diff --git a/includes/_git-basics.qmd b/includes/_git-basics.qmd index 37f731e..33626c8 100644 --- a/includes/_git-basics.qmd +++ b/includes/_git-basics.qmd @@ -1,76 +1,91 @@ In our work lives, we regularly work with files, either creating, -editing, moving, copying, or deleting them. These files can be -anything from text documents, to images, to code. When we work on these -files, we often make changes to them, and sometimes many changes. We -might want to keep track of these changes, so we can see *what* we've -done, *when* we did it, *why* we did it, and *who* did it. This is both helpful for -potential collaborators and our future selves. - -If a file has the ability to internally "track changes", like Word -does, you may have used that before, but likely only when getting -feedback from others. On the file level, you may have "tracked changes" -informally by saving multiple versions of a file with different names, -like in the example image below. - -![File naming in the commonly used *informal* 'version +editing, moving, copying, or deleting them. These files can be anything +from text documents, to images, to code. When we work on these files, we +often make changes to them, and sometimes many changes. We might want to +keep track of how our files change over time or "save" specific versions +of the files. This tracking of file changes over time is known as +*version control*. + +It can be useful to keep track of changes to files for many reasons. For +example, we might want to keep track of changes to a file so we can +revert back to a previous version of the file if we make a mistake or so +we can see how the file has changed over time. This is especially useful +when we are collaborating with others on a project, as we might want to +keep track of changes made or feedback given by different people. + +Tracking file changes is, however, also useful when we are working +mostly alone on a project, since we humans tend to forget things. This +could be why we made a certain change or what the file looked like at a +certain point in time (e.g., if we want to go back to an earlier version +of the file). + +If a file has the ability to internally "track changes", like Word does, +you may have used that before, maybe when getting feedback from others. +On the file level, you may have "tracked changes" informally by saving +multiple versions of a file with different names, like in the example +image below. + +![File naming in a commonly used *informal* 'version control'.](/images/informal-version-control.jpg) Does this way of saving files and keeping track of versions look -familiar? The above image may exaggerate how some people's versioning looks -like, but there is some truth to it: It is the most common approach to -"version control". +familiar? The above image may exaggerate what some people's versioning +looks like, but there is some truth to it: It is the most common +approach to "version control". This "informal" version control isn't ideal because it involves multiple copies of the same file. It makes it difficult to keep track of specific -changes and find the right version of the files. +changes and find the right version of the files. This also just +highlights the need for version control and the fact that it can be +difficult to keep track of file changes manually. -There are, however, "formal" version control systems that automatically -manage changes to files. One of the world's most popular version control -systems is called +Luckily for us, there exist "formal" version control systems that +automatically track changes to files. One of the world's most popular +version control systems is called [Git](https://git-scm.com/book/en/v2/Getting-Started-What-is-Git%3F). Git is used by millions of people around the world, including thousands of organisations and researchers. -With Git you can create snapshots of file changes, known as *commits*. Each commit -captures: +With Git you can create snapshots of file changes, known as *commits*. +Each commit captures: -- What specific changes were made to the file or files. -- Who made the changes to the files. -- When they made the changes to the files. +- *What* specific changes were made to the file or files. +- *Who* made the changes to the files. +- *When* they made the changes to the files. -Each commit also has a short message attached to it that can -describe *why* the changes were made. +Each commit also has a short message attached to it that can describe +*why* the changes were made. Git stores these commits in a history log. The history log allows you to quickly go back and explore the changes made to files, along with a message describing the changes. This is extremely useful when you -revisit your own work after a long time (because you *will* forget -things) and when you work in groups or with collaborators. +revisit your own work after a long time and when you work in groups or +with collaborators. Git only tracks changes to files *within a specific folder* (and it's -sub-folders). In Git terminology, this folder is called a -**repository** (or a *repo* for short). The best way to use a repository -is to store all files related to a specific project, like a research -project, in this repository (this folder). This way, you can track all -changes made to all files in the project. It keeps things more organised and +sub-folders). In Git terminology, this folder is called a **repository** +(or a *repo* for short). The best way to use a repository is to store +all files related to a specific project, like a research project, in +this repository (this folder). This way, you can track all changes made +to all files in the project. It keeps things more organised and self-contained, since everything related to a project is in one place. -Any type of file can be stored in the repository, including both -code and other non-code based files like Word or images. However, Git has -more features and tools for tracking specific changes when the file is +Any type of file can be stored in a repository, including both code and +other non-code based files like Word or images. However, Git has more +features and tools for tracking specific changes when the file is text-based, like a `.txt`, `.csv`, or code. Since these text-based files are literally only text characters, it is easier to track the changes to exact lines of text. Unlike files like images, or Word documents (that actually aren't just text), there are no "lines" to track changes on. -To understand how powerful formal version control like Git is, consider about these -questions: +To understand how powerful formal version control like Git is, consider +these questions: - How many files of different versions of a scientific document or thesis do you have laying around after getting feedback from your supervisor or co-authors? -- Have you ever wanted to test an analysis in a - file but ended up creating a new one to avoid modifying the original? +- Have you ever wanted to test an analysis in a file but ended up + creating a new one to avoid modifying the original? - Have you ever deleted something and wished you hadn't? - Have you ever forgotten what