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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no" />
<title>reveal-md</title>
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<body>
<div class="reveal">
<div class="slides"><section ><section data-markdown><script type="text/template"># 2020-07-01 Software Carpentry Workshop: git
</script></section><section data-markdown><script type="text/template">
## Let me tell you a story...
</script></section><section data-markdown><script type="text/template">
### Once upon a time...
* Wolfman and Dracula were been hired to plan a Mars mission (obviously)
* Wolfman and Dracula live on different continents
* They work on the same plan at the same time
* How to manage this?
* take turns on each file?
* email copies?
* The solution? **Version Control**
</script></section><section data-markdown><script type="text/template">
### Advantage of version control
* Nothing that is committed is *ever* lost (unless you try…)
* We can record who made which changes, and when
* We can revert to previous versions.
* We can identify and correct conflicts
The lab notebook of code development.
</script></section></section><section ><section data-markdown><script type="text/template">
## Version control with `git`
</script></section><section data-markdown><script type="text/template">
### What lies ahead…?
</script></section><section data-markdown><script type="text/template">
### Learning objectives
* Understand the basics of automated version control
* Understand the basics of `git`
</script></section><section data-markdown><script type="text/template">
### Do you recognise this?
(i.e. have you *ever* worked on the same document as someone else?)
</script></section><section data-markdown><script type="text/template">
### How version control works
* Version control is like a 'recording' of history
* Rewind and play back changes
</script></section><section data-markdown><script type="text/template">
### Multiple editors (branching)
* Two people work on a document
* Each makes their changes: docs diverge
* Changes are separate from the document
</script></section><section data-markdown><script type="text/template">
### Combining changes (merging)
* Several changes can be merged onto the same base document
* 'Merging'
</script></section><section data-markdown><script type="text/template">
### What version control systems do
* Version control systems manage this process
* track changes
* store metadata (who, when)
* record 'versions' (a.k.a. *commits*)
* give you access to any of those versions
`git` is a version control system.
</script></section></section><section ><section data-markdown><script type="text/template">
## Setting up `git`
</script></section><section data-markdown><script type="text/template">
### Learning objectives
* Configure `git` for first use on a computer
* Understand `git config --global`
</script></section><section data-markdown><script type="text/template">
### Setting global options
* `git` needs to know who you are for metadata
* `git` wants your preferences for display/editing
**Live Presentation**
```
git config --global user.name "Vlad Dracul"
git config --global user.email "[email protected]"
git config --global color.ui "auto"
git config --global core.editor "nano -w"
```
</script></section></section><section ><section data-markdown><script type="text/template">
## Creating a repository
</script></section><section data-markdown><script type="text/template">
### Learning objectives
* Create a local `git` repository
* What is in a repository?
* files
* commits
* metadata
</script></section><section data-markdown><script type="text/template">
### Creating a `git` repository
* A fictional project about planets
* (Wolfman and Dracula…)
**Live Presentation**
```
git init
git status
```
</script></section></section><section ><section data-markdown><script type="text/template">
## Tracking changes
</script></section><section data-markdown><script type="text/template">
### Learning objectives
* Practice the modify-add-commit cycle
* Understand where information is stored, in the `git` workflow
</script></section><section data-markdown><script type="text/template">
### My first untracked file
* We'll create a file, but do nothing with it
* "Is Mars suitable as a space base?"
**Live Presentation**
```
nano mars.txt
```
</script></section><section data-markdown><script type="text/template">
### My first `git` commit
* We tell `git` that it should *track* a file (watch for changes): `git add`
* We also `git commit` the file (keep a copy of the file in the *repository*, in its current state)
**Live Presentation**
```
git add mars.txt
git commit -m "start notes on Mars as a base"
git log
```
</script></section><section data-markdown><script type="text/template">
### The staging area
* We don't always want to commit all changes
* The *staging area* holds changes we want to commit
* (other files may also be changed, but we don't want to commit them)
</script></section><section data-markdown><script type="text/template">
### modify-add-commit
* Now we want to add more information to the file
* Modify file
* Add file to *staging area* (`git add`)
* Commit changes
**Live Presentation**
```
nano mars.txt
git diff
git add mars.txt
git diff
git commit
```
</script></section><section data-markdown><script type="text/template">
### Question
- Which command(s) below would save changes in `myfile.txt` to the local `git` repository?
