Friday, October 25, 2013

Git commands

See also my other posts labelled git:
I've started using GIT to track file modifications and I followed this advice to set it up:  create a repository.
I use git both on windows and on Ubuntu / Debian GNU-Linux.

The commands I've used to upload content to github.com/paul4forest/forestproductsdemand are:
git remote add origin https://github.com/paul4forest/forestproductsdemand
git pull origin master
git add
git commit -m "Explanatory message"
git push origin master
Alternatively "git commit -a"" is a replacement for "git add"" and "git commit". What is the difference between pull and clone: "I like to think of 'clone' as "make me a local copy of that repo" and 'pull' as "get me the updates from some specified remote."

The commands to setup a fresh repository from bitbucket :
mkdir /path/to/your/project
cd /path/to/your/project
git init
git remote add origin ssh://git@bitbucket.org/username/bbreponame.git
# Upload and set the local changes as upstream
git push -u origin master
See also this discussion on why do I need to set upstream?

Commands to copy an existing repository from bitbucket :
 git clone git@bitbucket.org/username/bbreponame.git

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
See also alias and git grep below.

 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'

 .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 -> master
Branch 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:
Workflow:
Turorial:

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