• Synchronize local Git directory with remote repository:

  git pull

  same as git fetch plus git merge.

• Modify files in local working directory.

• Add snapshots to staging area:

  git add FILES

• Commit: store snapshots permanently to (local) Git repository

  git commit -m "MESSAGE"

• Push commits to remote repository:

  git push

• Register for an account on a Git server, e.g., github.com.

• Upload your SSH public key to the server.

• Identify yourself at local machine, e.g.,

  git config --global user.name "Your Name"
  git config --global user.email "your_email@ucla.edu"

  Name and email appear in each commit you make.

• Initialize a project.

  • Create a repository, e.g., biostat-m280-2018-winter on the server.

  • Clone the repository to your local machine:

  git clone git@github.com:biostat-m280-2018-winter.git

• Working with your local copy.

  • git pull: update local Git repository with remote repository (fetch + merge).

  • git log FILENAME: display the current status of working directory.

  • git diff: show differences (by default difference from the most recent commit).

  • git add file1 file2 ...: add file(s) to the staging area.

  • git commit: commit changes in staging area to Git directory.

  • git push: publish commits in local Git repository to remote repository.

  • git reset --soft HEAD~1: undo the last commit.

  • git checkout FILENAME: go back to the last commit, discarding all changes made.

  • git rm FILENAME: remove files from git control.

On your local machine:

• Clone the repository, create develop branch, where your work on solutions.

  # clone the project
  git clone git@github.com:biostat-m280-2018-winter.git
  # enter project folder
  cd biostat-m280-2018-winter
  # what branches are there?
  git branch
  # create develop branch
  git branch develop
  # switch to the develop branch
  git checkout develop
  # create folder for HW1
  mkdir hw1
  cd hw1
  # let's write solutions
  echo "sample solution" > hw1.Rmd
  echo "some bug" >> hw1.Rmd
  # commit the code
  git add hw1.Rmd
  git commit -m "start working on problem #1"
  # push to remote repo
  git push

• Submit and tag HW1 solution to master branch.

  # which branch are we in?
  git branch
  # change to the master branch
  git checkout master
  # merge develop branch to master branch
  # git pull origin develop 
  git merge develop
  # push to the remote master branch
  git push
  # tag version hw1
  git tag hw1
  git push --tags

• RStudio has good Git integration. But practice command line operations also.

• Be judicious what to put in repository.

  • Not too less: Make sure collaborators or yourself can reproduce everything on other machines.

  • Not too much: No need to put all intermediate files in repository. Make good use of the .gitignore file.

  • Strictly version control system is for source files only. E.g. only xxx.Rmd, xxx.bib, and figure files are necessary to produce a pdf file. Pdf file doesn't need to be version controlled or, if version controlled, doesn't need to be frequently committed.

• Commit early, commit often and don't spare the horses.

• Adding an informative message when you commit is not optional. Spending one minute on commit message saves hours later for your collaborators and yourself. Read the following sentence to yourself 3 times:

Write every commit message like the next person who reads it is an axe-wielding maniac who knows where you live.