Merge pull request #91 from reconverse/04

04

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: reportfactory
 Title: Lightweight Infrastructure for Handling Multiple R Markdown Documents
-Version: 0.3.1.9000
+Version: 0.4.0
 Authors@R: c(
   person("Thibaut", "Jombart", role = "aut", email = "thibautjombart@gmail.com"),
   person("Amy", "Gimma", role = "ctb", email = "amyg225@gmail.com"),

NEWS.md

@@ -1,5 +1,7 @@
-# reportfactory (development version)
+# reportfactory 0.4.0
 
+* `list_deps()` now only checks the `report_sources` and `scripts` folders for
+  package dependencies.
 * `list_deps()` no longer uses the `checkpoint` package so the dependency has
   been dropped.
 

R/internals.R

@@ -37,6 +37,8 @@ factory_root <- function(directory = ".") {
   root
 }
 
+# -------------------------------------------------------------------------
+
 #' check whether a vector is "integer-like" to a given precision
 #'
 #' @param x vector to check
@@ -47,6 +49,8 @@ is.wholenumber <- function(x, tol = .Machine$double.eps^0.5)  {
   all(abs(x - round(x)) < tol)
 }
 
+# -------------------------------------------------------------------------
+
 #' copy a file from the skeleton directory
 #'
 #' @param file name of the file you want to copy
@@ -58,6 +62,7 @@ copy_skeleton_file <- function(file, dest) {
   file.copy(f, dest)
 }
 
+# -------------------------------------------------------------------------
 
 #' Change part of the front yaml matter from an Rmarkdown file
 #'
@@ -103,6 +108,7 @@ change_yaml_matter <- function(input_file, ..., output_file) {
   }
 }
 
+# -------------------------------------------------------------------------
 
 #' Return rows of one data.frame not in another
 #'

R/list_deps.R

@@ -1,7 +1,7 @@
 #' List dependencies of reports within a factory
 #'
-#' This function can be used to list package dependencies based of the reports
-#'   and R scripts within the factory.
+#' List package dependencies based on the reports and scripts within the
+#'   report_sources and scripts directories respectively.
 #'
 #' @inheritParams compile_reports
 #' @param missing A logical indicating if only missing dependencies should be
@@ -11,55 +11,92 @@
 #'   checked. Note that this will error if the script cannot be parsed.
 #' @param exclude_readme If TRUE (default) README files will not be checked for
 #'   dependencies.
+#' @param parse_first If `TRUE` code will first be parsed for validity and
+#'   unevaluated Rmd chunks will not be checked for dependencies. The default
+#'   value is `FALSE` and, in this case, files will simply be checked line by
+#'   line for calls to `library`, `require` or use of double, `::`, and triple,
+#'   `:::` function calls.
 #'
 #' @note This function requires that any R scripts present in the factory are
 #'   valid syntax else the function will error.
 #'
 #' @return A character vector of package dependencies.
 #'
 #' @export
-list_deps <- function(factory = ".", missing = FALSE, check_r = TRUE, exclude_readme = TRUE) {
+list_deps <- function(factory = ".", missing = FALSE, check_r = TRUE,
+                      exclude_readme = TRUE, parse_first = FALSE) {
 
   tmp <- suppressMessages(validate_factory(factory))
   root <- tmp$root
+  config <- as.data.frame(read.dcf(file.path(root, "factory_config")))
+  report_sources <- config$report_sources
+  root_report_sources <- file.path(root, report_sources)
+  root_scripts <- file.path(root, "scripts")
+  root_to_check <- c(root_report_sources, root_scripts)
 
-  # Find dependencies in R files
-  r_files <- list.files(root, pattern = "\\.[Rr]$", recursive = TRUE, full.names = TRUE)
+  # List of R files
+  r_files <- list.files(
+    root_to_check,
+    pattern = "\\.[Rr]$",
+    recursive = TRUE,
+    full.names = TRUE
+  )
+
+  # List of Rmd files
+  rmd_files <- list.files(
+    root_to_check, pattern = "\\.[Rr]md$",
+    recursive = TRUE,
+    full.names = TRUE
+  )
+  if (exclude_readme) {
+    readme <- list.files(
+      pattern = "README\\.Rmd",
+      recursive = TRUE,
+      ignore.case = TRUE,
+      full.names = TRUE
+    )
+    rmd_files <- rmd_files[!rmd_files %in% readme]
+  }
+
+  # Find R file dependencies
   r_files_deps <- character(0)
   if (length(r_files) && check_r) {
-    r_files_deps <- list_r_file_deps(r_files)
+    r_files_deps <- list_r_file_deps(r_files, parse = parse_first)
   }
 
