Remotes in GitHub

Estimated time: 45 minutes

Overview

Questions

• How do I share my changes with others on the web?

Objectives

• Explain what remote repositories are and why they are useful.
• Push to or pull from a remote repository.

Version control really comes into its own when we begin to collaborate with other people. We already have most of the machinery we need to do this; the only thing missing is to copy changes from one repository to another.

Systems like Git allow us to move work between any two repositories. In practice, though, it’s easiest to use one copy as a central hub, and to keep it on the web rather than on someone’s laptop. Most programmers use hosting services like GitHub, Bitbucket or GitLab to hold those main copies; we’ll explore the pros and cons of this in a later episode.

Let’s start by sharing the changes we’ve made to our current project with the world. To this end we are going to create a remote repository that will be linked to our local repository.

1. Create a remote repository

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Log in to GitHub, then click on the icon in the top right corner to create a new repository called amr-data-dictionary:

Name your repository “amr-data-dictionary” and then click “Create Repository”.

Note: Since this repository will be connected to a local repository, it needs to be empty. Leave “Initialize this repository with a README” unchecked, and keep “None” as options for both “Add .gitignore” and “Add a license.” See the “GitHub License and README files” exercise below for a full explanation of why the repository needs to be empty.

As soon as the repository is created, GitHub displays a page with a URL and some information on how to configure your local repository:

This effectively does the following on GitHub’s servers:

BASH

$ mkdir amr-data-dictionary
$ cd amr-data-dictionary
$ git init

If you remember back to the earlier episode where we added and committed our earlier work on index.qmd, we had a diagram of the local repository which looked like this:

Now that we have two repositories, we need a diagram like this:

Note that our local repository still contains our earlier work on index.qmd, but the remote repository on GitHub appears empty as it doesn’t contain any files yet.

2. Create a Personal Access Token (PAT)

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Before we can connect our local repository to the remote repository there are some things we need to setup.

The first is a secure connection to the GitHub server. To do this we will create a Personal Access Token (PAT)

Will work in the Console to generate and store the our Personal Access Token.

We will need to make use of the usethis package. If not already installed we will need to install the package, and tell R that we want to use the package.

BASH

install.packages("usethis")
library(usethis)

We can now generate our token using the following command in the console:

BASH

usethis::create_github_token()

We will generate our token within the GitHub interface by visiting https://github.com/settings/tokens.

This will open the generate token page on the GitHub website.

You will be asked to specify an expiration date, for this example I have chosen 90 days and to set the scope of the token. A suitable scope will be automatically selected.

Click Generate token.

Once we have generated the token, we need to copy this token and add to our R settings.

In the Console in RStudio we can enter the following:

BASH

gitcreds::gitcreds_set()

Paste the PAT in response to the dialogue in the console:

OUTPUT

? Enter password or token: ghp_xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-> Adding new credentials...
-> Removing credentials from cache...
-> Done.

We are now ready to connect the two repositories.

3. Connect local to remote repository

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Now we connect the two repositories. We do this by making the GitHub repository a remote for the local repository. The home page of the repository on GitHub includes the URL string we need to identify it:

Copy that URL from the browser, in RStudio open the Terminal from the Git tab. Checking that you are in the directory of your amr-data-dictionary repository, and run this command:

BASH

$ git remote add origin https://github.com/quirksahern/amr-data-dictionary.git

Make sure to use the URL for your repository rather than the instructor’s: the only difference should be your username instead of quirksahern.

origin is a local name used to refer to the remote repository. It could be called anything, but origin is a convention that is often used by default in git and GitHub, so it’s helpful to stick with this unless there’s a reason not to.

We can check that the command has worked by running git remote -v:

BASH

$ git remote -v

OUTPUT

origin   https://github.com/quirksahern/amr-data-dictionary.git (fetch)
origin   https://github.com/quirksahern/amr-data-dictionary.git (push)

We’ll discuss remotes in more detail in the next episode, while talking about how they might be used for collaboration.

4. Push local changes to a remote

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Now that authentication is setup, we can return to the remote. This command will push the changes from our local repository to the repository on GitHub:

BASH

$ git push origin main

OUTPUT

Enumerating objects: 15, done.
Counting objects: 100% (15/15), done.
Delta compression using up to 8 threads
Compressing objects: 100% (10/10), done.
Writing objects: 100% (15/15), 1.54 KiB | 33.00 KiB/s, done.
Total 15 (delta 2), reused 0 (delta 0), pack-reused 0
remote: Resolving deltas: 100% (2/2), done.
To github.com:quirksahern/amr-data-dictionary.git
 * [new branch]      main -> main

The files that we had created and edited locally are now available in the remote repository and are currntly in the same state.

