Merge branch 'add_file_extension_package_option' into 'main'

Add file extension package option

See merge request lpjml/lpjmlstats!10

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '337246'
+ValidationKey: '397120'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

.github/workflows/check.yaml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -35,7 +35,7 @@ jobs:
           # gms, goxygen, GDPuc) will usually have an outdated binary version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
+      - uses: actions/setup-python@v5
         with:
           python-version: 3.9
 
@@ -48,6 +48,11 @@ jobs:
         shell: Rscript {0}
         run: lucode2:::validkey(stopIfInvalid = TRUE)
 
+      - name: Verify that lucode2::buildLibrary was successful
+        if: github.event_name == 'pull_request'
+        shell: Rscript {0}
+        run: lucode2:::isVersionUpdated()
+
       - name: Checks
         shell: Rscript {0}
         run: |
@@ -56,6 +61,8 @@ 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"

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 exclude: '^tests/testthat/_snaps/.*$'
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: 2c9f875913ee60ca25ce70243dc24d5b6415598c  # frozen: v4.6.0
     hooks:
     -   id: check-case-conflict
     -   id: check-json
@@ -15,7 +15,7 @@ repos:
     -   id: mixed-line-ending
 
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.2.9019
+    rev: 7910e0323d7213f34275a7a562b9ef0fde8ce1b9  # frozen: v0.4.2
     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: 'lpjmlstats: Statistical tools for LPJmL data analysis'
-version: 0.1.7
-date-released: '2024-04-25'
+version: 0.2.0
+date-released: '2024-05-13'
 abstract: This package provides statistical tools for LPJmL data analysis to be used
   for benchmarking LPJmL outputs.
 authors:

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: lpjmlstats
 Title: Statistical tools for LPJmL data analysis
-Version: 0.1.7
+Version: 0.2.0
 Authors@R: c(person("David","Hötten", email = "[email protected]", role = c("aut", "cre")),
              person("Jannes","Breier", email = "[email protected]", role = c("aut")))
 Description: This package provides statistical tools for LPJmL data analysis
@@ -38,4 +38,4 @@ Config/testthat/edition: 3
 VignetteBuilder: knitr
 Depends:
     R (>= 3.5.0)
-Date: 2024-04-25
+Date: 2024-05-13

R/benchmark.R

@@ -177,7 +177,7 @@ benchmark <-
       list(
         baseline_dir = baseline_dir,
         under_test_dirs = under_test_dirs,
-        suffix = ".bin.json"
+        suffix = getOption("lpjmlstats.file_extension", default = ".bin.json")
       )
 
     sim_table <- create_simulation_table(paths)
@@ -285,11 +285,11 @@ create_simulation_table <- function(paths) {
   lpjml_version <- c()
 
   for (path in sim_paths) {
-    # read any file with a .bin.json extension in the directory
+    # read any file with the correct file extension in the directory
     # and extract the meta data
 
-    # get filename of any file with .bin.json extension in the directory
-    file <- list.files(path, pattern = ".bin.json", full.names = TRUE)[1]
+    # get filename of any fitting file
+    file <- list.files(path, pattern = paths$suffix, full.names = TRUE)[1]
 
     # get relevant meta information from that file
     meta <- lpjmlkit::read_meta(file)

R/package_settings.R

@@ -26,6 +26,9 @@
 #'   \item \code{metric_at_start}: A string to be matched against the
 #'   names of the metrics. The matched metrics will be run first
 #'   and displayed at the beginning of the report.
+#'
+#'   \item \code{file_extension}: A string indicating the file extension
+#'   to be used by read_io.
 #' }
 #'
 #'
@@ -76,6 +79,11 @@ set_lpjmlstats_settings <- function(...) {
           stop("metrics_at_start must be a character string")
         options(lpjmlstats.metrics_at_start = option_value) # nolint
       },
+      "file_extension" = {
+        if (!(is.character(option_value) | is.null(option_value)) | length(option_value) != 1)
+          stop("file_extension must be a character string")
+        options(lpjmlstats.file_extension = option_value) # nolint
+      },
       stop(paste("Invalid option:", option_name))
     )
   }

README.md

@@ -1,8 +1,8 @@
 # Statistical tools for LPJmL data analysis
 
-R package **lpjmlstats**, version **0.1.7**
+R package **lpjmlstats**, version **0.2.0**
 
-[![CRAN status](https://www.r-pkg.org/badges/version/lpjmlstats)](https://cran.r-project.org/package=lpjmlstats)  [![R build status](https://github.com/PIK-LPJmL/lpjmlstats//workflows/check/badge.svg)](https://github.com/PIK-LPJmL/lpjmlstats//actions) [![codecov](https://codecov.io/gh/PIK-LPJmL/lpjmlstats//branch/master/graph/badge.svg)](https://app.codecov.io/gh/PIK-LPJmL/lpjmlstats/) [![r-universe](https://pik-piam.r-universe.dev/badges/lpjmlstats)](https://pik-piam.r-universe.dev/builds)
+[![CRAN status](https://www.r-pkg.org/badges/version/lpjmlstats)](https://cran.r-project.org/package=lpjmlstats)  [![R build status](https://gitlab.pik-potsdam.de/lpjml/lpjmlstats/workflows/check/badge.svg)](https://gitlab.pik-potsdam.de/lpjml/lpjmlstats/actions) [![codecov](https://codecov.io/gh/lpjml/lpjmlstats/branch/master/graph/badge.svg)](https://app.codecov.io/gh/lpjml/lpjmlstats) [![r-universe](https://pik-piam.r-universe.dev/badges/lpjmlstats)](https://pik-piam.r-universe.dev/builds)
 
 ## Purpose and Functionality
 
@@ -48,7 +48,7 @@ In case of questions / problems please contact David Hötten <davidho@pik-potsda
 
 To cite package **lpjmlstats** in publications use:
 
-Hötten D, Breier J (2024). _lpjmlstats: Statistical tools for LPJmL data analysis_. R package version 0.1.7.
+Hötten D, Breier J (2024). _lpjmlstats: Statistical tools for LPJmL data analysis_. R package version 0.2.0.
 
 A BibTeX entry for LaTeX users is
 
@@ -57,6 +57,6 @@ A BibTeX entry for LaTeX users is
   title = {lpjmlstats: Statistical tools for LPJmL data analysis},
   author = {David Hötten and Jannes Breier},
   year = {2024},
-  note = {R package version 0.1.7},
+  note = {R package version 0.2.0},
 }
 ```