Testing.rmd

---
title: Testing
layout: default
---

# Testing

Testing is important to make sure that your package behaves as you expect it to do. You probably test your code already, but you may not have taken the next step to automate it. This chapter describes how to use the `testthat` package to create automated tests for your code.

## Motivation

I started automating my tests because I discovered I was spending too much time recreating bugs that I had previously fixed. While I was writing the original code or fixing the bug, I'd perform many interactive tests to make sure the code worked, but I never had a system for retaining these tests and running them, again and again. I think that this is a common development practice of R programmers: it's not that we don't test our code, it's that we don't store our tests so they can be re-run automatically.

It will always require a little more work to turn your casual interactive tests into reproducible scripts: you can no longer visually inspect the output, so instead you have to write code that does the inspection for you. However, this is an investment in the future of your code that will pay off in:

* Decreased frustration. Whenever I'm working to a strict deadline I always
  seem to discover a bug in old code. Having to stop what I'm doing to fix the
  bug is a real pain. This happens less when I do more testing, and I can
  easily see which parts of my code I can be confident in by looking at how
  well they are tested.

* Better code structure. Code that's easy to test is usually better designed.
  I have found writing tests makes me extract out the complicated parts of my
  code into separate functions that work in isolation. These functions are
  easier to test, have less duplication, are easier to understand and are
  easier to re-combine in new ways.

* Less struggle to pick up development after a break. If you always finish a
  session of coding by creating a failing test (e.g. for the feature you want
  to implement next) it's easy to pick up where you left off: your tests let
  you know what to do next.

* Increased confidence when making changes. If you know that all major
  functionality has a test associated with it, you can confidently make big
  changes with out worrying about accidentally breaking something. For me,
  this is particularly useful when I think of a simpler way to accomplish a
  task - often my simpler solution is only simpler because I've forgotten an
  important use case!

## testthat test structure

`testthat` has a hierarchical structure made up of expectations, tests and contexts. 

* An __expectation__ describes the expected result of a computation: Does it
  have the right value and right class? Does it produce error messages when it
  should? There are 11 types of built in expectations.

* A __test__ groups together multiple expectations to test one function, or
  tightly related functionality across multiple functions. A test is created
  with the `test_that` function.

* A __context__ groups together multiple tests that test related
  functionality.  Contexts are defined with the `context()` function.

These are described in detail below. 

Expectations give you the tools to convert your visual, interactive
experiments into reproducible scripts; tests and contexts are ways of
organising your expectations so that when something goes wrong you can easily
track down the source of the problem.

### Expectations

An expectation is the finest level of testing; it makes a binary assertion about whether or not a value is as you expect. If the expectation isn't true, `testthat` will raise an error.

An expectation is easy to read, since it is nearly a sentence already: `expect_that(a, equals(b))` reads as "I expect that a will equal b". 

There are 11 built in expectations:

* `equals()` uses `all.equal()` to check for equality with numerical tolerance.

      # Passes 
      expect_that(10, equals(10)) 
      # Also passes
      expect_that(10, equals(10 + 1e-7))  
      # Fails
      expect_that(10, equals(10 + 1e-6))  
      # Definitely fails! 
      expect_that(10, equals(11)) 
  
* `is_identical_to()` uses `identical()` to check for exact equality.

      # Passes
      expect_that(10, is_identical_to(10)) 
      # Fails
      expect_that(10, is_identical_to(10 + 1e-10))  

* `is_equivalent_to()` is a more relaxed version of `equals()` that ignores
  attributes:

      # Fails
      expect_that(c("one" = 1, "two" = 2), equals(1:2))
      # Passes
      expect_that(c("one" = 1, "two" = 2), is_equivalent_to(1:2))

* `is_a()` checks that an object `inherit()`s from a specified class.

      model <- lm(mpg ~ wt, data = mtcars)
      # Passes
      expect_that(model, is_a("lm"))  
      # Fails 
      expect_that(model, is_a("glm")) 

* `matches()` matches a character vector against a regular expression. The
  optional `all` argument controls whether all elements or just one element need
  to match. This code is powered by `str_detect()` from the `stringr`
  package.

      string <- "Testing is fun!"
      # Passes
      expect_that(string, matches("Testing")) 
      # Fails, match is case-sensitive
      expect_that(string, matches("testing")) 
      # Passes, match can be a regular expression
      expect_that(string, matches("t.+ting")) 

* `prints_text()` matches the printed output from an expression against a
  regular expression.

      a <- list(1:10, letters)
      # Passes
      expect_that(str(a), prints_text("List of 2"))
      # Passes
      expect_that(str(a), prints_text(fixed("int [1:10]"))

* `shows_message()` checks that an expression shows a message:

      # Passes
      expect_that(library(mgcv), shows_message("This is mgcv"))

* `gives_warning()` expects that you get a warning.

      # Passes
      expect_that(log(-1), gives_warning())
      expect_that(log(-1), 
        gives_warning("NaNs produced"))
      # Fails
      expect_that(log(0), gives_warning())

* `throws_error()` verifies that the expression throws an error. You can also
  supply a regular expression which is applied to the text of the error.

