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anopheles-genomic-surveillance / anopheles-genomic-surveillance.github.io

Lecture notes for a course on genomic surveillance of malaria vectors, developed by PAMCA and MalariaGEN
https://anopheles-genomic-surveillance.github.io/
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W5M3 update #228

Closed KellyLBennett closed 4 months ago

KellyLBennett commented 5 months ago

Data analysis has been restricted to release 3.0 to match the video examples. I also changed the map background to match. I would be grateful for a review @ahernank @jonbrenas and then I will run it in colab again to double check it. Resolves #220.

KellyLBennett commented 5 months ago

The notebooks are now updated and plots rendered. Thank you @ahernank.

ahernank commented 5 months ago

Thanks @KellyLBennett!

Some small things, would it be possible to rename this PR to start with W5M3? This makes it easier to review all notebooks on the same workshop together.

Also, I think the notebook here wasn't run on the developer environment with the latest API version, this is developer-training-nb-maintenance-mgen-9.0.0 on bespin. Would it be possible to re-run it using this environment to ensure we are testing all notebooks on this version?

Please do feel free to open other PRs for the other modules on W5 (if required), and we can also look at those together.

KellyLBennett commented 5 months ago

Thanks @ahernank I have run the notebook in developer-training-nb-maintenance-mgen-9.0.0. The rendering of the notebook is OK in terms of all analysis output but seems to add in some code boxes even though these are not present in the notebook. I am not sure how to resolve this.

ahernank commented 4 months ago

Thanks @KellyLBennett, yes, we've noticed the issue with the code boxes. Currently, we are leaving it unaddressed but it would be good to track it down & fix it before the next iteration.

KellyLBennett commented 4 months ago

Yes all seemed to render fine for me.

ahernank commented 4 months ago

Awesome, thanks!

ahernank commented 4 months ago

Will merge this now, and we can check that the HTML on the website looks all good & then make another quick check on Colab. :)

ahernank commented 4 months ago

Just a small thing here, @KellyLBennett - the HTML didn't seem to render correctly for one of the cells below in here (all the other ones on this & the other modules are looking great): 

ag3.plot_samples_interactive_map(sample_query="release == '3.0'", basemap='worldimagery')

Would be great to re-run this one so the map is showing, on a new PR, if it isn't too much trouble! Usually this happens if the widgets changed between saves.