Merge pull request #50 from ThinkR-open/47-escape-line

v0.2.5 - Prepare for CRAN

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: attachment
 Title: Deal with Dependencies
-Version: 0.2.4.9001
+Version: 0.2.5
 Authors@R:
     c(person(given = "Sébastien",
              family = "Rochette",

NEWS.md

@@ -1,11 +1,14 @@
-# attachment 0.2.4.900x
+# attachment 0.2.5
 ## Major changes
 
 * add `create_renv_for_dev()` and `create_renv_for_prod()` function to create `renv.lock` file based on development project (@VincentGuyader and @statnmap).
+* Quarto documents can be parsed with `att_from_rmds()`.
+* Documentation for bookdown and quarto dependencies extraction updated
 
 ## Minor changes
 
 * `att_amend_desc()` now saves file before processing
+* Newline escape code `\n` will not interfere with package discovery 
 
 # attachment 0.2.4
 

R/att_from_rmds.R

@@ -60,7 +60,13 @@ att_from_rmd <- function(path, temp_dir = tempdir(), warn = -1,
   yaml <- c("\n# yaml to parse \n",
             paste(yaml_pkg, "\n"))
   cat(yaml, file = r_file, append = TRUE)
-  att_from_rscript(r_file)
+  res <- att_from_rscript(r_file)
+
+  # clean tempdir
+  file.remove(runR)
+  file.remove(r_file)
+
+  return(res)
 }
 
 #' Get all packages called in vignettes folder
@@ -81,7 +87,7 @@ att_from_rmd <- function(path, temp_dir = tempdir(), warn = -1,
 
 #' @export
 att_from_rmds <- function(path = "vignettes",
-                          pattern = "*.[.](Rmd|rmd)$",
+                          pattern = "*.[.](Rmd|rmd|qmd)$",
                           recursive = TRUE, warn = -1,
                           inside_rmd = FALSE, inline = TRUE) {
 

R/att_from_rscripts.R

@@ -19,6 +19,8 @@
 att_from_rscript <- function(path) {
 
   file <- as.character(parse(path))
+  # Replace newlines `\n` by space
+  file <- gsub("\\\\n", " ", file)
 
   pkg_points <- file %>%
     .[grep("^#", ., invert = TRUE)] %>%

README.Rmd

@@ -108,20 +108,27 @@ for (i in to_install) {
 }
 ```
 
-### For bookdown
+### For bookdown, pagedown, quarto
 
-If you write a {bookdown} and want to publish it on Github using Travis for instance, you will need a DESCRIPTION file with list of dependencies just like for a package. In this case, you can use the function to description from import/suggest: `att_to_desc_from_is()`.
+If you write a {bookdown} and want to publish it on Github using GitHub Actions or GitLab CI for instance, you will need a DESCRIPTION file with list of dependencies just like for a package. In this case, you can use the function to description from import/suggest: `att_to_desc_from_is()`.
 
 ```{r, eval=FALSE}
+usethis::use_description()
 # bookdown Imports are in Rmds
 imports <- c("bookdown", attachment::att_from_rmds("."))
 attachment::att_to_desc_from_is(path.d = "DESCRIPTION",
                                 imports = imports, suggests = NULL)
 ```
 
+Then, install dependencies with
+```{r, eval=FALSE}
+remotes::install_deps()
+```
+
 
 ### To list information
-Of course, you can also use {attachment} out of a package to list all package dependencies of R scripts using `att_from_rscripts()` or Rmd files using `att_from_rmds()`.  
+
+Of course, you can also use {attachment} out of a package to list all package dependencies of R scripts using `att_from_rscripts()` or Rmd/qmd files using `att_from_rmds()`.  
 If you are running this inside a Rmd, you may need parameter `inside_rmd = TRUE`.  
 
 ```{r, eval=TRUE}
@@ -131,17 +138,18 @@ att_from_rscripts(path = dummypackage)
 att_from_rmds(path = file.path(dummypackage, "vignettes"), inside_rmd = TRUE)
 ```
 
-## Vignette
+## Vignettes
 
-Package {attachment} has a vignette to present the different functions available. There is also a recommendation to have a `dev_history.R` in the root directory of your package. (*Have a look at [dev_history.R](https://github.com/ThinkR-open/attachment/blob/main/dev/dev_history.R) in the present package*)
+Package {attachment} has vignettes to present the different functions available. There is also a recommendation to have a `dev_history.R` in the root directory of your package. (*Have a look at [dev_history.R](https://github.com/ThinkR-open/attachment/blob/main/dev/dev_history.R) in the present package*)
 
