Release rbi 1.0.1

.Rbuildignore

@@ -12,3 +12,5 @@ _pkgdown.yml
 docs/
 ^.lintr$
 ^CRAN-SUBMISSION$
+^\.claude$
+^\.coderabbit\.yaml$

.coderabbit.yaml

@@ -0,0 +1,2 @@
+reviews:
+  request_changes_workflow: true

.github/workflows/R-CMD-check-docker.yaml

@@ -37,7 +37,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/R-CMD-check.yaml

@@ -21,9 +21,10 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      OMP_NUM_THREADS: 1
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/_pkgdown.yml

@@ -20,7 +20,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/lint_changed_files.yaml

@@ -16,7 +16,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
 

.github/workflows/render_readme.yml

@@ -24,7 +24,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - name: Checkout repos
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Setup R
         uses: r-lib/actions/setup-r@v2

.github/workflows/test-coverage.yaml

@@ -19,7 +19,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -61,7 +61,7 @@ jobs:
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: rbi
-Version: 1.0.0.9000
+Version: 1.0.1
 Title: Interface to 'LibBi'
 Authors@R:
     c(
@@ -38,7 +38,7 @@ URL: https://github.com/sbfnk/rbi
 BugReports: https://github.com/sbfnk/rbi/issues
 SystemRequirements: LibBi (>= 1.4.2)
 LazyLoad: no
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.3
 Language: en-GB
 Encoding: UTF-8
 VignetteBuilder: knitr

NAMESPACE

@@ -105,5 +105,6 @@ importFrom(processx,run)
 importFrom(reshape2,melt)
 importFrom(stats,as.formula)
 importFrom(stats,median)
+importFrom(stats,na.omit)
 importFrom(stats,quantile)
 importFrom(stats,runif)

NEWS.md

@@ -1,6 +1,7 @@
-# rbi (development version)
+# rbi 1.0.1
 
-* work with character columns in sparse input data
+* Character columns in sparse input data are now correctly handled by
+  converting them to factors (#54).
 
 # rbi 1.0.0
 

R/bi_write.R

@@ -340,7 +340,7 @@ bi_write <- function(filename, variables, append = FALSE, overwrite = FALSE,
 
   nc_close(nc)
 
-  return(list(time_dim = time_dim, coord_dims = coord_dims, dims = dim_factors))
+  list(time_dim = time_dim, coord_dims = coord_dims, dims = dim_factors)
 }
 
 ##' Check if a variable is sparse
@@ -379,7 +379,7 @@ check_sparse_var <- function(x, coord_cols, value_column) {
     length(setdiff(levels(all_values[[x]]), all_values[[x]])) == 0
   }, logical(1))
 
-  return(any(!all[["all_equal"]]) || any(!all_factors))
+  any(!all[["all_equal"]]) || any(!all_factors)
 }
 
 ##' Create a coordinate variable
@@ -457,17 +457,19 @@ create_coord_var <- function(name, dims, dim_factors, coord_dim, index_table,
     coord_var_dims <- c(list(ns_dim), coord_var_dims)
   }
   var <- ncvar_def(coord_var, "", coord_var_dims)
-  return(list(
+  list(
     name = coord_var, values = values, var = var,
     dim = coord_index_dim, dim_factors = dim_factors
-  ))
+  )
 }
 
 ##' Get the factor levels of all character columns in data
 ##'
 ##' @param ... variable lists
 ##' @return a list with elements that represent the factor levels present in
 ##'   character columns
+##' @importFrom stats na.omit
+##' @keywords internal
 ##' @author Sebastian Funk
 get_char_levels <- function(...) {
   levels <- list()
@@ -484,14 +486,15 @@ get_char_levels <- function(...) {
       }
     }
   }
-  return(levels)
+  levels
 }
 
 ##' Convert character columns to factors in data
 ##'
 ##' @param levels factor levels, as a named list, each representing one column
 ##' @inheritParams bi_write
 ##' @return the \code{variables} argument with factorised columns
+##' @keywords internal
 ##' @author Sebastian Funk
 factorise <- function(variables, levels) {
   data_frames <- names(variables)[
@@ -504,9 +507,9 @@ factorise <- function(variables, levels) {
         if (col %in% colnames(df)) {
           df[[col]] <- factor(df[[col]], levels = levels[[col]])
         }
-        return(df)
+        df
       })
     }
   }
-  return(variables)
+  variables
 }

R/libbi.R

@@ -64,13 +64,13 @@ libbi <- function(model, path_to_libbi, dims, use_cache = TRUE, ...) {
   dot_options <- list(...)
   if ("norun" %in% names(dot_options) && dot_options[["norun"]]) {
     new_obj$model <- model
-    return(new_obj)
+    new_obj
   } else {
-    return(do.call(
+    do.call(
       run.libbi, c(
         list(x = new_obj, model = model, client = character(0)), dot_options
       )
-    ))
+    )
   }
 }
 
