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] > 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, although I couldn't find anything "bokeh" on Salsa (unless packaging efforts are being done elsewhere). > I hope my reply helps you? :-) Definitely! As always, thanks for your reply! Kind regards, Shayan Doust [1]: https://salsa.debian.org/med-team/gneiss/-/blob/master/gneiss/plot/_regression_plot.py On 08/07/2020 22:21, Nilesh Patra wrote: > Hi, > > On Thu, 9 Jul 2020, 01:20 Shayan Doust, <hello@shayandoust.me > <mailto:hello@shayandoust.me>> wrote: > > Hello, > > I was planning on packaging q2-gneiss, but gneiss is a missing > dependency which I am packaging right now[1]. Right now, I care about > getting gneiss to run properly hence the incomplete package. > > During nosetest, there is only one error[2]. This is because there is a > missing module called Bokeh. > > > 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. > > Looking at Bokeh's situation, it seems like > it isn't in the repository, but there has been interest for > packaging[3]. > > > 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 should also note that within setup.py, bokeh is not listed as a > requirement to build or install, so this makes me have the feeling that > perhaps bokeh is not important to have for this package's core > functionality? > > > 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 need some advice as to whether or not I should continue packaging > this, or if there is a suggestion to do something else to work around > this missing module or something. > > > I hope my reply helps you? :-) > > Kind regards, > Nilesh > > > [1]: https://salsa.debian.org/med-team/gneiss/ > [2]: https://paste.debian.net/1155647/ > [3]: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=756017 >
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