Примітки для викладача

Using a software tool to handle the versions of your project files lets you focus on the more interesting/innovative aspects of your project.

  • Переваги контролю версій
    • Його легко встановити
    • Кожна копія репозиторію Git є повною резервною копією проєкту та його історії
    • A few easy-to-remember commands are all you need for most day-to-day version control tasks
    • The GitHub hosting service provides a web-based collaboration service
  • Два основних поняття
    • commit: a recorded set of changes in your project’s files
    • repository: the history of all your project’s commits
  • Why use GitHub?
    • No need for a server: easy to set up
    • GitHub’s strong community: your colleagues are probably already there

Overall

Контроль версій може бути найважливішою темою, яку ми викладаємо, але Git, безумовно, є найскладнішим інструментом. However, GitHub presently dominates the open software repository landscape, so the time and effort required to teach fundamental Git is justified and worthwhile.

Через цю складність, ми не вчимо початківців багатьом цікавим темам, такі як гілки, хеші так об’єкти комітів.

Instead we try to convince them that version control is useful for researchers working in teams or not, because it is

  • a better way to “undo” changes,
  • a better way to collaborate than mailing files back and forth, and
  • a better way to share your code and other scientific work with the world.

Teaching Notes

  • Ви можете “розділити” ваш термінал так, щоб останні команди залишалися в полі зору за допомогою цього скрипту.

  • Make sure the network is working before starting this lesson.

  • Drawings are particularly useful in this lesson: if you have a whiteboard, use it!

  • Version control is usually not the first subject in a workshop, so get learners to create a GitHub account after the session before. Remind learners that the username and email they use for GitHub (and setup during Git configuration) will be viewable to the public by default. However, there are many reasons why a learner may not want their personal information viewable, and GitHub has resources for keeping an email address private.

  • If some learners are using Windows, there will inevitably be issues merging files with different line endings. (Even if everyone’s on some flavor of Unix, different editors may or may not add a newline to the last line of a file.) Take a moment to explain these issues, since learners will almost certainly trip over them again. If learners are running into line ending problems, GitHub has a page that helps with troubleshooting. Specifically, the section on refreshing a repository may be helpful if learners need to change the core.autocrlf setting after already having made one or more commits.

  • We don’t use a Git GUI in these notes because we haven’t found one that installs easily and runs reliably on the three major operating systems, and because we want learners to understand what commands are being run. That said, instructors should demo a GUI on their desktop at some point during this lesson and point learners at this page.

  • Instructors should show learners graphical diff/merge tools like DiffMerge.

  • When appropriate, explain that we teach Git rather than CVS, Subversion, or Mercurial primarily because of GitHub’s growing popularity: CVS and Subversion are now seen as legacy systems, and Mercurial isn’t nearly as widely used in the sciences right now.

  • Further resources:

Automated Version Control

  • Ask, “Who uses ‘undo’ in their editor?” Всі скажуть: “Я”. ‘Undo’ is the simplest form of version control.

  • Give learners a five-minute overview of what version control does for them before diving into the watch-and-do practicals. Most of them will have tried to co-author papers by emailing files back and forth, or will have biked into the office only to realize that the USB key with last night’s work is still on the kitchen table. Instructors can also make jokes about directories with names like “final version”, “final version revised”, “final version with reviewer three’s corrections”, “really final version”, and, “come on this really has to be the last version” to motivate version control as a better way to collaborate and as a better way to back work up.

Налаштування Git

  • We suggest instructors and students use nano as the text editor for this lessons because

    • він працює у всіх трьох основних операційних системах
    • він працює всередині терміналу (перемикання вікон може заплутати учнів), та
    • it has shortcut help at the bottom of the window.

    Please point out to students during setup that they can and should use another text editor if they’re already familiar with it.

  • When setting up Git, be very clear what learners have to enter: it is common for them to edit the instructor’s details (e.g. email). Check at the end using git config --list.

  • When setting up the default branch name, if learners have a Git version older than 2.28, the default branch name can be changed for the lesson using git branch -M main if there are currently commits in the repository, or git checkout -b main if there are no commits/the repository is completely empty.

Створення репозиторію

  • When you do git status, Mac users may see a .DS_Store file showing as untracked. Це файл, який Mac OS створює в кожній директорії.

  • The challenge “Places to create repositories” tries to reinforce the idea that the .git folder contains the whole Git repo and deleting this folder undoes a git init. It also gives the learner the way to fix the common mistake of putting unwanted folders (like Desktop) under version control.

    Instead of removing the .git folder directly, you can choose to move it first to a safer directory and remove it from there:

    BASH 

    $ mv .git temp_git
$ rm -rf  temp_git

    The challenge suggests that it is a bad idea to create a Git repo inside another repo. Для додаткової дискусії на цю тему, будь ласка, дивіться це питання.

Tracking Changes

  • It’s important that learners do a full commit cycle by themselves (make changes, git diff, git add, and git commit). The “bio repository” challenge does that.

  • This is a good moment to show a diff with a graphical diff tool. If you skip it because you’re short on time, show it once in GitHub.

  • One thing may cause confusion is recovering old versions. If, instead of doing $ git checkout f22b25e mars.txt, someone does $ git checkout f22b25e, they wind up in the “detached HEAD” state and confusion abounds. It’s then possible to keep on committing, but things like git push origin main a bit later will not give easily comprehensible results. It also makes it look like commits can be lost. Щоб “повторно прикріпити” HEAD, використовуйте git checkout main.

