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##Software Carpentry Unix Instructor Crib Sheet ####Oklahoma State University, May 2015 ####Kate L Hertweck, University of Texas at Tyler

####Before class:

  • set up shell:
    • enlarge text size
    • export PS1='$ '
    • export PROMPT_COMMAND="history 1 >> ~/Dropbox/GitHistory.txt"
  • check software installation for git AND account with GitHub
  • need proxy?
  • get slides setup
  • remind students to register for GitHub account

####Reources

####SETUP Objectives: get system set up for proper attribution of your work

  • Slides: run locally, Git.pdf
  • open shell, can be anywhere
  • specify your name, to be recorded in commits
  • git config --global user.name "k8hertweck"
    • specify your email, to be recorded in commits
  • git config --global user.email "k8hertweck@gmail.com"
    • specify text editor, to be used in committing
    • nano: git config --global core.editor "nano -w"
    • text wrangler: git config --global core.editor "edit -w"
    • notepad++: git config --global core.editor "'c:/program files (x86)/Notepad++/notepad++.exe' -multiInst -notabbar -nosession -noPlugin"
    • kate: git config --global core.editor "kate"
  • --global means will apply for every command entered afterward
  • check settings: git config –list
  • syntax for git: git VERB

####CREATING A REPO (WORKING LOCALLY) Objectives: start tracking versions in a particular folder/directory (repository)

  • start in home directory
  • create directory and change directories
  • mkdir planets
  • cd planets
  • tell git where to store old records and versions of file
    • git init
  • list contents: ls
  • list everything (including hidden files)
    • ls -a
  • result is a subdirectory with information about project
  • if this is removed, we don't have access to versioning anymore
  • ask status of project
  • git status
  • output also adds helpful comments
  • Socrative question 1

####TRACKING CHANGES: Objectives: practice workflow (modify-add-commit), explain where information is stored

  • create new file: nano mars.txt
  • copy and add text, exit and save, ls, cat mars.txt
  • show status of project: git status
    • draw attention to "untracked files": there's something not being tracked
  • add file: git add mars.txt
  • git status draw attention to "Changes to be committed": it's tracking, but the changes aren't recorded
  • commit file: git commit -m "creating script"
    • commits record to history in .git, called a revision, with short identifier
    • run without -m and will open editor to add comment (you've specified your preference earlier today)
    • good commits: brief (<50 characters), for more info, add empty line (adds in separate field)
  • git status
  • check history: git log
    • lists all revisions in reverse chronological order: full identifier (relate to short identifier, same initial characters),
    • when created, log message
  • make another change (this is just one way): nano mars.txt, cat mars.txt
  • check status: git status
  • look at differences: git diff first line: old and new version of files, similar to diff command in Unix second line: labels for revisions third and fourth: name of file changing last lines: actual changes commit changes: git commit -m "adding change" but change hasn't been added!: git add, git commit working through staging nano morning.txt, make change, cat morning.txt look at differences: git diff stage file: git add morning.txt, git diff (no output) git diff –staged (shows differences) git commit -m, git status, git log git commit workflow Socrative question 2

####EXPLORING HISTORY Objectives: identify and use Git commit numbers, compare versions, restore old versions

compare different versions of commits HEAD1 (HEAD minus 1) and HEAD2 refer to old commits: most recent end of chain is HEAD git diff HEAD1 mars.txt git diff HEAD2 mars.txt git log gives strings of digits and letters: git diff XXXXXXXX mars.txt can also just use first few characters: git diff XXX mars.txt how to revert to old version? make another change, git status git checkout to remove unstaged changes (default to previous committed version) git checkout XXX mars.txt remember that you want changes before most recent commit Socrative question3

####IGNORING THINGS Objectives: ignore some files, why ignoring is useful

sometimes backup files are created by other programs, or intermediate files we don't want to track create dummy files mkdir results, touch a.dat b.dat c.dat results/a.out results b.out git status: lots of stuff needs to be committed, but we don't want to! nano .gitignore, add *.dat and results/ git status: now .gitignore is the only thing there! git add .gitignore, git commit -m “add ignore file”, git status git add a.dat: error git status --ignored

####REMOTES IN GITHUB Objectives: explain why remote repos, clone remote repos, push/pull

Github is cool because collaboration! we've been working in local repo, so we're the only ones who can see our work GitHub is a remote repo that can be published for other folks to see log in to GitHub, click icon in top right corner, create repo called “planets” resulting page has info about configuring repository, it's done the mkdir planets, cd planets, git init process remotely connect the two repos: copy https url to clipboard go to local repo (in shell): git remote add origin https://github.com/k8hertweck/planets git remote -v: check that it worked origin is a nickname for remote repo now send local changes to remote repo: git push origin master check remote repo, changes should be there. create README file and add brief comment about the purpose of the materials, commit change, go back to terminal: git pull origin master

####COLLABORATING Objectives: collaborate pushing to common repo

pair up students in your planets repo on GitHub, click settings, select collaborators, enter partner's username partner should cd to another directory (Desktop) and make copy of partner's repo: git clone https://github.com/vlad/planets.git collaborator should make changes, add, commit, git push origin master original owner can pull changes onto their machine

####CONFLICTS Objectives: explain when conflicts occur, resolve conflicts from a merge

each partner adds a (different) line to mars.txt, adds, commits, pushes to github the second push will fail failed pusher should: git pull origin master reconcile change and remove markers add, status, commit, push other partner can pull without additional changes needing to take place COLLABORATION EXERCISE collaboration tool: https://github.com/ouinformatics/git-collaboration students can fork the repo explain forking: making own copy of a repo that isn't owned by you make changes to one of the countries submit pull request to original owner

####OPEN SCIENCE can use version control as electronic lab notebook for computational work more open means more citation and reuse

####HOSTING where to put code and data? can do this yourself by purchasing domain and paying ISP to host can also use public service includes web interface, plus other functionalities: ability to collaborate, get DOI, academic folks can get free private repos for education

####LICENSING adding license and citation info choosing licenses licensing vs. social expectations

####WRAPPING UP sticky notes for summary link to materials on GitHub: http://software-carpentry.org/lessons.html reminders about hosting other workshops, becoming an instructor