-  # Find dependencies in Rmd files. We knit the files first to ensure only
-  # dependencies of code that is actually run are returned.
+  # Find Rmd file dependencies
   op <- options(knitr.purl.inline = TRUE)
   on.exit(options(op))
-  rmd_files <- list.files(root, pattern = "\\.[Rr]md$", recursive = TRUE, full.names = TRUE)
-  if (exclude_readme) {
-    readme <- list.files(pattern = "README\\.Rmd", recursive = TRUE, ignore.case = TRUE, full.names = TRUE)
-    rmd_files <- rmd_files[!rmd_files %in% readme]
-  }
-
   rmd_files_deps <- character(0)
   if (length(rmd_files)) {
-    d <- tempdir()
-    fd <- sub(pattern = "(.*)\\..*$", replacement = "\\1", basename(rmd_files))
-    fd <- vapply(fd, function(x) file.path(d, x), character(1))
-    on.exit(unlink(fd), add = TRUE)
-    fefil <- tempfile()
-    on.exit(unlink(fefil), add = TRUE)
-    fe <- file(fefil, "w")
-    sink(fe, type = "message")
-    mapply(
-      function(x,y) try(knitr::purl(input = x, output = y, quiet = TRUE, documentation = 0), silent = TRUE),
-      rmd_files,
-      fd
-    )
-    sink(type = "message")
-    close(fe)
-    rmd_files_deps <- c("rmarkdown", list_r_file_deps(fd))
+    if (parse_first) {
+      d <- tempdir()
+      fd <- sub(pattern = "(.*)\\..*$", replacement = "\\1", basename(rmd_files))
+      fd <- vapply(fd, function(x) file.path(d, x), character(1))
+      on.exit(unlink(fd), add = TRUE)
+      fefil <- tempfile()
+      on.exit(unlink(fefil), add = TRUE)
+      fe <- file(fefil, "w")
+      sink(fe, type = "message")
+      mapply(
+        function(x,y) {
+          try(
+            knitr::purl(input = x, output = y, quiet = TRUE, documentation = 0),
+            silent = TRUE
+          )
+        } ,
+        rmd_files,
+        fd
+      )
+      sink(type = "message")
+      close(fe)
+      rmd_files_deps <- c("rmarkdown", list_r_file_deps(fd, parse = TRUE))
+    } else {
+      rmd_files_deps <- c("rmarkdown", list_r_file_deps(rmd_files, parse = FALSE))
+    }
   }
 
+  # return unique dependencies
   deps <- unique(c(r_files_deps, rmd_files_deps))
   if (missing) {
     installed <- basename(find.package(deps))
@@ -69,13 +106,17 @@ list_deps <- function(factory = ".", missing = FALSE, check_r = TRUE, exclude_re
   deps
 }
 
-list_r_file_deps <- function(filepaths) {
+# -------------------------------------------------------------------------
 
-  dat <- vapply(
-    filepaths,
-    function(x) paste(as.character(parse(x)), collapse = "\n"),
-    character(1)
-  )
+list_r_file_deps <- function(filepaths, parse = FALSE) {
+
+  if (parse) {
+    f <- function(x) paste(as.character(parse(x)), collapse = "\n")
+  } else {
+    f <- function(x) paste(readLines(x), collapse = "\n")
+  }
+
+  dat <- vapply(filepaths, f, character(1))
 
   colon_string <- r"---{([a-zA-Z][\w.]*)(?=:{2,3})}---"
   colon_greg <- gregexpr(colon_string, dat, perl = TRUE)

cran-comments.md

@@ -1,8 +1,6 @@
-# Reason for update
-* Fixes due to breaking changes in the upstream checkpoint package.
-
 # Tested on
-* Fedora 34, R Under development (unstable) (2021-06-16 r80504)
+* Fedora 34, R Under development (unstable) (2021-08-09 r80724)
+* Winbuilder, R Under development (unstable) (2021-08-05 r80717)
 
