User:Timothee Flutre/Notebook/Postdoc/2012/08/14: Difference between revisions
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* ''' | * '''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] | |||
** [http://mrchlblng.me/2014/09/practical-git-introduction/ practical intro] | |||
** 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] | |||
** a [http://nvie.com/posts/a-successful-git-branching-model/ branching model] | |||
* ''' | * '''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>; [https://github.com/blog/2019-how-to-undo-almost-anything-with-git (much) more] on "undo" | ||
** 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'; git config --global core.autocrlf input</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]) | |||
** make the [http://www.gnu.org/prep/standards/html_node/Change-Logs.html ChangeLog] file: <code>git log --no-merges --format="%an: %s" > ChangeLog</code> | |||
** collaborate with some using Windows: ask him to do <code>git config --global core.autocrlf true</code> | |||
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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> | |||
* '''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> | |||
* '''Personal repositories''': for some small project, I am the only one working on them and I want to keep them confidential, so I have my own server in my home on a computer cluster (~/opt/git) | |||
** <code>mkdir ~/smallproject; cd ~/smallproject; echo "hello" > README; git init; git add README; git commit -m "first commit"; cd ..; git clone --bare smallproject/.git</code> | |||
** edit <code>smallproject.git/config</code> to only keep section <code>[core]</code> and, inside, set <code>bare = true</code> | |||
** <code>mkdir -p ~/cluster1; sshfs -oworkaround=rename me@cluster1: ~/cluster1; cp -r smallproject.git ~/cluster1/opt/git</code> | |||
** <code>cd ~/smallproject; git remote add origin ~/cluster1/opt/git/smallproject.git</code> | |||
** I can now push and pull from this minimal server | |||
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Revision as of 01:58, 26 April 2016
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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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