collaborate.Rmd

---
output:
  html_document:
    pandoc_args: [
      "--number-offset=0"]
---

# Collaborate

```{r, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)

if (!require(librarian)){
  install.packages("librarian")
  library(librarian)
}
shelf(
  htmltools, mitchelloharawild/icons)

# icons::download_fontawesome()
# devtools::load_all("~/github/bbest/icons")
# icons::download_octicons()
```

## Learning Objectives {- .objectives}

1. Create a Github repository (or "repo").
1. Synchronize local files (using `git commit` & `git push` plus `git pull`) with a Github repository.
1. Use RStudio's Git pane.
1. Branch and Fork repos.
1. Handle file merge conflicts.
1. Contribute file changes to any public Github repo with `pull request`.
1. Manage projects in Github with Issues and Project boards. Understand how to reference Issues (e.g. `#2`) in Github commit messages as well as mention other Github users (e.g. `@bbest`).
1. Write markdown (e.g. `README.md`) to format text, and yaml (e.g. `_site.yml`) for configurations.
1. Use the 3 components of an Rmarkdown: 1) frontmatter in yaml; 2) markdown text; and 3) R code as chunks or inline.
1. Create an Rmarkdown website with a `_site.yml`.

## Prerequisites {-.prereq} 

**R Skill Level**: Beginner - you've run a few commands in R, hopefully from RStudio.

## Background: Software & Github Workflows

### What are Git & Github?

The two main version control tools are:

1. [**Git**](https://git-scm.com/) is a command-line version control system that lets you track changes to files over time. These files can be any kind of file (eg doc, pdf, xls), but free text differences are most easily visible (eg txt, csv, md). This facilitates a playground for collaboration, without fear of experimentation (you can always rollback changes).

1. [**Github**](https://github.com/) is a website for storing your git versioned files remotely. It has many nice features to be able visualize differences between [images](https://help.github.com/articles/rendering-and-diffing-images/), [rendering](https://help.github.com/articles/mapping-geojson-files-on-github/) & [diffing](https://github.com/blog/1772-diffable-more-customizable-maps) map data files, [render text data files](https://help.github.com/articles/rendering-csv-and-tsv-data/), and [track changes in text](https://help.github.com/articles/rendering-differences-in-prose-documents/).

### What are R & RStudio?

The two main programming tools you'll be using are:

1.  [**R**](https://cran.r-project.org) is the scientific programming language.

1.  [**RStudio**](https://www.rstudio.com/products/rstudio/download/#download) is the integrated development environment (IDE) that provides a robust coding environment to write and execute R code. I recommend reviewing the 2-page [RStudio IDE Cheat Sheet](https://github.com/rstudio/cheatsheets/raw/master/rstudio-ide.pdf) (also available in the RStudio interface through the menu **Help** -> **Cheat Sheets** -> **RStudio IDE Cheat Sheet**) for getting a quick grasp of the panes and keyboard shortcuts.

### Github Workflows

There are a variety of ways to interact with a Github repository, or **REPO** for short, which is a collection of files, possibly organized within folders. On Github every repo is associated with an **OWNER**, which can be a Github organization or a Github user. Repos are consistently found at **github.com/OWNER/REPO**.

If you have _write_ permissions to the repo, then you can `git push` changes to it directly. These changes are always first packaged as a set of file differences by a `git commit` that requires a message.

If you do not have _write_ permissions to the repo, then you need to `Github fork` that repo into your own user-writable space (user or organization). After you make changes to the files in your user-writable repo (with `git commit` and `git push`), you can then request those changes be pulled into the original repo with a `Github pull request`.

Furthermore, you can `git branch` a snapshot of the repo files into a _sandbox_ for continuing to make changes, such as to fix a _bug_ or implement a new _feature_. This branch won't affect the _main_ branch until you're ready to `git merge` those changes, so it isolates development.

