Version control systems allow you to record the history of files and share files among several computers and collaborators in a professional way. Especially when working with software development or technical writing, it is essential to have file changes documented and to ensure that every computer and person involved in the project have the most recent updates of the files.
Projects that you want to share among several computers or project workers are most conveniently stored at some web site "in the cloud", here called project hosting services. For efficient access to the files, and the possibility to work offline, you interact with local copies of the files on your computers. I strongly recommend you to use such sites and version control for all serious programming and scientific writing work.
The essence of project hosting services is that you have the files associated with a project in the cloud. Many people may share these files. Every time you want to work on the project you explicitly update your version of the files, edit the files as you like, and synchronize the files with the "master version" in the cloud. It is a trivial operation to go back to a previous version of a file, corresponding to a certain point of time or labeled with a comment. You can also use tools to see what various people have done with the files throughout the history of the project.
Greg Wilson's excellent Script for Introduction to Version Control provides a detailed motivation why you will benefit greatly from using version control systems. Here follows a shorter motivation and a quick overview of the basic concepts.
The simplest services for hosting project files are Dropbox and Google Drive. It is very easy to get started with these systems, and they allow you to share files among laptops and mobile units with as many users as you want. The systems offer a kind of version control in that the files are stored frequently (several times per minute), and you can go back to previous versions for the last 30 days. However, it is challenging to find the right version from the past when there are so many of them and when the different versions are not annotated with sensible comments. Another deficiency of Dropbox and Google Drive is that they sync all your files in a folder, a feature you clearly do not want if there are many large files (simulation data, visualizations, movies, binaries from compilations, temporary scratch files, automatically generated copies) that can easily be regenerated.
However, the most serious problem with Dropbox and Google Drive arises when several people edit files simultaneously: it can be difficult detect who did what when, roll back to previous versions, and to manually merge the edits when these are incompatible. Then one needs more sophisticated tools, which means a true version control system. The following text aims at providing you with the minimum information to started with Git, the leading version control system, combined with project hosting services for file storage.
The mentioned services host all your files in a specific project in what is known as a repository, or repo for short. When a copy of the files are wanted on a certain computer, one clones the repository on that computer. This creates a local copy of the files. Now files can be edited, new ones can be added, and files can be deleted. These changes are then brought back to the repository. If users at different computers synchronize their files frequently with the repository, most modern version control systems will be able to merge changes in files that have been edited simultaneously on different computers. This is perhaps one of the most useful features of project hosting services. However, the merge functionality clearly works best for pure text files and less well for binary files, such as PDF files, MS Word or Excel documents, and OpenOffice documents.
The installation of Git on various systems is described on the Git website under the Download section. Git involves compiled code so it is most convenient to download a precompiled binary version of the software on Windows, Mac and other Linux computers. On Ubuntu or any Debian-based system the relevant installation command is
Terminal> sudo apt-get install git gitk git-doc
This tutorial explains Git interaction through command-line applications in a terminal window. There are numerous graphical user interfaces to Git. Three examples are git-cola, TortoiseGit, and SourceTree.
Make a file
.gitconfig in your home directory with information on
your full name, email address, your favorite text editor, and
the name of an "excludes file" which defines the file types that Git
should omit when bringing new directories under version control.
Here is a simplified version of the author's
[user] name = Hans Petter Langtangen email = firstname.lastname@example.org editor = emacs [core] excludesfile = ~/.gitignore
excludesfile variable is important: it points to a
.gitignore, which must list,
using the Unix Shell Wildcard notation,
the type of files that you do not need to have under version control,
because they represent garbage or temporary information,
or they can easily be regenerated from
some other source files. A suggested .gitignore file looks like
# compiled files: *.o *.so *.a # temporary files: *.bak *.swp *~ .*~ *.old tmp* .tmp* temp* .#* \#* # tex files: *.log *.dvi *.aux *.blg *.idx *.nav *.out *.toc *.snm *.vrb *.bbl *.ilg *.ind *.loe # eclipse files: *.cproject *.project # misc: .DS_Store
You should be critical to what kind of files you really need a full
history of. For example, you do not want to populate the repository
with big graphics files of the type that can easily be regenerated by
some program. The suggested
.gitignore file above lists typical
files that are not needed (usually because they are automatically
generated by some program).
