GitHub

Go to github.com and create an account. Then go to your account settings (icon in the upper left corner of the page), choose SSH Keys, and provide your SSH key unless you have already registered this key with another GitHub account (see Appendix: Working with multiple GitHub accounts). Often, it is just a matter of pasting the contents of id_rsa.pub or id_dsa.pub files, located in the .ssh subdirectory of your home directory, into the Key box in the web page. Make sure to just cut and paste the text from, e.g., id_rsa.pub without any extra whitespaces or other text. How to generate these files is described in the link generating SSH keys above the SSH Keys box (or see the introduction to Bitbucket above).

If the account is a project account and not a personal account, I do not recommend to provide an SSH key although it can be done (see Appendix: Working with multiple GitHub accounts). It is easier to log in and add collaborators using their personal GitHub usernames.

Creating a new project

Click on New repository on the main page and fill out a project name, here My Project, click the check button Initialize this repository with a README, and click on Create repository. Unless you pay, all repos are public, but students and teachers can request free, private repos.

The next step is to clone the project on your personal computer. Click on the SSH button to see the address of the project, and paste this address into a terminal window, after git clone:

Terminal> git clone git://github.com:user/My-Project.git

Make sure you substitute user by your own username on GitHub.

The result of the git clone command is a new directory My-Project. It contains the file .git, which shows that it is a Git repository. It also contains a default README.md file with the project name and description. The extension .md signifies a file written in the Markdown format. You may use the reStructuredText format as an alternative (README.rst), or simply write a plain text file (README), but the git mv command must be used to change the filename.

You can now add files and directories into the My-Project directory. When your initial file collection has the desired form, you must run

Terminal> git add .
Terminal> git commit -am 'First set of files.'
Terminal> git push -u origin master

The daily file operations are explained in the section Using Git.

Collaborating

To give others permissions to push their edits of files to the repository, you click on the Settings link in the right sidebar, then click on Collaborators on the left, and fill in the name of a collaborator (her or his username on GitHub). Many find it convenient to be notified in email when others have pushed a new version of the files to the repo. Click on Service Hooks in the project's Settings menu, choose Email, fill in at most two whitespace-separated email addresses, mark the Send from Author and Active boxes, and click on Update Settings. More addresses must be dealt with through a mailing list and filling in the name of that list.

Anyone who participates in a project (has write access) or watches a project (having clicked the watch button) can monitor the development of the activity on their GitHub main page. Go to Account Settings and choose Notification Center. There you see two sections, Participating and Watching, for those participating in the project (granted write access) and those watching the project (having clicked the watch button), respectively.

Wiki pages

With every GitHub project there is an option to create wiki pages. Click on the Wiki button in the right sidebar on the main page of the project. Click on New Page to create a new page. The wiki pages can be written in different markup languages. Markdown is the default choice, but you can alternatively use MediaWiki and reStructuredText. Unfortunately, GitHub wiki pages do not allow LaTeX mathematics through MathJax, even though MediaWiki has support for LaTeX (the reason is security issues).

The wiki pages can be written and maintained through the web browser interface, but it is usually more convenient to clone them on your computer as this makes it easy to add figures and other documents you may want to link to. It also makes it straightforward to edit the wiki text in your favorite text editor. The wiki pages are stored in a separate repo and can be cloned by

Terminal> git clone git://github.com/user/My-Project.wiki.git

This command makes a local copy of the pages in the directory My-Project.wiki, which you may prefer to have at the same level as the project directory itself in your directory tree.

Each wiki page has its own file, where the extension reflects the markup language used, e.g., .md for Markdown, .rest for reStructuredText, .mediawiki for MediaWiki, and .creole for Creole wiki. The wiki files are handled as other files in a GitHub project, i.e., you need to pull before editing and then perform commit and push. After the push you can reload the page in the web browser to monitor the effect.

You may consider having the original text in doconce format and generate the wiki in the reStructuredText or MediaWiki format.

Do changes, commit the usual way, and push by

Terminal> git push git@github.com:user/My-project.wiki.git

The address can be stored as url in .git/config in the root directory of the wiki project so that just a standard git push works.

Project web pages

HTML pages stored in your repo cannot be linked to and properly rendered as web pages. Say you have some HTML file doc/file.html in the repo. The normal link to the file is

https://github.com/user/my-project/blob/master/doc/file.html

which shows up as a nicely typeset, colorful HTML code. The raw text file,

https://raw.githubusercontent.com/user/my-project/master/doc/file.html

shows up as pure text in a browser. If one wants to see the file rendered as HTML code, one can view it through htmlpreview.github.io. This means that one can use the link

http://htmlpreview.github.io/?https://raw.githubusercontent.com/user/my-project/master/doc/file.html

to produce the HTML document in a browser.