These aspects give rise to different _workflows_ with increasing complexity that we'll incrementally try out with exercises, so you can become comfortable managing your own code, contributing to other open-source projects, and working on a set of code without trampling on other people's work.

```{r icons, echo=F}
icon_down   <- icons::fontawesome$solid$`arrow-down`
icon_up     <- icons::fontawesome$solid$`arrow-up`
icon_right  <- icons::fontawesome$solid$`arrow-right`
icon_cloud  <- icons::fontawesome$solid$cloud
icon_plus   <- icons::octicons$plus
icon_pc     <- icons::octicons$device_desktop
icon_dl     <- icons::octicons$download
icon_ul     <- icons::octicons$upload
icon_commit <- icons::octicons$git_commit
icon_pull   <- icons::fontawesome$solid$`cloud-download-alt`
icon_push   <- icons::fontawesome$solid$`cloud-upload-alt`
icon_merge  <- icons::octicons$git_merge
icon_fork   <- icons::octicons$repo_forked
icon_pr     <- icons::octicons$git_pull_request
icon_clone  <- icons::octicons$repo_clone
icon_branch <- icons::octicons$git_branch
```

#### **Simple**: `push` & `pull`

The simplest workflow for tracking file changes is to simply `git push` changes into your Github repo, assuming you have _write_ permissions to that repo. If you're working with anyone else or editing on more than one computer, then you'll want to `git pull` changes at the beginning of each session to capture changes and minimize potential _conflicts_ before proceeding with any edits and subsequent `git commit` and `git push` commands.

The exact steps can be described in the table below. After the `Github create` repo step, you `git clone` it to get a copy of it onto your machine (with the hidden `.git` folder containing the configuration). Then you make changes on files and package differences with `git commit`, which requires a message every time and can happen offline. You'll need to be online to then run `git push` to publish those changes back to the Github repo. Then before subsequent changes, you'll want to update your machine with a `git pull`.\
    
repo location                          | initialize `r icon_down`                                                                                       | edit `r icon_up`                                                                                                                                   | update `r icon_down`
---------------------------------------|:--------------------------------------------------------------------------------------------------------------:|:--------------------------------------------------------------------------------------------------------------------------------------------------:|:---------------------------------------------------------------------------------:
`r icon_cloud` `github.com/OWNER/REPO` |  [**create**](https://help.github.com/articles/create-a-repo/) `r icon_plus`                                   |                                                                                                                                                    |
`r icon_pc` `~/github/REPO`            |  [**clone**](https://help.github.com/articles/fetching-a-remote) `r icon_dl` `r HTML("&nbsp;")` `r icon_right` | [**commit**](http://git-scm.com/docs/git-commit) `r icon_commit`,  [**push**](https://help.github.com/articles/pushing-to-a-remote/) `r icon_push` | [**pull**](https://help.github.com/articles/fetching-a-remote/#pull) `r icon_pull`
  
#### **Contribute**: `fork` & `pull request`

If you don't have _write_ access to a Github repo, such as with any open-source project, then you can `Github fork` somebody else's repo into your own user-writable space (i.e. OWNER being a Github user or organization) where you have write permissions. There you can make changes (using `git commit` and `git push`). When you're ready to submit changes to the original repo, you make a `pull request` queuing these changes up for the owner(s) of the original repo to review and accept with a `merge`, reject or ignore. Github facilitates the conversation that may follow, including the ability to update the `pull request` before performing the final `merge`.

repo location                          | `USER` permission | initialize `r icon_down`                                                                                         | edit `r icon_up`                                                                                                                                   | update `r icon_down`
---------------------------------------|:-----------------:|:----------------------------------------------------------------------------------------------------------------:|:--------------------------------------------------------------------------------------------------------------------------------------------------:|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------:
`r icon_cloud` `github.com/OTHER/REPO` | read only         |                                                                                                                  | [**merge**](https://help.github.com/articles/merging-a-pull-request) `r icon_merge`                                                                | 
`r icon_cloud` `github.com/OWNER/REPO` | read + write      | [**fork**](https://help.github.com/articles/fork-a-repo) `r icon_fork`                                           | [**pull request**](https://help.github.com/articles/creating-a-pull-request/) `r icon_pr`                                                          | [**pull request**](https://help.github.com/articles/creating-a-pull-request/) `r icon_pr`, [**merge**](https://help.github.com/articles/merging-a-pull-request) `r icon_merge`
`r icon_pc`    `~/github/REPO`         | read + write      | [**clone**](https://help.github.com/articles/fetching-a-remote) `r icon_clone` `r HTML("&nbsp;")` `r icon_right` | [**commit**](http://git-scm.com/docs/git-commit) `r icon_commit`,  [**push**](https://help.github.com/articles/pushing-to-a-remote/) `r icon_push` | [**pull**](https://help.github.com/articles/fetching-a-remote/#pull) `r icon_pull`

