let as.quitte support lists

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '610998170'
+ValidationKey: '612505180'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

.github/workflows/check.yaml

@@ -1,5 +1,3 @@
-# Run CI for R using https://eddelbuettel.github.io/r-ci/
-
 name: check
 
 on:
@@ -8,92 +6,44 @@ on:
   pull_request:
     branches: [main, master]
 
-env:
-  USE_BSPM: "true"
-  _R_CHECK_FORCE_SUGGESTS_: "false"
-  NO_BINARY_INSTALL_R_PACKAGES: 'c("madrat", "magclass", "citation", "gms", "goxygen", "GDPuc", "roxygen2")'
-
 jobs:
   check:
     runs-on: ubuntu-latest
 
     steps:
       - uses: actions/checkout@v3
 
-      - name: Bootstrap
-        run: |
-          sudo chown runner -R .
-          sudo locale-gen en_US.UTF-8
-          sudo add-apt-repository -y ppa:ubuntugis/ppa
-          curl -OLs https://eddelbuettel.github.io/r-ci/run.sh
-          chmod 0755 run.sh
-          ./run.sh bootstrap
-          rm -f bspm_*.tar.gz
-
-      - name: Enable r-universe repo, modify bspm integration
-        run: |
-          # install packages from https://pik-piam.r-universe.dev and CRAN
-          echo '
-          options(repos = c(universe = "https://pik-piam.r-universe.dev",
-                            CRAN = "https://cloud.r-project.org"))
-          ' >> .Rprofile
-          cat .Rprofile
-          # modify bspm integration to never install binary builds of PIK CRAN packages
-          sudo sed -i '/bspm::enable()/d' /etc/R/Rprofile.site
-          # need double % because of printf, %s is replaced with "$NO_BINARY_INSTALL_R_PACKAGES" (see "env:" above)
-          printf '
-          local({
-            expr <- quote({
-              if (!is.null(repos)) {
-                noBinaryInstallRPackages <- %s
-                pkgs <- c(bspm::install_sys(pkgs[!pkgs %%in%% noBinaryInstallRPackages]),
-                          pkgs[pkgs %%in%% noBinaryInstallRPackages])
-              }
-              type <- "source"
-            })
-            trace(utils::install.packages, expr, print = FALSE)
-          })
-          ' "$NO_BINARY_INSTALL_R_PACKAGES" | sudo tee --append /etc/R/Rprofile.site >/dev/null
-          cat /etc/R/Rprofile.site
-
-      - name: Set up Pandoc
-        uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v4
+      - uses: r-lib/actions/setup-r@v2
         with:
-          python-version: 3.9
+          use-public-rspm: true
+          extra-repositories: "https://rse.pik-potsdam.de/r/packages"
 
-      - name: Cache R libraries
-        if: ${{ !env.ACT }} # skip when running locally via nektos/act
-        uses: pat-s/always-upload-cache@v3
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: /usr/local/lib/R/
-          key: 3-${{ runner.os }}-usr-local-lib-R-${{ hashFiles('DESCRIPTION') }}
-          restore-keys: |
-            3-${{ runner.os }}-usr-local-lib-R-
-
-      - name: Restore R library permissions
-        run: |
-          sudo chmod 2777 /usr/local/lib/R /usr/local/lib/R/site-library
-
-      - name: Install dependencies
-        run: |
-          ./run.sh install_aptget libhdf5-dev libharfbuzz-dev libfribidi-dev
-          ./run.sh install_all
-          ./run.sh install_r_binary covr rstudioapi
-          ./run.sh install_r lucode2
+          extra-packages: |
+            any::lucode2
+            any::covr
+            any::madrat
+            any::magclass
+            any::citation
+            any::gms
+            any::goxygen
+            any::GDPuc
+          # piam packages also available on CRAN (madrat, magclass, citation,
+          # gms, goxygen, GDPuc) will usually have an outdated binary version
+          # available; by using extra-packages we get the newest version
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
 
       - name: Install python dependencies if applicable
         run: |
           [ -f requirements.txt ] && python -m pip install --upgrade pip wheel || true
           [ -f requirements.txt ] && pip install -r requirements.txt || true
 
-      - name: Remove bspm integration # to get rid of error when running install.packages
-        run: |
-          sudo sed -i '/  trace(utils::install.packages, expr, print = FALSE)/d' /etc/R/Rprofile.site
-          cat /etc/R/Rprofile.site
-
       - name: Verify validation key
         shell: Rscript {0}
         run: lucode2:::validkey(stopIfInvalid = TRUE)

.pre-commit-config.yaml

@@ -15,7 +15,7 @@ repos:
     -   id: mixed-line-ending
 
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.2.9013
+    rev: v0.3.2.9019
     hooks:
     -   id: parsable-R
     -   id: deps-in-desc

