Getting Started

Who are you?

Course Resources

• Syllabus: on Canvas
• GitHub: github.com/SoftwareDevEngResearch
• Other resources: on Canvas
• Slack chat room: researchsoftw-27f5620.slack.com

Textbook

http://physics.codes/

Chapters 1–6 should be review

Project

Most of your work in the class will be centered around a project developing a new software package for your research.

Rest of today: version control

What for?

• Back up changing files
• Store and access an annotated history
• Manage merging of changes between different change sets

Why important?

Image credit: Jorge Cham, PhD Comics

Saving copies

important_code.py

important_code-2.py

important_code-fix.py

important_code-final.py

important_code-final-4apr.py

Git commits

important_code.py

important_code.py

important_code.py

important_code.py

important_code.py

Git

Git is a knife whose handle is also a knife. – Philip Guo

Image credit: xkcd

Getting Started with Git

                    $ git --help

                    $ git config --global user.name "Kyle Niemeyer"
                    $ git config --global user.email "kyle.niemeyer@oregonstate.edu"
                    $ git config --global core.editor "vim"
                

                    ~ $ mkdir analysis_code
                    ~ $ cd analysis_code

                    ~/analysis_code $ git init
                    Initialized empty Git repository in ~/analysis_code/.git/
                

                    ~/analysis_code $ ls
                    ~/analysis_code $ ls -A
                    .git

                    ~/analysis_code $ cd .git && ls -A
                    HEAD    config    description    hooks    index    info    logs    objects    packed-refs    refs
                

Try this yourself.

Adding files

                    ~/analysis_code $ touch README.md
                

                    ~/analysis_code $ git add README.md
                

                    ~/analysis_code $ git status
                

Try this yourself.

Committing changes

Snapshot of repository = revision

Committing a revision:

• Saves current state with a unique ID (hash)
• Names you as author
• Allows you to add a message

                    ~/analysis_code $ git commit
                

Try this yourself.

Options to save time:

                    ~/analysis_code $ git commit -m "This is my message"
                

                    ~/analysis_code $ git commit -am "This is my message
                                      committing all changes"
                

Commit messages:

Bad commit message:

                    Fixed bug
                

Good commit message:

                    Fixed bug in mass calculation

                    Due to incorrect density value, mass was being calculated
                    orders of magnitude larger than it should. The correct value
                    of density fixed this problem.
                

Image credit: xkcd

Viewing the history and differences

                    ~/analysis_code $ git log
                

                    ~/analysis_code $ git diff
                

Undoing work

Un-add a file:

                    ~/analysis_code $ git reset new-file.txt
                

Reset repository to previous commit:

                    ~/analysis_code $ git reset [mode] [commit]
                

Remove uncommitted changes:

                    ~/analysis_code $ git checkout -- README.md
                

Branches

                    ~/analysis_code $ git branch
                    * master

                    ~/analysis_code $ git branch experimental
                    ~/analysis_code $ git branch
                      experimental
                    * master

                    ~/analysis_code $ git branch new
                    ~/analysis_code $ git branch -d new

                    ~/analysis_code $ git checkout experimental
                    ~/analysis_code $ git branch
                    * experimental
                      master
                

Merging Branches

                    ~/analysis_code $ git checkout master
                    ~/analysis_code $ git merge experimental
                    ~/analysis_code $ git log