However, there is another technique available where all HTML files in a special branch gh-pages of the repository are automatically rendered correctly as HTML documents in a browser. This is the recommended technique for publishing a collection of HTML files related to the project in a simple and convenient way. The recipe is described in detail below.

1. Go to the project page on github.com and click Settings.
2. Click on Automatic Page Generator under the GitHub Pages.
3. Proceed clicking Continue to Layouts, choose a design of the index.html page that GitHub will create for you, and click Publish.
4. Go to the root directory of the project, My-Project and run git fetch origin.
5. Run git checkout gh-pages.

The index.html page is invoked by the web address

http://user.github.io/My-Project/index.html

where user is the GitHub username and My-Project is the project name.

The web pages and project files are now in two different branches. To see the branches, type git branch, and the one you are in will be marked with * in the output. Switching to the master branch is done by git checkout master. Similarly, git checkout gh-pages switches to the gh-pages branch.

My personal preference is to have the master and gh-pages synchronized, at least in projects where I want to link to various source code files or other files from the web documentation. Sometimes I also update files in the gh-pages branch without remembering to switch to the master branch. To this end, one needs to merge the branches, i.e., automatically edit files in the current branch such that they are up-to-date and identical to files in another branch.

To merge the current branch with some branch named otherbranch, run

Terminal> git merge otherbranch

Git applies smart algorithms that very often manage to merge the files without human interaction. However, occasionally these algorithms are not able to resolve conflicts between two files. A message about the failure of the merge is seen in the terminal window, and the corresponding files have markers in them showing which sections that needs manual editing to resolve the conflicts. Run git diff to show the problems (you can tailor this command to your needs as explained in the section Replacing pull by fetch and merge). After a manual edit, do git commit -a. More details on merging appears in the section Merging files with Git.

If you want to keep the master branch and the gh-pages branch synchronized, start with merging the gh-pages branch with the master branch and push the complete file collection to the gh-pages branch. Then switch to the master branch and merge with gh-pages so you get the autogenerated index.html file and associated files and directories for web pages in the root directory of the master branch as well:

Terminal> git merge master
Terminal> touch .nojekyll
Terminal> git push origin gh-pages
Terminal> git checkout master
Terminal> git merge gh-pages

You must add an empty file .nojekyll in the top directory of the project pages if you want to use Sphinx-generated HTML pages (or other pages using javascripts, style sheets, and images in subdirectories whose names start with an underscore).

You can now add the documentation to the project files and maintain them in the master branch. Before publishing documents online, make sure to update the gh-pages branch by

Terminal> git commit -am 'Ensure commit of master branch'
Terminal> git push origin master
Terminal> git checkout gh-pages
Terminal> git pull origin gh-pages
Terminal> git merge master
Terminal> git push origin gh-pages
Terminal> git checkout master

Personally, I like to move the generated index.html file and all associated scripts, stylesheets, and images from the root directory to some more isolated place, say doc/web:

Terminal> git mv index.html params.json stylesheets/ images/ \
                 javascripts/ doc/web/

The URL of the index.html file is

http://user.github.io/My-Project/doc/web/index.html

Linking to source code files or other files in the project is easy: just find the file in GitHub's web interface, choose which version of the file you want to link to (nicely HTML formatted version or the raw file), right-click on the link, choose Copy Link, and paste the link into the document you want. You can test that the link works by the Unix command curl -O <link>. Note that the link to a file is different from the source file's intuitive path in the repository. Typically, a source file dir/f.py in project prj is reached through

https://github.com/user/prj/blob/master/dir/f.py?raw=true

Sometimes you want to link to another HTML file, PDF file, movie file, or a file that is to be interpreted as a web resource by the browser. Do not use the path to the file in the repo as explained above as it will just bring the reader to the repo page. Instead, make sure the file is in the gh-pages branch and use a local link, like ../doc.pdf, or the complete gh-pages URL to the file, say

http://user.github.com/My-Project/doc/misc/doc.pdf

User web pages

GitHub also allows you to create user pages and organization pages not tied to any specific project. Your personal site has address http://user.github.com. Go to your home page on github.com and click New repository, and give it the project name user.github.com. Then follow the instructions that come up:

Terminal> mkdir user.github.com
Terminal> cd user.github.com
Terminal> git init
Terminal> # make an index.html file with some test text
Terminal> git add index.html
Terminal> git commit -m 'First commit'
Terminal> git remote add origin \
          git@github.com:user/user.github.com.git
Terminal> git push -u origin master

Go to http://user.github.com and see how the index.html is rendered. You can now add various contents as in any ordinary Git repository. If you want to use Sphinx generated HTML pages, recall to add an empty file .nojekyll.

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