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Discuss code-local testing

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hyginn 2020-09-25 00:25:15 +10:00
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1 changed files with 27 additions and 11 deletions
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RPR-Unit_testing.R
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@ -1,20 +1,15 @@
# tocID <- "RPR-Unit_testing.R" # tocID <- "RPR-Unit_testing.R"
# #
# ---------------------------------------------------------------------------- #
# PATIENCE ... #
# Do not yet work wih this code. Updates in progress. Thank you. #
# boris.steipe@utoronto.ca #
# ---------------------------------------------------------------------------- #
#
# Purpose: A Bioinformatics Course: # Purpose: A Bioinformatics Course:
# R code accompanying the RPR-Unit_testing unit. # R code accompanying the RPR-Unit_testing unit.
# #
# Version: 1.1 # Version: 1.2
# #
# Date: 2017 10 - 2019 01 # Date: 2017 10 - 2019 01
# Author: Boris Steipe (boris.steipe@utoronto.ca) # Author: Boris Steipe (boris.steipe@utoronto.ca)
# #
# Versions: # Versions:
# 1.2 2020 Updates. Discuss local tests.
# 1.1 Change from require() to requireNamespace() # 1.1 Change from require() to requireNamespace()
# 1.0 New code # 1.0 New code
# #
@ -35,10 +30,11 @@
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> ------------------------------------------------- #TOC> -------------------------------------------------
#TOC> 1 Unit Tests with testthat 46 #TOC> 1 Unit Tests with testthat 42
#TOC> 2 Organizing your tests 165 #TOC> 2 Organizing your tests 165
#TOC> 2.1 Testing scripts 189 #TOC> 2.1 Testing scripts 189
#TOC> 3 Task solutions 204 #TOC> 2.2 Rethinking testing 202
#TOC> 3 Task solutions 220
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -56,7 +52,7 @@ if (! requireNamespace("testthat", quietly = TRUE)) {
# data(package = "testthat") # available datasets # data(package = "testthat") # available datasets
# testthat is one of those packages that we either use A LOT in a script, # testthat is one of those packages that we either use A LOT in a script,
# or not at all. Therfore it's more reasonable to depart from our usual # or not at all. Therefore it's more reasonable to depart from our usual
# <package>::<function>() idiom, and load the entire library. In fact, if # <package>::<function>() idiom, and load the entire library. In fact, if
# we author packages, it is common practice to load testthat in the part # we author packages, it is common practice to load testthat in the part
# of the package that automates testing. # of the package that automates testing.
@ -122,7 +118,8 @@ expect_error(log(v[1,2])) # This appears oK, but ...
expect_error(log(v[1,2]), "non-numeric") # ... it's actually a different error! expect_error(log(v[1,2]), "non-numeric") # ... it's actually a different error!
# Producing unit tests simply means: we define a function, and then we check # Producing unit tests simply means: we define a function, and then we check
# whether all test pass. Consider a function that is loaded on startup: # whether all test pass. Consider a function that is loaded on startup from
# the .utilities.R script:
biCode biCode
@ -144,6 +141,9 @@ expect_error(biCode(), "argument \"s\" is missing, with no default")
# test_that("<descriptive string>, {<code block>}) # test_that("<descriptive string>, {<code block>})
test_that("NA values are preserved", { test_that("NA values are preserved", {
# bicode() respects vector length: input and output must have the smae length.
# Therefore NA's can't be simply skipped, bust must be properly passed
# into output:
expect_true(is.na((biCode(NA)))) expect_true(is.na((biCode(NA))))
expect_equal(biCode(c("first", NA, "last")), expect_equal(biCode(c("first", NA, "last")),
c("FIRST", NA, "LAST.")) c("FIRST", NA, "LAST."))
@ -199,6 +199,22 @@ if (FALSE) {
} }
# == 2.2 Rethinking testing ================================================
# However, it is important to keep in mind that different objectives lead to
# different ideas of what works best. There is never a "best" in and of itself,
# the question is always: "Best for what?" While automated unit testing is a
# great way to assure the integrity of packages and larger software artefacts as
# they are being developed, more loosely conceived aggregates of code - like the
# scripts for this course for example - have different objectives and in this
# case I find the testthat approach to actually be inferior. The reason is its
# tendency to physically separate code and tests. Keeping assets, and functions
# that operate on those assets separated is always poor design. I have found
# over time that a more stable approach is to move individual functions into
# their individual scripts, all in one folder, one function (and its helpers)
# per file, and examples, demos and tests in an if (FALSE) { ... } block, as
# explained above.
# = 3 Task solutions ====================================================== # = 3 Task solutions ======================================================