Merge pull request #79 from reconhub/fix77

change argument ordering (closes #77)

NEWS.md

@@ -1,8 +1,17 @@
 # reportfactory (development version)
 
+## Bug fixes
+* Fixes (#74) where files generated within the Rmd were not being copied
+  over to the output folder.
+
+## Breaking changes
+* Following user feedback `compile_reports()` now takes `reports` as a first
+  argument and `factory` as the second (previously these were the other way
+  round).
+
 # reportfactory 0.1.3
 
-* Implements slighlty less strict folder validation.
+* Implements slightly less strict folder validation.
 * Fix for CRAN. One additional test skipped on macs.
 
 # reportfactory 0.1.2

R/compile_reports.R

@@ -1,12 +1,12 @@
 #' Compile one or several R Markdown reports
 #'
-#' @param factory The path to the report factory or a folder within the desired
-#'   factory. Defaults to the current directory.
 #' @param reports Either a regular expression (passed directly to `grep()`) that
 #'   matches to the report paths you would like to compile or an integer/logical
 #'   vector.  If `reports` is an integer or logical vector then a call of
 #'   `compile_reports(factory, reports = idx)` is equivalent to
 #'   `compile_reports(factory, list_reports(factory)[idx])`.
+#' @param factory The path to the report factory or a folder within the desired
+#'   factory. Defaults to the current directory.
 #' @param params A named list of parameters to be used for compiling reports,
 #'   passed to `rmarkdown::render()` as the params argument. Values specified
 #'   here will take precedence over default values specified in YAML headers of
@@ -31,7 +31,7 @@
 #'
 #' @importFrom utils write.table
 #' @export
-compile_reports <- function(factory = ".", reports = NULL,
+compile_reports <- function(reports = NULL, factory = ".",
                             params = NULL, quiet = TRUE, subfolder = NULL,
                             timestamp = format(Sys.time(), "%Y-%m-%d_T%H-%M-%S"),
                             ...) {

README.md

@@ -125,16 +125,16 @@ always clear what will be built.
 compile_reports( 
   reports = "example_report.Rmd"
 )
-#> >>> Compiling report: /example_report
+#> >>> Compiling report: example_report
 #> All done!
 ```
 
 Use `list_ouputs()` to view the report outputs.
 
 ``` r
 list_outputs()
-#> [1] "example_report/2021-01-21_T10-44-57/example_report.html"
-#> [2] "example_report/2021-01-21_T10-44-57/example_report.Rmd"
+#> [1] "example_report/2021-03-08_T09-16-24/example_report.html"
+#> [2] "example_report/2021-03-08_T09-16-24/example_report.Rmd"
 ```
 
 `compile_reports()` can also be used to pass a set of parameters to use
@@ -147,14 +147,14 @@ compile_reports(
   params = list(grouped_plot = FALSE),
   subfolder = "regional"
 )
-#> >>> Compiling report: /example_report
+#> >>> Compiling report: example_report
 #>       - with parameters: grouped_plot = FALSE
 #> All done!
 list_outputs()
-#> [1] "example_report/2021-01-21_T10-44-57/example_report.html"         
-#> [2] "example_report/2021-01-21_T10-44-57/example_report.Rmd"          
-#> [3] "example_report/regional/2021-01-21_T10-44-58/example_report.html"
-#> [4] "example_report/regional/2021-01-21_T10-44-58/example_report.Rmd"
+#> [1] "example_report/2021-03-08_T09-16-24/example_report.html"         
+#> [2] "example_report/2021-03-08_T09-16-24/example_report.Rmd"          
+#> [3] "example_report/regional/2021-03-08_T09-16-25/example_report.html"
+#> [4] "example_report/regional/2021-03-08_T09-16-25/example_report.Rmd"
 ```
 
