Moving things around: `cnv_frequencies` is treated differently from `snp_frequencies` and `hap_frequencies`, and `plot_frequencies_heatmap` is not in a good place

[jonbrenas]

While snp_frequencies and hap_frequencies each have their own file while cnv_frequencies is stuck in anopheles.py. It would probably make more sense to give it its own file as well.

On the other hand, plot_frequencies_heatmap is in snp_frq.py when it is used to plot all kinds of frequencies heat maps. It could probably be moved to util.py (if there are parasite functions that want to use a similar function) or anopheles.py.

[leehart]

Thanks @jonbrenas . We should probably split these into two separate issues, partly because I expect the two proposals might have different implications.

I can certainly see the benefits to consistency putting cnv_frequencies into its own file. I'm not sure why that is currently different, but I guess it just hasn't been been moved over yet. I can't imagine a technical reason, yet. Maybe @alimanfoo has some knowledge of this?

I'm less comfortable with migrating plot_frequencies_heatmap to util.py or anopheles.py. I'm wary about files like util.py becoming a general purpose catch-all place for all kinds of stuff, like that stereotypical one kitchen drawer! And if we're talking about moving stuff out of anopheles.py, which sounds like a pretty high-level place, something seems wrong about moving other stuff into it, especially plotting functions, within the same breath. But I would need to refresh my memory on the scope of those particular modules. In principle, I would go with grouping like-with-like, but you know those sort of decisions can become subjective or aesthetic, rather than perfectly rational.

Where do we usually put functions (e.g. plotting functions) that are used by both parasite and vector? Is it really util.py?

[jonbrenas]

I am closing this issue to be replaced by 2 new ones as advised by @leehart .

[leehart]

Reopening as a parent issue rather than unplanned.