Re: [autopkgtest 879622]

[Kalou.Katerina]

​Dear Andreas,
>
​
>
>
> export DEBEMAIL=aik.ka...@gmail.com
> export DEBFULLNAME='Katerina Kalou'
>
> in your environment - than dch knows for sure what user ID to choose.
>
> ​Thank you, i was just searching on how to do that!!

​

> There is also some care needed to make sure that there is no changelog
> entry left for UNRELEASED.  I merged those two entries.  I've pushed and
> uploaded now.
>

​Thank you again! And i will more careful next time!​

> I would also kindly like to express my interest to apply to either
> > outreachy or GSoC. I had a look to the Outreachy announcement for this
> > round of applications and as i did not see any proposed project by the
> > debian med team (especially the one about adding autopkgtest suites),  i
> > was thinking about the GSoC as an alternative. As my PhD thesis will be
> > ready in the end of March but i will still be a student until the
> beginning
> > of June, i was thinking if it would be possible for me to apply.
>
> Please note:  I'm *always* confused about all the bureaucracy around.  I
> remember that in the past GSoC *and* Outreachy picked from the project
> list that has the GSoC headline.  I as a mentor do not mind at all to
> what project you subscribe.  I do not even have a clear advise whom to
> ask for clarification - sorry. :-(
>
​
Actually that was helpful for me - i will go on with the Outreachy
application (also maybe send the organisers an email asking for some
clarification) and i will let you know!!

Thank you again for everything :)

Kind regards,
Kate​


> ​
>
>
>

Re: [autopkgtest 879622]

[Andreas Tille]

Dear Katerina,

On Mon, Feb 19, 2018 at 08:03:50PM +0200, Kalou.Katerina wrote:
> Dear Andreas,
> 
> Thank you so much for all your comments! I confirm i pushed the changelog
> entry , i hope i did it right ;)

There is some room for enhancement. ;-)

I'd suggest to use

export DEBEMAIL=aik.ka...@gmail.com
export DEBFULLNAME='Katerina Kalou'

in your environment - than dch knows for sure what user ID to choose.

There is also some care needed to make sure that there is no changelog
entry left for UNRELEASED.  I merged those two entries.  I've pushed and
uploaded now.

> I would love to go on with adding an autopkgtest to another package, i was
> thinking to continue with rsem (n.890792
>  ), if that is ok
> for everyone!

I've put the rsem bug in CC.
 
> I would also kindly like to express my interest to apply to either
> outreachy or GSoC. I had a look to the Outreachy announcement for this
> round of applications and as i did not see any proposed project by the
> debian med team (especially the one about adding autopkgtest suites),  i
> was thinking about the GSoC as an alternative. As my PhD thesis will be
> ready in the end of March but i will still be a student until the beginning
> of June, i was thinking if it would be possible for me to apply.

Please note:  I'm *always* confused about all the bureaucracy around.  I
remember that in the past GSoC *and* Outreachy picked from the project
list that has the GSoC headline.  I as a mentor do not mind at all to
what project you subscribe.  I do not even have a clear advise whom to
ask for clarification - sorry. :-(
 
> Anyway, apart of the internships, i would like to continue contributing to
> the debian med project , it is a truly unique experience!

That's really appreciated.  Thank you for this.

> Thank you so much again for all the help and comments!

You are welcome as any contributor

Andreas.

-- 
http://fam-tille.de

Re: [autopkgtest 879622]

[Kalou.Katerina]

Dear Andreas,

Thank you so much for all your comments! I confirm i pushed the changelog
entry , i hope i did it right ;)

I would love to go on with adding an autopkgtest to another package, i was
thinking to continue with rsem (n.890792
 ), if that is ok
for everyone!

I would also kindly like to express my interest to apply to either
outreachy or GSoC. I had a look to the Outreachy announcement for this
round of applications and as i did not see any proposed project by the
debian med team (especially the one about adding autopkgtest suites),  i
was thinking about the GSoC as an alternative. As my PhD thesis will be
ready in the end of March but i will still be a student until the beginning
of June, i was thinking if it would be possible for me to apply.