 Note that reports can also be an integer or a logical vector, in which
@@ -172,7 +172,7 @@ the `factory_overview()` function:
 
 ``` r
 factory_overview()
-#> /tmp/Rtmp1gGdYE/my_factory
+#> /tmp/RtmpWSy7OS/my_factory
 #> ├── README.md
 #> ├── data
 #> │   ├── clean
@@ -181,11 +181,11 @@ factory_overview()
 #> ├── factory_config
 #> ├── outputs
 #> │   └── example_report
-#> │       ├── 2021-01-21_T10-44-57
+#> │       ├── 2021-03-08_T09-16-24
 #> │       │   ├── example_report.Rmd
 #> │       │   └── example_report.html
 #> │       └── regional
-#> │           └── 2021-01-21_T10-44-58
+#> │           └── 2021-03-08_T09-16-25
 #> │               ├── example_report.Rmd
 #> │               └── example_report.html
 #> ├── report_sources

tests/testthat/test-compile_reports.R

@@ -16,8 +16,8 @@ test_that("test parameteriesed report output", {
 
   # compile report
   compile_reports(
-    f,
     "parameterised",
+    f,
     params = list(test1 = "three", test2 = "four")
   )
 
@@ -49,8 +49,8 @@ test_that("test output folder gets recreated if not there", {
 
   # compile report
   compile_reports(
-    f,
     "parameterised",
+    f,
     params = list(test1 = "three", test2 = "four")
   )
 
@@ -78,8 +78,8 @@ test_that("parameteriesed report with missing param output but input", {
 
   # compile report
   compile_reports(
-    f,
     "parameterised",
+    f,
     params = list(test2 = "four", test3 = "five")
   )
 
@@ -106,8 +106,8 @@ test_that("non parameteriesed report with param input", {
 
   # compile report
   compile_reports(
-    f,
     "simple",
+    f,
     params = list(test2 = "four", test3 = "five")
   )
 
@@ -136,8 +136,8 @@ test_that("parameteriesed report with missing param (but in environment)", {
 
   # compile report
   compile_reports(
-    f,
-    "parameterised"
+    "parameterised",
+    f
   )
 
   # check the output
@@ -174,7 +174,7 @@ test_that("integer index for reports", {
 
   # compile report
   idx <- c(1, 3)
-  compile_reports(f, idx, timestamp = "test")
+  compile_reports(idx, f, timestamp = "test")
   nms <- path_ext_remove(list_reports(f))[idx]
   nms <- paste(nms, collapse = "|")
   expected_files <- c(
@@ -234,7 +234,7 @@ test_that("logical index for reports", {
 
   # compile report
   idx <- c(TRUE, FALSE)
-  compile_reports(f, idx, timestamp = "test")
+  compile_reports(idx, f, timestamp = "test")
   nms <- path_ext_remove(list_reports(f))[idx]
   nms <- paste(nms, collapse = "|")
   expected_files <- c(
@@ -282,7 +282,7 @@ test_that("figures folders copied correctly reports", {
   file_delete(path(f, "report_sources", "example_report.Rmd"))
 
   # compile report
-  compile_reports(f, timestamp = "test")
+  compile_reports(factory = f, timestamp = "test")
   nms <- path_ext_remove(list_reports(f))
   nms <- paste(nms, collapse = "|")
   expected_files <- c(

tests/testthat/test-list_outputs.R

@@ -21,7 +21,7 @@ test_that("list_output works with nested and unnested files", {
   # remove the other example report
   file_delete(path(f, "report_sources", "example_report.Rmd"))
 
-  compile_reports(f, timestamp = "test")
+  compile_reports(factory = f, timestamp = "test")
   output_files <- list_outputs(f)
   expected_files <- c(
     file.path("simple", "test", "simple.Rmd"),
@@ -73,7 +73,7 @@ test_that("list_output works, one file compiled", {
     nested_dir
   )
 
-  compile_reports(f, "parameterised", timestamp = "test")
+  compile_reports(factory = f, "parameterised", timestamp = "test")
   output_files <- list_outputs(f)
   expected_files <- c(
     file.path("nested", "parameterised", "test", "parameterised.Rmd"),
@@ -105,7 +105,7 @@ test_that("list_output works, with subfolders", {
     nested_dir
   )
 
-  compile_reports(f, "parameterised", timestamp = "test", subfolder = "bob")
+  compile_reports(factory = f, "parameterised", timestamp = "test", subfolder = "bob")
   output_files <- list_outputs(f)
   expected_files <- c(
     file.path("nested", "parameterised", "bob", "test", "parameterised.Rmd"),