 ```{r, eval=FALSE}
-vignette("fill-pkg-description", package = "attachment")
+vignette("a-fill-pkg-description", package = "attachment")
+vignette("b-bookdown-and-scripts", package = "attachment")
+vignette("use_renv", package = "attachment")
 ```
 
-The vignette is available on the {pkgdown} page: <https://thinkr-open.github.io/attachment/articles/fill-pkg-description.html>
+The vignettes are available on the {pkgdown} page, in the "Articles" menu: <https://thinkr-open.github.io/attachment/>
 
-See full documentation realized using {pkgdown} at <https://thinkr-open.github.io/attachment/>  
 
 ## Code of Conduct
 

README.md

@@ -85,13 +85,13 @@ dummypackage <- file.path(tmpdir, "dummypackage")
 # browseURL(dummypackage)
 att_amend_desc(path = dummypackage, inside_rmd = TRUE)
 #> Updating dummypackage documentation
-#> Updating roxygen version in /tmp/RtmpdAJaCu/dummypackage/DESCRIPTION
+#> Updating roxygen version in /tmp/RtmpK2L9Ud/dummypackage/DESCRIPTION
 #> ℹ Loading dummypackage
 #> Writing NAMESPACE
 #> Writing NAMESPACE
 #> Package(s) Rcpp is(are) in category 'LinkingTo'. Check your Description file to be sure it is really what you want.
 #> [-] 1 package(s) removed: utils.
-#> [+] 2 package(s) added: stats, ggplot2.
+#> [+] 2 package(s) added: stats, glue.
 ```
 
 ### For installation
@@ -130,24 +130,32 @@ for (i in to_install) {
 }
 ```
 
-### For bookdown
+### For bookdown, pagedown, quarto
 
-If you write a {bookdown} and want to publish it on Github using Travis
-for instance, you will need a DESCRIPTION file with list of dependencies
-just like for a package. In this case, you can use the function to
-description from import/suggest: `att_to_desc_from_is()`.
+If you write a {bookdown} and want to publish it on Github using GitHub
+Actions or GitLab CI for instance, you will need a DESCRIPTION file with
+list of dependencies just like for a package. In this case, you can use
+the function to description from import/suggest:
+`att_to_desc_from_is()`.
 
 ``` r
+usethis::use_description()
 # bookdown Imports are in Rmds
 imports <- c("bookdown", attachment::att_from_rmds("."))
 attachment::att_to_desc_from_is(path.d = "DESCRIPTION",
                                 imports = imports, suggests = NULL)
 ```
 
+Then, install dependencies with
+
+``` r
+remotes::install_deps()
+```
+
 ### To list information
 
 Of course, you can also use {attachment} out of a package to list all
-package dependencies of R scripts using `att_from_rscripts()` or Rmd
+package dependencies of R scripts using `att_from_rscripts()` or Rmd/qmd
 files using `att_from_rmds()`.  
 If you are running this inside a Rmd, you may need parameter
 `inside_rmd = TRUE`.
@@ -158,26 +166,25 @@ dummypackage <- system.file("dummypackage", package = "attachment")
 att_from_rscripts(path = dummypackage)
 #> [1] "stats"        "testthat"     "dummypackage"
 att_from_rmds(path = file.path(dummypackage, "vignettes"), inside_rmd = TRUE)
-#> [1] "knitr"     "rmarkdown" "ggplot2"
+#> [1] "knitr"     "rmarkdown" "glue"
 ```
 
-## Vignette
+## Vignettes
 
-Package {attachment} has a vignette to present the different functions
+Package {attachment} has vignettes to present the different functions
 available. There is also a recommendation to have a `dev_history.R` in
 the root directory of your package. (*Have a look at
-[dev\_history.R](https://github.com/ThinkR-open/attachment/blob/main/dev/dev_history.R)
+[dev_history.R](https://github.com/ThinkR-open/attachment/blob/main/dev/dev_history.R)
 in the present package*)
 
 ``` r
-vignette("fill-pkg-description", package = "attachment")
+vignette("a-fill-pkg-description", package = "attachment")
+vignette("b-bookdown-and-scripts", package = "attachment")
+vignette("use_renv", package = "attachment")
 ```
 
-The vignette is available on the {pkgdown} page:
-<https://thinkr-open.github.io/attachment/articles/fill-pkg-description.html>
-
-See full documentation realized using {pkgdown} at
-<https://thinkr-open.github.io/attachment/>
+The vignettes are available on the {pkgdown} page, in the “Articles”
+menu: <https://thinkr-open.github.io/attachment/>
 
 ## Code of Conduct
 

dev/dev_history.R

@@ -111,7 +111,8 @@ rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"))
 
 # Check content
 # remotes::install_github("ThinkR-open/checkhelper")
-checkhelper::find_missing_tags()
+out <- checkhelper::find_missing_tags()
+View(out)
 
 # Check spelling
 # usethis::use_spell_check()
@@ -137,6 +138,7 @@ aa
 # _win devel
 devtools::check_win_devel()
 devtools::check_win_release()
+devtools::check_mac_release()
 