#### **Sandbox**: `branch` & `merge`

Even if you're able to _write_ directly to the repo, you may be collaborating with others and not want to step on their proverbial coding toes. By performing a `git branch`, you're taking a snapshot of the files and isolating them into your own _sandbox_. For instance let's say you're working on a new feature, then you might call your branch generically _new-feature_. Subsequent changes to the files in the Github repo (with `git commit` and `git push`) do not then affect the _main_ branch until a `git merge` is executed to fold these changes of _new-feature_ into the _main_ branch.

repo location                                                | `USER` permission | initialize `r icon_down`                                                                                               | edit `r icon_up`                                                                                                                                                              | update `r icon_down`
-------------------------------------------------------------|:-----------------:|:----------------------------------------------------------------------------------------------------------------------:|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------:|:--------------------------------------------------------------------------------:
`r icon_cloud` `github.com/OWNER/REPO` branch: _main_        | read + write      |                                                                                                                        |                                                                                                                                                                               | 
`r icon_pc`    `~/github/REPO` branch: _main_                | read + write      | [**clone**](https://help.github.com/articles/fetching-a-remote) `r icon_clone`                                         | [**merge**](https://www.atlassian.com/git/tutorials/using-branches/git-merge) `r icon_merge`, [**push**](https://help.github.com/articles/pushing-to-a-remote/) `r icon_push` |
`r icon_pc`    `~/github/REPO` branch: _new-feature_         | read + write      | [**branch**](https://www.atlassian.com/git/tutorials/using-branches) `r icon_branch` `r HTML("&nbsp;")` `r icon_right` | [**commit**](http://git-scm.com/docs/git-commit) `r icon_commit`                                                                                                              | [**pull**](https://help.github.com/articles/fetching-a-remote/#pull) `r icon_pull`

The scenario above shows the `branch` and `merge` happening locally, but you can also execute these on Github. The RStudio IDE provides the ability to create a new branch locally, but then to perform the `git merge` you need to do this in its Terminal.

#### **Pro**: `branch`, `pull request` & `merge`

Extending the **Sandbox** workflow to full "professional" status, even if you have the administrative ability on the repo to perform a `git merge` you may wish to first advertise your proposed file changes to other contributors with a `pull request`. This then allows others to review and discuss changes before an admin then performs the final `git merge`. This is the recommended workflow described in [Understanding the GitHub flow · GitHub Guides](https://guides.github.com/introduction/flow/):

`r img(src='figs/github_flow.png', width=600)`

We want go over this entire workflow in this lesson, but it simply combines all the techniques above.

## Setup Github & Git & RStudio

1. Create **Github** account at <http://github.com>, if you don't already have one. For username, I recommend all lower-case letters, short as you can. If you use an email ending in `.edu`, you can request free private repositories via [GitHub Education](https://education.github.com/) discount.

1. Install the latest software, per [Setup](./setup.html):
    
    1.  [**R**](https://cran.r-project.org) scientific programming language
    1.  [**RStudio**](https://www.rstudio.com/products/rstudio/download/#download)
        integrated development environment
    1.  [**Git**](https://git-scm.com/) version control\
    \
    
1. Configure **git** with global commands to tell it who you are. Open the Terminal in RStudio and type the following. Be sure to replace `USER` and `USER@SOMEWHERE.ORG` with yours (e.g. mine is `bbest` and `ben@ecoquants.com`):
    
    ```bash
    # display your version of git
    git --version
    
    # display the path to git on Mac/Linux
    which git
    
    # display the path to git on Windows
    where git

    # replace USER with your Github user account
    git config –-global user.name USER
    
    # replace USER@SOMEWHERE.ORG with the email you used to register with Github
    git config –-global user.email USER@SOMEWHERE.ORG
    
    # use git merge (default) instead of git rebase to resolve git pull conflicts
    git config --global pull.rebase true
    
    # list your config to confirm user.* variables set
    git config --list
    ```
    
1. Tell **RStudio** where to find **Git**. In the RStudio menu, go to **Tools** -> **Global Options** and select the **Git/SVN** sidebar menu:
    
    `r img(src='figs/rstudio_setup-git.png', width=400)`
    
    Here you **Browse** and select the **Git executable** based on the path found from the above commands dependening on your operating system in the Terminal (`which git` on Mac/Linux; `where git` on Windows).
    