you were doing on a project, or why you chose a particular strategy or analysis? @@ -78,16 +93,17 @@ questions: All these problems can be fixed by using formal version control! There are many good reasons to use version control, especially in science: -- Transparency of work done to demonstrate or substantiate your - scientific claim and protect against accusations of fraud. -- Claim to first discovery, since you have a time-stamped history of - your work. -- Evidence of contributions and work, since who does what is tracked. -- Easier collaboration, because you can work on a single file/folder - in a single central location rather than emailing file versions - around. - Organized files and folders, since there is one single project folder and one single version of each file, rather than multiple versions of the same file. +- Ability to see previous versions of files using the history log. - Less time spent on finding things related to your projects, because everything is organized and in one place. +- Easier collaboration, because you can work on a single file/folder + in a single central location rather than emailing file versions + around. +- Transparency of work done to demonstrate or substantiate your + scientific claim and protect against accusations of fraud. +- Claim to first discovery, since you have a time-stamped history of + your work. +- Evidence of contributions and work, since who does what is tracked. diff --git a/includes/_github-basics.qmd b/includes/_github-basics.qmd index 20ac665..92d51c1 100644 --- a/includes/_github-basics.qmd +++ b/includes/_github-basics.qmd @@ -18,9 +18,9 @@ that use Git (meaning, Git repositories). This means that your Git repositories can be stored on GitHub, and you can manage your files and projects using Git through GitHub's web interface. -Everything we do in this workshop (including storing and managing files) -will be done through the GitHub website, which under the hood uses Git -to track the changes. +Everything we do in this workshop (including storing and managing files +and folders) will be done through the GitHub website, which uses Git +behind the scenes to track changes. In the simplest terms, GitHub is a company and website while Git is software. GitHub is a website that hosts Git repositories and builds on @@ -33,7 +33,7 @@ For instance: - Viewing the changes you've made in files is easier and nicer on GitHub than with Git. - Viewing the history log of changes is easier and more pleasant on - GitHub than on Git. + GitHub than only using Git. GitHub offers many tools to help you manage your project if its files are stored there. For instance, GitHub has "Issues" that allow you to @@ -47,28 +47,38 @@ benefit of being faster (you do work locally, so don't need to wait for the internet) and more flexible (you can do more things with Git on your computer than on GitHub). Then you can use GitHub as a place to keep backups of your repository, to track tasks, and to make use of the other -features GitHub has. How you would use Git with GitHub would look -something like @fig-git-sync-github. +features GitHub has. How you would use Git locally with GitHub would +look something like the figure below. ```{mermaid} %%| label: fig-git-sync-github %%| fig-cap: "How Git and GitHub can work together by synchronising changes between GitHub and your computer." %%| fig-alt: "A diagram showing two boxes, one of a Git repository on your computer and another of a Git repository on GitHub, along with an arrow between each box showing them synchronise between both." graph - github(Git repository
on GitHub) <-- Synch --> git(Git repository
on your computer) + github(Git repository
on GitHub) <-- Sync --> git(Git repository
on your computer) ``` +Using GitHub on its own is a great way to get started with Git. It +allows you to learn the concepts of version control and Git without +needing to install anything on your computer and without needing to +learn some of the more technical details of Git. Since GitHub is a +website it also makes it easier to share your work with others and to +collaborate with others. This is one of the main reasons why GitHub is +so popular. + ::: callout-note You may notice that GitHub sounds a bit like file synching tools such as OneDrive or Dropbox. So how is GitHub different? Unlike OneDrive or Dropbox, GitHub (via Git) tracks line-level changes to files, not just file-level changes. This means you can see the specific changes made in -a file, not just that it was changed. OneDrive and Dropbox also use a -simple way of handling conflicts when synching between the cloud and -your computer by either creating a new file with some details appending -to it or by overwriting which ever is newer. GitHub, on the other hand, -uses a more complex way of handling conflicts by showing you the changes -and asking you to resolve them. +a file, not just that it was changed. The messages you attach to commits +can also help you keep track of *why* the changes were made. + +OneDrive and Dropbox also use a simple way of handling conflicts when +synching between the cloud and your computer by either creating a new +file with some details appending to it or by overwriting which ever is +newer. GitHub, on the other hand, uses a more complex way of handling +conflicts by showing you the changes and asking you to resolve them. File synching tools are really good for easily sharing files within a team or group, but they aren't as good for collaboratively working diff --git a/pre-workshop/git-and-github.qmd b/pre-workshop/git-and-github.qmd index 5a0c411..fdd31c9 100644 --- a/pre-workshop/git-and-github.qmd +++ b/pre-workshop/git-and-github.qmd @@ -1,7 +1,9 @@ # Version control with Git and GitHub {#sec-git-and-github} This reading is meant as a primer to the workshop. It will introduce you -to the concepts of *version control*, *Git*, and *GitHub*. +to the concepts of *version control*, *Git*, and *GitHub* which are +central concepts of the workshop and to working with files on GitHub in +general. ## What is version control and Git? {#sec-what-is-version-control} @@ -17,7 +19,8 @@ to the concepts of *version control*, *Git*, and *GitHub*. track of changes to your files and projects. - A Git *repository* is a place where you store all the files for your project along with their history. -- GitHub is a website that hosts Git repositories. +- GitHub is a website that hosts Git repositories, allowing you to + store and share your files and projects online. - Through GitHub you can manage your files and projects using Git. diff --git a/pre-workshop/pre-survey.qmd b/pre-workshop/pre-survey.qmd index f1361b4..fbe62e7 100644 --- a/pre-workshop/pre-survey.qmd +++ b/pre-workshop/pre-survey.qmd @@ -4,7 +4,7 @@ If you haven't read the sections under "Workshop overview" and "Pre-workshop tasks", **please read them now**. Also make sure to read the [Code of -Conduct](https://guides.rostools.org/conduct.html), since the survey +conduct](https://guides.rostools.org/conduct.html), since the survey involves a question about it. We want to make sure this workshop is a supportive and safe environment for learning, so this is quite important.