User:Timothee Flutre/Notebook/Postdoc/2012/08/14: Difference between revisions

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(→‎About Git: put "conflicts" in a separate section)
(→‎About Git: add tips SSL certificate)
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* '''Start using git''': first you need to [http://git-scm.com/downloads download] it. Then you need to read some [http://git-scm.com/doc documentation] about it. And finally you can start using it. Typical cases are when developing a software or writing an article.
* '''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], [http://www.ndpsoftware.com/git-cheatsheet.html cheatsheet]
** 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
** make your repositories freely available online via [https://github.com/ github] (see its [https://help.github.com/ help pages] too) or [https://bitbucket.org/ bitbucket]
** 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!
** [http://fr.openclassrooms.com/informatique/cours/gerez-vos-codes-source-avec-git tutoriel en français]




* '''Need some help''': the learning curve for git is quite steep at the beginning, so it's always worth browsing [https://help.github.com/ help pages], reading [http://gitref.org/ Git Reference], and searching for questions and answers on [http://stackoverflow.com/ stackoverflow].
* '''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''':
* '''Tips''':
** undo uncommitted changes: <code>git checkout myfile.txt</code>
** undo uncommitted changes: <code>git checkout myfile.txt</code>
** usual config: <code>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'</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 color.diff auto; git config --global color.status auto; git config --global color.branch auto; 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>
** create release on github: first create tags, and then create the release (automatic via tag name) <code>curl --user "timflutre" --data '{"tag_name":"v1.0","target_commitish":"master","name":"v1.0","body":"first release"}' https://api.github.com/repos/timflutre/eqtlbma/releases</code>
** get download count of release: <code>curl -u "timflutre" -i https://api.github.com/repos/timflutre/eqtlbma/releases/:id/assets</code> where the release id can be obtained via <code>curl -u "timflutre" -i https://api.github.com/repos/timflutre/eqtlbma/releases/</code>
** avoid being rejected by github because SSL certificates are not installed on your machine: add <code>export GIT_SSL_NO_VERIFY=true</code> to your <code>~/.bash_profile</code> ([http://stackoverflow.com/a/4454754/597069 source])




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*** 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.
*** 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>.
*** 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>




* '''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. In the following, branch1 can be master and branch2 can be origin/master, or branch1 can be tim and branch2 can be master.
* '''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.
** The first solution is to edit the files by hand and choose which version we want to keep for each conflict.
** first I log on cluster2 and I clone the repo from github: <code>git clone https://github.com/timflutre/myproject.git</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>.
** 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>
** 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>.
** 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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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.



  • 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
    • split a big commit in several smaller commits: git add -p myfile.txt
    • usual config: git config --global user.name 'Timothée Flutre'; git config --global user.email 'timflutre@gmail.com'; git config --global color.diff auto; git config --global color.status auto; git config --global color.branch auto; git config --global core.editor emacs; git config --global i18n.commitEncoding 'utf8'; git config --global i18n.logOutputEncoding 'utf8'
    • remote via ssh tunnel: first open the tunnel ssh gateway.foo.bar -l tflutre -Nf -L 20400:maincluster:22, then add the remote git remote add mcl ssh://tflutre@localhost:20400/home/tflutre/myproject/.git
    • create release on github: first create tags, and then create the release (automatic via tag name) curl --user "timflutre" --data '{"tag_name":"v1.0","target_commitish":"master","name":"v1.0","body":"first release"}' https://api.github.com/repos/timflutre/eqtlbma/releases
    • get download count of release: curl -u "timflutre" -i https://api.github.com/repos/timflutre/eqtlbma/releases/:id/assets where the release id can be obtained via curl -u "timflutre" -i https://api.github.com/repos/timflutre/eqtlbma/releases/
    • avoid being rejected by github because SSL certificates are not installed on your machine: add export GIT_SSL_NO_VERIFY=true to your ~/.bash_profile (source)


  • 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


  • 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.


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