    If you run into any problems, please consult more thorough documentation in [Chapter 13 Detect Git from RStudio | Happy Git and GitHub for the useR](https://happygitwithr.com/rstudio-see-git.html#tell-rstudio-where-to-find-git). If you're still stuck, please email me ben@ecoquants.com or better yet look at existing [Issues · noaa-iea/r3-train](https://github.com/noaa-iea/r3-train/issues) and from there **Create a new issue** describing the problem, any error messages and the operating system with version numbers of software being used.
    
## Create Github Repository

Now you will create a Github repository. This will be the source code of an Rmarkdown website that will house your work completing all the exercises for this course.

1. With your web browser, sign into [Github.com](https://github.com) and visit your Github user page (i.e. `https://github.com/USER`) and [Create a repository](https://help.github.com/articles/create-a-repo/) called `r3-exercises`.

    `r img(src='figs/github_repo-create.png', width=200)`
    
    Please tick the box to **Add a README file**. I optionally included "Exercises from https://noaa-iea.github.io/r3-train" in the **Description**. Otherwise the defaults are fine.
    
    `r img(src='figs/github_create_r3-exercises.png', width=600)`
    
You should now see this repo at `https://github.com/USER/r3-exercises`.

  `r img(src='figs/github_initial_r3-exercises.png', width=600)`

## `README.md` {- .callout}

Notice that the only file in the repo so far is the `README.md`, which is in _**markdown**_ format (`.md`) and its contents are displayed directly below, which is the special case for any `README.md` file in a Github folder. Clicking on the pencil icon to edit, reveals the source for this file:

```md
# r3-exercises
Exercises from https://noaa-iea.github.io/r3-train
```

Clicking on the **Preview** tab shows the formatted result. Note how the `#` is used to create a header and the link is automatically generated:

`r img(src='figs/github_readme.md-preview.png', width=400)`

For more on formatting text with markdown within Github, check out [Mastering Markdown · GitHub Guides](https://guides.github.com/features/mastering-markdown/).

## Create RStudio Project

Next, you'll use RStudio to initialize this project in two important ways:

1. You'll let RStudio run `git clone` to copy the git repository onto your machine containing the `README.md` and importantly a hidden folder `.git/` which contains all file history and the configuration on where to synchronize files, i.e. Github.

1. By creating an **RStudio Project**, you'll create an `r3-exercises.Rproj` file. This will be an executable that you can double-click on from Windows Explorer or Mac Finder that will open RStudio and set the working directory to that containing folder. This assures that others who similarly open the project will start with the same working directory, so relative paths to other files in the repo will work regardless of where that repo lives on an individual machine. This is important for making your R code portable for others to use.

From **RStudio** menu **File** -> **New Project...** 

`r img(src='figs/rstudio_new-project.png', width=500)`

Choose **Version Control** -> **git** and enter the **Repository URL** with the `.git` extension.

`r img(src='figs/rstudio_clone-repo.png', width=500)`

This **Repository URL** is also easily copied into your clipboard from your web **browser** by clicking on the green Code button of your new repository (i.e. `https://github.com/USER/r3-exercises`):

`r img(src='figs/github_code-clone.png', width=400)`

Then paste (Ctrl + V) into the **Repository URL** field of the form.

I chose to Create the project as a subdirectory of `~/github/bbest` which means my home directory (`~`) and subfolder `bbest` of folder `github`, but you can create it wherever makes sense on your computer. Be sure to swap any instance of USER `bbest` with your Github username.

If it all works correctly then you should see the files downloaded and showing up in the **Files** pane of RStudio. If RStudio is configured correctly to work with **Git**, then you should also see a Git pane.

`r img(src='figs/rstudio_init.png', width=600)`

## `.gitignore` {- .callout}

Besides the desired **RStudio Project** file `r3-exercises.Rproj`, you should also see the `.gitignore`. This file describes files that `git` should ignore and so not prompt for asking. If you open the file in RStudio, you see it's a simple text file listing hidden files (i.e. those starting with a `.` and not normally shown in Windows Explorer or Mac Finder) that RStudio uses. 

```
.Rproj.user
.Rhistory
.RData
.Ruserdata
```

## **Simple** `commit` & `push`

Note that in the **Git** pane, the yellow box question marks under **Status** next to `.gitignore` and `r3-exercises.Rproj` indicate these files are not known to the version control system (and asking should they be?). Ticking the boxes under **Staged** changes the **Status** to a turquoise `A` for added:

`r img(src='figs/rstudio_git-add-files.png', width=300)`

Now click the **Commit** button in the Git pane to open the Review Changes dialog window. Every commit requires a message.