1. `git commit -m "add recent changes"`
2. `git init myfile.txt; git commit -m "add recent changes"`
3. `git add myfile.txt; git commit -m "add recent changes"`
4. `git commit -m myfile.txt "add recent changes"`
</script></section><section data-markdown><script type="text/template">
### Challenge 1 (5min)
* Make a one-line change to `mars.txt`.
* Create file `earth.txt` with one-line comment on Earth.
* Commit both changes (*as a **single*** `commit`)
</script></section><section data-markdown><script type="text/template">
### The modify-add-commit lifecycle
</script></section><section data-markdown><script type="text/template">
### In which I predict the future…
</script></section></section><section ><section data-markdown><script type="text/template">
## Exploring history
</script></section><section data-markdown><script type="text/template">
### Is history bunk?
* How can I identify old versions of files?
* How do I review changes between commits?
* How can I recover old file versions?
</script></section><section data-markdown><script type="text/template">
### Learning objectives
* Understand what the `HEAD` of a repository is
* Identify and use `git` commit numbers
* Compare various versions of tracked files
* Restore old versions of files
</script></section><section data-markdown><script type="text/template">
### Commit history
* Most recent commit: `HEAD`
* Next-most recent: `HEAD~1`
* Next-next-most recent: `HEAD~2`
</script></section><section data-markdown><script type="text/template">
### History with `git diff`
* We can use `git diff` to see what changed for a file at each commit
**Live Presentation**
```
git diff HEAD~1 mars.txt
git diff HEAD~2 mars.txt
```
</script></section><section data-markdown><script type="text/template">
### History with commit IDs
* We can use the unique ID for a commit in the same way
**Live Presentation**
```
git diff d22195b9ec3c8fb4c2ce0f52f344b95ce5d0d0e3 mars.txt
git diff d221 mars.txt
```
</script></section><section data-markdown><script type="text/template">
### Restoring older versions
* How can we restore older versions/backtrack?
* Let's say we accidentally overwrite a file…
**Live Presentation**
```
git checkout HEAD mars.txt
```
</script></section><section data-markdown><script type="text/template">
### `git checkout`
* `git checkout` "checks out" files from the repo
* Can use any commit identifier
* Check out the commit *before* the edit you want to replace!
</script></section><section data-markdown><script type="text/template">
### Question
- Which command(s) below will let Jennifer recover the last committed version of her Python script called `data_cruncher.py` (but no other files)?
1. `$ git checkout HEAD`
2. `$ git checkout HEAD data_cruncher.py`
3. `$ git checkout HEAD~1 data_cruncher.py`
4. `$ git checkout <unique ID of last commit> data_cruncher.py`
</script></section></section><section ><section data-markdown><script type="text/template">
## Ignoring things
</script></section><section data-markdown><script type="text/template">
### Learning objectives
* Configure `git` to ignore files and directories
* Understand why this is useful
</script></section><section data-markdown><script type="text/template">
### Not all files are useful
* Editor backup files
* Temporary files
* Intermediate analysis files
**Live Presentation**
```
mkdir results
touch a.dat results/a.out
```
</script></section><section data-markdown><script type="text/template">
### `.gitignore`
* `.gitignore` is a special file in your repository root
* It tells `git` to ignore specified files/directories
* It should be committed in your repository
**Live Presentation**
```
nano .gitignore
git status --ignored
git add -f b.dat
```
</script></section></section><section ><section data-markdown><script type="text/template">
## Remotes in GitHub
</script></section><section data-markdown><script type="text/template">
### Learning objectives
* What remote repositories are and why they are useful
* To clone a remote repository
* To push to and pull from a remote repository
</script></section><section data-markdown><script type="text/template">
### Remote repositories
* Version control most useful for collaboration
* Easiest to have a single repository
* Repository may be hosted off-site (for at least one collaborator)
* Services available:
* GitHub, BitBucket, GitLab
* We're using GitHub
</script></section><section data-markdown><script type="text/template">
### GitHub Saved My Life!
</script></section><section data-markdown><script type="text/template">
### Log in to GitHub
* Register for an account, if you don't have one - then log in
</script></section><section data-markdown><script type="text/template">
### Create a remote repository
* Essentially, on GitHub's servers:
```
mkdir planets
cd planets
git init
```
**Live Presentation**
</script></section><section data-markdown><script type="text/template">
### A freshly-made GitHub repository
* There's nothing in the remote repository!
