Allow styling of Rnw files from style_dir() and style_pkg() and add a few more tests

jonmcalder · jonmcalder · commit 6b56ba48d41f · 2018-10-27T21:52:25.000+02:00
diff --git a/R/set-assert-args.R b/R/set-assert-args.R
@@ -38,10 +38,10 @@ set_and_assert_arg_filetype <- function(filetype) {
 #' @param lowercase_filetype A vector with file types to check, all lower case.
 #' @keywords internal
 assert_filetype <- function(lowercase_filetype) {
-  if (!all(lowercase_filetype %in% c("r", "rmd"))) {
+  if (!all(lowercase_filetype %in% c("r", "rmd", "rnw"))) {
     stop(
       "filetype must not contain other values than 'R'",
-      "or 'Rmd' (case is ignored).",
+      "'Rmd' or 'Rnw' (case is ignored).",
       call. = FALSE
     )
   }
diff --git a/R/ui.R b/R/ui.R
@@ -19,8 +19,8 @@ NULL
 #'   conveniently constructed via the `style` argument and `...`. See
 #'   'Examples'.
 #' @param filetype Vector of file extensions indicating which file types should
-#'   be styled. Case is ignored, and the `.` is optional, e.g. `c(".R", ".Rmd")`
-#'   or `c("r", "rmd")`.
+#'   be styled. Case is ignored, and the `.` is optional, e.g. `c(".R", ".Rmd",
+#'   ".Rnw")` or `c("r", "rmd", "rnw")`.
 #' @param exclude_files Character vector with paths to files that should be
 #'   excluded from styling.
 #' @param include_roxygen_examples Whether or not to style code in roxygen
@@ -102,6 +102,16 @@ prettify_pkg <- function(transformers,
     readme <- dir(pattern = "^readme\\.rmd$", ignore.case = TRUE)
   }
 
+  if ("\\.rnw" %in% filetype) {
+    vignette_files <- append(
+      vignette_files,
+      dir(
+        path = "vignettes", pattern = "\\.rnw$",
+        ignore.case = TRUE, recursive = TRUE, full.names = TRUE
+      )
+    )
+  }
+
   files <- setdiff(c(r_files, vignette_files, readme), exclude_files)
   transform_files(files, transformers, include_roxygen_examples)
 }
diff --git a/man/prettify_any.Rd b/man/prettify_any.Rd
diff --git a/man/style_dir.Rd b/man/style_dir.Rd
diff --git a/man/style_pkg.Rd b/man/style_pkg.Rd
diff --git a/tests/testthat/public-api/xyzpackage-rnw/DESCRIPTION b/tests/testthat/public-api/xyzpackage-rnw/DESCRIPTION
@@ -0,0 +1,15 @@
+Package: xyzpackage
+Title: What the Package Does (one line, title case)
+Version: 0.0.0.9000
+Authors@R: person("First", "Last", email = "first.last@example.com", role = c("aut", "cre"))
+Description: What the package does (one paragraph).
+Depends: R (>= 3.3.2)
+License: What license is it under?
+Encoding: UTF-8
+LazyData: true
+Suggests: testthat
+LinkingTo: 
+    Rcpp
+Imports: 
+    Rcpp
+RoxygenNote: 6.0.1.9000
diff --git a/tests/testthat/public-api/xyzpackage-rnw/NAMESPACE b/tests/testthat/public-api/xyzpackage-rnw/NAMESPACE
@@ -0,0 +1,2 @@
+# Generated by roxygen2: do not edit by hand
+
diff --git a/tests/testthat/public-api/xyzpackage-rnw/R/RcppExports.R b/tests/testthat/public-api/xyzpackage-rnw/R/RcppExports.R
@@ -0,0 +1,6 @@
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+timesTwo <- function(x) {
+  .Call("_xyzpackage_timesTwo", PACKAGE = "xyzpackage", x)
+}
diff --git a/tests/testthat/public-api/xyzpackage-rnw/R/hello-world.R b/tests/testthat/public-api/xyzpackage-rnw/R/hello-world.R
@@ -0,0 +1,3 @@
+hello_world <- function() {
+  print("hello, world")
+}
diff --git a/tests/testthat/public-api/xyzpackage-rnw/README.Rmd b/tests/testthat/public-api/xyzpackage-rnw/README.Rmd
@@ -0,0 +1,33 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r setup, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-"
+)
+```
+# styler
+
+The goal of styler is to ...
