Merge pull request #212 from pascal-sauer/master

fix "Selection:" prompt during puc creation (actually during .fillRenvCache)

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '62025600'
+ValidationKey: '62126626'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

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: 3.12.0
-date-released: '2024-06-06'
+version: 3.12.1
+date-released: '2024-07-02'
 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
@@ -14,7 +14,7 @@ authors:
 - family-names: Dietrich
   given-names: Jan Philipp
   email: [email protected]
-  orcid: 0000-0002-4309-6431
+  orcid: https://orcid.org/0000-0002-4309-6431
   affiliation: Potsdam Institute for Climate Impact Research
 - family-names: Baumstark
   given-names: Lavinia
@@ -51,7 +51,8 @@ authors:
   email: [email protected]
   affiliation: Potsdam Institute for Climate Impact Research
 license: BSD-2-Clause
-keywords: tool
+keywords:
+- tool
 repository-code: https://github.com/pik-piam/madrat
 doi: 10.5281/zenodo.1115490
 

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: madrat
 Title: May All Data be Reproducible and Transparent (MADRaT) *
-Version: 3.12.0
-Date: 2024-06-06
+Version: 3.12.1
+Date: 2024-07-02
 Authors@R: c(
     person("Jan Philipp", "Dietrich", , "[email protected]", role = c("aut", "cre"),
            comment = c(affiliation = "Potsdam Institute for Climate Impact Research", ORCID = "0000-0002-4309-6431")),
@@ -66,4 +66,4 @@ VignetteBuilder:
 Config/Keywords: tool
 Encoding: UTF-8
 LazyData: no
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

R/retrieveData.R

@@ -350,28 +350,24 @@ retrieveData <- function(model, rev = 0, dev = "", cachetype = "def", puc = iden
 
   vcat(3, paste(utils::capture.output({
     dummyProject <- withr::local_tempdir()
-    initRenv <- function() {
+    initHydrateSnapshotRenv <- function(requiredPackages) {
       renv::init()
-      return(normalizePath(renv::paths$library()))
+      # hydrate requiredPackages into throwaway renv to ensure they can be restored from cache on this machine
+      if (utils::packageVersion("renv") >= numeric_version("0.17.0")) {
+        renv::hydrate(packages = requiredPackages, report = TRUE, prompt = FALSE)
+      } else {
+        # call without `report = TRUE, prompt = FALSE` as these were unavailable before renv 0.17.0
+        renv::hydrate(packages = requiredPackages)
+      }
+      # create an renv.lock file documenting all package versions, see renv parameter of pucAggregate
+      renv::snapshot(type = "all", prompt = FALSE)
     }
     # init renv in separate session to prevent changes to current session's libpath
-    dummyLibPath <- callr::r(initRenv, wd = dummyProject, spinner = FALSE, show = TRUE)
-
-    # hydrate requiredPackages into throwaway renv to ensure they can be restored from cache on this machine
-    # run renv::hydrate outside of callr, otherwise site library would not be used if running in renv
-    if (utils::packageVersion("renv") >= numeric_version("0.17.0")) {
-      renv::hydrate(packages = requiredPackages, library = dummyLibPath, project = dummyProject,
-                    report = TRUE, prompt = FALSE)
-    } else {
-      # call without `report = TRUE, prompt = FALSE` as these were unavailable before renv 0.17.0
-      renv::hydrate(packages = requiredPackages, library = dummyLibPath, project = dummyProject)
-    }
-
-    # create an renv.lock file documenting all package versions, see renv parameter of pucAggregate
-    renv::snapshot(project = dummyProject, library = dummyLibPath, prompt = FALSE,
-                   lockfile = "./renv.lock", type = "all")
+    callr::r(initHydrateSnapshotRenv, args = list(requiredPackages = requiredPackages),
+             wd = dummyProject, spinner = FALSE, show = TRUE)
 
     # (unlikely) caveat: if packages are updated while retrieveData is running a package's version
     # in the created renv.lock might not match the version used to run the full functions
   }), collapse = "\n"))
+  return(invisible(NULL))
 }

README.md

@@ -1,6 +1,6 @@
 # May All Data be Reproducible and Transparent (MADRaT) *
 
-R package **madrat**, version **3.12.0**
+R package **madrat**, version **3.12.1**
 
 [![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 (2024). _madrat: May All Data be Reproducible and Transparent (MADRaT)_. doi:10.5281/zenodo.1115490 <https://doi.org/10.5281/zenodo.1115490>, R package version 3.12.0, <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 (2024). _madrat: May All Data be Reproducible and Transparent (MADRaT)_. doi:10.5281/zenodo.1115490 <https://doi.org/10.5281/zenodo.1115490>, R package version 3.12.1, <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 = {2024},
-  note = {R package version 3.12.0},
+  note = {R package version 3.12.1},
   url = {https://github.com/pik-piam/madrat},
   doi = {10.5281/zenodo.1115490},
 }

tests/testthat/test-toolAggregate.R

@@ -222,7 +222,7 @@ test_that("Edge cases work", {
 test_that("columns with only zeros in weight produce a warning", {
   weight <- pm
   weight[, , ] <- 0
-  expect_message(toolAggregate(pm, rel, weight = weight), "Weight sum is 0")
+  expect_warning(toolAggregate(pm, rel, weight = weight), "Weight sum is 0")
   expect_error(toolAggregate(pm, rel, weight = weight, zeroWeight = "stop"), "Weight sum is 0")
   expect_silent(toolAggregate(pm, rel, weight = weight, zeroWeight = "allow"))
 })