From 74be387bb4ea784cc3925c7843f6f01e88581477 Mon Sep 17 00:00:00 2001
From: Dorchies David <david.dorchies@irstea.fr>
Date: Tue, 21 Apr 2020 12:34:13 +0200
Subject: [PATCH] test: Implementation of the testthat framework and first
tests on vignette execution (failed) Refs #52
---
.gitignore | 8 +++++
tests/testthat.R | 4 +++
tests/testthat/helper_vignettes.R | 60 +++++++++++++++++++++++++++++++
tests/testthat/test-vignettes.R | 26 ++++++++++++++
4 files changed, 98 insertions(+)
create mode 100644 tests/testthat.R
create mode 100644 tests/testthat/helper_vignettes.R
create mode 100644 tests/testthat/test-vignettes.R
diff --git a/.gitignore b/.gitignore
index 894f5a91..1c2a1b2e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,13 @@
# Specific files for airGR
packrat/lib*/
+# Compiled files
+/src/*.o
+/src/*.dll
+
+# Test temporary files
+/tests/tmp/
+
######################################################################################################
### Generic .gitignore for R (source: https://github.com/github/gitignore/blob/master/R.gitignore) ###
######################################################################################################
@@ -52,3 +59,4 @@ docs/
.vscode/*
*.code-workspace
.history/
+.Rproj.user
diff --git a/tests/testthat.R b/tests/testthat.R
new file mode 100644
index 00000000..0a429218
--- /dev/null
+++ b/tests/testthat.R
@@ -0,0 +1,4 @@
+library(testthat)
+library(airgr)
+
+test_check("airgr")
diff --git a/tests/testthat/helper_vignettes.R b/tests/testthat/helper_vignettes.R
new file mode 100644
index 00000000..81009d93
--- /dev/null
+++ b/tests/testthat/helper_vignettes.R
@@ -0,0 +1,60 @@
+#' Extract chunks from Rmd files (knitr::purl) and source them
+#'
+#' @param fileRmd Rmd file to
+#' @param tmpFolder Folder storing the script containing extracted chunks
+#' @param force.eval Force execution of chunks with parameter eval=FALSE
+RunRmdChunks <- function(fileRmd,
+ tmpFolder = "../tmp",
+ force.eval = FALSE) {
+ dir.create(tmpFolder, showWarnings = FALSE)
+ output = file.path(tmpFolder,
+ gsub("\\.Rmd", "\\.R", basename(fileRmd), ignore.case = TRUE))
+ knitr::purl(fileRmd, output = output, quiet = TRUE)
+ sTxt = readLines(output)
+ if (force.eval) {
+ sectionLines = grep("^## ----", sTxt)
+ chunksEvalStart = grep("^## ----.*eval=F", sTxt)
+ if (length(chunksEvalStart) > 0) {
+ if (sectionLines[length(sectionLines)] == chunksEvalStart[length(chunksEvalStart)]) {
+ lastEvalStart = length(chunksEvalStart) - 1
+ } else {
+ lastEvalStart = length(chunksEvalStart)
+ }
+ # Search for end lines of eval=F chunks
+ chunksEvalEnd = sectionLines[sapply(chunksEvalStart[1:lastEvalStart], function(x) {which(sectionLines == x)}) + 1] - 1
+ if(lastEvalStart) {
+ # Add last line if last chunk is eval=FALSE
+ chunksEvalEnd = c(chunksEvalEnd, length(sTxt))
+ }
+ chunksEvalStart = chunksEvalStart + 1 # Chunks begin one line after the section comment
+ for (i in 1:length(chunksEvalStart)) {
+ # Remove comments on eval=F chunk lines
+ sTxt[chunksEvalStart[i]:chunksEvalEnd[i]] = gsub(pattern = "^## ",
+ replace = "",
+ x = sTxt[chunksEvalStart[i]:chunksEvalEnd[i]])
+ }
+ }
+
+ }
+ # Remove line of code displaying data
+ removeFromGrep <- function(pattern, x) {
+ i <- grep(pattern, x)
+ if (length(i) > 0) {
+ x <- x[-i]
+ }
+ return(x)
+ }
+ sTxt <- removeFromGrep("^summary\\(.*\\)$", sTxt)
+ sTxt <- removeFromGrep("^str\\(.*\\)$", sTxt)
+ # Switch echo off for some functions
+ sTxt = gsub("trace\\s?=\\s?[0-9]+", "trace = 0", sTxt)
+ # Add parameters to example calls
+ exLines = grep("^example\\(.*\\)", sTxt)
+ sTxt[exLines] = paste0(substr(sTxt[exLines], 1, nchar(sTxt[exLines]) - 1), ", local = TRUE, echo = FALSE, verbose = FALSE, ask = FALSE)")
+ # Remove question "Hit <Return> to see next plot"
+ sTxt = c("par(ask=F)", sTxt)
+ # Write the transformed script
+ writeLines(sTxt, output)
+ # Silently run the chunks
+ invisible(capture.output(suppressMessages(suppressWarnings(source(output))), type="output"))
+}
diff --git a/tests/testthat/test-vignettes.R b/tests/testthat/test-vignettes.R
new file mode 100644
index 00000000..c6eb47a1
--- /dev/null
+++ b/tests/testthat/test-vignettes.R
@@ -0,0 +1,26 @@
+context("Test vignette chunks")
+
+test_that("V01_get_started works", {
+ RunRmdChunks("../../vignettes/V01_get_started.Rmd")
+
+})
+
+test_that("V02.1_param_optim works", {
+ RunRmdChunks("../../vignettes/V02.1_param_optim.Rmd", force.eval = TRUE)
+
+})
+
+test_that("V02.2_param_mcmc works", {
+ RunRmdChunks("../../vignettes/V02.2_param_mcmc.Rmd", force.eval = TRUE)
+
+})
+
+test_that("V03_param_sets_GR4J works", {
+ RunRmdChunks("../../vignettes/V03_param_sets_GR4J.Rmd", force.eval = TRUE)
+
+})
+
+test_that("V04_cemaneige_hysteresis works", {
+ RunRmdChunks("../../vignettes/V04_cemaneige_hysteresis.Rmd", force.eval = TRUE)
+
+})
--
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