 ## R CMD check results for above environments
 Status: OK

inst/skeletons/example_report.Rmd

@@ -12,6 +12,10 @@ output:
 knitr::opts_chunk$set(echo = TRUE, collapse = TRUE, fig.width = 8, fig.height = 6, dpi = 70)
 ```
 
+```{r, eval = FALSE}
+base::mean(c(1,2))
+```
+
 This is an example report to illustrate how `reportfactory` can be used.
 It loads the `fs` library purely for demonstration purposes. 
 

tests/testthat/test-compile_reports.R

@@ -25,7 +25,7 @@ test_that("test parameteriesed report output", {
   md_file <- grep("\\.md", list_outputs(f), value = TRUE)
   md_file <- path(f, "outputs", md_file)
 
-  expect_snapshot_file(md_file, "param_report_check.md", binary = FALSE)
+  expect_snapshot_file(md_file, "param_report_check.md", compare = compare_file_text)
 })
 
 test_that("test ignore_case works report output", {
@@ -54,7 +54,7 @@ test_that("test ignore_case works report output", {
   md_file <- grep("\\.md", list_outputs(f), value = TRUE)
   md_file <- path(f, "outputs", md_file)
 
-  expect_snapshot_file(md_file, "param_report_check.md", binary = FALSE)
+  expect_snapshot_file(md_file, "param_report_check.md", compare = compare_file_text)
 
   # Should error if not case insensitive
   expect_error(
@@ -98,7 +98,7 @@ test_that("test output folder gets recreated if not there", {
   md_file <- grep("\\.md", list_outputs(f), value = TRUE)
   md_file <- path(f, "outputs", md_file)
 
-  expect_snapshot_file(md_file, "outputs_deleted_param_report_check.md", binary = FALSE)
+  expect_snapshot_file(md_file, "outputs_deleted_param_report_check.md", compare = compare_file_text)
 })
 
 
@@ -127,7 +127,7 @@ test_that("parameteriesed report with missing param output but input", {
   md_file <- grep("\\.md", list_outputs(f), value = TRUE)
   md_file <- path(f, "outputs", md_file)
 
-  expect_snapshot_file(md_file, "missing_param_report_check.md", binary = FALSE)
+  expect_snapshot_file(md_file, "missing_param_report_check.md", compare = compare_file_text)
 })
 
 test_that("non parameteriesed report with param input", {
@@ -155,7 +155,7 @@ test_that("non parameteriesed report with param input", {
   md_file <- grep("\\.md", list_outputs(f), value = TRUE)
   md_file <- path(f, "outputs", md_file)
 
-  expect_snapshot_file(md_file, "nonparameterised_with_params.md", binary = FALSE)
+  expect_snapshot_file(md_file, "nonparameterised_with_params.md", compare = compare_file_text)
 })
 
 test_that("parameteriesed report with missing param (but in environment)", {
@@ -184,7 +184,7 @@ test_that("parameteriesed report with missing param (but in environment)", {
   md_file <- grep("\\.md", list_outputs(f), value = TRUE)
   md_file <- path(f, "outputs", md_file)
 
-  expect_snapshot_file(md_file, "missing_param_but_envir.md", binary = FALSE)
+  expect_snapshot_file(md_file, "missing_param_but_envir.md", compare = compare_file_text)
 })
 
 

tests/testthat/test-list_deps.R

@@ -1,6 +1,6 @@
 library(fs)
 
-test_that("list_deps works", {
+test_that("non parsing list_deps works", {
 
   f <- new_factory(path = path_temp(), move_in = FALSE)
   on.exit(dir_delete(f))
@@ -9,13 +9,37 @@ test_that("list_deps works", {
   file_copy(path("test_reports", "package_calls.Rmd"), path(f, "report_sources"))
   file_copy(path("test_reports", "example.R"), path(f, "report_sources"))
 
-  expected_deps_package_calls <- c("purrr", "readxl", "fs", "rmarkdown", "utils", "yaml", "callr", "rprojroot")
+  # non parsed expected_deps
+  expected_deps_package_calls_rmd <- c("purrr", "readxl", "fs", "rmarkdown")
+  expected_deps_example_r <- c("fs", "yaml", "callr", "utils", "rprojroot")
+  expected_deps_example_report <- c("base", "knitr", "fs")
+  expected_deps <- c(expected_deps_package_calls_rmd,
+                     expected_deps_example_r,
+                     expected_deps_example_report)
 
-  expected_deps_example_report <- c("knitr", "fs", "rmarkdown")
-  expected_deps_readme <- "rmarkdown"
-  expected_deps <- c(expected_deps_package_calls,
-                     expected_deps_example_report,
-                     expected_deps_readme)
   deps <- list_deps(f)
   expect_equal(sort(deps), sort(unique(expected_deps)))
 })
+
+
+test_that("parsing list_deps works", {
+
+  f <- new_factory(path = path_temp(), move_in = FALSE)
+  on.exit(dir_delete(f))
+
+  # copy test reports over (as this has inline code)
+  file_copy(path("test_reports", "package_calls.Rmd"), path(f, "report_sources"))
+  file_copy(path("test_reports", "example.R"), path(f, "report_sources"))
+
+  # non parsed expected_deps
+  expected_deps_package_calls_rmd <- c("purrr", "readxl", "fs", "rmarkdown")
+  expected_deps_example_r <- c("fs", "yaml", "callr", "utils", "rprojroot")
+  expected_deps_example_report <- c("knitr", "fs")
+  expected_deps <- c(expected_deps_package_calls_rmd,
+                     expected_deps_example_r,
+                     expected_deps_example_report)
+
+  deps <- list_deps(f, parse_first = TRUE)
+  expect_equal(sort(deps), sort(unique(expected_deps)))
+})
+