Hello Nilesh, > Ah, then this is being used for the data visualization part here, and is > probably not a test-only dependency. > I suppose the _core_ functionality (analysis) will remain unaffected, > but the visualisation part will be unusable. > Can you try to use this module - maybe try reading docs and see how > broken/not-brokem it looks? > If there's no visualization, maybe this isn't fit to go to the archive yet. From what I can see by reading the source, only one exposed function is not functional due to the missing module. Specifically, from the gneiss.plot module, the importation of "radialplot" is the only one that depends on bokeh. This seems to be agreeable with the unit test where only one unit test failed. I am not sure if the failure on one visualisation module (out of multiple) would constitute a low-standard to where a package is held back, or if there are presumably some ways around this, as of course primarily the package installation should handle everything itself and not rely on some end-user intervention for further third party installation. I did also ping within the bug report for bokeh with your suggestion, but then I stumbled across bokehjs[1], which seems to be a subset / included within bokeh as a whole. From what I can see, bokeh seems big and complex, so that puts a doubt as to when its upload would happen :(. Kind regards, Shayan Doust [1]: https://wiki.debian.org/Javascript/Nodejs/Tasks/bokehjs On 08/07/2020 23:01, Nilesh Patra wrote: > > > On Thu, 9 Jul 2020, 03:15 Shayan Doust, <hello@shayandoust.me > <mailto:hello@shayandoust.me>> wrote: > > Hello Nilesh, > > > If it's a test-only dependency, IMO you can simply skip that > particular > > test for now. > > And enable testing it when bokeh is packaged and accepted into the > archive. > > > Yeah, I'd anticipate probably not needed. > > All the upstream tests but one pass, as you reported above - this > sounds > > more convincing that it's very likely not needed. > > > > FWIW: Bokeh is a data visualization module, and maybe that's used in > > tests to visualize and confirm the results of gneiss and nothing more. > > I'm skeptic about this being a test-only module. Imports to bokeh are > done more-so within the gneiss files and not the test files itself, for > instance in the regression plot file[1] > > > Ah, then this is being used for the data visualization part here, and is > probably not a test-only dependency. > I suppose the _core_ functionality (analysis) will remain unaffected, > but the visualisation part will be unusable. > Can you try to use this module - maybe try reading docs and see how > broken/not-brokem it looks? > If there's no visualization, maybe this isn't fit to go to the archive yet. > > > > As an additional work - you can enquire about the status of bokeh > > packaging by replying to the bug, CC'ing Diane (who's doing the > original > > work) > > I will perhaps ping the bug report and see if there is anything, > > > I suppose that makes sense. Maybe we'll have to wait till Bokeh gets > uploaded, replying might help speed up the process. > > although I couldn't find anything "bokeh" on Salsa (unless packaging > efforts are being done elsewhere). > > > Here[2] > > Kind regards, > Nilesh > > > [1]: > https://salsa.debian.org/med-team/gneiss/-/blob/master/gneiss/plot/_regression_plot.py > > > [2]: https://github.com/detrout/python-bokeh
Attachment:
0x6D7D441919D02395.asc
Description: application/pgp-keys
Attachment:
signature.asc
Description: OpenPGP digital signature