> > https://github.com/Electrostatics/apbs-pdb2pqr/releases
> > On SourceForge there are 2 versions of apbs (1.4.1 and 1.4.2), but they
> > both don't have source archive. Version 1.4.0 is old.
> > I asked maintainers via gitter channel to add latest apbs source package
> > to SourceForge, let's see if they'll do it.
> > But probably changing debian/watch to take releases from github might be
> > the option.
> > I also translated debian/copyright to machine-readable format, but I
> > haven't checked if something is missing. There are also MAPBS (matlab
> > scripts) inside tools/ directory, they have their own license, but I
> > haven't installed them and haven't checked if their license present in
> > debian/copyright yet.
> >
> > Regarding pymol, I'll fix debian/copyright now.
> >
> > 2016-08-17 10:57 GMT+03:00 Andreas Tille :
> >
> >> Hi Tanya,
> >>
> >> On Tue, Aug 16, 2016 at 08:01:46PM +0300, merlettaia wrote:
> >> > Could you please take a look at pymol?
> >>
> >> I did now.  I fixed some minor lintian issues (DEP3, override for
> >> spelling).  I also added some Breaks and a versioned dependency which is
> >> important for upgrades when splitting a package.  Please have a look at
> >> the commits to debian/control which might be an interesting lesson for
> >> other packages.
> >>
> >> > I made almost everything possible, except solving this warnings (but I
> >> can
> >> > fix them too):
> >> >
> >> >I: pymol: desktop-entry-lacks-keywords-entry
> >> > usr/share/applications/pymol.desktop
> >>
> >> Please just let me know if you want to fix this.
> >>
> >> >W: pymol: command-in-menu-file-and-desktop-file pymol
> >> > usr/share/menu/pymol:7
> >>
> >> Fixed by removal of menu file.
> >>
> >> Thanks again for your tough work.  I'll upload once I hear from you
> >> about the desktop file.  I'd also upload if you confirm: "Uhhmmm, no
> >> idea what keyword would be appropriate."
> >>
> >> Kind regards
> >>
> >>Andreas.
> >>
> >> --
> >> http://fam-tille.de
> >>
> >
> >
> >
> > --
> > Best wishes,
> > Tanya.
> >
> 
> 
> 
> -- 
> Best wishes,
> Tanya.

-- 
http://fam-tille.de

Re: [Outreachy] pymol

[Andreas Tille]

Hi Tanya,

On Sat, Aug 20, 2016 at 01:19:03PM +0300, merlettaia wrote:
> I've made testsuite for apbs (I took its own tests "(cd tests; python
> apbs_tester.py -c test_cases.cfg)", installed them to usr/share/apbs, and
> made sure that they work when installed).
> Regarding python interface, which is used by pdb2pqr, it is not present in
> source archive.
> apbs source releases are available on github, but they contain both apbs
> and pdb2pqr (probably because they both are developed in the same
> repository)
> https://github.com/Electrostatics/apbs-pdb2pqr/releases
> On SourceForge there are 2 versions of apbs (1.4.1 and 1.4.2), but they
> both don't have source archive. Version 1.4.0 is old.
> I asked maintainers via gitter channel to add latest apbs source package to
> SourceForge, let's see if they'll do it.
> But probably changing debian/watch to take releases from github might be
> the option.

Thanks for your work on this.  I'm a bit offline-ish this week and thus
a short notice.  If I where you I'd point d/watch to Github and package
the latest upstream version.  May be some Daniel or Michael might
comment here.  Moving the packaging from SVN to Git might be also a
sensible thing to do but DebiChem team might raise their option as well.

> I also translated debian/copyright to machine-readable format, but I
> haven't checked if something is missing. There are also MAPBS (matlab
> scripts) inside tools/ directory, they have their own license, but I
> haven't installed them and haven't checked if their license present in
> debian/copyright yet.

As long as we have no sign that the scripts work with Octave as well and
thus are usable with free software I personally would not care about
this.
 
> Regarding pymol, I'll fix debian/copyright now.

Thanks for working on this.  Just ping if something needs uploading.  If
someone else might take over the sponsoring that would be nice - please
respond to the according mail to let me know.

Kind regards

 Andreas.

-- 
http://fam-tille.de