In addition to a default
.gitignore file in your home directory, it
may be wise to have a
.gitignore file tailored your repo in the
root directory of the repo.
Large data files, even when you want to version them, fill up your repo and should be taken care of through the special service Git Large File Storage.
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
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.,
without any extra whitespaces or other text. How to generate these
files is described in the link generating SSH keys above the SSH Keys
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.
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
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
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
You may use the reStructuredText format as an alternative
README.rst), or simply write a plain text file (
git mv command must be used to change the filename.
You can now add files and directories into the
When your initial file collection has the desired form, you must
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.
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.
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,
.mediawiki for MediaWiki,
.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 email@example.com:user/My-project.wiki.git
The address can be stored as
.git/config in the
root directory of the wiki project so that just a standard
git push works.
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
which shows up as a nicely typeset, colorful HTML code. The raw text file,
shows up as pure text in a browser. If one wants to see the file
rendered as HTML code, one can view it through
This means that one can use the link
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.
github.comand click Settings.
index.htmlpage that GitHub will create for you, and click Publish.
git fetch origin.
git checkout gh-pages.
git rm). You can populate the root directory and subdirectories of your gh-pages branch with HTML and other files as you like. The key issue is that the people out there will only see the web pages that correspond to your HTML files in the gh-pages branch!
index.html page is invoked by the web address
user is the GitHub
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
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.
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
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
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
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
The URL of the
index.html file is
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
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
The ordinary GitHub URL of image files can be used
in web pages to insert images from your repo, provided the image files
are in the raw format - click the Raw button when viewing a file at
github.com and use the corresponding URL in the
img tag in
the HTML code.
GitHub also allows you to create user pages and organization pages not
tied to any specific project.
Your personal site has address
Go to your home page on
github.com and click New repository,
and give it the project name
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 \ firstname.lastname@example.org:user/user.github.com.git Terminal> git push -u origin master
http://user.github.com and see how the
rendered. You can now add various contents as in any ordinary
If you want to use Sphinx generated HTML pages, recall to add an empty file
Most Mac and Linux users prefer to work with Git via commands in a terminal window. Windows users may prefer a graphical user interface (GUI), and there are many options in this respect. There are also GUIs for Mac users. Here we concentrate on the efficient command-line interface to Git.
You get started with your project on a new machine, or another user can get started with the project, by running
Terminal> git clone email@example.com:user/My-Project.git Terminal> cd My-Project ls
Recall to replace
user by your real username and
My-Project by the
actual project name.
The typical work flow with the "My Project" project starts with
updating the local repository by going to the
Terminal> git pull origin master
You may want to do
git fetch and
git merge instead
git pull as explained in the section Replacing pull by fetch and merge,
especially if you work with branches.
You can now edit files, make new files, and make new directories.
New files and directories must be added with
There are also Git commands for deleting, renaming, and moving
files. Typical examples on these Git commands are
Terminal> git add file2.* dir1 dir2 # add files and directories Terminal> git rm file3 Terminal> git rm -r dir2 Terminal> git mv oldname newname Terminal> git mv oldname ../newdir
When your chunk of work is ready,
it is time to commit your changes (note the
Terminal> git commit -am 'Description of changes.'
If typos or errors enter the message, the
git commit --amend command
can be used to reformulate the message. Running
git diff prior to
git commit makes it
easier to formulate descriptive commit messages since this command
gives a listing of all the changes you have made to the files since
the last commit or pull command.
You may perform many commits (to keep track of small changes), before you push your changes to the global repository:
Terminal> git push origin master
It is recommended to pull, commit, and push frequently if the work takes place in several clones of the repo (i.e., there are many users or you work with the repo on different computers). Infrequent push and pull easily leads to merge problems (see the section Merging files with Git). Also remember that others (human and machines) cannot get your changes before they are pushed!
