Re: q2-* - did a few
On 8 August 2021 2:57:46 am IST, "Steffen Möller" <steffen_moeller@gmx.de> wrote:
>
>On 07.08.21 22:13, Nilesh Patra wrote:
>>> [...]
>> Do you need some help?
>
>There is a partial dependency of
>https://salsa.debian.org/med-team/gneiss (dep of q2-gneiss) on
>https://github.com/bokeh/bokeh . The latter seems to produce nice
>graphics, no idea how much work that would be to package. Should go to
>science rather than med, I suggest. If you could pioneer the packaging
>of bokeh then this would be nice.
Bokeh is a beast, and I honestly don't have the time to get it all by myself. However I can ofcourse hell in the process.
I think Shayan (in CC) was doing something to package Bokeh. @Shayan, any updates on this?
>I do not think that the upload of
>gneiss should be blocked by that missing dependency, but anyway, this
>looks good to have and the circular diagrams that gneiss depends on
>bokeh for (if I understood this right) are indeed a thing in microbiome
>analyses since no absolute abundances of microbiomes can be measured -
>only relative, as nicely representable in a circle.
So I think we have two options:
a) Upload gneiss w/o support of Bokeh for now, and add Bokeh related support/enable Bokeh related tests when we have Bokeh packaged. We have an entire release to get it in
b) Only one or two sub parts of gneiss use Bokeh, so
For now, translate the code that uses Bokeh to something that we have in the archive. For instance code that uses Bokeh to use matplotlib, or seaborn for dataset visualisations.
What do you suggest/think?
>Otherwise, you typically bring packages to another level and I
>appreciate whatever you find time to address - once the release is out,
>I suggest.
:-)
>I do not know yet about what qiime2 tutorial (from
>https://docs.qiime2.org/2021.4/tutorials/ I presume) I want to run on
>Debian. Suggestions are welcome. The simplest as a start :) I kind of
>picture a Wiki page that references an established tutorial and then it
>should be possible to come up with a "qiime2-debian-test" package that
>runs that code. A side-effect I hope to be that I improve the package
>descriptions of the q2-* packages.
I think it'd be worth asking upstream too about it, right?
>>> Q2-taxa needs a bit of
>>> cleanup with the JavaScript it is shipping. But otherwise, I tend to
>>> think we are done.
>> I believe I made q2-taxa ready for its entry to the archive. What $cleanup does it need exactly?
>
>Aargh. I just still had the "D3-scale-chromatic,
node-d3-scale-chromatic was my first ever contribution to Debian :-)
It was done two years ago
> thenBy, natural-sort
>JavaScript dependencies" note in the spreadsheet and apparently
>missed/forgot about your patches on the mailing list.
I had packaged all of these, and q2-taxa is in the archive, and will be a part of bullseye too
> To hear that this
>is out of the way is really nice!
\o/
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