 # Check reverse dependencies
 # remotes::install_github("r-lib/revdepcheck")
@@ -146,14 +148,17 @@ usethis::use_build_ignore("revdep/")
 devtools::revdep()
 library(revdepcheck)
 # In another session
+revdepcheck::revdep_todo()
+# revdepcheck::revdep_add(packages = "fusen")
 id <- rstudioapi::terminalExecute("Rscript -e 'revdepcheck::revdep_check(num_workers = 4)'")
 rstudioapi::terminalKill(id)
 # See outputs
-revdep_details(revdep = "pkg")
-revdep_summary()                 # table of results by package
+revdep_details(revdep = "fusen")
+revdep_summary()
+# table of results by package
 revdep_report() # in revdep/
 # Clean up when on CRAN
-revdep_reset()
+revdepcheck::revdep_reset()
 
 # Update NEWS
 # Bump version manually and add list of changes

tests/testthat/escape_newline.R

@@ -0,0 +1,41 @@
+# This code contains knitr on a newline and should not be read with `\nknitr`
+
+create_vignette_head <- function(pkg, vignette_name, yaml_options = NULL) {
+  pkgname <- basename(pkg)
+
+  # Get all yaml options except Title, output, editor_options
+  yaml_options <- yaml_options[
+    !names(yaml_options) %in% c("output", "title", "editor_options")]
+
+  enc2utf8(
+    glue(
+      '---
+title: ".{vignette_name}."
+output: rmarkdown::html_vignette',
+      ifelse(length(yaml_options) != 0,
+             glue::glue_collapse(
+               c("",
+                 glue("{names(yaml_options)}: \"{yaml_options}\""), ""),
+               sep = "\n"),
+             "\n"),
+      'vignette: >
+  %\\VignetteIndexEntry{.{vignette_name}.}
+  %\\VignetteEngine{knitr::rmarkdown}
+  %\\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+```{r setup}
+library(.{pkgname}.)
+```
+    ',
+    .open = ".{", .close = "}."
+    )
+  )
+}

tests/testthat/quarto.qmd

@@ -0,0 +1,47 @@
+---
+title: "quarto demo"
+date: "5/22/2021"
+format: 
+  html:
+    fig-width: 8
+    fig-height: 4
+    code-fold: true
+---
+
+## Air Quality
+
+@fig-airquality further explores the impact of temperature on ozone level.
+
+```{r}
+#| label: fig-airquality
+#| fig-cap: Temperature and ozone level.
+#| warning: false
+
+plot(pressure)
+utils::packageVersion("knitr")
+library("findme.quarto")
+# library("dontfindme.quarto")
+
+```
+
+## Python should not be parsed
+
+```{python}
+#| label: fig-polar
+#| fig-cap: "A line plot on a polar axis"
+
+import numpy as np
+import matplotlib.pyplot as plt
+
+r = np.arange(0, 2, 0.01)
+theta = 2 * np.pi * r
+fig, ax = plt.subplots(
+  subplot_kw = {'projection': 'polar'} 
+)
+ax.plot(theta, r)
+ax.set_rticks([0.5, 1, 1.5, 2])
+ax.grid(True)
+plt.show()
+```
+
+

tests/testthat/test-rmd.R

@@ -18,7 +18,9 @@ all_to_be_found <- c(
   "find.inline",
   "bookdown",
   "rmarkdown",
-  "emo"
+  "emo",
+  "findme.quarto",
+  "utils"
 )
 
 # One Rmd with YAML ---
@@ -29,7 +31,9 @@ test_that("rmd well parsed", {
 
   # One output
   res <- sort(attachment::att_from_rmd(path = "f1.Rmd"))
-  expect_equal(sort(res), sort(sort(setdiff(all_to_be_found, c("emo", "rmarkdown")))))
+  expect_equal(sort(res),
+               sort(sort(setdiff(
+                 all_to_be_found, c("emo", "rmarkdown", "findme.quarto", "utils")))))
 })
 
 # A directory ----
@@ -57,4 +61,11 @@ test_that("test inside rmd works", {
   }
 })
 
-
+# Test quarto and new way of chunk options with knitr>=1.35 ----
+if (utils::packageVersion("knitr") >= "1.35") {
+  test_that("test inside qmd works", {
+    res <- attachment::att_from_rmds(path = ".")
+    expect_true("findme.quarto" %in% res)
+    expect_true(!"dontfindme.quarto" %in% res)
+  })
+}

tests/testthat/test-rscript.R

@@ -53,3 +53,13 @@ test_that("att_from_rscripts well parsed", {
   expect_false("base" %in% res_files)
 
 })
+
+# Test escape code not used ----
+newline_script <- att_from_rscript(path = "escape_newline.R")
+
+test_that("newline correctly escaped", {
+  expect_equal(sort(c("rmarkdown", "glue", "knitr")),
+               sort(newline_script))
+  expect_true(!"nknitr" %in% newline_script)
+
+})