You should run
git status -s frequently to see the status of
A for added,
M for modified,
R for renamed,
?? for not being registered in the repo. Pay particular attention
?? files and examine if all of them are redundant or easily
regenerated from other files - of not, run
The simplest way of adding files to the repo is to do
Terminal> git add .
The dot adds every file, and this is seldom what you want, since
your directories frequently contain large redundant files or files
that can easily be regenerated. You therefore need a
.gitignore file, see the section Configuring Git,
either in your home directory or in the root directory of the repo.
.gitignore file will ignore undesired files when you do
git add ..
A nice graphical tool allows you to view all changes, or just the latest ones:
Terminal> gitk --all Terminal> gitk --since="2 weeks ago"
You can also view changes to all files, some selected ones, or a subdirectory:
Terminal> git log -p # all changes to all files Terminal> git log -p filename # changes to a specific file Terminal> git log --stat --summary # compact summary Terminal> git log --stat --summary subdir
--follow will print the history of file versions before the
file got its present name.
To show the author who is responsible for the last modification of each
line in the file, use
Terminal> git blame filename Terminal> git blame --since="1 week" filename
A useful command to see the history of who did what, where individual
edits of words are highlighted (
git log -p --stat --word-diff filename
Removed words appear in brackets and added words in curly braces.
Looking for when a particular piece of text entered or left the file,
say the text
def myfunc, one can run
Terminal> git log -p --word-diff --stat -S'def myfunc' filename
This is useful to track down particular changes in the files to see when
they occurred and who introduced them. One can also search for regular
expressions instead of exact text: just replace
Occasionally you need to go back to an earlier version of a file,
e.g., a file called
f.py. Start with viewing the history:
Terminal> git log f.py
Find a commit candidate from the list that you will compare the
present version to, copy the commit hash (string like
c7673487...), and run
Terminal> git diff c7673487763ec2bb374758fb8e7efefa12f16dea f.py
where the long string is the relevant commit hash. You can now view the
differences between the most recent version and the one in
the commit you picked (see the section Replacing pull by fetch and merge for how to
configure the tools used by the
git diff command). If you want to restore the old file, write
Terminal> git checkout c7673487763ec2bb374758fb8e7efefa12f16dea f.py
To go back to another version (the most recent one, for instance),
find the commit hash with
git log f.py, and do
<commit hash> f.py.
f.py changed name from
e.py at some point and you want
e.py back, run
git log --follow f.py to find the commit
e.py existed, and do a
git checkout <commit hash> e.py.
f.py no longer exists, run
git log -- f.py to
see its history before deletion. The last commit shown does
not contain the file, so you need to check out the next last
to retrieve the latest version of a deleted file.
Often you just need to view the old file, not replace the current
one by the old one, and then
git show is handy. Unfortunately,
it requires the full path from the root git directory:
Terminal> git show \ c7673487763ec2bb374758fb8e7efefa12f16dea:dir1/dir2/f.py
git log on some file and find the commit hash of the date
or message when want to go back to. Run
git checkout <commit hash>
to change all files to this state.
The problem of going back to the most recent state is that
has no newer commits than the one you checked out. The trick is to say
git checkout master to set all files to most recent version again.
If you want to reset all files to an old version and commit this state as the valid present state, you do
Terminal> git checkout c7673487763ec2bb374758fb8e7efefa12f16dea . Terminal> git commit -am 'Resetting to ...'
Note the period at the end of the first command (without it, you only get the possibility to look at old files, but the next commit is not affected).
Sometimes accidents with many files happen and you want to go back to the last commit. Find the hash of the last commit and do
Terminal> git reset --hard c867c487763ec2
This command destroys everything you have done since the last commit. To push it as the new state of the repo, do
Terminal> git push origin HEAD --force
git pull command fetches new files from the repository and
tries to perform an automatic merge if there are conflicts between
the local files and the files in the repository. Alternatively,
you may run
git fetch and
git merge to do the same
thing as described in the section Replacing pull by fetch and merge.
We shall now address what do to if the merge goes wrong, which
Git will write a message in the terminal window
if the merge is unsuccessful for one or
more files. These files will have to be edited manually.
