Merge branch 'fix_run_lpjml_inside_jobs' into 'master'

Fix run_lpjml call for jobs; change default to new HPC system.

See merge request lpjml/lpjmlkit!110

Author: stephnwirth

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '3612220'
+ValidationKey: '34827570'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

.github/workflows/check.yaml

@@ -4,11 +4,13 @@ on:
   push:
     branches: [main, master]
   pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
     branches: [main, master]
 
 jobs:
   check:
     runs-on: ubuntu-latest
+    if: github.event.pull_request.draft == false
 
     steps:
       - uses: actions/checkout@v4
@@ -58,9 +60,31 @@ jobs:
           lucode2::check(runLinter = FALSE)
 
       - name: Test coverage
+        if: ${{ github.event_name != 'pull_request' }}
         shell: Rscript {0}
         run: |
           nonDummyTests <- setdiff(list.files("./tests/testthat/"), c("test-dummy.R", "_snaps"))
-          if(length(nonDummyTests) > 0 && !lucode2:::loadBuildLibraryConfig()[["skipCoverage"]]) covr::codecov(quiet = FALSE)
+          if(length(nonDummyTests) > 0 && !lucode2:::loadBuildLibraryConfig()[["skipCoverage"]]) {
+            coverage <- covr::package_coverage(quiet = FALSE)
+            # The following function might be unnecessary if r-lib/covr#616 gets merged
+            to_simple_codecov <- function(coverage) {
+              fullLineCoverage <- covr:::per_line(coverage)
+              data <- Map(function(fileCoverage) {
+                resultCoverage <- lapply(fileCoverage$coverage, jsonlite::unbox)
+                names(resultCoverage) <- seq_along(resultCoverage)
+                return(resultCoverage)
+              }, fullLineCoverage)
+              return(jsonlite::toJSON(list("coverage" = data), na = "null"))
+            }
+            writeLines(to_simple_codecov(coverage), "simple-codecov.json")
+          }
         env:
           NOT_CRAN: "true"
+
+      - uses: codecov/codecov-action@v4
+        if: ${{ github.event_name != 'pull_request' }}
+        with:
+          file: ./simple-codecov.json
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}

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: 'lpjmlkit: Toolkit for Basic LPJmL Handling'
-version: 1.7.9
-date-released: '2025-04-02'
+version: 1.7.10
+date-released: '2025-10-06'
 abstract: A collection of basic functions to facilitate the work with the Dynamic
   Global Vegetation Model (DGVM) Lund-Potsdam-Jena managed Land (LPJmL) hosted at
   the Potsdam Institute for Climate Impact Research (PIK). It provides functions for

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: lpjmlkit
 Type: Package
 Title: Toolkit for Basic LPJmL Handling
-Version: 1.7.9
+Version: 1.7.10
 Authors@R: c(
     person("Jannes", "Breier", , "jannesbr@pik-potsdam.de", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9055-6904")),
     person("Sebastian","Ostberg", , "ostberg@pik-potsdam.de", role = "aut", comment = c(ORCID = "0000-0002-2368-7015")),
@@ -56,4 +56,4 @@ Suggests:
     R6
 Config/testthat/edition: 3
 VignetteBuilder: knitr
-Date: 2025-04-02
+Date: 2025-10-06

R/run_lpjml.R

@@ -38,6 +38,9 @@
 #' @param output_path Argument is deprecated as of version 1.0; use sim_path
 #'   instead.
 #'
+#' @param debug Logical. If `TRUE`, only the command to run LPJmL is printed
+#'   and parallelization is switched off.
+#'
 #' @return See `x`, extended by columns `"type"`, `"job_id"` and `"status"`.
 #'
 #' @details
@@ -164,17 +167,23 @@
 #'
 #' @md
 #' @export
-run_lpjml <- function(x,
+run_lpjml <- function(x, # nolint:cyclocomp_linter.
                       model_path = ".",
                       sim_path = NULL,
-                      run_cmd = "srun --propagate",
+                      run_cmd = "mpirun ",
                       parallel_cores = 1,
                       write_stdout = FALSE,
                       raise_error = TRUE,
-                      output_path = NULL) {
+                      output_path = NULL,
+                      debug = FALSE) {
 
   warn_runner_os("run_lpjml")
 
+  if (run_cmd != "" && !grepl(" $", run_cmd)) {
+    run_cmd <- paste0(run_cmd, " ")
+    message("Note: Added trailing space to run_cmd")
+  }
+
   # Check if model_path is set or unit test flag provided
   if (!dir.exists(model_path)) {
     stop("Folder of model_path \"", model_path, "\" does not exist.")
@@ -212,9 +221,10 @@ run_lpjml <- function(x,
     for (order in unique(sort(x$order))) {
       sim_names <- x$sim_name[which(x$order == order)]
 
-      if (parallel_cores == 1) {
+      if (parallel_cores == 1 || debug) { # nolint:undesirable_function_linter.
         do_sequential(
-          sim_names, model_path, sim_path, run_cmd, write_stdout, raise_error
+          sim_names, model_path, sim_path, run_cmd, write_stdout, raise_error,
+          debug = debug # nolint:undesirable_function_linter.
         )
       } else if (parallel_cores > 1 && Sys.getenv("SLURM_JOB_ID") != "") {
         do_parallel(
@@ -230,9 +240,10 @@ run_lpjml <- function(x,
     }
 
