Sample project for the git lesson of embl software carpentry course

• The official git webpage and documentation is in this link

• Create the repo in GitHub and clone to a local directory

• To check the repo settings:

git config -l

• To set user email and preferences

git config --global user.email [email protected]
git config --global user.name "Irene de Teresa"
git config --global core.editor nano

• Add, commit:

git add filename
git commit -m "the message"

or, to not have restrictions to message length:

git commit

The basic process is file -> add (which brings to a 'stage') -> commit (adds the version to .git) .git is the directory where the repo will be developed so do not modify

• To see the history of versons and commits

git log #or
git log --oneline

• diff is a tool that shows changes between versions and repository copies:

git diff

in stage:

git diff --staged

or between two versions in the local repo:

git diff b856f26 b1f794b

to check changes since some version to the current one:

git diff 9bdd448

to color the changes:

git diff --color-words 9bdd448

• To undo commits!:

git checkout -- README.md

• To go back in time:

  First, you have to be in a clean state (commit all changes)

  And then go to the desired working copy, e.g. b856f26:

   git checkout b856f26

  Now the HEAD will be in that point in time

  • Now one can do a branch

   git checkout -b one_sample_branch

• To push to a remote repository in GitHub:

git push

• To pull changes from remote repo

git pull

• If the other person has already commited changes to the remote repo, you have to first pull those changes and then push:

git pull
# Add a message to explain why you will pull
git push

• When both change the same piece of the repository, the merging can't be done automatically. In the corresponding file one sees the <<<<<<< >>>>>>> symbols and tokens related to the different versions. So one has to edit manually and decide what to chose:

nano conflicting_file_name

then delete weird symbols and choose...

git add ...
git commit ...
git push

• To protect the repository from potential changes by collaborators: in github -> settings -> branches ...

• new branch

git checkout -b whateverbranchname

• Create a repo locally:

mkdir repo_directory
cd repo_directory
git init

• Then create the corresponding repo in GitHub (e.g. at https://github.com/username/new-repo) and then link them together:

git remote add origin https://github.com/username/new-repo
git pull https://github.com/username/new-repo
git push https://github.com/username/new-repo

• For bullets, use a small '-'
• Create bold text use '**'
• Create emphasized text use '*'
• Code formatting with backticks
• For links one uses 'link name'

• The commit message should be descriptive