Paul Martin: Git commands

Go back in time

Display the modification log

git log

Display the log of a particular branch (after a fetch for example)

git log origin/master

Display a compact log for one file or one directory only

git log --abbrev-commit --pretty=oneline path_to_file

Identify the commit identity in the log and copy its sha number. Then to go back to this state for the whole folder:

git reset --hard commit_sha

To go back to this state for only one file, see git checkout

git checkout commit_hash path_to_file/file_name

No commit hash to get to get the file back to the latest commit.

Chekout the older revision of a file under a new name

git show commit_sha:filename > new_file_name

Help

Get help on a command (will start a web browser):

git init --help

Configure user name and email

Display your user name, email and remote repositories

git config -l

To change username and email

git config --global user.name "Your Name"

git config --global user.email you@example.com

Setting your email in git explains how to change the email for the current repository only.

Branching

To start work in a new branch:

git branch new_branch_name
git checkout new_branch_name

To compare a file between 2 branches:

git diff branch1 branch2 file_name

To merge changes back to the master branch:

git checkout master
git merge branch1

If there were conflicts, they will be presented in this way:

"The area where a pair of conflicting changes happened is marked with markers <<<<<<<, =======, and >>>>>>>. The part before the ======= is typically your side, and the part afterwards is typically their side."

I might need to delete a branch at some point:

git branch -d branchname

Delete a remote branch (stackoverflow question)

git push --delete origin temp

Deleting your master branch.

If I am on a detached head, it is recommended to create a temporary branch (stackoverflow).

git branch temp
git checkout temp
git add -a
git commit -m "description of changes"
git checkout master
git merge temp

Delete uncommitted changes in current working directory:

git checkout branch_name .

See also below git clean.

Add minor change to the previous commit (git commit --amend):

git commit --amend

Tagging

Creating an annotated tag

git tag -a v1.4 -m 'my version 1.4'

You can add a tag after the fact. To tag an earlier commit, specify the commit checksum or part of it:

git log --pretty=oneline
git tag -a v1.2 -m 'version 1.2' 9fceb02

Delete a tag

git tag -d tag_name

A regular push command won't push a tag (bitbucket), to push all your tags :

git push origin --tags

Display changes

To view modified files that have not been committed and to view commit history you can use:

git status
git log
git log --pretty=oneline

Shows the changes between the working directory and the index.

git diff

Shows the changes between the index and the HEAD

git diff --cached

Shows all the changes between the working directory and HEAD

git diff HEAD

The 3 lines above were copied from this question on git diff.

Show when the tip of branches have been updated

git reflog

Alternatively, call the repository browser with:

gitk

To view a shorter version of the log file, and get an idea at where I am in the history:

git log --graph --decorate --all --pretty=oneline

You can define an alias for git log as explained be Fred here:

git config --global alias.lg "log --color --graph --pretty=format:'%Cred%h%Creset -%C(yellow)%d%Creset %s %Cgreen(%cr)%C(bold blue)<%an>%Creset' --abbrev-commit"

The new alias can then be used with

git lg

Use tags to specify important points in history, such as software versions.

Working with files

Get back a file to the last commit

git checkout path_to_file/file_name

Get back a file to a previous commit, using the commit hash

git checkout 4fb987f175210c09daaa4d0240070ffc9641120b path_to_file/file_name

Rename a file

git mv file_name file_name_new

Change the case of a file on a windows FAT 32 system:

git mv load.r load2.R
git mv load2.R load.R

Sometimes the vi editor starts. To exit the vi editor:

ESC:q!

If a file or folder has been renamed outside of git, I get this warning:

$ git add .
warning: You ran 'git add' with neither '-A (--all)' or '--ignore-remo
whose behaviour will change in Git 2.0 with respect to paths you removed
Paths like 'docs/efi/efi_logo_rgb_small_siw.jpg' that are
removed from your working tree are ignored with this version of Git.

* 'git add --ignore-removal ', which is the current default,
ignores paths you removed from your working tree.

* 'git add --all ' will let you also record the removals.

Therefore I think I should always run "git add --all "

Remove local (untracked) files from my current Git branch
Show what will be deleted with the -n option:

git clean -f -n

Then - beware: this will delete files - run:

git clean -f

Alternatively clean in interactive mode:

git clean -i

Search text

Search all files in the subdirectory "subdir" for lines containing the words "factor" and "item". Show 2 lines of context (2 leading and 2 trailing lines).

git grep -e item --and -e factor -C 2 -- subdir/

Stackoverflow: How to search committed code in the git history?

Bulk replace strings

Use git grep to replace strings in many files in the directory :

git grep -l 'original_text' | xargs sed -i 's/original_text/new_text/g'

Save local modification temporarily

# I had edited the current file in between so needed to use
git stash # save local modifications away
git checkout __commit__hash__
# do some stuff in there ...
# Get back to most recent version of the code
git checkout branch_name
git stash pop # reload local modifications

.gitignore

To ignore all files in a folder but not the folder itself. Put this .gitignore into the folder, then git add .gitignore

*
!.gitignore

To exclude everything except a specific directory foo/bar (note the /* - without the slash, the wildcard would also exclude everything within foo/bar):

    /*
    !/foo
    /foo/*
    !/foo/bar

Remote

When a repository is connected to several remote repositories, to change the default git remote, push with :

git push -u origin master

Then later push of that branch to that remote can be made simply with:

git push

Another command without specifying the remote and the branch

$ git push -u

fatal: The current branch master has no upstream branch.
To push the current branch and set the remote as upstream, use

git push --set-upstream origin master

After I run this set upstream flag, I can push to the remote server. Then I get this message

[...]
* [new branch] master -> masterBranch master set up to track remote branch master from origin.

I'll have to figure out what this does.

Using the gh-branch to publish project documentation on github

SO Answer to the question "How to add a git repo as a submodule of itself? (Or: How to generate GitHub Pages programmatically?)": An alternative to using Git Submodules to generate GitHub Pages is to use Git Subtree Merge Strategy.

In fact I didn't use quite that strategy and I instead cloned a temporary copy of my repository. Created the gh-page branch. Pushed it to github. Then I went back to the original repository (where I have a few large untracked data files I find handy to keep for analyses purposes).

Then within the inst folder, I cloned only the gh-branch. To clone only one branch:

git clone -b mybranch --single-branch git://sub.domain.com/repo.git

Then I renamed the folder to "web", so that I had a inst/web folder, tracking the gh-branch. inst/web is ignored in the main repository.

References

Presentations:

Power Your Workflow With Git (towards 43 minutes, an animation of branches and merging) A recommendation if you work in a team, don't use pull, but use fetch + merge.
Getting Started with GitHub + Git

Workflow:

Mixing private and public repository in Git workflow

Turorial:

Git foundations

Paul Martin

Friday, October 25, 2013

Git commands