   } else {
-    if (parallel_cores == 1) {
+    if (parallel_cores == 1 || debug) { # nolint:undesirable_function_linter.
       do_sequential(
-        x$sim_name, model_path, sim_path, run_cmd, write_stdout, raise_error
+        x$sim_name, model_path, sim_path, run_cmd, write_stdout, raise_error,
+        debug = debug # nolint:undesirable_function_linter.
       )
     } else if (parallel_cores > 1 && Sys.getenv("SLURM_JOB_ID") != "") {
       do_parallel(
@@ -258,7 +269,8 @@ do_run <- function(sim_name,
                    sim_path,
                    run_cmd,
                    write_stdout,
-                   raise_error) {
+                   raise_error,
+                   debug) {
 
   config_file <- paste0("config_",
                         sim_name,
@@ -279,6 +291,9 @@ do_run <- function(sim_name,
                            sim_path,
                            "/configurations/",
                            config_file)
+  if (debug) { # nolint:undesirable_function_linter.
+    message("Debug mode is on, only printing command:\n", inner_command)
+  }
 
   stdout_file <- ifelse(write_stdout,
                         paste0(sim_path,
@@ -328,7 +343,8 @@ do_sequential <- function(sim_names,
                           sim_path,
                           run_cmd,
                           write_stdout,
-                          raise_error) {
+                          raise_error,
+                          debug) {
 
   # tryCatch to unset and set MPI for function call outside of slurm job on
   #   an HPC cluster even when function call is interrupted or has thrown
@@ -343,12 +359,13 @@ do_sequential <- function(sim_names,
       mpi_var <- NULL
       # If not specified by the user set number of processes to 1 to run lpjml
       #  in interactive mode
-      if (run_cmd == "mpirun") {
+      if (run_cmd == "mpirun " && Sys.getenv("SLURM_JOB_ID") == "") {
         run_cmd <- paste0(run_cmd, " -np 1 ")
       }
     }
     for (sim_name in sim_names) {
-      do_run(sim_name, model_path, sim_path, run_cmd, write_stdout, raise_error)
+      do_run(sim_name, model_path, sim_path, run_cmd, write_stdout, raise_error,
+             debug = debug) # nolint:undesirable_function_linter.
     }
   }, finally = {
     # Check if slurm is available

README.md

@@ -1,6 +1,6 @@
 # <a href=''><img src='inst/img/logo.png' align='right' alt='logo' height=139 /></a> Toolkit for Basic LPJmL Handling
 
-R package **lpjmlkit**, version **1.7.9**
+R package **lpjmlkit**, version **1.7.10**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/lpjmlkit)](https://cran.r-project.org/package=lpjmlkit) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7773134.svg)](https://doi.org/10.5281/zenodo.7773134) [![R build status](https://github.com/PIK-LPJmL/lpjmlkit/workflows/check/badge.svg)](https://github.com/PIK-LPJmL/lpjmlkit/actions) [![codecov](https://codecov.io/gh/PIK-LPJmL/lpjmlkit/branch/master/graph/badge.svg)](https://app.codecov.io/gh/PIK-LPJmL/lpjmlkit) [![r-universe](https://pik-piam.r-universe.dev/badges/lpjmlkit)](https://pik-piam.r-universe.dev/builds)
 
@@ -76,7 +76,7 @@ In case of questions / problems please contact Jannes Breier <jannesbr@pik-potsd
 
 To cite package **lpjmlkit** in publications use:
 
-Breier J, Ostberg S, Wirth S, Minoli S, Stenzel F, Hötten D, Müller C (2025). "lpjmlkit: Toolkit for Basic LPJmL Handling." doi:10.5281/zenodo.7773134 <https://doi.org/10.5281/zenodo.7773134>, Version: 1.7.9, <https://github.com/PIK-LPJmL/lpjmlkit>.
+Breier J, Ostberg S, Wirth S, Minoli S, Stenzel F, Hötten D, Müller C (2025). "lpjmlkit: Toolkit for Basic LPJmL Handling." doi:10.5281/zenodo.7773134 <https://doi.org/10.5281/zenodo.7773134>, Version: 1.7.10, <https://github.com/PIK-LPJmL/lpjmlkit>.
 
 A BibTeX entry for LaTeX users is
 
@@ -85,9 +85,9 @@ A BibTeX entry for LaTeX users is
   title = {lpjmlkit: Toolkit for Basic LPJmL Handling},
   author = {Jannes Breier and Sebastian Ostberg and Stephen Björn Wirth and Sara Minoli and Fabian Stenzel and David Hötten and Christoph Müller},
   doi = {10.5281/zenodo.7773134},
-  date = {2025-04-02},
+  date = {2025-10-06},
   year = {2025},
   url = {https://github.com/PIK-LPJmL/lpjmlkit},
-  note = {Version: 1.7.9},
+  note = {Version: 1.7.10},
 }
 ```