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Re: COBRApy available as a Debian package



I think pandas should be recommended (some functions have the option to return pandas Dataframes which will fail if they are not installed). However, I think that you are correct by changing matplotlib to suggested.

As far as the COBRA toolbox goes, it's still used pretty heavily. However, I'm not sure if it's tested on GNU Octave (and obviously you can't have MATLAB as a dependency). In any case, its primary maintainer is Ronan Fleming (ronan.mt.fleming@uni.lu) if you want to discuss it further with someone.

On Thu, Jul 23, 2015 at 8:55 PM, Afif Elghraoui <afif@ghraoui.name> wrote:
Thanks for your feedback-- (see inline)

On الخميس 23 تـمـوز 2015 19:50, Ali Ebrahim wrote:
> Hello Afif,
>
> Thank you very much for doing this!
>

No problem.

> I have the following comments for the next version (I'll be releasing
> beta 2 soon, so maybe you can do it when you make  an updated package
> for that).
>

Just to make sure we're on the same page, I'm going by definitions of
the suggests/recommends fields at:
https://www.debian.org/doc/debian-policy/ch-relationships.html#s-binarydeps

> 1) Please remove jython from sug. cobrapy is no longer developed or
> tested on jython.
> 2) Please make the data required, as its necessary for some cobrapy
> functions.

Committed.

> (Also please make sure that cobra.test.data_directory
> contains the test files).
>

I separated the data so they could be shared by the different python
versions of the package, but there is a symlink in the appropriate place
so as not to break the software.

In light of the policy definitions linked above, I was also going to
change matplotlib and pandas from 'recommended' to 'suggested'. Do you
think I should keep them as recommended? Recommended packages get
installed by default.

> Once again, this is awesome.
>

By the way, is there a reason to also package the cobra toolbox or is
that on its way out of use?

Regards
Afif

--
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name


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