User:Timothee Flutre/Notebook/Postdoc/2012/08/14

About Git

• Motivation: nowadays, it's pretty common to use a computer for a project in which one wants to: keep history of the changes, access them on different machines with different operating systems, share our work with someone else, etc. In such cases, it's very useful to use a distributed versioning system, such as Git.

• Start using git: first you need to download it. Then you need to read some documentation about it. And finally you can start using it. Typical cases are when developing a software or writing an article.

• Need some help: the learning curve for git is quite steep at the beginning, so it's always worth browsing help pages, reading Git Reference, and searching for questions and answers on stackoverflow.

• Conflicts: when updating one branch with the content of another one (git checkout branch1; git merge branch2), some conflicts can happen, and it is usually hard to know how to solve them properly (but see a concrete example here). In the following, branch1 can be master and branch2 can be origin/master, or branch1 can be master and branch2 can be dev.
  • The first solution is to edit each conflicted files by hand, then run git add fileX.txt (staging indicates to git that the conflict is resolved) and finally run git commit -m "merge branch2 and solve conflicts" fileX.txt.
  • The second solution is to ignore the conflicts and overwrite the files of branch1 with the content of branch2, one file at a time: git checkout --patch branch2 fileX.txt.
  • The third solution, even more radical, is to "overwrite" all of branch1 with the content of the branch2, all files at once: git reset --hard branch2.

• Tips:
  • undo uncommitted changes: git checkout myfile.txt
  • usual config: git config --global user.name 'Timothée Flutre'; git config --global user.email 'timflutre@gmail.com'; git config --global i18n.commitEncoding 'utf8'; git config --global i18n.logOutputEncoding 'utf8'

• Writing a paper: in this example, I am writing a paper with two colleagues. We decide to do it as a centralized workflow, the shared repository being hosted by github.
  • Setting up the infrastructure:
    • Each of us needs to create a free account.
    • I need to upgrade my account in order to have the right to manage private repositories ($7/month).
    • I create a private repository named "paper" and add my colleagues as collaborators to it.
    • I retrieve the repository on my local machine: git clone git://github.com/timflutre/paper.git
    • I create my first file, for instance "paper_main.tex", and add it to git in my local repository: git add paper_main.tex followed by git commit -m "first commit" paper_main.tex.
    • I create one branch per collaborator (the default branch being "master"): git branch tim, then git branch colleague1 and finally git branch colleague2. I can list the local branches with git branch and I can switch to my branch with git checkout tim for instance.
    • I push the changes I made from my local repo onto github: git push origin master, this for each branch I created.
    • I send an email to my colleagues telling them that they can retrieve the content of the repository from github into their local machine(s): git clone https://github.com/timflutre/paper.git.
  • Typical working cycle:
    • Each of us can make modifications on its own branch, and push them on github in order to allow the others to access the changes: git push origin colleague1 for instance.
    • From time to time, one of us has the responsibility to merge the changes and update the "master" branch with the latest version.
    • Once this is done, the others need to retrieve the new content of "master" in their local repo: git checkout master, git fetch origin, git diff master origin/master, git merge origin/master.
    • Then, they need to update their local branch with the new content of "master": git checkout colleague1, git diff --name-status colleague1..master. This will list the files having differences between their local branch and the new content of "master".
    • One can look at the differences file by file: git diff --color-words colleague1:paper_main.tex master:paper_main.tex. The options "--color-words" is especially useful in LaTeX.
    • To merge the content of the recently-updated local "master" into his own local branch, we do: git merge master.
  • Tips: don't version the output pdf in the repository because, as it is binary, git can't merge it properly. But you can add a Makefile (see below) and, by entering make main -i on the command-line, it will compile your pdf document when you need it

all: main supp

main:
	latex paper_main.tex
	bibtex paper_main
	latex paper_main.tex
	latex paper_main.tex
	pdflatex paper_main

supp:
	latex paper_supplements.tex
	bibtex paper_supplements
	latex paper_supplements.tex
	latex paper_supplements.tex
	pdflatex paper_supplements

clean:
	rm -f *~ *.aux *.dvi *.log *.pdf *.bbl *.blg *.toc