+
+## Installation
+
+You can install styler from github with:
+
+```{r gh-installation, eval = FALSE}
+# install.packages("devtools")
+devtools::install_github("jonmcalder/styler")
+```
+
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+```{r example}
+## basic example code
+```
diff --git a/tests/testthat/public-api/xyzpackage-rnw/src/.gitignore b/tests/testthat/public-api/xyzpackage-rnw/src/.gitignore
@@ -0,0 +1,3 @@
+*.o
+*.so
+*.dll
diff --git a/tests/testthat/public-api/xyzpackage-rnw/src/RcppExports.cpp b/tests/testthat/public-api/xyzpackage-rnw/src/RcppExports.cpp
@@ -0,0 +1,28 @@
+// Generated by using Rcpp::compileAttributes() -> do not edit by hand
+// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#include <Rcpp.h>
+
+using namespace Rcpp;
+
+// timesTwo
+NumericVector timesTwo(NumericVector x);
+RcppExport SEXP _xyzpackage_timesTwo(SEXP xSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< NumericVector >::type x(xSEXP);
+    rcpp_result_gen = Rcpp::wrap(timesTwo(x));
+    return rcpp_result_gen;
+END_RCPP
+}
+
+static const R_CallMethodDef CallEntries[] = {
+    {"_xyzpackage_timesTwo", (DL_FUNC) &_xyzpackage_timesTwo, 1},
+    {NULL, NULL, 0}
+};
+
+RcppExport void R_init_xyzpackage(DllInfo *dll) {
+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+    R_useDynamicSymbols(dll, FALSE);
+}
diff --git a/tests/testthat/public-api/xyzpackage-rnw/src/timesTwo.cpp b/tests/testthat/public-api/xyzpackage-rnw/src/timesTwo.cpp
@@ -0,0 +1,27 @@
+#include <Rcpp.h>
+using namespace Rcpp;
+
+// This is a simple example of exporting a C++ function to R. You can
+// source this function into an R session using the Rcpp::sourceCpp
+// function (or via the Source button on the editor toolbar). Learn
+// more about Rcpp at:
+//
+//   http://www.rcpp.org/
+//   http://adv-r.had.co.nz/Rcpp.html
+//   http://gallery.rcpp.org/
+//
+
+// [[Rcpp::export]]
+NumericVector timesTwo(NumericVector x) {
+  return x * 2;
+}
+
+
+// You can include R code blocks in C++ files processed with sourceCpp
+// (useful for testing and development). The R code will be automatically
+// run after the compilation.
+//
+
+/*** R
+timesTwo(42)
+*/
diff --git a/tests/testthat/public-api/xyzpackage-rnw/tests/testthat.R b/tests/testthat/public-api/xyzpackage-rnw/tests/testthat.R
@@ -0,0 +1,4 @@
+library(testthat)
+library(xyzpackage)
+
+test_check("xyzpackage")
diff --git a/tests/testthat/public-api/xyzpackage-rnw/tests/testthat/test-package-xyz.R b/tests/testthat/public-api/xyzpackage-rnw/tests/testthat/test-package-xyz.R
@@ -0,0 +1,5 @@
+context("testing styler on package")
+
+test_that("hi there", {
+  I(am(a(package(x))))
+})
diff --git a/tests/testthat/public-api/xyzpackage-rnw/vignettes/random.Rmd b/tests/testthat/public-api/xyzpackage-rnw/vignettes/random.Rmd
@@ -0,0 +1,58 @@
+---
+title: "Vignette Title"
+author: "Vignette Author"
+date: "`r Sys.Date()`"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Vignette Title}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+Vignettes are long form documentation commonly included in packages. Because they are part of the distribution of the package, they need to be as compact as possible. The `html_vignette` output type provides a custom style sheet (and tweaks some options) to ensure that the resulting html is as small as possible. The `html_vignette` format:
+
+- Never uses retina figures
+- Has a smaller default figure size
+- Uses a custom CSS stylesheet instead of the default Twitter Bootstrap style
+
+## Vignette Info
+
+Note the various macros within the `vignette` section of the metadata block above. These are required in order to instruct R how to build the vignette. Note that you should change the `title` field and the `\VignetteIndexEntry` to match the title of your vignette.
+
+## Styles
+
+The `html_vignette` template includes a basic CSS theme. To override this theme you can specify your own CSS in the document metadata as follows:
+
+    output: 
+      rmarkdown::html_vignette:
+        css: mystyles.css
+
+## Figures
+
+The figure sizes have been customised so that you can easily put two images side-by-side. 
+
+```{r, fig.show='hold'}
+plot(1:10)
+plot(10:1)
+```
+
+You can enable figure captions by `fig_caption: yes` in YAML:
+
+    output:
+      rmarkdown::html_vignette:
+        fig_caption: yes
+
+Then you can use the chunk option `fig.cap = "Your figure caption."` in **knitr**.