      # Fails
      expect_that(1 / 2, throws_error()) 
      # Passes
      expect_that(1 / "a", throws_error()) 
      # But better to be explicit
      expect_that(1 / "a", throws_error("non-numeric argument"))

* `is_true()` is a useful catchall if none of the other expectations do what
  you want - it checks that an expression is true. `is_false()` is the
  complement of `is_true()`.

If you don't like the readable, but verbose, `expect_that` style, you can use one of the shortcut functions:

<table>
  <tr>
    <th>Full</th><th>Abbreviation</th>
  </tr>
  <tr><td><code>expect_that(x, is_true())</code></td><td><code>expect_true(x)</code></td></tr>
  <tr><td><code>expect_that(x, is_false())</code></td><td><code>expect_false(x)</code></td></tr>
  <tr><td><code>expect_that(x, is_a(y))</code></td><td><code>expect_is(x, y)</code></td></tr>
  <tr><td><code>expect_that(x, equals(y))</code></td><td><code>expect_equal(x, y)</code></td></tr>
  <tr><td><code>expect_that(x, is_equivalent_to(y))</code></td><td><code>expect_equivalent(x, y)</code></td></tr>
  <tr><td><code>expect_that(x, is_identical_to(y))</code></td><td><code>expect_identical(x, y)</code></td></tr>
  <tr><td><code>expect_that(x, matches(y))</code></td><td><code>expect_match(x, y)</code></td></tr>
  <tr><td><code>expect_that(x, prints_text(y))</code></td><td><code>expect_output(x, y)</code></td></tr>
  <tr><td><code>expect_that(x, shows_message(y))</code></td><td><code>expect_message(x, y)</code></td></tr>
  <tr><td><code>expect_that(x, gives_warning(y))</code></td><td><code>expect_warning(x, y)</code></td></tr>
  <tr><td><code>expect_that(x, throws_error(y))</code></td><td><code>expect_error(x, y)</code></td></tr>
</table>

Running a sequence of expectations is useful because it ensures that your code behaves as expected. You could even use an expectation within a function to check that the inputs are what you expect. However, they're not so useful when something goes wrong: all you know is that something is not as expected, not anything about where the problem is. Tests, described next, organise expectations into coherent blocks that describe the overall goal of a set of expectations.

### Tests

Each test should test a single item of functionality and have an informative name. The idea is that when a test fails, you should know exactly where to look for the problem in your code. You create a new test with `test_that`, with parameters name and code block. The test name should complete the sentence "Test that" and the code block should be a collection of expectations. When there's a failure, it's the test name that will help you figure out what's gone wrong.

The following code shows one test of the `floor_date` function from `lubridate`. There are 7 expectations that check the results of rounding a date down to the nearest second, minute, hour, etc. Note how we've defined a couple of helper functions to make the test more concise so you can easily see what changes in each expectation.

    test_that("floor_date works for different units", {
      base <- as.POSIXct("2009-08-03 12:01:59.23", tz = "UTC")

      is_time <- function(x) equals(as.POSIXct(x, tz = "UTC"))
      floor_base <- function(unit) floor_date(base, unit)

      expect_that(floor_base("second"), is_time("2009-08-03 12:01:59"))
      expect_that(floor_base("minute"), is_time("2009-08-03 12:01:00"))
      expect_that(floor_base("hour"),   is_time("2009-08-03 12:00:00"))
      expect_that(floor_base("day"),    is_time("2009-08-03 00:00:00"))
      expect_that(floor_base("week"),   is_time("2009-08-02 00:00:00"))
      expect_that(floor_base("month"),  is_time("2009-08-01 00:00:00"))
      expect_that(floor_base("year"),   is_time("2009-01-01 00:00:00"))
    })

Each test is run in its own environment so it is self-contained. The exceptions are actions which have effects outside the local environment. These include things that affect:

* the filesystem: creating and deleting files, changing the working directory,
  etc.

* the search path: package loading \& detaching, {\tt attach}.

* global options, like `options()` and `par()`.

When you use these actions in tests, you'll need to clean up after yourself. Many other testing packages have set-up and teardown methods that are run automatically before and after each test. These are not so important with `testthat` because you can create objects outside of the tests and rely on R's copy-on-modify semantics to keep them unchanged between test runs. To clean up other actions you can use regular R functions.

You can run a set of tests just by `source()`ing a file, but as you write more and more tests, you'll probably want a little more infrastructure. The first part of that infrastructure is contexts, described below, which give a convenient way to label each file, helping to locate failures when you have many tests.

## Contexts

Contexts group tests together into blocks that test related functionality, and are established with the code `context("My context")`. Normally there is one context per file, but you can have more if you want, or you can use the same context in multiple files.