Merge markers of the type
<<<<< have been
inserted by Git to mark sections of a file where the version in the
repository differ from the local version. You must decide which
lines that are to appear in the final, merged version. When done,
git commit and the conflicts are resolved.
Graphical merge tools may ease the process of merging text files. You
git mergetool --tool=meld to open the merge tool
every file that needs to be merged (or specify the name of a
particular file). Other popular merge tools supported by Git are
Below is a Unix shell script illustrating how to make a global
repository in Git, and how two users clone this repository and
perform edits in parallel. There is one file
myfile in the
#!/bin/sh # Demo script for exemplifying git and merge rm -rf tmp1 tmp2 tmp_repo # Clean up previous runs mkdir tmp_repo # Global repository for testing cd tmp_repo git --bare init --shared cd .. # Make a repo that can be pushed to tmp_repo mkdir _tmp cd _tmp cat > myfile <<EOF This is a little test file for exemplifying merge of files in different git directories. EOF git init git add . # Add all files not mentioned in ~/.gitignore git commit -am 'first commit' git push ../tmp_repo master cd .. rm -rf _tmp # Make a new hg repositories tmp1 and tmp2 (two users) git clone tmp_repo tmp1 git clone tmp_repo tmp2 # Change myfile in the directory tmp1 cd tmp1 # Edit myfile: insert a new second line perl -pi -e 's/a little\n/a little\ntmp1-add1\n/g' myfile # Register change in local repository git commit -am 'Inserted a new second line in myfile.' # Look at changes in this clone git log -p # or a more compact summary git log --stat --summary # or graphically #gitk # Register change in global repository tmp_repo git push origin master cd .. # Change myfile in the directory tmp2 "in parallel" cd tmp2 # Edit myfile: add a line at the end cat >> myfile <<EOF tmp2-add1 EOF # Register change locally git commit -am 'Added a new line at the end' # Register change globally git push origin master # Error message: global repository has changed, # we need to pull those changes to local repository first # and see if all files are compatible before we can update # our own changes to the global repository. # git writes #To /home/hpl/vc/scripting/manu/py/bitgit/src-bitgit/tmp_repo # ! [rejected] master -> master (non-fast-forward) #error: failed to push some refs to ... git pull origin master # git writes: #Auto-merging myfile #Merge made by recursive. # myfile | 1 + # 1 files changed, 1 insertions(+), 0 deletions(-) cat myfile # successful merge! git commit -am merge git push origin master cd .. # Perform new changes in parallel in tmp1 and tmp2, # this time causing hg merge to fail # Change myfile in the directory tmp1 cd tmp1 # Do it all right by pulling and updating first git pull origin master # Edit myfile: insert "just" in first line. perl -pi -e 's/a little/tmp1-add2 a little/g' myfile # Register change in local repository git commit -am 'Inserted "just" in first line.' # Register change in global repository tmp_repo git push origin master cd .. # Change myfile in the directory tmp2 "in parallel" cd tmp2 # Edit myfile: replace little by modest perl -pi -e 's/a little/a tmp2-replace1\ntmp2-add2\n/g' myfile # Register change locally git commit -am 'Replaced "little" by "modest"' # Register change globally git push origin master # Not possible: need to pull changes in the global repository git pull origin master # git writes #CONFLICT (content): Merge conflict in myfile #Automatic merge failed; fix conflicts and then commit the result. # we have to do a manual merge cat myfile echo 'Now you must edit myfile manually'
You may run this file git_merge.sh named
sh -x git_merge.sh.
At the end, the versions of
myfile in the
repository and the
tmp2 directory are in conflict. Git tried
to merge the two versions, but failed. Merge markers are left in
<<<<<<< HEAD This is a tmp2-replace1 tmp2-add2 ======= This is tmp1-add2 a little >>>>>>> ad9b9f631c4cc586ea951390d9415ac83bcc9c01 tmp1-add1 test file for exemplifying merge of files in different git directories. tmp2-add1
Launch a text editor and edit the file, or use
so that the file becomes correct.
git commit -am merge to finalize the merge.
