Re: RRID update on salsa on packages starting with A+B

[Andreas Tille]

On Thu, Mar 29, 2018 at 08:48:01PM +0200, Steffen Möller wrote:
> 
> > > But I found artemis
> > > (https://salsa.debian.org/med-team/artemis/tree/master/debian/upstream)
> > > which was not touched for a while and looks syntactically just fine but 
> > > has
> > > its RRIDs not shown.
> 
> Please kindly have a look at clonalframe - it has a ref
> for SciCrunch, is yamllint clean but nothing shows up.

H, good catch.  

 clonalframe   | SciCrunch | SCR_016060

is in UDD.  I have no idea why it is not displayed on the tasks page.
Needs further investigation.  And flexbar is also fully read:

 flexbar   | OMICtools | OMICS_01087
 flexbar   | bio.tools | flexbar
 flexbar   | SciCrunch | SCR_013001

I need to check this in the next couple of days. 

Kind regards

   Andreas.

-- 
http://fam-tille.de

Re: RRID update on salsa on packages starting with A+B

[Steffen Möller]

On 3/29/18 8:48 PM, Steffen Möller wrote:


On 3/28/18 1:14 PM, Andreas Tille wrote:

On Wed, Mar 28, 2018 at 12:03:54PM +0200, Steffen Möller wrote:

But I found artemis
(https://salsa.debian.org/med-team/artemis/tree/master/debian/upstream)
which was not touched for a while and looks syntactically just fine 
but has

its RRIDs not shown.


Please kindly have a look at clonalframe - it has a ref
for SciCrunch, is yamllint clean but nothing shows up.


For flexbar it is only the missing \n that is missing.

Cheers,

Steffen

Re: RRID update on salsa on packages starting with A+B

[Steffen Möller]

On 3/28/18 1:14 PM, Andreas Tille wrote:

On Wed, Mar 28, 2018 at 12:03:54PM +0200, Steffen Möller wrote:

But I found artemis
(https://salsa.debian.org/med-team/artemis/tree/master/debian/upstream)
which was not touched for a while and looks syntactically just fine but has
its RRIDs not shown.


Please kindly have a look at clonalframe - it has a ref
for SciCrunch, is yamllint clean but nothing shows up.

Many thanks

Steffen

Re: Bug#879619: Autopkgtest for ncbi-tools6

[Aaron M. Ucko]

Liubov Chuprikova  writes:

> Please, have an eye on my last commits
> ! I'd like to
> ask one question (most likely it is to Aaron): Are there tools that I
> didn't include, but you would strongly recommend for testing? Then I will
> concentrate on them to finish.

These tests are shaping up nicely; thanks again for putting them
together.  Of the remaining tools, I would prioritize testing tbl2asn
and perhaps asnmacro.  (Also, please fix the typo in the asn2gb test's
leading echo statement.)

Спасибо!

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu

Re: Bug#879619: Autopkgtest for ncbi-tools6

[Andreas Tille]

On Thu, Mar 29, 2018 at 02:35:01PM +, Liubov Chuprikova wrote:
> 
> Thanks a lot for your attention to my work on the project!

I'd like to confirm that this is because of your pretty good work. ;-)

> Please, have an eye on my last commits
> ! I'd like to
> ask one question (most likely it is to Aaron): Are there tools that I
> didn't include, but you would strongly recommend for testing? Then I will
> concentrate on them to finish.

Definitely Aaron is the expert here.  I personally have no idea, sorry.

Kind regards

 Andreas.

-- 
http://fam-tille.de

Re: Bug#879619: Autopkgtest for ncbi-tools6

[Liubov Chuprikova]

Dear Andreas, dear Aaron,

ср, 28 мар. 2018 г. в 5:07, Aaron M. Ucko :

> Liubov Chuprikova  writes:
>
> > Thanks a lot for helping me out with this project! I saw your messages to
> > Aaron and it was a relief for me that there was a "real" problem to build
> > the package. I had it too, but thought, this was with updating package
> > dependencies on my computer..
>
> Thanks for adding these tests, and sorry you ran into dpkg errors along
> the way!  Please let me know if you have usage questions about any of
> this package's tools.