Proxy

If the network you are connected to uses a proxy, there is a chance that your last command failed with “Could not resolve hostname” as the error message. To solve this issue, you need to tell Git about the proxy:

BASH

$ git config --global http.proxy http://user:password@proxy.url
$ git config --global https.proxy https://user:password@proxy.url

When you connect to another network that doesn’t use a proxy, you will need to tell Git to disable the proxy using:

BASH

$ git config --global --unset http.proxy
$ git config --global --unset https.proxy

Our local and remote repositories are now in this state:

The ‘-u’ Flag

You may see a -u option used with git push in some documentation. This option is synonymous with the --set-upstream-to option for the git branch command, and is used to associate the current branch with a remote branch so that the git pull command can be used without any arguments. To do this, simply use git push -u origin main once the remote has been set up.

We can pull changes from the remote repository to the local one as well:

BASH

$ git pull origin main

OUTPUT

From https://github.com/quirksahern/amr-data-dictionary
 * branch            main     -> FETCH_HEAD
Already up-to-date.

Pulling has no effect in this case because the two repositories are already synchronized. If someone else had pushed some changes to the repository on GitHub, though, this command would download them to our local repository.

Are the Push/Pull Commands Grayed Out?

Grayed out Push/Pull commands generally mean that RStudio doesn’t know the location of your remote repository (e.g. on GitHub). To fix this, open a terminal to the repository and enter the command: git push -u origin main. Then restart RStudio.

GitHub GUI

Browse to your amr-data_dictionary repository on GitHub. Under the Code tab, find and click on the text that says “XX commits” (where “XX” is some number). Hover over, and click on, the three buttons to the right of each commit. What information can you gather/explore from these buttons? How would you get that same information in the shell?

Show me the solution

The left-most button (with the picture of a clipboard) copies the full identifier of the commit to the clipboard. In the shell, git log will show you the full commit identifier for each commit.

When you click on the middle button, you’ll see all of the changes that were made in that particular commit. Green shaded lines indicate additions and red ones removals. In the shell we can do the same thing with git diff. In particular, git diff ID1..ID2 where ID1 and ID2 are commit identifiers (e.g. git diff a3bf1e5..041e637) will show the differences between those two commits.

The right-most button lets you view all of the files in the repository at the time of that commit. To do this in the shell, we’d need to checkout the repository at that particular time. We can do this with git checkout ID where ID is the identifier of the commit we want to look at. If we do this, we need to remember to put the repository back to the right state afterwards!

Uploading files directly in GitHub browser

Github also allows you to skip the command line and upload files directly to your repository without having to leave the browser. There are two options. First you can click the “Upload files” button in the toolbar at the top of the file tree. Or, you can drag and drop files from your desktop onto the file tree. You can read more about this on this GitHub page.

GitHub Timestamp

Create a remote repository on GitHub. Push the contents of your local repository to the remote. Make changes to your local repository and push these changes. Go to the repo you just created on GitHub and check the timestamps of the files. How does GitHub record times, and why?

Show me the solution

GitHub displays timestamps in a human readable relative format (i.e. “22 hours ago” or “three weeks ago”). However, if you hover over the timestamp, you can see the exact time at which the last change to the file occurred.

Push vs. Commit

In this episode, we introduced the “git push” command. How is “git push” different from “git commit”?

Show me the solution

When we push changes, we’re interacting with a remote repository to update it with the changes we’ve made locally (often this corresponds to sharing the changes we’ve made with others). Commit only updates your local repository.

GitHub License and README files

In this episode we learned about creating a remote repository on GitHub, but when you initialized your GitHub repo, you didn’t add a README.md or a license file. If you had, what do you think would have happened when you tried to link your local and remote repositories?

Show me the solution

In this case, we’d see a merge conflict due to unrelated histories. When GitHub creates a README.md file, it performs a commit in the remote repository. When you try to pull the remote repository to your local repository, Git detects that they have histories that do not share a common origin and refuses to merge.

BASH

$ git pull origin main

OUTPUT

warning: no common commits
remote: Enumerating objects: 3, done.
remote: Counting objects: 100% (3/3), done.
remote: Total 3 (delta 0), reused 0 (delta 0), pack-reused 0
Unpacking objects: 100% (3/3), done.
From https://github.com/quirksahern/amr-data-dictionary
 * branch            main     -> FETCH_HEAD
 * [new branch]      main     -> origin/main
fatal: refusing to merge unrelated histories

You can force git to merge the two repositories with the option --allow-unrelated-histories. Be careful when you use this option and carefully examine the contents of local and remote repositories before merging.

BASH

$ git pull --allow-unrelated-histories origin main

OUTPUT

From https://github.com/quirksahern/amr-data-dictionary
 * branch            main     -> FETCH_HEAD
Merge made by the 'recursive' strategy.
README.md | 1 +
1 file changed, 1 insertion(+)
create mode 100644 README.md

Key Points

• A local Git repository can be connected to one or more remote repositories.
• Use the SSH protocol to connect to remote repositories.
• git push copies changes from a local repository to a remote repository.
• git pull copies changes from a remote repository to a local repository.