12_final-workflow.qmd

---
title: "Final Workflow"
abstract: "This section outlines a workflow built from the best practices and tools outlined in this training."
format: 
  html: 
    code-line-numbers: true
    fig-align: "center"
editor_options: 
  chunk_output_type: console
bibliography: references.bib
---

```{r hidden-here-load}
#| include: false

exercise_number <- 1
```

## Final Workflow

We've learned many best practices and explored a lot of tools. How can we put it all together into a sustainable workflow?

### Setup

1. Create a folder for your project. 
    - Add any project-relevant materials you already have (e.g. that data someone emailed to you and that paper that that inspired the project). 
2. Optional: Create a Zotero library or group for relevant literature
3. Create a .Rproj
4. Create a README
5. `init` a local Git repository
6. `add` and `commit` the .Rproj and README
7. Create a remote GitHub repository with the same name as the folder. Connect the local and remote repositories using the instruction on GitHub.
8. Initialize a virtual environment with `library(renv)`.

### Analysis Development

1. Create GitHub issues that organize progress on your work.
2. For each issue, checkout a branch with the name `iss<number>`.
3. Develop your analysis
    - Use Quarto. Render early and often.
    - Regularly commit and push changes to GitHub.
    - Keep your renv up-to-date. 
    - Adopt defensive programming techniques like modular, well-tested code and assertions.
4. When you think you've addressed an issue, open a pull request from `iss<number>` to `main` and flag someone as a reviewer.
5. Close the issue when the PR is approved and merged into `main`.

### Closing Up a Project

1. Ensure that all Quarto documents have been rendered with the most up-to-date `.qmd` documents.
2. Ensure that `renv` reflects the software layer of the computing environment.
3. Ensure that all local changes have been pushed to the GitHub repository.
4. Ensure all necessary branches have been merged into `main`. 
5. Update the README with instructions for how to reproduce the analysis.
6. Consider building a GitHub page for your analysis.