вт, 27 мар. 2018 г. в 16:01, Andreas Tille :

> On Tue, Mar 27, 2018 at 01:33:58PM +, Liubov Chuprikova wrote:
>
> > > I noticed that you pushed a commit featuring the copyright information
> > > of the test data.  Do you consider the package ready for upload now or
> > > are you busy to enhance the test?  From my point of view an upload with
> > > the current status would be fine but I'm waiting for your OK for the
> > > upload.  In any case I added a closes: #879619 (which should mark the
> > > bug "pending upload" if the hook on Salsa works properly which I hereby
> > > want to test).
> > >
> >
> > Sorry, but yes, I had no time to enhance the test by this evening. The
> > package has more commands to test and I need to figure out how. I will be
> > able to finish it no later than tomorrow's evening.  I will let you know
> > once it will be done.
>
> That's perfectly fine and I'll stay patient.  Feel free to take all time
> you need.
>

Thanks a lot for your attention to my work on the project! Frankly, I am
stunned with the huge amount of different file formats required or
generated! :-) Unfortunately, I could not add tests for all commands in the
package so far. It appears I need more time to recognise what their inputs
should look like and where to find them.

Please, have an eye on my last commits
! I'd like to
ask one question (most likely it is to Aaron): Are there tools that I
didn't include, but you would strongly recommend for testing? Then I will
concentrate on them to finish.

Kind regards,
Liubov

Re: Help with new package version?

[Andreas Tille]

Hi Benjamin,

On Wed, Mar 28, 2018 at 09:37:05PM -0400, Benjamin Redelings wrote:
> I've released a new version 3.0.3 of bali-phy, and I realize that I don't
> understand how to manage the salsa repo using git.  I've tried something
> like this (mostly locally), but I'm pretty sure there is a way of doing this
> with gbp that is recommended instead:
> 
>     git fetch upstream
>     git fetch upstream --tags
>     git checkout upstream
>     git merge -X theirs 3.0.3
>     git tag upstream/3.0.3+dfsg
>     git checkout master
>     git merge upstream

I assume the problem is that you most probably intend to maintain the
Debian repository in your upstream repository.  I know that this is
somehow possible but I'm lacking experience with this and thus can not
give any helpful hint for this approach.  We actually had some clones of
upstream directories created by other maintainers but I was always
running into problems with this (most probably just me!) and since those
Debian maintainers got busy with other stuff I turned the repositories
in what we consider default repository layout in Debian Med policy[1].

So if qou want to avoid any hassle I'd recommend to do the following:

   gbp clone g...@salsa.debian.org:med-team/bali-phy.git

(may be you rename the resulting dir to bali-phy_debian ??) change
to this dir and do

   uscan --verbose
   gbp import-orig --pristine-tar 

This approach is well tested and if something unexpected might happen
you can quickly get help here.

BTW, I base my assumption that you are using your development Git on the
fact that yesterday arrived lots of tags in the Salsa Git repository.  I
took the freedom to do

  for tag in `git tag | grep -v -e '^debian' -e '^upstream'` ; do 
git tag -d $tag
git push origin :refs/tags/$tag
  done

since these tags do not make any sense in the current repository on
Salsa.

> I also tried gbp dch, but it tried to create version 3.0.2+dfsg-2 instead of
> 3.0.3+dfsg-1.

Well, dch does not know what version bump you intend to do.  Just use
your editor to fix the version number.

> Would it be possible to give me the quick overview?  My
> apologies for the basic nature of this question.

Your question is perfectly valid and I'm happy to help.  Just keep
on with asking about any problem you might face.

Hope this helps

  Andreas.


[1] 
https://debian-med.alioth.debian.org/docs/policy.html#git-repository-structures

-- 
http://fam-tille.de