Re: New package bali-phy

[Benjamin Redelings]

Hi Andreas,

On 03/09/2018 06:20 PM, Andreas Tille wrote:

Hi again,

On Fri, Mar 09, 2018 at 10:42:11PM +0100, Andreas Tille wrote:

I wondered about this.  I was unsure if /usr/share/doc/ is a good place for
non-Debian systems, so I did not change the upstream default.  But for
Debian it is indeed the natural place for me to look.  It seems there are a
few options:
1. Change upstream to install to /usr/share/doc/ everywhere
2. Edit meson.build to put the examples in /usr/share/doc/
3. #2 + make symlink to /usr/share//examples
4. Make a symlink from /usr/share/doc//examples to
/usr/share//examples
I'm not sure #1 works everywhere. #2 has the problem that the path to the
examples would be distribution-dependent. #3 and #4 both seem OK though.

I admit I have no real preference.  I can not see any problem in #1 in
general but I'll leave the freedom of decision to you.

That's now the last open question.
I guess you are right.  I changed the upstream default to put the 
examples in /usr/share/doc.
I also updated README.{html,xhtml,pdf} to mention the new location. I 
can tag this as 3.0.2 if that makes life easier, since I'm not sure how 
to modify README.pdf with a patch.





how to do it.  Do we do this with a quilt patch? Because that would be a
very large patch, and I didn't like the idea of removing the local boost via
a patch that was the same size as boost :-P  But it is not really
important.  Also, if we strip them out, do they still need to be in the
copyright file?  That would shrink the copyright file nicely.

I'll take this as agreement that I'll do what I suggested as an example
and will confirm here once this is done (probably tomorrow).

Done now.

OK, thanks.




In addition, anything from the autotools build system can also be removed.
This includes:
   m4/
   configure.ac
   bootstrap.sh
   scripts/git_version.sh
   $(find . -name Makefile.am)

I'll do this as well.

Besides these I removed src/dlfcn-win32

Please check and confirm that you are OK with this solution.

That looks good.

-BenRI

Re: New package bali-phy

[Andreas Tille]

Hi Benjamin,

On Sat, Mar 10, 2018 at 09:28:55AM -0500, Benjamin Redelings wrote:
> > > I admit I have no real preference.  I can not see any problem in #1 in
> > > general but I'll leave the freedom of decision to you.
> > That's now the last open question.
> I guess you are right.  I changed the upstream default to put the examples
> in /usr/share/doc.
> I also updated README.{html,xhtml,pdf} to mention the new location. I can
> tag this as 3.0.2 if that makes life easier, since I'm not sure how to
> modify README.pdf with a patch.

Using a new release tag is most probably the easiest way to deal with
this.
 
> > Please check and confirm that you are OK with this solution.
> That looks good.

Fine.  So I'll upload as soon as you issued the new release tag.

Kind regards

   Andreas. 

-- 
http://fam-tille.de

Outreachy round 16 | Applying to Debian

[Rupal Jain]

Hi, Andreas. Hi, Molly.

I am Rupal Jain,  a 3rd-year undergrad studying at IIIT Delhi, India. I am
majoring in Computer Science and minoring in Computational Biology. I am
applying to Outreachy 2018 round 16. I am particularly interested in
the "*Quality
assurance for biological applications inside Debian project*".

A little background of mine:

I have been into programming since class 11th. Have been coding primarily
in C, C++. Also, have done projects in and have a good understanding of
Matlab, Python, and Java. I am a decent and confident coder having written
decently complex codes since my college days. I have a fair understanding
of Operating Systems, and strong in data structures and algorithms, and
their analysis and design. I'm a newbie to the world of open source. which
is the prime reason why I'm applying to Outreachy i.e to get a head-start.
And so that FOSS doesn't sound alien to me anymore. :P

The prime reason as to why I am interested in Bioinformatics project inside
Debian is that, I am Computational Biology enthusiast. I have been involved
in the field since past one year and have done/doing relevant courses at my
institute and doing projects in them.

*Relevant courses I took/taking*: Quantitative Biology, Computational
Neuroscience, Chemoinformatics, Network Biology, Network Science.
Alongside, I am also doing research projects in these domains as a part of
my courses.

*Self-learning*: Mathematical models in Biology. Studying it by myself as
I'm fascinated with the mathematical logic and aspect behind most of the
things I study.

Due to this exposure, I could resonate so well with this project under
Debian. *And*, I am excited to learn about bioinformatics from a whole new
aspect with Debian.

In addition to just sounding cool, the work looks challenging too. Being a
total beginner to Debian packaging or concepts along this line, the project
surely has a good learning curve for me.

So, I'll just list the things I have gone through and am aware of and other
trivial stuff and what question I have:

1. First and foremost, I have subscribed to your mailing list (have also
cc'ed it here as I have read that you guys prefer to keep most of your
conversations public, which does make sense to me).
2. I went through the archived conversations through the mailing lists for
GSoC/Outreachy program to know what questions did past applicants have,
what you answered them and also, to see whether there are already many
potential applicants for this project and whether you have finalized one of
them to be an intern, etc.
3. I have gone through this
 policy document as
I saw that you have redirected many individuals to this document as an
essential reading. I got to know about Debian Pure Blend, motivation and
aim of the "Debian Med project", and also reading like, "Developers
reference" and "New Maintainers guide", although I couldn't understand the
technical portion too well.
4. I also came across the *MoM *program here
, I want to be a part of it and in
the process of learning Debian packaging during MoM, I can also make
appropriate contributions to the project for Outreachy.
5. On this  tasks page, it shows a
whole list of Debian Med packages, so is there a particular package on
which I will be working on in the beginning or is it still to be decided?
Because based on names of meta packages, I feel more interested in some
packages more than other (broad fascination with themes), but I'm sure
you'll know it better that which one I should be working on.
6. Is this  the right link for me to head
towards setting up Debian environment?

I have just looked up to the internet to know what do we *mean *by
packaging in Debian, to get a gist of what is there to be done, but this
gave me a very broad view/glimpse of what it means, but only *theoretically.
*But to get into actual coding and building packages and understanding the
*workflow*, without which there wouldn't be much of a point to go on
solving bugs, I'll need help (as a beginner would do). Like MoM program,
maybe.

I am not sure if I am late in contacting you as the deadline is 22nd March
for submitting contributions. Although, the contributions we make after
that (till the results are announced) might also be counted.

Let me know what you think.



---

Thanks and regards

*Rupal Jain*2015081
CSE undergrad(3rd year) | IIITD‌

Re: EDFbrowser 1.63 (new version available)

[Andreas Tille]

Hi Teunis,

On Fri, Mar 09, 2018 at 09:45:20PM +0100, Teunis van Beelen wrote:
> EDFbrowser 1.63 is available at:
> 
> https://www.teuniz.net/edfbrowser/

Thanks for the update.  You might like to fix

I: edfbrowser: spelling-error-in-binary usr/bin/edfbrowser evironment 
environment

in your next upstream release.

Kind regards

  Andreas.

-- 
http://fam-tille.de