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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="" xml:lang="">
<head>
<title>Advanced git</title>
<meta charset="utf-8" />
<meta name="author" content="🐝, 🐜, 🐞, 🐝, 🐞, 🐞, 🐝" />
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<textarea id="source">
class: center, middle, inverse, title-slide
# Advanced <code>git</code>
## Best practices and debugging
### 🐝, 🐜, 🐞, 🐝, 🐞, 🐞, 🐝
### SFG
### 2019/08/21
---
# Outline
If you haven't, `fork` and `clone` the repo from: [https://github.com/emlab-ucsb/adv_git.git](https://github.com/emlab-ucsb/adv_git.git)
- Boring
- Best practices
- Hands-on
- Repo tour
- Tests
- functions / packages
- `shiny` Apps
- Finding the error
- Fixing the error
---
class: center, middle, inverse
# Best practices
---
# Use the terminal
- It doesn't have to be scary
- You'll mostly use `pull`, `add`, `commit`, and `push`
- It forces you to think about what you have to `stage` and `commit`
- It's good to get comfortable, especially when you have to fix a repo
---
# Commit frequency
- Try to keep commits as small as possible
- Don't just `stage` all and `commit` "updated repo" (we all do it)
- If possible, break it down to files / topics / improvements
- If possible, break it down to sections within a file
- You don't have to `push` all your changes
- `commit` through the day, and `push` at the end
---
# Testing your code
Create tests for possible breaks:
- Test for data integrity
- Number of records
- Dimensions of a key `data.frame`
- Dates in your `Raster*` objects
- Test for function behavior
- Returns correct output
- Handles `NA`s or `NULL`s correctly
- Test for know breaks
--
**Test before pushing big changes**
---
# Using tags
If something (ever) works, mark it!
- After your `commit`, you can do:
`git tag -a version -m "message"`
For example:
```bash
**run tests in R**
git add scripts/foo.R #Stages the foo.R script
git commit -m "Added foo.R script" #This is our commit message
git tag -a v0.1 -m "foo.R working" #Add a tagg and a message
```
---
# Using tags
In the repo, try:
`git tag`
You should get:
```bash
v0.1
v0.2
v0.3
```
Not very informative, right?
---
# Using tags
Now try:
`git show v0.2`
```bash
tag v0.3
Tagger: jcvdav <juancarlos.villader@gmail.com>
Date: Mon Aug 19 16:27:56 2019 -0700
Tests working with more precision
commit c581a28de5a13d576654cf6ae6491142f551d9bf (tag: v0.3)
Author: jcvdav <juancarlos.villader@gmail.com>
Date: Mon Aug 19 16:27:20 2019 -0700
Updated tests for more precision
```
---
# Using tags
Now try
```bash
git logline
# that's a shortcut for
git log --graph --pretty=format:'%Cred%h%Creset -%C(yellow)%d%Creset %s %Cgreen(%cr) %C(bold blue)<%an>%Creset' --abbrev-commit
```
or
```bash
git logone
# short for
git log --pretty=oneline
```
---
class: center, middle, inverse
# Repo tour
---
# Repo
```
-- adv.Rproj
-- basic_app
|__app.R
|__tests
-- DESCRIPTION
-- man
|__gal2lit.Rd
-- NAMESPACE
-- R
|__gal2lit.R
-- README.md
-- tests
|__testthat
|__testthat.R
```
---
class: center, middle, inverse
# Tests
---
# Shiny Apps
- The shiny app is under `basic_app/app.R`
- Run `shiny::runApp("basic_app")` or open the file and run the app
- Stop the instance
- Now let's run the tests:
- Run `shinytest::testApp("basic_app")` or
- Open the `app.R` file
- Top-right corner, click on `Run App` >> `Run Tests`
- Top-right corner, click on `Compare Results`
- Inspect the differences:
- The app is not returning the correct conversion of gallons to liters
- But is this an error in the app, or in the underlying code?
---
# Packages / functions
- In your root directory for the repo, look for a `tests` folder
- There is a `testthat.R` file, and folder with the same name
- Open `tests/testthat/test_gal2lit.R`
- To test the package (*i.e.* run all tests):
- You can run `devtools::test()`
- Take advantage of the Rstudio IDE:
- Go to the `Build` pane
- Click on `More`
- Select `Test package` (or simply `Ctrl` + `Shift` + `T`)
---
```bash
==> devtools::test()
Loading adv
Testing adv
v | OK F W S | Context
x | 0 2 | gal2lit converts correctly
---------------------------------------------
test_gal2lit.R:8: failure: gal2lit
gal2lit(1) not equal to 3.78541.
1/1 mismatches
[1] 3.79 - 3.79 == -0.00041
test_gal2lit.R:9: failure: gal2lit
gal2lit(1/3.78541) not equal to 1.
1/1 mismatches
[1] 1 - 1 == -0.000108
---------------------------------------------
v | 3 | gal2lit handles input types
== Results ==================================
OK: 3
Failed: 2
Warnings: 0
Skipped: 0
```
---
class: center, middle, inverse
# Well 💩, 💩, 💩, 💩, 💩, 💩, 💩
Turns out our basic function is not working...
Now what?
We (sort of?) know *where* the error is (this is an easy one)
But *when* / *how* / *why* / (**who???** 😠)?
Enter: `git bisect`
---
# `git bisect`
## Why not go into GitHub?
- You want to be able to track incremental changes
- Let's you see how changes relate to tests / status of the repo
- If you use the `git bisect` approach, no need to leave RStudio!
---
# `git bisect`
## What does it do?
- You start by telling it that the present commit (state of the repo) is `bad`
- You then tell it when things worked (remember `tags`?)
- It choses a point (roughly) between them and checks out a version of how things looked like
- Then, you iterate:
- Running your tests
- Tagging each commit as `good` or `bad`
- `git bisect` will advance in the logical direction
- Do until it finds the last good commit
---
# `git bisect`
## Workflow: finding
```bash
git logline #To see the history
git bisect start #Start bisecting
git bisect bad #Tagg current state as bad
git bisect good HASH / tag #Specify a state where things worked
# git bisect will take you to somewhere in the middle
**Run tests in R**
# If it works
git bisect good
#marks this point as working and moves forward in time
# If it fails
git bisect bad
#marks this pointas not working and moves backward in time
**Run tests in R**
... #Until test pass
```
---
# `git bisect`
## Workflow: fixing
We know *when* (*i.e.* HASH) things changed, let's dig deeper:
```bash
git bisect reset #Exit bisect mode (go back to the present)
git show HASH #Check the changes of the guilty commit
```
---
# `git bisect`
## Workflow: fixing
---
Let's fix the problem:
```bash
git branch #To check existing branches
git checkout -b fix_bug #To create a new branch and switch into it
git revert HASH #Will undo changes in that commit
# It is equivalent to just making the change yourself
# in `gal2lit.R` and `add` and `commit` the result
**Run tests in R**
```
---
# `git bisect`
## Workflow
```bash
git checkout master #Get back to master branch
git branch #Confirm that you are on master
git merge fix_bug master #Bring the changes in fix_bug into master
**Run tests in R** #optional, at this point
git tag -a vx.x -m "Fixed bug" #(Optionally, add a tag)
git push #Push changes
```
</textarea>
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