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greenelab / deep-review

A collaboratively written review paper on deep learning, genomics, and precision medicine
https://greenelab.github.io/deep-review/
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Upgrading repo to track manubot-rootstock #680

Closed dhimmel closed 6 years ago

dhimmel commented 6 years ago

The Deep Review predates the Manubot (the CI-based system we use to process the manuscript). In fact, greenelab/manubot-rootstock (a template GitHub repo for Manubot instances) and greenelab/manubot (a python package for processing the manuscript) were both derived from the code from Deep Review. In other words, Deep Review gave birth to these projects.

However, the Manubot has now diverged considerably from the codebase and architecture present in this repository. The manuscript processing code in this repository has not been receiving any rootstock updates. As time goes on, the reconciliation of the codebases becomes more difficult. However, once synchronized, incremental updates should generally be straightforward.

In https://github.com/greenelab/deep-review/issues/678#issuecomment-341539497, I proposed merging in the latest manubot-rootstock. @agitter replied:

@dhimmel maybe we should open a new issue to preview and discuss how much would be involved in the merge. I'm hesitant to create a lot of new work when the current version of deep review is running smoothly even if it lacks some (important) features.

The merge certainly could be difficult. I'm happy to take on the task with a focus on minimizing disruption to open pull requests. The main benefits I see to the upgrade are:

Anyways, I'll attempt a merge and PR, so we can see exactly what the upgrade will entail. Most likely we will have to remove the current author scripts and re-engineer them, which I am willing to do.

agitter commented 6 years ago

Good luck with the merge. This will also add proper figure and table support, which we'll need for the revisions.

How much has changed from the author perspective? The citation syntax is slightly different now. Is that it? We already asked all of the contributors learn one custom writing platform so I want to be conscious of how many new requirements we impose.

dhimmel commented 6 years ago

How much has changed from the author perspective?

https://github.com/greenelab/deep-review/pull/681/commits/12ce17cdfa572cca61f16457fa99e705826719c9 contains the changes to the manuscript body. Really the only change that users will need to be aware of is to semicolon separate references. Once we see the effect on open PRs, I can post a message on every open PR regarding if any upgrade steps are needed and offer help if neccessary.

dhimmel commented 6 years ago

I'd also like to start phasing in "one line per sentence" rather than word wrap. I think the best way to do this would be to operate on sections without any open PRs. And then when editing sections, we can encourage one line per sentence. However, this would be in future PRs not #681

agitter commented 6 years ago

I'd also like to start phasing in "one line per sentence" rather than word wrap

We had an issue about that and there was broad consensus that we should convert. Someone had a simple script to implement the change. I don't have the issue number accessible right now though.

dhimmel commented 6 years ago

We had an issue about that

https://github.com/greenelab/deep-review/issues/624 proposed by @michaelmhoffman. @michaelmhoffman if you are interested in doing this, then you can take the lead (wait for #681 to be merged). Otherwise I can.

michaelmhoffman commented 6 years ago

I would like to punt to @evancofer who already wrote a script to do this.