Reference

Quick reference

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Navigating the shell

pwd

print working directory

ls

list directory

• -l: list file information

• -lh: list human readable file information

• -a: also list hidden files (names starting with .)

cd

change directory

Interacting with files in the shell

mkdir

make directory

touch

create an empty file

cat

send file or files to output (in most cases, print to shell)

head

output first parts of a file or files

tail

output last parts of a file or files

less

view a file one screen at a time (quit with q)

mv

rename or move a file or files. Syntax for renaming a file: mv FILENAME NEWFILENAME

cp

copy a file or files. Syntax: cp FILENAME NEWFILENAME

>

redirect output. Syntax with cat: cat FILENAME1 FILENAME2 > NEWFILENAME

rm

remove a file or files. NB: USE WITH CAUTION!!!

Git commands

Git cheat sheet handouts:

• GitHub git cheat sheet
• Tower client git cheat sheet

git init

create a new local git repository

git status

view the status of your files in the working directory and staging area

git add

tell git to start tracking a file, or a series of files

git commit

save file changes from the staging area permanently to the project history

git push

upload all commits to a remote repository, such as one on Codeberg

git log

show history of commits in reverse chronological order

git diff

show changes made to tracked files

git pull

download upstream changes and merge them into your local repository

git remote add origin

add a remote repository named ‘origin’, to upload changes to or download changes from

Codeberg

Issue

a task, question or problem report in a repository, with a discussion; can be open or closed

Label, milestone, assignee

ways to organise issues: by topic or status, by target date, by responsible person

Fork

your own copy of someone else’s repository on Codeberg

Pull request (GitLab: merge request)

a request to merge the changes from one branch (often in a fork) into another branch

Closes #1

in a pull request description, closes issue number 1 when the pull request is merged

Further reading

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• The Codeberg documentation is a good place to start, for example the introduction to pull requests and the Codeberg Pages documentation.
• The Forgejo user guide describes the software that Codeberg is built on.
• The free book Pro Git covers Git in depth.
• Atlassian has in-depth but clear tutorials on using git.
• The Turing Way is a community handbook on reproducible, ethical and collaborative data science, with chapters on version control and research data management.

Useful Git repositories for research data management

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• dini-ag-kim/fdm-lernziele: Learning objectives matrix for research data management (LZM-FDM / LOM-RDM), developed and versioned in a Git repository; the learning objectives of this lesson are based on it.
• the-turing-way/the-turing-way: Source of The Turing Way handbook, written collaboratively by hundreds of contributors with issues and pull requests.
• citation-file-format/citation-file-format: Specification of the CITATION.cff file, which tells others how to cite the software or data in your repository.
• frictionlessdata: Open standards and tools for describing and packaging tabular data (Data Package), developed on GitHub.
• NFDI4Objects OER templates: Templates for creating FAIR open educational resources with Git, including a metadata schema.
• Software Heritage: Archive that preserves the source code and history of public Git repositories, including those on Codeberg.