`r img(src='figs/rstudio_git-commit.png', width=500)`

Click the **Commit** button in the Review Changes dialog window. You should see something like:

`r img(src='figs/rstudio_git-committed.png', width=500)`

This is confirmation that these `2` files were changed with `17` new lines and the hash `8367334` uniquely identifies this commit. **Close** this dialog. Note how now "Your branch is ahead of 'orgin/main' by 1 commit":

`r img(src='figs/rstudio_git-ahead-1-commit.png', width=500)`

The previous `git commit` operation happened only on the local machine. The "origin" is Github and "main" referring to the main branch. Next, you need to **Push** these changes by clicking on the button in the upper right. You should get confirmation like:

`r img(src='figs/rstudio_git-pushed.png', width=500)`

You should now see these two new files showing up in your repo at `https://github.com/USER/r3-exercises`. These files are displayed with the filename, most recent commit message associated with any changes and the time since last update.

`r img(src='figs/github_2-new-files.png', width=500)`

## Create `index.Rmd`

Next we'll create an Rmarkdown file and render it to html. By calling it `index.Rmd` and rendering to `index.html`, this will become the default web page of the repository since web servers serve `index.html` as the default for the folder.

Rmarkdown files weave markdown text with chunks of R code to be evaluated and output content like tables and plots.

In the RStudio menu choose **File** -> **New File** -> **Rmarkdown...**. Give it a Title like "R3 Exercises" and go with Default Output Format HTML.

`r img(src='figs/rstudio_new-rmd-doc-html.png', width=500)`

After you click OK, **File** -> **Save as** (or Ctrl + S) `index` (which will get named with the filename extension `index.Rmd`).

`r img(src='figs/rstudio_new-rmd-source.png', width=600)`

Some initial text is already provided for you. Let's go ahead and render to html by clicking the **Knit** button (highlighted with a pink box above).

`r img(src='figs/rstudio_new-rmd-rendered.png', width=600)`

The **Viewer** pane now shows the rendered html. Also notice the unversioned files. Let's get these onto our Github repo by going into the **Git** pane like previously, ticking the **Staged** boxes, clicking **Commit**, adding a message like "+ index":

`r img(src='figs/rstudio_git-add-index.png', width=500)`

Click on **Commit** in the dialog. Close the Git Commit window and then click on **Push** so your branch is not ahead of the origin Github.

You should now see these two new index.* files showing up in your repo at `https://github.com/USER/r3-exercises`.

We'll get back to Rmarkdown, but first let's get this website served up.

## Setup Github Pages website

[Github Pages](https://pages.github.com) allows you to serve up simple websites from your Github repo. Let's turn on this feature by visiting the **Settings** tab in `https://github.com/USER/r3-exercises`. Then click the **Pages** menu from the left navbar, choose Branch: **main**, folder **/ (root)**:

`r img(src='figs/github_settings-pages.png', width=700)`

Click **Save**. You should now see that the site is "ready to be published":

`r img(src='figs/github_settings-pages-saved.png', width=700)`

You should now be able to visit the website URL:

- `https://USER.github.io/r3-exercises`

Notice how the URL is a slight rearrangement of your Github repo URL:

- `https://github.com/USER/r3-exercises`

For easily referencing the website, I recommend returning to the Github repo `https://github.com/USER/r3-exercises`, clicking the upper right **About** cog and adding it to the **Website** entry:

`r img(src='figs/github_about-website.png', width=500)`

You should now see a handy link to get to your website similar to this:

`r img(src='figs/github_about-website-saved.png', width=300)`

## **Contribute** website with `fork` & `pull request`

So far you've been using the **Simple** workflow with `git push` and `git pull`. Next, you'll learn how to contribute towards a repo for which you don't have write permissions.

The task is to suggest a revision with your information to [roster.csv](https://github.com/noaa-iea/r3-train/blob/master/data/roster.csv), which is used to generate the course [Roster](https://noaa-iea.github.io/r3-train/roster.html).

To do so, please visit [github.com/noaa-iea/r3-train](https://github.com/noaa-iea/r3-train) and in the upper right, click **Fork**:

`r img(src='figs/github_fork-repo.png', width=300)`

Next, choose your Github USER name as the owner:

`r img(src='figs/github_fork-repo-owner.png', width=300)`

Notice how the URL changed from `github.com/noaa-iea/r3-train` to `github.com/USER/r3-train`:

`r img(src='figs/github_fork-repo-done.png', width=300)`

You now have _write_ permissions on this repo. Please proceed with previous steps above to **Create Github RStudio Project**, except this time using `https://github.com/USER/r3-train.git` as the URL. Be sure to replace USER with your Github username.

