# Meeting notes 1/26/2022

hi!!!! :)
hello

- Workflow for contributing to manuscript
- Adding new text
- Submitting a pull request
- Reviewing a pull request
- Citations
- Picking topics
- Finalizing figure teams
- Timeline
- Paragraph/Topic first drafts by Feb 16(?)
- Expectation: gather citations, high-level overview of why this component is important
- Everyone does read through for general edits by Feb 23(?)
- Figures and tables ____
- Everyone has a chance to incorporate edits by ____
- A few authors do a final read through by ____
- Do we want to draft a letter to Nature EcoEvo editor?
- Next meeting (Feb 23rd)

> [Matt] We need some discussion on what people use GitHub for now (I have a few ideas how to do this using the lens.org search/API)
>
| Topic | Author |
| -------- | -------- |
| Storing and archiving version controlled data |Dylan, Emma, Pedro |
| virtual lab notebook | Luna |
| responding to reviewer comments | Eric |
| classroom teaching / education materials | Cole |
| Project management | Kaitlyn, Madison |
| Building website | Emma |
| Making code citable | Rob, Dylan, Emma |
| Collaborative code editing | Kaitlyn, Madison, Pedro |
| Writing manuscript | Pedro? :) |
| Open science discussions | Freddy, Emily |
| Project continuity | Brandon, Viv |
| Asynchronous working | Matt|
| GitHub organizations | Cole, Katherine, Pedro |
| Misc other uses | Rob |
|Discussion - What can GitHub enable in EcoEvo | Matt |
|Discussion - Why aren't more people using GitHub | Saeed |
|Discussion - Limitations |Emma, Ali, Pedro|
|Discussion - 5 or 10 tips to gain knowledge/experience with github | Freddy, Ali, Emma |

| Figure / Table | Lead ||
| -------- | -------- |------|
| [Table 1](https://docs.google.com/presentation/d/1b_8r7FHeVzP1tQ1H5mHVxw6xYU5A2KWCT3VbyrypWjs/edit?usp=sharing): Comparison table |Dylan |Luna, Saeed|
| [Figure 1 first option](https://docs.google.com/presentation/d/1TOuQlpWMEt-cfWIii1O6YccC2QjQ67LH7i0x5GDouMw/edit?usp=sharing) [Second option](https://docs.google.com/presentation/d/1b_8r7FHeVzP1tQ1H5mHVxw6xYU5A2KWCT3VbyrypWjs/edit?usp=sharing): GitHub use and technical difficulty | Rob |Luna, Ali, Matt|
| [Figure 2](https://docs.google.com/presentation/d/1b_8r7FHeVzP1tQ1H5mHVxw6xYU5A2KWCT3VbyrypWjs/edit?usp=sharing): Non-programming aspects of respository | Cole |Brandon, Vivienne, Madison|
|[Figure 3](https://docs.google.com/presentation/d/1b_8r7FHeVzP1tQ1H5mHVxw6xYU5A2KWCT3VbyrypWjs/edit?usp=sharing): Collaborator personas |Eric |Kaitlyn|
| [Figure 4](https://docs.google.com/presentation/d/1b_8r7FHeVzP1tQ1H5mHVxw6xYU5A2KWCT3VbyrypWjs/edit?usp=sharing): 10 efficient ways to improve github knowledge | Emma |Matt, Ali, Saeed, Pedro|
| [Table 2](https://docs.google.com/presentation/d/1b_8r7FHeVzP1tQ1H5mHVxw6xYU5A2KWCT3VbyrypWjs/edit?usp=sharing) | Saeed |Highlight papers that review GitHub functions/uses|

## Workflow for editing manuscript demo

- Github repo for hosting manuscript
- Manuscript is automatically generated to a webpage, so you can see the most updated version.
- Go through the README for instructions on contribution
- *NOTE*: Because git tracks *lines*, each sentence added should be on a separate line.

1. Either create a **branch** or **fork** the repository (and create a branch)
2. Make commits (frequently!)
3. Make pull request to main branch
4. Pull request will be reviewed (required)
- Can view changes and comment line-by-line in PR review
5. After review, changes can be merged

>Who does code review?

**anyone** can review the code at this stage.

>And who does this code merge?

The person that reviews can also do the merge.

### Merge Conflicts
Sometimes merging can't happen because of conflicts. Can resolve conflicts on GitHub. Conflicts highlighted like:

<<<<<<< branchname
changes on pull request branch
=======
text on main branch
>>>>>>> main

Just delete whatever text shouldn't be there, plus the `<<<`, `===`, and `>>>` lines. Commit those changes on GitHub interface, then you should be able to merge the PR.

### Discussion Tab
Discussion tab on GitHub repo is for introductions and broader discussion about editing or adding text. Feel free to create a new discussion.

# Other Discussion

>Could we add hackmd notes, google slides notes, etc. to README?

Sounds good. Rob will work on a PR

>5-10 tips for learning more: is it a figure or text in the Discussion?

a way to wrap up and send people to more info
could be a table with more in-depth discussion in text

This is also very fun to look at for a visual of everything (pull requests, merges, new branches, etc.) that’s been going on: https://github.com/SORTEE-Github-Hackathon/manuscript/network

good question! I noted this and will look further into this question! If there is nothing already built within Manubot or something that other users developed, we should be able to pull something by converting the .md files to TeX or .docx using a pandoc command within pandoc, which are formats that are accepted by journals.

The nitty-gritty of editing and making the manuscript match journal requirements could be done with rticles (or, less elegantly, manually)

Yeah I certainly think citing/referencing tutorials will be valuable