The following code shows the context that tests the operation of the `str_length()` function in `stringr`. The tests are very simple, but cover two situations where `nchar()` in base R gives surprising results.

    context("String length")

    test_that("str_length is number of characters", {
      expect_that(str_length("a"), equals(1))
      expect_that(str_length("ab"), equals(2))
      expect_that(str_length("abc"), equals(3))
    })

    test_that("str_length of missing is missing", {
      expect_that(str_length(NA), equals(NA_integer_))
      expect_that(str_length(c(NA, 1)), equals(c(NA, 1)))
      expect_that(str_length("NA"), equals(2))
    })

    test_that("str_length of factor is length of level", {
      expect_that(str_length(factor("a")), equals(1))
      expect_that(str_length(factor("ab")), equals(2))
      expect_that(str_length(factor("abc")), equals(3))
    })

## Running tests

There are two situations in which you want to run your tests: interactively while you're developing your package to make sure that everything works ok, and then as a final automated check before releasing your package. 

* run all tests in a file or directory `test_file()` or `test_dir()`

* automatically run tests whenever something changes with `autotest`.

* have `R CMD check` run your tests.

### Testing files and directories

You can run all tests in a file with `test_file(path)`. The following code shows the difference between `test_file` and `source` for the `stringr` tests, as well as those same tests for `nchar`. You can see the advantage of `test_file` over `source`: instead of seeing the first failure, you see the performance of all tests.

    > source("test-str_length.r")
    > test_file("test-str_length.r")
    .........

    > source("test-nchar.r")
    Error: Test failure in 'nchar of missing is missing'
    * nchar(NA) not equal to NA_integer_
    'is.NA' value mismatch: 0 in current 1 in target
    * nchar(c(NA, 1)) not equal to c(NA, 1)
    'is.NA' value mismatch: 0 in current 1 in target

    > test_file("test-nchar.r")
    ...12..34

    1. Failure: nchar of missing is missing ---------------------------------
    nchar(NA) not equal to NA_integer_
    'is.NA' value mismatch: 0 in current 1 in target

    2. Failure: nchar of missing is missing ---------------------------------
    nchar(c(NA, 1)) not equal to c(NA, 1)
    'is.NA' value mismatch: 0 in current 1 in target

    3. Failure: nchar of factor is length of level --------------------------
    nchar(factor("ab")) not equal to 2
    Mean relative difference: 0.5

    4. Failure: nchar of factor is length of level --------------------------
    nchar(factor("abc")) not equal to 3
    Mean relative difference: 0.6666667

Each expectation is displayed as either a green dot (indicating success) or a red number (including failure). That number indexes into a list of further details, printed after all tests have been run. What you can't see is that this display is dynamic: new dot is printed each time a test passes, and it's rather satisfying to watch.

`test_dir` will run all of the test files in a directory, assuming that test files start with `test` (so it's possible to intermix regular code and tests in the same directory). This is handy if you're developing a small set of scripts rather than a complete package. The following shows the output from the `stringr` tests. You can see there are 12 contexts with between 2 and 25 expectations each. As you'd hope in a released package, all the tests pass.

    > test_dir("inst/tests/")
    String and pattern checks : ......
    Detecting patterns : .........
    Duplicating strings : ......
    Extract patterns : ..
    Joining strings : ......
    String length : .........
    Locations : ............
    Matching groups : ..............
    Test padding : ....
    Splitting strings : .........................
    Extracting substrings : ...................
    Trimming strings : ........

If you want a more minimal report, suitable for display on a dashboard, you can use a different reporter. `testthat` comes with three reporters: stop, minimal and summary. The stop reporter is the default and `stop()`s whenever a failure is encountered, and the summary report is the default for `test_file` and `test_dir`. The minimal reporter is shown below: it prints `.` for success, `E` for an error and `F` a failure. The following output shows the results of running the `stringr` test suite with the minimal reporter.

    > test_dir("inst/tests/", reporter="minimal")
    ...............................................

### Autotest

Tests are most useful when run frequently, and `autotest` takes that idea to the limit by rerunning your tests whenever your code or tests changes. `autotest()` has two arguments, `code_path` and `test_path`, which point to a directory of source code and tests respectively.

Once run, `autotest()` will continuously scan both directories for changes. If a test file is modified, it will test that file; if a code file is modified, it will reload that file and rerun all tests. To quit, you'll need to press Ctrl + Break on windows, Escape in the mac gui, or Ctrl + C if running from the command line.

This promotes a workflow where the _only_ way you test your code is through tests. Instead of modify-save-source-check you just modify and save, then watch the automated test output for problems.

## R CMD check

When developing a package, put your tests in `inst/tests` (note that your test files must begin with `test`), and then create a file `tests/run-all.R` (note that it must be a capital R), which contains the following code:

    library(testthat)
    library(mypackage)
    
    test_package("mypackage")

This will evaluate your tests in the package namespace (so you can test non-exported functions), and it will throw an error if there are any test failures. This means you'll see the full report of test failures and `R CMD check` won't pass unless all tests pass.

This also makes it easy for your users to check that you package works correctly in their run-time environment.