User:Timothee Flutre/Notebook/Postdoc/2012/08/14: Difference between revisions
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==About Git== | ==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 operating | * '''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 [http://en.wikipedia.org/wiki/Git_%28software%29 Git]. | ||
* '''Documentation''': | |||
** try it [http://try.github.io/levels/1/challenges/1 online] | |||
** if you liked, [http://git-scm.com/downloads download] it | |||
** official [http://git-scm.com/doc book] | |||
** [http://gitref.org/ quick ref] | |||
** tutorial for [http://nyuccl.org/pages/GitTutorial/ scientists] (another by a [http://kbroman.github.io/github_tutorial/ geneticist]) | |||
** [http://gitready.com/ resources] depending on your level | |||
** use [https://github.com/ github] to make your repositories freely available online (see its [https://help.github.com/ help pages] too) | |||
** ask questions on [http://stackoverflow.com/ stackoverflow] | |||
** manage your code, papers, talks, courses and even [http://www.wired.com/wiredenterprise/2013/06/cades-witty-headline-here/ books] with it! | |||
* '''Conflicts''': when updating one branch with the content of another one (<code>git checkout branch1; git merge branch2</code>), some conflicts can happen, and it is usually hard to know how to solve them properly (but see a concrete example [http://git-scm.com/book/en/Git-Branching-Basic-Branching-and-Merging 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 <code>git add fileX.txt</code> (staging indicates to git that the conflict is resolved) and finally run <code>git commit -m "merge branch2 and solve conflicts" fileX.txt</code>. | |||
** The second solution is to ignore the conflicts and overwrite the files of branch1 with the content of branch2, one file at a time: <code>git checkout --patch branch2 fileX.txt</code>. | |||
** The third solution, even more radical, is to "overwrite" all of branch1 with the content of the branch2, all files at once: <code>git reset --hard branch2</code>. | |||
* '''Tips''': | |||
** undo uncommitted changes: <code>git checkout myfile.txt</code> | |||
** split a big commit in several smaller commits: <code>git add -p myfile.txt</code> | |||
** usual config: <code>git config --global user.name 'Timothée Flutre'; git config --global user.email 'timflutre@gmail.com'; git config --global core.editor emacs; git config --global i18n.commitEncoding 'utf8'; git config --global i18n.logOutputEncoding 'utf8'</code> | |||
** remote via ssh tunnel: first open the tunnel <code>ssh gateway.foo.bar -l tflutre -Nf -L 20400:maincluster:22</code>, then add the remote <code>git remote add mcl ssh://tflutre@localhost:20400/home/tflutre/myproject/.git</code> | |||
* '''Writing a paper''': in this example, I am writing a paper with two colleagues. We decide to do it as a [http://git-scm.com/book/en/Distributed-Git-Distributed-Workflows centralized workflow], the shared repository being hosted by [https://github.com/ github]. | * '''Writing a paper''': in this example, I am writing a paper with two colleagues. We decide to do it as a [http://git-scm.com/book/en/Distributed-Git-Distributed-Workflows centralized workflow], the shared repository being hosted by [https://github.com/ github]. | ||
** Each of us needs to [https://github.com/signup/free create a free account]. | ** Setting up the infrastructure: | ||
** I need to upgrade my account in order to have the right to manage private repositories ([https://github.com/plans/ $7/month]). | *** Each of us needs to [https://github.com/signup/free create a free account]. | ||
** I create a private repository named "paper" and add my colleagues as collaborators to it. | *** I need to upgrade my account in order to have the right to manage private repositories ([https://github.com/plans/ $7/month]). | ||
** I retrieve the repository on my local machine: <code>git clone git://github.com/timflutre/paper.git</code> | *** I create a private repository named "paper" and add my colleagues as collaborators to it. | ||
** I create | *** I retrieve the repository on my local machine: <code>git clone git://github.com/timflutre/paper.git</code> | ||
** I create one branch per collaborator (the default branch being "master"): <code>git branch tim</code>, then <code>git branch colleague1</code> and finally <code>git branch colleague2</code>. I can list the local branches with <code>git branch</code> and I can switch to my branch with <code>git checkout tim</code> for instance. | *** I create my first file, for instance "paper_main.tex", and add it to git in my local repository: <code>git add paper_main.tex</code> followed by <code>git commit -m "first commit" paper_main.tex</code>. | ||
** I push the changes I made from my local repo onto github: <code>git push origin master</code>, this for each branch I created. | *** I create one branch per collaborator (the default branch being "master"): <code>git branch tim</code>, then <code>git branch colleague1</code> and finally <code>git branch colleague2</code>. I can list the local branches with <code>git branch</code> and I can switch to my branch with <code>git checkout tim</code> for instance. | ||
** 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): <code>git clone | *** I push the changes I made from my local repo onto github: <code>git push origin master</code>, this for each branch I created. | ||
** 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. | *** 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): <code>git clone https://github.com/timflutre/paper.git</code>. | ||
** From time to time, one of us has the responsibility to merge the changes and update the "master" branch with the latest version. | ** Typical working cycle: | ||
** Once this is done, the others need to retrieve the new content of "master" in their local repo: <code>git checkout master</code>, <code>git fetch origin</code>, <code>git diff master origin/master</code>, <code>git merge origin/master</code>. | *** 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: <code>git push origin colleague1</code> for instance. | ||
** Then, they need to update their local branch with the new content of "master": <code>git checkout colleague1</code>, <code>git diff --name-status colleague1..master</code>. This will list the files having differences between their local branch and the new content of "master". | *** From time to time, one of us has the responsibility to merge the changes and update the "master" branch with the latest version. | ||
** One can look at the differences file by file: <code>git diff --color-words colleague1:paper_main.tex master:paper_main.tex</code>. The options "--color-words" is especially useful in LaTeX. | *** Once this is done, the others need to retrieve the new content of "master" in their local repo: <code>git checkout master</code>, <code>git fetch origin</code>, <code>git diff master origin/master</code>, <code>git merge origin/master</code>. | ||
** To merge the content of "master" into his own branch, we do: <code>git merge master</code>. | *** Then, they need to update their local branch with the new content of "master": <code>git checkout colleague1</code>, <code>git diff --name-status colleague1..master</code>. 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: <code>git diff --color-words colleague1:paper_main.tex master:paper_main.tex</code>. 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: <code>git merge master</code>. | |||
** 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 <code>make main -i</code> on the command-line, it will compile your pdf document when you need it | |||
<nowiki> | |||
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 | |||
</nowiki> | |||
* '''Two remotes''': let's imagine that on cluster1 I have 2 branches, "master" and "dev", on github I only have "master", and I want to work with "dev" on cluster2. | |||
** first I log on cluster2 and I clone the repo from github: <code>git clone https://github.com/timflutre/myproject.git</code> | |||
** then I add my repo from cluster1 as a remote: <code>cd myproject/; git remote add cluster1 ssh://tflutre@cluster1:/home/tflutre/myproject/.git</code> | |||
** finally I fetch the remotes and create a "dev" branch which tracks the one on cluster1: <code>git remote update; git checkout -b dev cluster1/dev</code> | |||
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Revision as of 18:27, 8 October 2013
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About Git
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
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