Branching and stashing are nice features of Git that allow you to try
out new things without affecting the stable version of your files.
Usually, you extend and modify files quite often and perform a
commit every time you want to record the changes in your local
repository. Imagine that you want to correct a set of errors in some
files and push these corrections immediately. The problem is that
such a push will also include the latest, yet unfinished files that you
A better organization of your work would be to keep the latest, ongoing developments separate from the more official and stable version of the files. This is easily achieved by creating a separate branch where new developments takes place:
Terminal> git branch newstuff # create new branch Terminal> git checkout newstuff Terminal> # extend and modify files... Terminal> git commit -am 'Modified ... Added a file on ...' Terminal> git checkout master # swith back to master Terminal> # correct errors Terminal> git push origin master Terminal> git checkout newstuff # switch to other branch Terminal> git merge master # keep branch up-to-date w/master Terminal> # continue development work... Terminal> git commit -am 'More modifications of ...'
At some point, your developments in
are mature enough to be incorporated
in the master branch:
Terminal> git checkout newstuff Terminal> git merge master # synchronize newstuff w/master Terminal> git checkout master Terminal> git merge newstuff # synchronize master w/newstuff
You no longer need the
newstuff branch and can delete it:
Terminal> git branch -d newstuff
This command deletes the branch locally. To also delete the branch in the remote repo, run
Terminal> git push origin --delete newstuff
You can learn more in an excellent introduction and demonstration of Git branching.
It is not possible to switch branches unless you have committed the
files in the current branch. If your work on some files is in a mess
and you want to change to another branch or fix other files in the
current branch, a "global" commit affecting all files might be
immature. Then the git stash command is handy. It
records the state of your files and sets you back to the state of the
last commit in the current branch. With
git stash apply you will update the
files in this branch to the state when you did the last
Let us explain a typical case. Suppose you have performed some
extensive edits in some files and then you are suddenly
interrupted. You need to fix some typos in some other files, commit
the changes, and push. The problem is that many files are in an
unfinished state - in hindsight you realize that those files should
have been modified in a separate branch. It is not too late to create
that branch! First run
git stash to get the files back to the state
they were at the last commit. Then run
git stash branch newstuff to
create a new branch
newstuff containing the state of the files when
you did the (last)
git stash command. Stashing used this way is a
convenient technique to move some immature edits after the last commit
out in a new branch for further experimental work.
You can get the stashed files back by
git stash apply. It is
possible to multiple
git stash and
git stash apply
commands. However, it is easy to run into trouble with multiple
stashes, especially if they occur in multiple branches, as it becomes
difficult to recognize which stashes that belong to which branch. A
good advice is therefore to do
git stash only once to get back to
a clean state and then move the unfinished messy files to a separate
git stash branch newstuff.
git pull command actually performs two steps that are sometimes
advantageous to run separately. First, a
get fetch is run to fetch
new files from the repository, and thereafter a
git merge command is
run to merge the new files with your local version of the files.
git pull tries to do a lot and be smart in the merge, very
often with success, the merge step may occasionally lead to
trouble. That is why it is recommended to run a
separately, especially if you work with branches.
To fetch files from your repository at GitHub, which usually has
origin, you write
Terminal> git fetch origin
You now have the possibility to check out in detail what the differences are between the new files and local ones:
Terminal> git diff origin/master
This command produces comparisons of the files in the current local branch
master branch at
origin (the GitHub repo).
In this way you can exactly see the differences between branches.
It also gives you an overview of what others have done with
When you are ready to merge in the new files from the
origin with the files in the current local branch, you say
Terminal> git merge origin/master
Especially when you work with multiple branches, as outlined in
the section Git working style with branching and stashing, it is wise to first do a
get fetch origin and then update each branch separately. The
git fetch origin command will list the branches, e.g.,
* master gh-pages next
master as described, you can continue with another branch:
Terminal> git checkout next Terminal> git diff origin/next Terminal> git merge origin/next Terminal> git checkout master
git diff command launches by default the
diff tool in the terminal window.
