In emlab-ucsb/adv_git: What the Package Does (One Line, Title Case)

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Outline

If you haven't, fork and clone the repo from: 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

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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

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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 NAs or NULLs 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:

**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

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Using tags

In the repo, try:

git tag

You should get:

v0.1
v0.2
v0.3

Not very informative, right?

---

Using tags

Now try:

git show v0.2

tag v0.3
Tagger: jcvdav <[e-mail]>
Date:   Mon Aug 19 16:27:56 2019 -0700

Tests working with more precision

commit c581a28de5a13d576654cf6ae6491142f551d9bf (tag: v0.3)
Author: jcvdav <[e-mail]>
Date:   Mon Aug 19 16:27:20 2019 -0700

    Updated tests for more precision

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Using tags

Now try

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

git logone

# short for
git log --pretty=oneline

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Repo tour

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Repo

-- adv.Rproj
-- basic_app
   |__app.R
   |__tests
-- DESCRIPTION
-- man
   |__gal2lit.Rd
-- NAMESPACE
-- R
   |__gal2lit.R
-- README.md
-- tests
   |__testthat
   |__testthat.R

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Tests

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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)

---

==> 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

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Well r rep(emo::ji("poop"), 7)

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??? r emo::ji("angry"))?

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

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:

git bisect reset #Exit bisect mode (go back to the present)

git show HASH #Check the changes of the guilty commit

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git bisect

Workflow: fixing

---

Let's fix the problem:

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

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

emlab-ucsb/adv_git documentation built on Nov. 4, 2019, 11:54 a.m.