@@ -510,7 +510,16 @@ run.libbi <- function(x, client, proposal = c("model", "prior"), model, fix,
             )
           )
         )
-      stop_msg <- paste0("LibBi terminated with \"", error_msg[1], "\".")
+      if (length(error_msg) == 0 || is.na(error_msg[1])) {
+        stop_msg <- paste0(
+          "LibBi terminated with exit code ", p$status, "."
+        )
+        if (nchar(p$stderr) > 0) {
+          stop_msg <- paste0(stop_msg, "\nstderr: ", p$stderr)
+        }
+      } else {
+        stop_msg <- paste0("LibBi terminated with \"", error_msg[1], "\".")
+      }
       if (length(x$log_file_name) > 0) {
         stop_msg <- paste0(
           stop_msg, "\nYou can view a full log using \"print_log('",
@@ -533,13 +542,13 @@ run.libbi <- function(x, client, proposal = c("model", "prior"), model, fix,
       x <- update(x)
       ## get original model back if it has been modified
       x$model <- save_model
-      return(x)
+      x
     }
   } else {
     ## if run from the constructor, just write the model and add all the options
     write_model(x)
     x$options <- all_options
-    return(x)
+    x
   }
 }
 
@@ -878,7 +887,7 @@ attach_data.libbi <- function(x, file, data, in_place = FALSE, append = FALSE,
     x$options[[paste0(file, "-file")]] <- target_file_name
     x$timestamp[[file]] <- file.mtime(target_file_name)
   }
-  return(x)
+  x
 }
 
 #' @export
@@ -1063,7 +1072,7 @@ read_libbi <- function(name, ...) {
 
   new_obj$supplement <- read_obj$supplement
 
-  return(new_obj)
+  new_obj
 }
 
 #' @export
@@ -1199,7 +1208,7 @@ summary.libbi <- function(object, type = c("param", "state", "noise", "obs"),
         na.rm = na.rm
       ))
     ), by = summarise_columns]
-    return(dt)
+    dt
   }))
   ## reorder table
   numeric_columns <- c(
@@ -1225,7 +1234,7 @@ summary.libbi <- function(object, type = c("param", "state", "noise", "obs"),
   )
   setDF(summary_table)
 
-  return(summary_table)
+  summary_table
 }
 
 #' @keywords internal
@@ -1336,7 +1345,7 @@ sample_obs <- function(x, ...) {
     x$options[["without-transform-obs-to-state"]]
   pr$model <- x$model
 
-  return(pr)
+  pr
 }
 
 #' @export
@@ -1395,9 +1404,9 @@ logLik.libbi <- function(object, ...) {
   assert_files(object)
   res <- bi_read(object)
   if (is.vector(res$loglikelihood)) {
-    return(res$loglikelihood)
+    res$loglikelihood
   } else {
-    return(res$loglikelihood$value)
+    res$loglikelihood$value
   }
 }
 
@@ -1432,7 +1441,7 @@ update.libbi <- function(x, ...) {
       x$timestamp[["output"]] <- file.mtime(x$output_file_name)
     }
   }
-  return(x)
+  x
 }
 #' @export
 update.default <- function(x, ...) {
@@ -1455,5 +1464,5 @@ create_working_folder <- function(x) {
   reg.finalizer(x$.gc_env, function(env) {
     unlink(env$folder, recursive = TRUE)
   }, onexit = TRUE)
-  return(x)
+  x
 }

codecov.yml

@@ -1,2 +1,11 @@
 codecov:
  token: 14c79f07-68d5-4cc4-b1fd-66a5aae3251e
+
+coverage:
+  status:
+    project:
+      default:
+        enabled: false
+    patch:
+      default:
+        enabled: false

cran-comments.md

@@ -1,13 +1,7 @@
 ## Test environments
-* local macOS install, R 4.3.1
-* github Actions (macOS and Linux)
-* checked with devtools::check_win_devel()
+* local macOS install (aarch64), R 4.5.2
+* GitHub Actions (macOS), R release
+* GitHub Actions (Ubuntu), R release, R devel, R oldrel-1
 
 ## R CMD check results
-There were no ERRORs or WARNINGs, or NOTEs.
-
-## Downstream dependencies
-0 packages with problems.
-
-## Updates after initial submission.
-A reverse dependency issue with rbi.helpers is expected and being fixed by submitting an updated version of rbi.helpers to CRAN.
+There were no ERRORs, WARNINGs, or NOTEs.

tests/testthat/test-libbi.r

@@ -1,5 +1,7 @@
 context("Testing running libbi")
 
+options(libbi_args = list(assert = FALSE))
+
 model_str <- "
 model test {
   const no_a = 2
@@ -60,7 +62,7 @@ test_output <-
 bi <- attach_data(bi, "output", test_output)
 
 config_tmp_file <- tempfile(fileext = ".conf")
-writeLines("--enable-assert", config_tmp_file)
+writeLines("--disable-assert", config_tmp_file)
 log_tmp_file <- tempfile(fileext = ".log")
 output_tmp_file <- tempfile(fileext = ".nc")
 model_tmp_file <- tempfile(fileext = ".bi")