Many users prefer to use other diff tools, and the desired one
can be specified in
~/.gitconfig file. However, a much recommended approach is to
wrap a shell script around the call to the diff program, because
git diff actually calls the diff program with a series of
command-line arguments that will confuse diff programs that take
the names of the two files to be compared as arguments.
~/.gitconfig you specify a script to do the diff:
[diff] external = ~/bin/git-diff-wrapper.sh
It remains to write the
The 2nd and 5th command-line arguments passed to this script are the
name of the files to be compared in the diff. A typical script may
therefore look like
#!/bin/sh diff "$2" "$5" | less
Here we use the standard (and quite primitive) Unix
but we can replace
diff by, e.g.,
pdiff, or others. With a Python script you can easily check
for the extensions of the files and use different diff tools for
different types of files, e.g.,
latexdiff for LaTeX files
pdiff for pure text files.
Occasionally it becomes desirable to replace all files in the local repo with those in the repo at the file hosting service. One possibility is removing your repo and cloning again, or use the Git commands
Terminal> git fetch --all Terminal> git reset --hard origin/master
Say you have two branches, A and B, and want to merge a file
in A with the latest version in B. To merge this single file, go to
the directory where
f.txt resides and do
Terminal> git checkout A Terminal> git checkout --patch B f.txt
f.txt is not present in branch A, and if you want to include more
files, drop the
--patch option and specify files with full path relative
to the root in the repo:
Terminal> git checkout A Terminal> git checkout B doc/f.txt src/files/g.py
g.py from branch B will be included in branch A as well.
In small collaboration teams it is natural that everyone has push access to the repo. On GitHub this is known as the Shared Repository Model. As teams grow larger, there will usually be a few people in charge who should approve changes to the files. Ordinary team members will in this case not clone a repo and push changes, but instead fork the repo and send pull requests, which constitutes the Fork and Pull Model.
Say you want to fork the repo
The first step is to press the Fork button on the project page for
somebody/proj1 project on GitHub.
This action creates a new repo
proj1, known as the forked repo,
on your GitHub account.
Clone the fork as you clone any repo:
Terminal> git clone https://github.com/user/proj1.git
When you do
git push origin master, you update your fork.
However, the original
repo is usually under development too, and you need to pull from that
one to stay up to date. A
git pull origin master pulls from
origin which is your fork. To pull from the original repo, you
create a name
upstream, either by
Terminal> git remote add upstream \ https://github.com/somebody/proj1.git
if you cloned with such an
https address, or by
Terminal> git remote add upstream \ firstname.lastname@example.org:somebody/proj1.git
if you cloned with a
email@example.com (SSH) address.
git pull upstream master would seem to be the command for
pulling the most recent files in
the original repo. However,
it is not recommended to update the forked repo's files this way
because heavy development of the
sombody/proj1 project may
lead to serious merge problems.
It is much better to replace the pull by a separate
fetch and merge.
The typical workflow is
Terminal> git fetch upstream # get new version of files Terminal> git merge upstream/master # merge with yours Terminal> # Your files are up to date - ready for editing Terminal> git commit -am 'Description...' Terminal> git push origin master # store changes in your fork
At some point you would like to push your changes back to the original
somebody/proj1. This is done by a pull request. Make sure you
have selected the right branch on the project page of your forked
project. Press the Pull Request button and fill out the form that
pops up. Trusted people in the
somebody/proj1 project will now
review your changes and if they are approved, your files are merged
into the original repo. If not, there are tools for keeping a dialog
about how to proceed.
Also in small teams where everyone has push access, the fork and pull request model is beneficial for reviewing files before the repo is actually updated with new contributions.
An annoying feature of Git for beginners is the fact that if you
clone a repo, you only get the
master branch. There are seemingly
no other branches:
Terminal> git branch * master
To see which branches that exist in the repo, type
Terminal> git branch -a * master remotes/origin/HEAD -> origin/master remotes/origin/gh-pages remotes/origin/master remotes/origin/next
If there is only one remote repo that
you pull/push from/to, you can simply switch branch with
the usual way:
Terminal> git checkout gh-pages Terminal> git branch * gh-pages master Terminal> git checkout next Terminal> git branch gh-pages master * next
You might need to do
git fetch origin to see new branches made
on other machines.