Once you have the r3-train RStudio Project open, please open from the **Files** pane `data/roster.csv` by clicking on it and **View File**:

`r img(src='figs/rstudio_edit-roster-csv.png', width=700)`

Enter your information at the end of the file instead of:

```
USER,FIRST LAST,https://USER.github.io/r3-exercises
```

Save the changes and in the **Git** pane tick the **Staged** box next to `data/roster.csv` showing a blue `M` for Modified. Click on **Commit** and enter a message like "+ USER" except swapping your Github username. **Push** the changes.

In your browser return to `https://github.com/USER/r3-train`. You'll notice that this branch is "1 commit ahead of noaa-iea:master". Click on **Contribute**:

`r img(src='figs/github_contribute-pull-request.png', width=700)`

Then click on **Open pull request**. You should be taken to a screen asking for confirmation:

`r img(src='figs/github_create-pull-request.png', width=700)`

Click on **Create pull request**. Normally, you'd like a comment explaining what this pull request is for:

`r img(src='figs/github_create-pull-request-issue.png', width=700)`

Click on the final **Create pull request**. Now you should be taken to [github.com/noaa-iea/r3-train](https://github.com/noaa-iea/r3-train) (not your USER forked copy) and under the **Pull requests** see yours:

`r img(src='figs/github_pull-request-issue-admin-merge-option.png', width=700)`

The image above shows a **Merge pull request** since I have admin privileges on this repo. You wouldn't so would see it grayed out (or similar). 

Good job! Nothing left for you to do except wait for me (as admin of this repo) to click on **Merge pull request**. Then I'll re-render [roster.Rmd](https://github.com/noaa-iea/r3-train/blob/master/roster.Rmd) to [roster.html](https://noaa-iea.github.io/r3-train/roster.html).

## **Sandbox** an Rmarkdown website with `branch` & `merge`

Next, you'll up your Git skills by isolating development of your code in a new `branch`, which is like a **Sandbox** separate from the _main_ branch, while converting your website from a simple Rmarkdown to an **Rmarkdown website** for sharing a common navigation menu across created Rmarkdown web pages.

In RStudio's **Git** pane click on the **New Branch** button and enter a **Branch Name** like "rmd-website":

`r img(src='figs/rstudio_new-branch.png', width=500)`

Click **Create**. You should now see your new branch. Notice how when you click on the dropdown of branches you see both LOCAL and REMOTE: ORIGIN (as in on Github) versions.

`r img(src='figs/rstudio_new-branch-created.png', width=500)`

Following guidance from [10.5 rmarkdown’s site generator | R Markdown: The Definitive Guide](https://bookdown.org/yihui/rmarkdown/rmarkdown-site.html), create a `_site.yml` by going to RStudio's menu **File** -> **New File** -> **Text File** and paste the following:

```yaml
name: "R<sup>3</sup>"
navbar:
  title: "R<sup>3</sup> Exercises"
  left:
    - text: "Home"
      href: index.html
    - text: "Collaborate"
      href: collaborate.html
output_dir: "."
```

**Save** this file as `_site.yml`. Next create overwrite your `index.Rmd` with this simpler content:

```markdown
---
title: "Welcome"
---

Hello, Website!
```

Add another page `collaborate.Rmd`:

```markdown
---
title: "Collaborate"
---

Like branches of a tree.
```

Finally, render the website by running the following in your R Console:

```r
rmarkdown::render_site()
```

You might need to install the package `rmarkdown`, which you can do from RStudio's **Packages** pane, **Install** button and typing "rmarkdown".