</script></section><section data-markdown><script type="text/template">
### Connecting local and remote repositories
* We tell the *local* repository that the GitHub repository is its *remote* repository.
* `origin` is a local nickname for the remote repo (a common choice)
* Once set up, we *push* changes/history to the remote repo
**Live Presentation**
```
git remote add origin https://github.com/widdowquinn/planets.git
git push origin master
```
</script></section><section data-markdown><script type="text/template">
### Remote GitHub repo after first *push*
* We only *push* the repository, not the staging area
</script></section><section data-markdown><script type="text/template">
### My first remote *pull*
* To synchronise the local repo with the remote repo, we *pull*
**Live Presentation**
```
git pull origin master
```
</script></section></section><section ><section data-markdown><script type="text/template">
## GitHub collaboration
</script></section><section data-markdown><script type="text/template">
### Learning objectives
* Collaborate pushing changes to someone else's remote repository
</script></section><section data-markdown><script type="text/template">
### Starting a collaboration
* Pair up as 'owner' and 'collaborator'
- doing this remotely will be fine
* as _owner_: give GitHub repo access to your collaborator
* as *collaborator*: clone the _owner's_ repo
```
cd /tmp/
git clone https://github.com/<collaborator>/planets.git
git remote -v
```
</script></section><section data-markdown><script type="text/template">
### Make a collaborative change
**Collaborator:**
* Add a file called `pluto.txt` - (content your own)
* Commit that file and push your commits
```
cd planets
nano pluto.txt
git add pluto.txt
git commit -m "Notes on Pluto"
git push origin master
```
</script></section><section data-markdown><script type="text/template">
### Pull a collaborator's change
**Owner:**
* Change back to your **own** repository
* Check with `git remote -v`
* `git pull` the changes made by your collaborator
```
cd ~/planets/
git pull origin master
```
</script></section></section><section ><section data-markdown><script type="text/template">
## Resolving `git` conflicts
</script></section><section data-markdown><script type="text/template">
### Learning objectives
* Understand what conflicts are, and when they occur
* To be able to resolve conflicts resulting from a merge
</script></section><section data-markdown><script type="text/template">
### Why conflicts occur
* People working in parallel
* different changes to same part of a file
* not keeping local repo in sync before making local changes
* not keeping remote repo in sync after making local changes
* `git pull` before working; `git push` when done
</script></section><section data-markdown><script type="text/template">
### Seriously, `git push` when done…
</script></section><section data-markdown><script type="text/template">
### Let's make a conflict
**in your pairs**
* As the *owner*: add a line to `mars.txt`
* Commit and push the change
**then**
* As the *collaborator*: add a line to `mars.txt`
* Commit and push the change
```
cd ~/planets
nano mars.txt
git push origin master
cd /tmp/planets
nano mars.txt
git push origin master
```
</script></section><section data-markdown><script type="text/template">
### The conflict message
```
To https://github.com/<collaborator>/planets.git
! [rejected] master -> master (fetch first)
error: failed to push some refs to 'https://github.com/<collaborator>/planets.git'
hint: Updates were rejected because the remote contains work that you do
hint: not have locally. This is usually caused by another repository pushing
hint: to the same ref. You may want to first integrate the remote changes
hint: (e.g., 'git pull ...') before pushing again.
hint: See the 'Note about fast-forwards' in 'git push --help' for details.
```
</script></section><section data-markdown><script type="text/template">
### The conflicting changes
</script></section><section data-markdown><script type="text/template">
### Resolving a conflict
* `git` detects overlapping changes
* `git` defers to humans for how to resolve: **communicate**!
* To resolve:
* *pull* remote changes
* *merge* changes into our working copy
* *push* the merged changes
</script></section></section><section ><section data-markdown><script type="text/template">
## Wrapping up
* GitHub/version control can be an open electronic lab book as part of Open Science workflows
* Collect data - store in OA repository (Zenodo/FigShare)
* Use GitHub to store work in progress: analysis lab book
* Post preprint to (Bio)arXiv
* Even if you don't work openly, it's more reproducible (and auditable)
</script></section><section data-markdown><script type="text/template">
### You're ready to leave this behind…
</script></section></section></div>
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