Merge pull request pik-piam#188 from robinhasse/devMappings

extend toolGetMapping() to also fetch mappings from packages during development, i.e. loaded via devtools::load_all()

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '70925670'
+ValidationKey: '7275680'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

.github/workflows/check.yaml

@@ -56,6 +56,8 @@ jobs:
 
       - name: Test coverage
         shell: Rscript {0}
-        run: covr::codecov(quiet = FALSE)
+        run: |
+          nonDummyTests <- setdiff(list.files("./tests/testthat/"), c("test-dummy.R", "_snaps"))
+          if(length(nonDummyTests) > 0) covr::codecov(quiet = FALSE)
         env:
           NOT_CRAN: "true"

CITATION.cff

@@ -2,8 +2,8 @@ cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
 title: 'madrat: May All Data be Reproducible and Transparent (MADRaT) *'
-version: 3.6.10
-date-released: '2023-10-17'
+version: 3.7.0
+date-released: '2023-11-03'
 abstract: Provides a framework which should improve reproducibility and transparency
   in data processing. It provides functionality such as automatic meta data creation
   and management, rudimentary quality management, data caching, work-flow management

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: madrat
 Title: May All Data be Reproducible and Transparent (MADRaT) *
-Version: 3.6.10
-Date: 2023-10-17
+Version: 3.7.0
+Date: 2023-11-03
 Authors@R: c(
     person("Jan Philipp", "Dietrich", , "[email protected]", role = c("aut", "cre")),
     person("Lavinia", "Baumstark", , "[email protected]", role = "aut"),

R/toolGetMapping.R

@@ -95,34 +95,44 @@ toolGetMapping <- function(name, type = NULL, where = NULL,
 }
 
 .searchNamePackage <- function(name, type, packageName) {
-  tmpfname <- .typedName(name, type)
-  fname <- system.file("extdata", tmpfname, package = packageName)
-  if (fname == "" && !is_dev_package(packageName)) fname <- system.file("inst/extdata", tmpfname, package = packageName)
-  if (fname == "") fname <- system.file("extdata", strsplit(tmpfname, split = "/")[[1]][2], package = packageName)
-  if (fname == "" && !is_dev_package(packageName))
-    fname <- system.file("inst/extdata", strsplit(tmpfname, split = "/")[[1]][2], package = packageName)
-  return(fname)
+  packageLocation <- if (is_dev_package(packageName)) {
+    # If <packageName> was attached using devtools::load_all(), system.file()
+    # might or might not be shimmed with pkgload:::shim_system.file()
+    # (depending on whether madrat was loaded normally or
+    # through devtools::load_all()), and will yield different results.
+    # base::system.file() will return the directory from where <packageName> was
+    # loaded, and we append inst/ manually.
+    file.path(base::system.file(package = packageName), "inst")
+  } else {
+    # If <packageName> was attached normally, system.file() (shimmed or not)
+    # will return correct results.
+    system.file(package = packageName)
+  }
+
+  # From packageLocation/extdata, check both the subdirectory indicated by
+  # <type> and the extdata/ directory, picking the first over the second should
+  # both exist.  If nothing is found, return an empty string.
+  fname <- file.path(packageLocation, "extdata",
+                     c(.typedName(name, type), name))
+  return(c(fname[file.exists(fname)], "")[[1]])
 }
 
 .typedName <- function(name, type) {
   if (is.null(type)) {
     return(name)
   }
-  return(paste0(type, "/", name))
+  return(file.path(type, name))
 }
 
 .readMapping <- function(fname) {
   filetype <- tolower(file_ext(fname))
   if (filetype == "csv") {
-    if (grepl(pattern = ";", x = readLines(fname, 1))) {
-      return(read.csv(fname, sep = ";", stringsAsFactors = FALSE, comment.char = "*"))
-    } else {
-      return(read.csv(fname, sep = ",", stringsAsFactors = FALSE, comment.char = "*"))
-    }
+    sep <- if (grepl(pattern = ";", x = readLines(fname, 1))) ";" else ","
+    return(read.csv(fname, sep = sep, stringsAsFactors = FALSE, comment.char = "*"))
   } else if (filetype == "rda") {
     data <- NULL
     load(fname)
-    if (is.null(data)) stop(fname, " did not contain a object named \"data\"!")
+    if (is.null(data)) stop(fname, " did not contain an object named \"data\"!")
     return(data)
   } else if (filetype == "rds") {
     return(readRDS(fname))

README.md

@@ -1,6 +1,6 @@
 # May All Data be Reproducible and Transparent (MADRaT) *
 
-R package **madrat**, version **3.6.10**
+R package **madrat**, version **3.7.0**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/madrat)](https://cran.r-project.org/package=madrat) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1115490.svg)](https://doi.org/10.5281/zenodo.1115490) [![R build status](https://github.com/pik-piam/madrat/workflows/check/badge.svg)](https://github.com/pik-piam/madrat/actions) [![codecov](https://codecov.io/gh/pik-piam/madrat/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/madrat) [![r-universe](https://pik-piam.r-universe.dev/badges/madrat)](https://pik-piam.r-universe.dev/builds)
 
@@ -55,7 +55,7 @@ In case of questions / problems please contact Jan Philipp Dietrich <dietrich@pi
 
 To cite package **madrat** in publications use:
 
-Dietrich J, Baumstark L, Wirth S, Giannousakis A, Rodrigues R, Bodirsky B, Leip D, Kreidenweis U, Klein D, Sauer P (2023). _madrat: May All Data be Reproducible and Transparent (MADRaT)_. doi:10.5281/zenodo.1115490 <https://doi.org/10.5281/zenodo.1115490>, R package version 3.6.10, <https://github.com/pik-piam/madrat>.
+Dietrich J, Baumstark L, Wirth S, Giannousakis A, Rodrigues R, Bodirsky B, Leip D, Kreidenweis U, Klein D, Sauer P (2023). _madrat: May All Data be Reproducible and Transparent (MADRaT)_. doi:10.5281/zenodo.1115490 <https://doi.org/10.5281/zenodo.1115490>, R package version 3.7.0, <https://github.com/pik-piam/madrat>.
 
 A BibTeX entry for LaTeX users is
 
@@ -64,7 +64,7 @@ A BibTeX entry for LaTeX users is
   title = {madrat: May All Data be Reproducible and Transparent (MADRaT)},
   author = {Jan Philipp Dietrich and Lavinia Baumstark and Stephen Wirth and Anastasis Giannousakis and Renato Rodrigues and Benjamin Leon Bodirsky and Debbora Leip and Ulrich Kreidenweis and David Klein and Pascal Sauer},
   year = {2023},
-  note = {R package version 3.6.10},
+  note = {R package version 3.7.0},
   doi = {10.5281/zenodo.1115490},
   url = {https://github.com/pik-piam/madrat},
 }

tests/testthat/test-toolGetMapping.R

@@ -36,7 +36,7 @@ test_that("toolGetMapping works", {
   a <- 1
   save(a, file = paste0(getConfig("mappingfolder"), "/test.rda"))
   writeLines("abc", paste0(getConfig("mappingfolder"), "/test.xyz"))
-  expect_error(toolGetMapping("test.rda", where = "mappingfolder"), "did not contain a object")
+  expect_error(toolGetMapping("test.rda", where = "mappingfolder"), "did not contain an object")
   expect_error(toolGetMapping("test.xyz"), "Unsupported filetype")
 
   readTest <- function() {