Re: q2-* - did a few
On 07.08.21 23:49, Nilesh Patra wrote:
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?
My suggestion would be to have a section reserved on the spreadsheet
that summarizes all the bokeh dependencies and whatever needs to be done
for it.
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?
a.
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?
Yes.
What I would very much like to see online inspectable is the output of
the tutorial-package test runs. If you happen to have ideas how to get
there - I would love this as a "tangible" proof of the Debian package's
reliable and as educational material.
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/
These JavaScript packages are both really cumbersome and also something
that Debian can be proud of.
Best,
Steffen
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