Remove manuscript Rmd and its associated files

[lshandross]

The last step of splitting out the manuscript into its own separate repo (hubEnsemblesManuscript), as we decided in this issue which was transferred over to the new repo, is deleting all of the associated files in this original hubEnsembles repo. I have a couple of questions I was hoping to get others' opinions on before committing to the permanent deletion:

What exactly should we be deleting from the hubEnsembles repo? The entire software-manuscript branch? Just the manuscript directory on this branch? Note that all the manuscript files live on the software-manuscript branch in the manuscript directory

Feel free to add any other thoughts on manuscript deletion stuff from this repo @eahowerton @annakrystalli @elray1 @nickreich

[elray1]

Is there anything that's a part of the actual package or its documentation that's on the branch but not merged into main? If not, I think it's fine to just delete the whole branch. I think deletion of the branch should be our goal, so if there is anything that belongs on main that's not there yet, let's get it there and then delete the branch :)

[eahowerton]

Do we want to keep the example-complex-hub data with the package? I believe this is only on the software-manuscript branch right now (.rda files and corresponding scripts to generate them)

[elray1]

sure, let's keep those :) sounds like the working plan is to have data files like that within each package.

[eahowerton]

I just did a quick browse through the other diffs, and I don't see anything else that should be on main

[lshandross]

Do we want to also keep the changes to the example-simple-hub data (addition of mean and pmf output types) on the software-manuscript branch? I think @eahowerton originally made the changes to be used in the examples section (which would persist in the vignette), but I haven't been keeping track of whether all the examples in the manuscript have switched to using the example-complex-hub data.

[eahowerton]

@lshandross, you're referring to what is in the inst folder? I think those should be removed. What @elray1 implemented in example-complex-forecast-hub is a better version of my initial attempt (currently in inst). The pmf output type example data I had generated was entirely random, and instead the example-complex-forecast-hub data has pmf output type data that aligns with the corresponding quantile forecasts.

I think it'd be better to keep only the example-complex-forcast-hub data to avoid confusion.

[lshandross]

@eahowerton yes, thanks for the explanation. Do you mind copying the example-complex-forecast-hub files onto the main branch? I'm not sure how you want to structure those data files in the repo for use in the vignette, so it might be simpler for you to make the changes instead of describing the organization to me

[lshandross]

Summarizing a discussion @eahowerton and I had on Slack:

We will not yet be deleting the old example-simple-forecast-hub files to avoid breaking the vignette (even though it is out of date). Once the manuscript is fully finished, the vignette will be updated with the relevant sections. The larger deletion of the software-manuscript-branch can proceed as planned.

[elray1]

@lshandross just checking -- is this issue still active, or can it be closed?

[lshandross]

I was leaving it open because there are a couple of example data files used in the vignette that are out of date compared to what's in the manuscript now, but Emily and I thought it would be better to leave them in so the vignette doesn't break until we're ready to update the vignette when the manuscript is done.

[lshandross]

Remaining task of replacing example data with updated versions consistent with the manuscript is summarized on Issue #104, so I'm closing this issue since the other parts of it are finished