Anyway, apart of the internships, i would like to continue contributing to
the debian med project , it is a truly unique experience!

Thank you so much again for all the help and comments!

Kind regards,
Kate

On Mon, Feb 19, 2018 at 11:01 AM, Andreas Tille  wrote:

> Dear Kate,
>
> On Mon, Feb 19, 2018 at 12:21:35AM +0200, Kalou.Katerina wrote:
> > Thank you for your comments!! I tried to push the files again , i think
> > that now it worked :)
>
> I confirm the push worked now.  I've pushed some more commits - partly
> related to your work.  Please keep on reading my comments below.
>
> > > > Any
> > > > comments and corrections will be much welcome!! In my linux machine
> the
> > > > 'autopkgtest -- null' command reports a pass.
> > > >
> > > > In the example folder i have put two sample data that i managed to
> found
> > > at
> > > > 'https://github.com/arq5x/bedtools2'. These two files are '.BED'
> file
> > > > extensions. The example at the macs package install instructions is
> using
> > > > the 'BAM' extension , if anyone has any recommendation on where to
> find
> > > > these, it will be much appreciated!! :)
> > >
> > > In any case make sure you document the origin of the example filese in
> > > debian/README.source (may be you add your question also in this file).
>
> I've seen you have give some (rather vague) pointer in README.test
> (which is fine - no need to create an extra README.source.  Besides the
> fact that all Debian related stuff needs to be in debian/ dir (I just
> moved the file) I wished you would add some more specific pointer.  The
> best thing would be something like
>
> wget URL_to_example_file1
> wget URL_to_example_file2
>
> So everybody can immediately reproduce what you did to get the files.
> To express what I mean I did so in the latest commit.  I also left the
> files compressed as downloaded which requires an extra file
>
> debian/source/include-binaries
>
> (dpkg-buildpackage will tell you about this so this is no knowledge you
> need to keep by heart. ;-) )
>
> Regarding how to get BAM files instead of BED files I'm hoping for
> comments here on the list but for the moment macs2 seems to do something
> sensible which should qualify for a first test.
>
> > > > Finally , i included the files 'README.test',
> > > 'macs-example-data.install'
>
> The file macs-example-data.install is wrong.  In the other package you
> worked on we have created an extra data package.  I do not think that
> the amount of extra data in the macs example rectifies an additional
> package and thus we have no such package macs-example-data defined in
> debian/control.  Thus this file is simply ignored.  You rather need to
> put files in debian/macs.examples (and make sure those files are really
> existing - since I bumped debian/compat in some unrelated change
> mentioning non-existing files has lead to build problems).
>
> > > > and 'macs.install', taking inspiration from the previous packages
> like
> > > > rapmap i worked on. The purpose was to send the examples folder to
> the
> > > > 'usr/share/doc' directory during installation , i do not know if i
> did it
> > > > right!
>
> I've now fixed it - please check all my according commits.
>
> Finally please always add a changelog entry to the package documenting
> your changes.  I'd recommen to use the dch tool for this.  For instance
> you can do
>
> dch --team "Add autopkgtest (Closes: #879622)"
>
> specifically the "Closes:" is important to automatically close the bug.
> (You can also use `dch --team` and add the string manually with the
> editor.)
>
> I would like you to take over the changelog entry (that's why the --team
> option - see `man dch`) since I want to give credit to the person who
> has written the test and has fixed the bug.
>
> I think the package is ready once you have done the changelog entry and
> I'll upload once I have seen your commit.  Yesterday I added a set of
> new bugs for packages in need of an autopkgtest.  So there is a plenty
> to pick from and as I wrote here before I issued an according GSoC
> project proposal (which can be also picked for outreachy as far as I
> 

Fwd: [force11/force11-sciwg] Experience with Debian Science's Citations project? (#45)

[Michael Crusoe]

FYI

-- Forwarded message --
From: Katrin Leinweber 
Date: 2018-02-17 23:11 GMT+02:00
Subject: [force11/force11-sciwg] Experience with Debian Science's Citations
project? (#45)
To: force11/force11-sciwg 
Cc: Subscribed 


Hi!