Once complete, you should see that you're working from the new branch selected in your RStudio Git pane, then click on the file to be presented with options:

`r img(src='figs/rstudio_new-rmd-website-files.png', width=600)`

Select **View in Web Browser** to open your new website locally:

`r img(src='figs/rmd-website-new.png', width=600)`

Now you're ready to **Commit** and **Push** your changes. Once you've done that, please visit `https://USER.github.io/r3-exercises`. Notice that it's still the old default Rmarkdown page. Now visit `https://github.com/USER/r3-exercises` and at first it looks like the changes are not showing up, but now you simply need to select the `rmd-website` **branch** to see those files in their own little sandbox:

`r img(src='figs/github_rmd-website-show-branch.png', width=400)`

Returning to RStudio, you're ready to `git merge` the changes in the `rmd-website` branch to the `main` branch. In RStudio's **Git** pane switch back to the `main` branch:

`r img(src='figs/rstudio_switch-to-main-branch.png', width=400)`

You'll probably see a warning like this:

`r img(src='figs/rstudio_warning-file-missing.png', width=300)`

That's OK. It's just Rstudio saying that it doesn't see this file in your filesystem anymore since we just switched to the `main` branch's snapshot of files. Click **Yes** and proceed with closing any other files with a similar prompt.

RStudio doesn't provide a user interface to run the `git merge` command so you'll have to do this in RStudio's **Terminal** pane:

`r img(src='figs/rstudio_git-merge-branch.png', width=400)`

by entering:

```bash
git merge rmd-website
```

You've now merged your LOCAL changes from the `rmd-website` branch to the `main` branch, and see in the **Git** pane that "Your branch is ahead of 'origin/main' by 1 commit." This means that you're ready to `git push` them to the ORIGIN on Github by running good ol' **Push**.

Now at last you should see these file changes showing up at `https://github.com/USER/r3-exercises`.

It might take a minute or so before they show up on your website at `https://USER.github.io/r3-exercises`. This is because Github Pages were originally designed to render static webpages with some templating capability (e.g. comman navigation menu) using Jekyll. To speed up rendering and disable Jekyll create an empty text file called `.nojekyll`. On a Mac, you can run this command in **Terminal**:

```
touch .nojekyll
```

Be sure to **Commit** and **Push** these changes to Github.

## Create an Issue to resolve a file conflict

Next we're going to play with some of the [Github Project management](https://github.com/features/project-management/) features while learning how to resolve file conflicts when `git` has a conflict automatically merging competing commits.

Let's visit your Github repo `https://github.com/USER/r3-exercises` and click on **Issues**:

`r img(src='figs/github_issues.png', width=400)`

Click on the green **New issue** button and enter a title and comment like:

- Title: "resolve a file conflict"
- Comment:

```markdown
Reference:

* [22.4 Dealing with conflicts | Happy Git and GitHub for the useR](https://happygitwithr.com/git-branches.html#dealing-with-conflicts)
```

`r img(src='figs/github_new-issue.png', width=600)`

When you switch the comment from **Write** to **Preview**, you'll see how the **markdown** source gets formatted into html with a single item bulleted list and link. Now you're ready to **Submit new issue**.

Ok, let's create file conflict by editing the same line in two different places: 1) the Github website through your web browser, 2) your local machine through RStudio.


In your web browser, go to the **Code** tab of your Github repo at `https://github.com/USER/r3-exercises`. Click on `index.Rmd` and click the pencil icon to change it to:

```markdown
---
title: "Welcome"
---

Hello, Github!
```

Scroll down and notice enter a message under the **Commit changes** header of "edit from Github":

`r img(src='figs/github_edit-from-Github.png', width=600)`

Click on the green **Commit changes** button. Since you're already on Github, you don't need to **Push**.

Now go to RStudio, open the `index.Rmd` and change it to:

```markdown
---
title: "Welcome"
---

Hello, RStudio!
```

Be sure to **Commit** those changes with the message "edit from RStudio".

Next, **Pull** changes from Github. Now you'll get a long and messy message about a conflict like:

```
>>> /usr/bin/git pull
From https://github.com/bbest/r3-exercises
   719143f..17f3524  main       -> origin/main
First, rewinding head to replay your work on top of it...
Applying: edit from RStudio
Using index info to reconstruct a base tree...
M	index.Rmd
Falling back to patching base and 3-way merge...
Auto-merging index.Rmd
CONFLICT (content): Merge conflict in index.Rmd
error: Failed to merge in the changes.
hint: Use 'git am --show-current-patch' to see the failed patch
Patch failed at 0001 edit from RStudio
Resolve all conflicts manually, mark them as resolved with
"git add/rm <conflicted_files>", then run "git rebase --continue".
You can instead skip this commit: run "git rebase --skip".
To abort and get back to the state before "git rebase", run "git rebase --abort".
```

Close that. Now in the **Git Commit** dialog window, you'll see:

