Remote chapter added

Author: axiezai

_episodes/04-remote.md

@@ -0,0 +1,210 @@
+---
+title: "Collaborating with GitHub"
+teaching: 25
+exercises: 0
+questions:
+- "What is a remote repository?"
+- "How can I use GitHub to work from multiple locations?"
+objectives:
+- "Understand how to set up remote repository"
+- "Understand how to push local changes to a remote repository"
+- "Understand how to clone a remote repository"
+keypoints:
+- "Git is the version control system: GitHub is a remote repositories provider."
+- "`git clone` to make a local copy of a remote repository"
+- "`git push` to send local changes to remote repository"
+---
+To collaborate with your colleagues as well as _your self_, we will need to set up a remote destination to save our work *AND* our history.
+
+### GitHub
+
+[GitHub](http://GitHub.com) is a company which provides remote repositories for
+Git and a range of functionalities supporting their use. GitHub allows users to
+set up  their private and public source code Git repositories. It provides
+tools for browsing, collaborating on and documenting code. GitHub, like other
+services such as [GitLab](https://about.gitlab.com/) and
+[Bitbucket](https://bitbucket.org),  supports a wealth of resources to support
+projects including:
+
+* Browsing code from within a web browser, with syntax highlighting
+* Software release management
+* Issue and bug tracking
+* Project management tools
+
+### GitHub for research
+
+GitHub **isn't** the only remote repositories provider.
+It is very popular, however, particularly within the open source communities.
+
+Also, GitHub has [functionality which is particularly useful
+for researchers](https://github.com/blog/1840-improving-github-for-sciences)
+such as making code citable!
+
+---
+
+### Get a GitHub account
+
+[Sign up](https://GitHub.com) or [sign in](https://GitHub.com) if you already have an account.
+
+### Create a new repository
+
+Now, we can create a repository on GitHub,
+
+* Log in to [GitHub](https://GitHub.com/)
+* Click on the **Create** icon on the top right
+* Enter Repository name: "git-papers"
+* For the purpose of this exercise we'll create a public repository
+* Since we'll be importing a local repository, make sure that **Initialize this repository with a README** is **unselected**
+* Click **Create Repository**
+
+You'll get a page with new information about your repository. We already have our local repository and we will be *pushing* it to GitHub, so we can do the following:
+
+```
+$ git remote add origin https://github.com/<USERNAME>/git-papers.git
+```
+{: .language-bash}
+
+This line sets up an alias `origin`, to correspond to the URL of our new repository on GitHub.
+
+### Push locally tracked files to a remote repository
+
+Now we can execute the following:
+
+```
+$ git push -u origin master
+```
+{: .language-bash}
+```
+Counting objects: 32, done.
+Delta compression using up to 8 threads.
+Compressing objects: 100% (28/28), done.
+Writing objects: 100% (32/32), 3.29 KiB | 0 bytes/s, done.
+Total 32 (delta 7), reused 0 (delta 0)
+To https://github.com/emdupre/git-papers.git
+ * [new branch]      master -> master
+Branch master set up to track remote branch master from origin.
+```
+{: .output}
+
+This **pushes** our `master` branch to the remote repository, (named via the alias `origin`) and creates a new `master` branch in the remote repository.
+
+Now, on GitHub, we should see our code,
+and if we click the `Commits` tab we should see our complete history of commits.
+
+Our local repository is now available on GitHub. This means that anywhere we can access GitHub, we can access our repository!
+
+### Push other local branches to a remote repository
+
+Let's push each of our local branches into our remote repository:
+
+```
+$ git push origin branch_name
+```
+{: .language-bash}
+
+The branch should now be created in our GitHub repository.
+
+To list all branches (local and remote):
+
+```
+$ git branch -a
+```
+{: .language-bash}
+
+> ## Deleting branches (for information only)
+> **Don't do this now.** This is just for information.
+> To delete branches, use the following syntax:
+>
+> ```
+> $ git branch -d <branch_name>			# For local branches
+> $ git push origin --delete <branch_name>	# For remote branches
+> ```
+> {: .language-bash}
+{: .callout}
+
+### Cloning a remote repository
+
+Now, let's do something drastic!
+But before that step,
+**make sure that you pushed all your local branches into the remote repository!**
+
+```
+$ cd ..
+$ rm -rf git-papers
+```
+{: .language-bash}
+
+Gulp! We've just wiped our local repository!
+But, because we've pushed to GitHub, we have still have a copy!
+We can just copy the repository down using `git clone`:
+
+```
+$ git clone https://github.com/<USERNAME>/git-papers.git
+```
+{: .language-bash}
+```
+Cloning into 'git-papers'...
+remote: Counting objects: 32, done.
+remote: Compressing objects: 100% (21/21), done.
+remote: Total 32 (delta 7), reused 32 (delta 7), pack-reused 0
+Unpacking objects: 100% (32/32), done.
+Checking connectivity... done.
+```
+{: .output}
+
+Cloning creates an exact copy of the repository. By default it creates
+a directory with the same name as the name of the repository.
+
+Now, if we change into *git-papers* we can see that we have our repository,
+
+```
+$ cd git-papers
+$ git log
+```
+{: .language-bash}
+and we can see our Git configuration files too:
+
+```
+$ ls -A
+```
+{: .language-bash}
+
+In order to see the other branches locally, we can check them out as before:
+
+```
+$ git branch -r					# Show remote branches
+$ git checkout paperWJohn			# Check out the paperWJohn branch
+```
+{: .language-bash}
+
+### Push changes to a remote repository
+
+We can use our cloned repository just as if it were the original, local repository !
+So, let's make some changes to our files and commit these.
+
+```
+$ git checkout master				# We'll continue working on the master branch
+$ vim journal.md				# Add results section
+$ git add journal.md				# Stage changes
+$ git commit
+```
+{: .language-bash}
+
+Having done that, how do we send our changes back to the remote repository?
+We can do this by *pushing* our changes:
+
+```
+$ git push origin master
+```
+{: .language-bash}
+
+If we now check our GitHub page we should be able to see our new changes under
+the *Commit* tab.
+
+To see all configured remotes for this repository (we can have multiple!),
+type:
+
+```
+$ git remote -v
+```
+{: .language-bash}