I learned about https://wiki.debian.org/DebianScience/Citations recently
and was wondering whether anyone here knows about that initiative? The "med"
& "science" blends were apparently discussing

and implementing (not sure how far) a system-wide way for users to gather
citation info from packages they were using.



-- 
Michael R. Crusoe
Co-founder & Lead, Common Workflow Language project

Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania
https://orcid.org/-0002-2961-9670

m...@commonwl.org
+1 480 627 9108

Direktoriaus kontaktai - tai Jūsų klientas

[Gautas pranešimas]

Laba diena,


Noriu Jus informuoti apie šių metų pasikeitimą dėl atnaujintos visos Lietuvos 
įmonių bazės 2018 metų sausio vidurio.
Visi juridiniai asmenys pateikti bazėje yra veikiantys, realiai vykdantys 
veiklą, turintys įdarbintų darbuotojų. Duomenys pagal Sodrą, Registrų centrą.
 
Bazėje nurodoma ir apyvarta, darbuotojų atlyginimai, darbuotojų skaičius, 
transporto skaičius ir daug kitų duomenų, kuriuos matysite pavyzdyje.
 
Duomenis galima filtruoti pagal veiklas, miestus ir kitus duomenis.
 
 
Šią bazę verta turėti visoms įmonėms. Pateiksiu priežastis:
 
1) Kontaktai pateikti bazėje direktorių ir kitų atsakingų asmenų, didelė 
tikimybė Jums surasti naujų klientų, partnerių, tiekėjų, kai tiesiogiai 
bendrausite su direktoriais, komercijos vadovais.
 
2) Konkurentų analizavimas, tiekėjų atsirinkimas pagal Jums reikalingus 
kriterijus, galite atsifiltruoti pagal įmonės dydį, bazėje nurodoma kiek įmonės 
skolingos Sodrai.
 
3) Lengva, greita ir patogu dirbti su šia baze, elektroninius pašto adresus 
galite importuoti į elektroninių laiškų siuntimo programas ar sistemas iš kurių 
siunčiate elektroninius laiškus.
Taip pat galite importuoti mobiliųjų telefonų numerius į SMS siuntimo programas.
 
 
Išsirinkite iš "Veiklų sąrašo" veiklas kurių Jums reikia.
( Sąrašas prisegtas laiške excel faile )
 
Parašykite, kurias veiklas išsirinkote 
ir atsiųsime pavyzdį ir pasiūlymą su sąlygomis įmonių bazei įsigyti



Pagarbiai,
Tadas Giedraitis
Tel. nr. +37067881041


Veiklos.xlsx
Description: Binary data

Bug#890755: marked as done (ITP: ctdconverter -- Convert CTD files into Galaxy tool and CWL CommandLineTool files)

[Debian Bug Tracking System]

Your message dated Mon, 19 Feb 2018 11:01:30 +
with message-id 
and subject line Bug#890755: fixed in ctdconverter 2.0-1
has caused the Debian Bug report #890755,
regarding ITP: ctdconverter -- Convert CTD files into Galaxy tool and CWL 
CommandLineTool files
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
890755: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=890755
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: ctdconverter
  Version : 2.0
  Upstream Author : WorkflowConversion
* URL : https://github.com/WorkflowConversion/CTDConverter/
* License : GPL-3 / Apache-2.0
  Programming Lang: Python
  Description : Convert CTD files into Galaxy tool and CWL CommandLineTool 
files

Common Tool Descriptors (CTDs) are XML documents that represent the inputs,
outputs, parameters of command line tools in a platform-independent way.

CTDConverter, given one or more Common Tool Descriptors (CTD) XML files,
generates Galaxy tool wrappers and Common Workflow Language (CWL) Command
Line Tool v1.0 standard descriptions from CTD files.