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: 'quitte: Bits and pieces of code to use with quitte-style data frames'
-version: 0.3121.0
-date-released: '2023-08-08'
+version: 0.3122.0
+date-released: '2023-09-19'
 abstract: A collection of functions for easily dealing with quitte-style data frames,
   doing multi-model comparisons and plots.
 authors:

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: quitte
 Title: Bits and pieces of code to use with quitte-style data frames
-Version: 0.3121.0
-Date: 2023-08-08
+Version: 0.3122.0
+Date: 2023-09-19
 Authors@R: c(
     person("Michaja", "Pehl", , "[email protected]", role = c("aut", "cre")),
     person("Nico", "Bauer", , "[email protected]", role = "aut"),

Makefile

@@ -11,8 +11,9 @@ HELP_PARSING = 'm <- readLines("Makefile");\
 help:           ## Show this help.
 	@Rscript -e $(HELP_PARSING)
 
-build:          ## Build the package using lucode2::buildLibrary().
-	Rscript -e 'lucode2::buildLibrary()'
+build:          ## Build the package using lucode2::buildLibrary(). You can pass the
+                ## updateType with 'make build u=3'
+	Rscript -e 'lucode2::buildLibrary(updateType = "$(u)")'
 
 check:          ## Build documentation and vignettes, run testthat tests,
                 ## and check if code etiquette is followed using lucode2::check().

NAMESPACE

@@ -2,6 +2,7 @@
 
 S3method(as.quitte,character)
 S3method(as.quitte,data.frame)
+S3method(as.quitte,list)
 S3method(as.quitte,magpie)
 S3method(as.quitte,quitte)
 export(ISOyear)

R/as.quitte.R

@@ -228,7 +228,17 @@ as.quitte.magpie <- function(x, periodClass = "integer", addNA = FALSE, na.rm =
     class(x) <- c("quitte", class(x))
 
     return(x)
-  }
+}
+
+#' @method as.quitte list
+#' @export
+as.quitte.list <- function(x, periodClass = "integer", addNA = FALSE, na.rm = FALSE) { # nolint
+    out <- NULL
+    for (xi in x) {
+      out <- rbind(out, as.quitte(xi, periodClass = periodClass, addNA = addNA, na.rm = na.rm))
+    }
+    return(out)
+}
 
 qaddNA <- function(x) {
   for (col in colnames(x)) {

README.md

@@ -1,6 +1,6 @@
 # Bits and pieces of code to use with quitte-style data frames
 
-R package **quitte**, version **0.3121.0**
+R package **quitte**, version **0.3122.0**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/quitte)](https://cran.r-project.org/package=quitte)  [![R build status](https://github.com/pik-piam/quitte/workflows/check/badge.svg)](https://github.com/pik-piam/quitte/actions) [![codecov](https://codecov.io/gh/pik-piam/quitte/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/quitte) [![r-universe](https://pik-piam.r-universe.dev/badges/quitte)](https://pik-piam.r-universe.dev/builds)
 
@@ -47,7 +47,7 @@ In case of questions / problems please contact Michaja Pehl <michaja.pehl@pik-po
 
 To cite package **quitte** in publications use:
 
-Pehl M, Bauer N, Hilaire J, Levesque A, Luderer G, Schultes A, Dietrich J, Richters O (2023). _quitte: Bits and pieces of code to use with quitte-style data frames_. R package version 0.3121.0, <https://github.com/pik-piam/quitte>.
+Pehl M, Bauer N, Hilaire J, Levesque A, Luderer G, Schultes A, Dietrich J, Richters O (2023). _quitte: Bits and pieces of code to use with quitte-style data frames_. R package version 0.3122.0, <URL: https://github.com/pik-piam/quitte>.
 
 A BibTeX entry for LaTeX users is
 
@@ -56,7 +56,7 @@ A BibTeX entry for LaTeX users is
   title = {quitte: Bits and pieces of code to use with quitte-style data frames},
   author = {Michaja Pehl and Nico Bauer and Jérôme Hilaire and Antoine Levesque and Gunnar Luderer and Anselm Schultes and Jan Philipp Dietrich and Oliver Richters},
   year = {2023},
-  note = {R package version 0.3121.0},
+  note = {R package version 0.3122.0},
   url = {https://github.com/pik-piam/quitte},
 }
 ```

tests/testthat/test-as.quitte.R

@@ -74,3 +74,15 @@ test_that(
                      as.quitte(semicolonfile))
   }
 )
+
+test_that(
+  'as.quitte understands lists()',
+  {
+    expect_identical(quitte_example_data, as.quitte(list(list(quitte_example_data))))
+    miffile <- tempfile(fileext = ".mif")
+    writeLines(c("Model,Scenario,Region,Variable,Unit,2005,2010",
+                 "REMIND,Base,World,FE,EJ/yr,12,14"),
+               con = miffile, sep = "\n")
+    expect_identical(as.quitte(miffile), as.quitte(list(miffile)))
+  }
+)