`r img(src='figs/rstudio_git-conflict.png', width=600)`

The orange `U` refers to an Unresolved conflict. We now need to "manually resolve this conflict". The conflicted portions are compared above and below the `=======`. The conflict begins with `<<<<<<< HEAD` referring to the most recent commit from the ORIGIN on  Github, versus ending with `>>>>>>> edit from RStudio` as the most recent LOCAL commit. Let's change the entire contents of this file to:

```markdown
---
title: "Welcome"
---

Hello, everyone!
```

Then in the **Git** pane mark `index.Rmd` as Staged, **Commit** and enter the message "resolved file conflict; fixes #1":

`r img(src='figs/rstudio_git-commit-cnflict-resolved-ref-issue.png', width=600)`

**Commit** this change and notice that we're still "detached":

```
[detached HEAD 216c243] resolved file conflict #1
 1 file changed, 1 insertion(+), 1 deletion(-)
```
 
Next, we need to associate the detached HEAD with a new temporary branch and reset the main branch with it before pushing changes back to Github. Please run the following commands in the RStudio **Terminal**:

```bash
# associate detached HEAD with new branch temp
git checkout -b temp

# reset master branch with temp branch as starting point
git checkout -B main temp

# delete temp branch
git branch -d temp

# update Github with local main
git push origin main
```

For more details, see [git - How can I reconcile detached HEAD with master/origin? - Stack Overflow](https://stackoverflow.com/questions/5772192/how-can-i-reconcile-detached-head-with-master-origin#answer-5772882).

Now visit `https://github.com/USER/r3-exercises/issues/1`. You'll notice that your commit message automatically associated with that issue by simply including `#1` and closed it by prefixing the number with `fixes`.

The point is to be able to associate specific line by line file changes with fixing **bugs** and implementing **new features** of our code.


## Organize Issues in a Github Project

Let's create a couple **Issues** with the following titles to cue up next week's session:

- `read a csv and output a table`
- `read a wide csv and output a long table`

You should then see these at `https://github.com/USER/r3-exercises/issues`:

`r img(src='figs/github_plus-two-issues.png', width=600)`


Now visit the **Projects** tab, so `https://github.com/USER/r3-exercises/projects`:

`r img(src='figs/github_projects.png', width=600)`

And click the **Create new project** button.

`r img(src='figs/github_new-project.png', width=600)`

Choose the **Automated kanban** style and a title like "management" before clicking **Create project**. You'll next be presented with options to drag existing issues over into any of the columns: **To do**, **In progress** or **Done**:

`r img(src='figs/github_new-project-init.png', width=600)`

Drag the two issues over into **In progress** in the order of priority top to bottom:

`r img(src='figs/github_new-project-issues-dragged.png', width=600)`

A Project board helps answer the question, "What do I need to work on next?"

## Further Reading

### Git & Github

* [GitHub Guides](https://guides.github.com/)
* [Version Control with Git](http://swcarpentry.github.io/git-novice/)
* [How to Use Git/GitHub with R](https://rfortherestofus.com/2021/02/how-to-use-git-github-with-r/)

### RStudio with Git & Github

* [Happy Git and GitHub for the useR](https://happygitwithr.com/)
* [Chapter 18 Git and GitHub | R Packages](https://r-pkgs.org/git.html)
* [Version Control with Git and SVN – RStudio Support](https://support.rstudio.com/hc/en-us/articles/200532077-Version-Control-with-Git-and-SVN)
* [Using RStudio Projects – RStudio Support](https://support.rstudio.com/hc/en-us/articles/200526207-Using-Projects)

### Rmarkdown

* [Lesson 1 | Rmarkdown](https://rmarkdown.rstudio.com/lesson-1.html?_ga=2.141207218.1461543799.1623615738-155442495.1623419383)
* [Getting started with R Markdown - RStudio](https://www.rstudio.com/resources/webinars/getting-started-with-r-markdown/)
* [Reproducible Reporting - RStudio](https://www.rstudio.com/resources/webinars/reproducible-reporting/)
* [R Markdown: The Definitive Guide](https://bookdown.org/yihui/rmarkdown/)

#### Rmarkdown websites

* [10.5 rmarkdown’s site generator | R Markdown: The Definitive Guide](https://bookdown.org/yihui/rmarkdown/rmarkdown-site.html)
* [Creating websites in R](https://www.emilyzabor.com/tutorials/rmarkdown_websites_tutorial.html)
* [Making free websites with RStudio’s R Markdown](https://jules32.github.io/rmarkdown-website-tutorial/)