+
+## More Examples
+
+You can write math expressions, e.g. $Y = X\beta + \epsilon$, footnotes^[A footnote here.], and tables, e.g. using `knitr::kable()`.
+
+```{r, echo=FALSE, results='asis'}
+knitr::kable(head(mtcars, 10))
+```
+
+Also a quote using `>`:
+
+> "He who gives up [code] safety for [code] speed deserves neither."
+([via](https://twitter.com/hadleywickham/status/504368538874703872))
diff --git a/tests/testthat/public-api/xyzpackage-rnw/vignettes/random.Rnw b/tests/testthat/public-api/xyzpackage-rnw/vignettes/random.Rnw
@@ -0,0 +1,22 @@
+\documentclass{article}
+
+\begin{document}
+
+This is all you need to do if you want to use the xyzpackage package:
+
+<<setup, include=FALSE>>=
+library(xyzpackage)
+@
+
+The quick brown fox jumps over the lazy dog the quick brown fox jumps over the
+lazy dog the quick brown fox jumps over the lazy dog.
+
+<<test>>=
+1 + 1
+rnorm(30)
+@
+
+The quick brown fox jumps over the lazy dog the quick brown fox jumps over the
+lazy dog the quick brown fox jumps over the lazy dog.
+
+\end{document}
diff --git a/tests/testthat/public-api/xyzpackage-rnw/xyzpackage.Rproj b/tests/testthat/public-api/xyzpackage-rnw/xyzpackage.Rproj
@@ -0,0 +1,16 @@
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+Encoding: UTF-8
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace
diff --git a/tests/testthat/test-public_api.R b/tests/testthat/test-public_api.R
@@ -180,3 +180,29 @@ test_that("styler handles malformed Rnw file and invalid R code in chunk", {
     style_file(testthat_file("public-api", "xyzfile-rnw", "random4.Rnw"), strict = FALSE)
   ))
 })
+
+context("public API - Rnw in style_pkg()")
+
+test_that("styler can style R, Rmd and Rnw files via style_pkg()", {
+  msg <- capture_output(
+    style_pkg(testthat_file("public-api", "xyzpackage-rnw"),
+              filetype = c("R", "Rmd", "Rnw"))
+  )
+  expect_true(any(grepl("hello-world.R", msg, fixed = TRUE)))
+  expect_true(any(grepl("test-package-xyz.R", msg, fixed = TRUE)))
+  expect_true(any(grepl("random.Rmd", msg, fixed = TRUE)))
+  expect_true(any(grepl("random.Rnw", msg, fixed = TRUE)))
+  expect_false(any(grepl("RcppExports.R", msg, fixed = TRUE)))
+})
+
+test_that("styler can style Rnw files only via style_pkg()", {
+  msg <- capture_output(
+    style_pkg(testthat_file("public-api", "xyzpackage-rnw"),
+              filetype = "Rnw")
+  )
+  expect_false(any(grepl("hello-world.R", msg, fixed = TRUE)))
+  expect_false(any(grepl("test-package-xyz.R", msg, fixed = TRUE)))
+  expect_false(any(grepl("random.Rmd", msg, fixed = TRUE)))
+  expect_true(any(grepl("random.Rnw", msg, fixed = TRUE)))
+  expect_false(any(grepl("RcppExports.R", msg, fixed = TRUE)))
+})

Original file line number	Diff line number	Diff line change
`@@ -38,10 +38,10 @@ set_and_assert_arg_filetype <- function(filetype) {`
`38`	`38`	`#' @param lowercase_filetype A vector with file types to check, all lower case.`
`39`	`39`	`#' @keywords internal`
`40`	`40`	`assert_filetype <- function(lowercase_filetype) {`
`41`		`- if (!all(lowercase_filetype %in% c("r", "rmd"))) {`
	`41`	`+ if (!all(lowercase_filetype %in% c("r", "rmd", "rnw"))) {`
`42`	`42`	`stop(`
`43`	`43`	`"filetype must not contain other values than 'R'",`
`44`		`- "or 'Rmd' (case is ignored).",`
	`44`	`+ "'Rmd' or 'Rnw' (case is ignored).",`
`45`	`45`	`call. = FALSE`
`46`	`46`	`)`
`47`	`47`	`}`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+# Generated by roxygen2: do not edit by hand`
	`2`	`+`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+hello_world <- function() {`
	`2`	`+ print("hello, world")`
	`3`	`+}`