Will assist in including CWL descriptions in the seqan-apps, openms/topp,
flexbar, and lambda-align packages

Will be team-maintained by Debian Med
--- End Message ---
--- Begin Message ---
Source: ctdconverter
Source-Version: 2.0-1

We believe that the bug you reported is fixed in the latest version of
ctdconverter, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 890...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Michael R. Crusoe  (supplier of updated ctdconverter 
package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


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Format: 1.8
Date: Sun, 18 Feb 2018 02:17:55 -0800
Source: ctdconverter
Binary: ctdconverter
Architecture: source all
Version: 2.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Description:
 ctdconverter - Convert CTD files into Galaxy tool and CWL CommandLineTool files
Closes: 890755
Changes:
 ctdconverter (2.0-1) unstable; urgency=medium
 .
   * Initial release. (Closes: #890755)
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Re: [autopkgtest 879622]

[Andreas Tille]

Dear Kate,

On Mon, Feb 19, 2018 at 12:21:35AM +0200, Kalou.Katerina wrote:
> Thank you for your comments!! I tried to push the files again , i think
> that now it worked :)

I confirm the push worked now.  I've pushed some more commits - partly
related to your work.  Please keep on reading my comments below.
 
> > > Any
> > > comments and corrections will be much welcome!! In my linux machine the
> > > 'autopkgtest -- null' command reports a pass.
> > >
> > > In the example folder i have put two sample data that i managed to found
> > at
> > > 'https://github.com/arq5x/bedtools2'. These two files are '.BED' file
> > > extensions. The example at the macs package install instructions is using
> > > the 'BAM' extension , if anyone has any recommendation on where to find
> > > these, it will be much appreciated!! :)
> >
> > In any case make sure you document the origin of the example filese in
> > debian/README.source (may be you add your question also in this file).

I've seen you have give some (rather vague) pointer in README.test
(which is fine - no need to create an extra README.source.  Besides the
fact that all Debian related stuff needs to be in debian/ dir (I just
moved the file) I wished you would add some more specific pointer.  The
best thing would be something like

wget URL_to_example_file1
wget URL_to_example_file2

So everybody can immediately reproduce what you did to get the files.
To express what I mean I did so in the latest commit.  I also left the
files compressed as downloaded which requires an extra file

debian/source/include-binaries

(dpkg-buildpackage will tell you about this so this is no knowledge you
need to keep by heart. ;-) )

Regarding how to get BAM files instead of BED files I'm hoping for
comments here on the list but for the moment macs2 seems to do something
sensible which should qualify for a first test.

> > > Finally , i included the files 'README.test',
> > 'macs-example-data.install'

The file macs-example-data.install is wrong.  In the other package you
worked on we have created an extra data package.  I do not think that
the amount of extra data in the macs example rectifies an additional
package and thus we have no such package macs-example-data defined in
debian/control.  Thus this file is simply ignored.  You rather need to
put files in debian/macs.examples (and make sure those files are really
existing - since I bumped debian/compat in some unrelated change
mentioning non-existing files has lead to build problems).

> > > and 'macs.install', taking inspiration from the previous packages like
> > > rapmap i worked on. The purpose was to send the examples folder to the
> > > 'usr/share/doc' directory during installation , i do not know if i did it
> > > right!

I've now fixed it - please check all my according commits.

Finally please always add a changelog entry to the package documenting
your changes.  I'd recommen to use the dch tool for this.  For instance
you can do

dch --team "Add autopkgtest (Closes: #879622)"

specifically the "Closes:" is important to automatically close the bug.
(You can also use `dch --team` and add the string manually with the
editor.)

I would like you to take over the changelog entry (that's why the --team
option - see `man dch`) since I want to give credit to the person who
has written the test and has fixed the bug.

I think the package is ready once you have done the changelog entry and
I'll upload once I have seen your commit.  Yesterday I added a set of
new bugs for packages in need of an autopkgtest.  So there is a plenty
to pick from and as I wrote here before I issued an according GSoC
project proposal (which can be also picked for outreachy as far as I
know).

Kind regards

   Andreas.

-- 
http://fam-tille.de