Build stand-alone pathogenesis manuscript

[rando2]

Is your feature request related to a problem? Please describe.
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
Because we have split everything up, we will need to build docx versions of the manuscripts for submission. We're almost at that point with pathogenesis (#744).

Describe the solution you'd like
A clear and concise description of what you want to happen.
This will require a few pieces:

1. Select info from metadata.yaml depending on the unique author list for this manuscript
2. Generate a box defining all authors who belong to the consortium (how exactly do we want to phrase this?)
3. Render text from 07.pathogenesis.md only
4. Generate reference list from 07.pathogenesis.md text (see Managing References for Sections Separately #732)

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.
Some manual hijinks with docx involving a lot of copy and paste -- but that would not really work for the reference list.
Could also copy the text into a separate manubot project

Additional context
Add any other context or screenshots about the feature request here.

[agitter]

Because pathogenesis is being submitted first, I suggest we treat it as a special case. If we get it to work, we can generalize to generate all of the individual manuscripts. I'll make a pull request to get started.

We can add additional keys to each author in the metadata to help us select the named authors for each manuscript. Then the front matter for each manuscript can select only those authors. Imagine something like

authors:
  -
    name: Author A
    contributions:
      - Project Administration
      - Writing - Original Draft
      - Writing - Review & Editing
      - Methodology
    manuscripts:
      - pathogenesis
      - evolution
   -
    name: Author B
    contributions:
      - Writing - Original Draft
      - Writing - Review & Editing
    manuscripts:
      - pathogenesis
      - therapeutics

I'm leaving out most of the existing fields. That assumes the contributions are the same for all manuscripts, which is not really true. I'm also not yet sure how to order authors. Maybe we need to manually list the order for each manuscript

authors:
  -
    name: Author A
    contributions:
      - Project Administration
      - Writing - Original Draft
      - Writing - Review & Editing
      - Methodology
    manuscripts:
      pathogenesis: 1
      evolution: 5
   -
    name: Author B
    contributions:
      - Writing - Original Draft
      - Writing - Review & Editing
    manuscripts:
      Pathogenesis: 3
      Therapeutics: 6

If we need to support manuscript-specific contributions, we could nest those too:

authors:
  -
    name: Author A
    pathogenesis:
      order: 1
      contributions:
        - Project Administration
        - Writing - Original Draft
        - Writing - Review & Editing
        - Methodology
    evolution:
      order: 5
      contributions:
        - Project Administration
        - Writing - Review & Editing
   -
    name: Author B
    pathogenesis:
      order: 3
      contributions:
      - Writing - Original Draft
      - Writing - Review & Editing
    therapeutics:
      order: 6
      contributions:
      - Writing - Original Draft
      - Writing - Review & Editing

For the box, we could create a new markdown file that is included in all of the individual manuscripts. It could list all authors who are in the consortium. It will require some trial and error but seems feasible. Excluding named authors from the consortium list in the respective individual manuscripts would be harder.

[rando2]

Awesome @agitter! I think this sounds great. Perhaps for the box, we can just list consortium members in alphabetical order or using some other metric that would be easy to standardize across all of the manuscripts!

I do think nesting might be easier to work with from a project management perspective if it doesn't complicate things too much on the technical side. Looking at pathogenesis, there are definitely some people who edited that section but have other roles in other sections (the best example is @RLordan, who did a bunch of editing there, but is leading the nutraceuticals section and will have several additional roles for that manuscript).

I will keep an eye out for your PR!

[agitter]

Perhaps for the box, we can just list consortium members in alphabetical order or using some other metric that would be easy to standardize across all of the manuscripts!

That's a good goal. I may try to get some of the other elements working before adding that.

I do think nesting might be easier to work with from a project management perspective

We should do whatever makes the data entry easiest for you and all the authors. I should be able to adapt the front matter to any yaml format. However, I should test whether it is possible to sort authors by an order value like I proposed above before we start editing the metadata file.

[rando2]

Excellent, thank you so much for looking into all of this!

[agitter]

#763 added support for standalone manuscripts. The remaining TODOs are:

• Deciding how authors are randomized or sorted if they have the same order listed in the metadata
• Building all of the individual manuscripts listed in content/individual-manuscripts.txt
• Adding contributions for the individual manuscripts

I'll work on all of the individual manuscripts as soon as we need it. It will be a minor change to the build script. I can also add support for randomization once we finalize the desired behavior.