When you have more than one remote, which is usually the case if you have forked a repo, see the section Team work with forking and pull requests, you must use do a checkout with specifying the remote branch you want:
Terminal> git checkout -b gh-pages --track remote/gh-pages Terminal> git checkout -b next --track upstream/next
Files can be edited, added, or removed as soon as you have done the local checkout.
It is possible to write a little script that takes the output of
git branch -a after a
git clone command and automatically check
out all branches via
Although the purpose of these notes is just to get the reader started with Git, it must be mentioned that there are advanced features of Git that have led to very powerful workflows with files and people, especially for software development. There is an official Git workflow model that outlines the basic principles, but it can be quite advanced for those with modest Git knowledge. A more detailed explanation of a recommended workflow for beginners is given in the developer instructions for the software package PETSc. This is highly suggested reading. The associated "quick summary" of Git commands for their workflow is also useful.
git ls-files is the command:
Terminal> git ls-files # list all tracked files Terminal> git ls-files -o # list non-tracked files Terminal> git ls-files myfile # prints myfile if it's tracked Terminal> git ls-files myfile --error-unmatch
The latter command prints an error message if
myfile is not tracked.
man git-ls-files for the many options this utility has.
git gc can compress a git repository and should be
run regularly on large repositories. Greater effect
is achieved by
git gc --aggressive --prune=all. You can measure the
size of a repo before and after compression by
git gc using
du -s repodir, where
repodir is the name of the root directory of
Occasionally big or sensitive files are removed from the repo and you want to
permanently remove these files from the revision history. This is
achieved using git filter-branch. To remove a file or directory with path
doc/src/mydoc relative to the root directory of the repo, go to this root directory, make sure all branches are checked out on your computer, and run
Terminal> git filter-branch --index-filter \ 'git rm -r --cached --ignore-unmatch doc/src/mydoc' \ --prune-empty -- --all Terminal> rm -rf .git/refs/original/ Terminal> git reflog expire --expire=now --all Terminal> git gc --aggressive --prune=now Terminal> git push origin master --force # do this for each branch Terminal> git checkout somebranch Terminal> git push origin somebranch --force
You must repeat the
push command for each branch as indicated.
If other users have created their own branches in this repo, they
need to rebase,
merge, when updating the branches!
Sometimes you accidentally remove files from a repo, either by
git rm or
rm. You can get the files back as long as they are in the remote
repo. In case of a plain
rm command, run
Terminal> git checkout `git ls-files`
to restore all missing files in the current directory.
In case of a
git rm command, use
git log --diff-filter=D --summary to find the commit hash
corresponding to the last commit
the files were in the repo. Restoring a file is then done by
Terminal> git checkout <commit hash> filename
Working against different GitHub accounts is easy if each project you work with on each account adds you as a collaborator. The term "you" here means your primary username on GitHub. My strong recommendation is to always check out a project using your primary GitHub username.
Occasionally you want to create a new GitHub account, say for a project
For such a non-personal account, do not provide an SSH key of any
particular user. The reason is that this user will then get two
GitHub identities, and switching between these identities will require
some special tweakings. Just forget about the SSH key for a project
account and add
collaborators to repos using each collaborators personal GitHub username.
If you really need to operate the
XYZ account as a
personal account, you must provide an SSH key that is different from
any other key at any other GitHub account (you will get an error message
if you try to register an already registered SSH key, but it is possible to
get around the error message by providing
id_rsa.pub key on one account and an
id_dsa.pub on another - that
will cause trouble). Jeffrey Way has written a recipe for how to operate multiple GitHub accounts
using multiple identities.
To debug which identity that is used when you pull and push to GitHub accounts, you can first run
Terminal> ssh -Tv firstname.lastname@example.org
to see your current identity and which SSH key that was used to identify you. Typing
Terminal> ssh-add -l
lists all your SSH keys. The shown strings can be compared with the string in the SSH key field of any GitHub account.