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Address lint violations from updated gDRstyle rules: - Fix trailing whitespace and blank lines - Replace nrow/ncol with NROW/NCOL - Fix paste_linter (paste0+collapse, toString, strrep, file.path) - Fix seq_linter (seq_along, seq_len) - Refactor cyclocomp_linter violations (extract helper functions) - Fix test linters (yoda, expect_true_false) - Remove undesirable operators (|> pipes)
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Code Review
This pull request standardizes row counting by replacing nrow() with NROW() across several R files and performs general code cleanup, including the removal of trailing whitespace. Review feedback suggests simplifying the barcode generation logic in R/generate_data.R for better efficiency. Additionally, a change in the vignette from paste0 to paste was flagged as it introduces unwanted extra spaces in the output formatting.
| add_data_replicates <- function(df_layout) { | ||
| df_layout_duplicates <- Reduce(rbind, list(df_layout)[rep(1, times = 3)]) | ||
| barcode <- do.call(c, lapply(paste0("plate_", seq_len(3)), function(x) rep(x, nrow(df_layout)))) | ||
| barcode <- do.call(c, lapply(paste0("plate_", seq_len(3)), function(x) rep(x, NROW(df_layout)))) |
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The generation of the barcode vector can be simplified and made more efficient by using the each argument of the rep function. This avoids the overhead of lapply and do.call(c, ...) while producing the same result.
barcode <- rep(paste0("plate_", seq_len(3)), each = NROW(df_layout))| ```{r echo=FALSE} | ||
| yml_path <- system.file(package = "gDRtestData", "testdata", "synthetic_list.yml") | ||
| cat(paste0("* ", names(yaml::read_yaml(yml_path)), collapse = ", \n"), ".") | ||
| cat(paste("* ", names(yaml::read_yaml(yml_path)), collapse = ", \n"), ".") |
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Changing paste0 to paste here introduces an unwanted extra space between the bullet point "* " and the dataset name. This is because paste uses a single space as the default separator (sep = " "). Since the prefix string already ends with a space, the resulting output will have two spaces (e.g., "* dataset_name"). To maintain the original formatting while addressing linting concerns, you should use paste0 or explicitly set sep = "".
cat(paste0("* ", names(yaml::read_yaml(yml_path)), collapse = ", \n"), ".")
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Description
What changed?
Related JIRA issue: GDR-1014
Why was it changed?
Updated gDRstyle linting rules require compliance across all gDR packages.
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