  • This is a good moment to show a log within a Git GUI. If you skip it because you’re short on time, show it once in GitHub.

Ignoring Things

Just remember that you can use wildcards and regular expressions to ignore a particular set of files in .gitignore.

Віддалені репозиторії у GitHub

  • Make it clear that Git and GitHub are not the same thing: Git is an open source version control tool, GitHub is a company that hosts Git repositories in the web and provides a web interface to interact with repos they host.

  • It is very useful to draw a diagram showing the different repositories involved.

  • When pushing to a remote, the output from Git can vary slightly depending on what leaners execute. The lesson displays the output from git if a learner executes git push origin main. However, some learners might use syntax suggested by GitHub for pushing to a remote with an existing repository, which is git push -u origin main. Learners using syntax from GitHub, git push -u origin main, will have slightly different output, including the line Branch main set up to track remote branch main from origin by rebasing.

Співпраця

  • Decide in advance whether all the learners will work in one shared repository, or whether they will work in pairs (or other small groups) in separate repositories. The former is easier to set up; the latter runs more smoothly.

  • Role playing between two instructors can be effective when teaching the collaboration and conflict sections of the lesson. One instructor can play the role of the repository owner, while the second instructor can play the role of the collaborator. If it is possible, try to use two projectors so that the computer screens of both instructors can be seen. This makes for a very clear illustration to the students as to who does what.

  • It is also effective to pair up students during this lesson and assign one member of the pair to take the role of the owner and the other the role of the collaborator. In this setup, challenges can include asking the collaborator to make a change, commit it, and push the change to the remote repository so that the owner can then retrieve it, and vice-versa. The role playing between the instructors can get a bit “dramatic” in the conflicts part of the lesson if the instructors want to inject some humor into the room.

  • If you don’t have two projectors, have two instructors at the front of the room. Each instructor does their piece of the collaboration demonstration on their own computer and then passes the projector cord back and forth with the other instructor when it’s time for them to do the other part of the collaborative workflow. It takes less than 10 seconds for each switchover, so it doesn’t interrupt the flow of the lesson. And of course it helps to give each of the instructors a different-colored hat, or put different-colored sticky notes on their foreheads.

  • If you’re the only instructor, the best way to create is clone the two repos in your Desktop, but under different names, e.g., pretend one is your computer at work:

    BASH 

    $ git clone https://github.com/vlad/planets.git planets-at-work

  • It’s very common that learners mistype the remote alias or the remote URL when adding a remote, so they cannot push. You can diagnose this with git remote -v and checking carefully for typos.

    • To fix a wrong alias, you can do git remote rename <old> <new>.
    • To fix a wrong URL, you can do git remote set-url <alias> <newurl>.

  • Before cloning the repo, be sure that nobody is inside another repo. Найкращий спосіб досягти цього - перейти на Робочий стіл перед клонуванням: cd && cd Desktop.

  • If both repos are in the Desktop, have them to clone their collaborator repo under a given directory using a second argument:

    BASH 

    $ git clone https://github.com/vlad/planets.git vlad-planet

  • Найпоширенішою помилкою є те, що учні відправляють зміни перед тим, як отримати їх. If they pull afterward, they may get a conflict.

  • Conflicts, sometimes weird, will start to arise. Зберігайте спокій: конфлікти розглядаються у наступному епізоді.

  • Learners may have slightly different output from git push and git pull depending on the version of git, and if upstream (-u) is used.

Конфлікти

  • Очікуйте, що учні зроблять помилки. Очікуйте, що ви можете зробити помилки. Це відбувається тому, що урок триває вже достатньо довго і всі втомилися.

  • If you’re the only instructor, the best way to create a conflict is:

    • Clone your repo in a different directory, pretending is your computer at work: git clone https://github.com/vlad/planets.git planets-at-work.
    • At the office, you make a change, commit and push.
    • At your laptop repo, you (forget to pull and) make a change, commit and try to push.
    • git pull now and show the conflict.

  • Learners usually forget to git add the file after fixing the conflict and just (try to) commit. You can diagnose this with git status.

  • Памʼятайте, що можна відкинути одного з двох батьків злиття:

    • відкинути віддалений файл, git checkout --ours conflicted_file.txt
    • відкинути локальний файл, git checkout --theirs conflicted_file.txt

    Ви все ще повинні зробити git add та git commit після цього. Особливо це корисно при роботі з бінарними файлами.

  • Keep in mind that depending on the Git version used, the outputs for git push and git pull can vary slightly.

Відкрита наука

Ліцензування

We teach about licensing because questions about who owns what, or can use what, arise naturally once we start talking about using public services like GitHub to store files. Also, the discussion gives learners a chance to catch their breath after what is often a frustrating couple of hours.

The Creative Commons family of licenses is recommended for many types of works (including software documentation and images used in software) but not software itself. Creative Commons recommends a software-specific license instead.

Цитування

Хостинг

A common concern for learners is having their work publicly available on GitHub. Хоча ми заохочуємо відкриту науку, іноді приватні репо є єдиним вибором. Завжди цікаво згадати варіанти розміщення приватних репозиторіїв.

Автоматизований контроль версій

Налаштування Git

Створення репозиторію

Відстеження змін

Дослідження історії

Ігнорування файлів

Віддалені репозиторії у GitHub

Співпраця

Конфлікти

Відкрита наука

Ліцензування

Цитування

Хостинг

Додатково: Використання Git з RStudio