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Merged
Bai-Li-NOAA merged 1 commit into from
Jan 15, 2026
Merged

Style code and document #1110

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24 changes: 12 additions & 12 deletions vignettes/fims-user-setup-guide.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -37,37 +37,37 @@ knitr::opts_chunk$set(echo = TRUE)
extract_remote_markdown <- function(url, header_pattern) {
lines <- try(readLines(url, warn = FALSE), silent = TRUE)
tmp <- tempfile(fileext = ".md")

if (inherits(lines, "try-error")) {
writeLines("_Documentation temporarily unreachable._", tmp)
return(tmp)
}

# Find the starting line (e.g., the line containing "## WSL2")
start_idx <- grep(header_pattern, lines, ignore.case = TRUE)

if (length(start_idx) > 0) {
# Determine the level of the header found (count the # symbols)
header_line <- lines[start_idx]
header_level <- nchar(gsub("(^#+).*", "\\1", header_line))

# Find headers that are at the SAME level or HIGHER (fewer or equal #)
# We want to ignore ### if we are looking for a ## section
stop_pattern <- paste0("^#{1,", header_level, "} ")
all_potential_stops <- grep(stop_pattern, lines)

# The end index is the next header that isn't the current one
end_idx <- all_potential_stops[all_potential_stops > start_idx][1]

if (is.na(end_idx)) end_idx <- length(lines) else end_idx <- end_idx - 1

# Extract and add blank lines for proper RMarkdown list rendering
content <- c("", lines[(start_idx + 1):end_idx], "")
content <- c("", lines[(start_idx + 1):end_idx], "")
writeLines(content, tmp)
} else {
writeLines("_Section not found in remote documentation._", tmp)
}

return(tmp)
}
```
Expand All @@ -92,8 +92,8 @@ common_script <- "bash <(curl -sL https://raw.githubusercontent.com/NOAA-FIMS/FI
# The R script to verify FIMS is ready to be used
fims_demo_rscript <- "
knitr::purl(
input = 'https://raw.githubusercontent.com/NOAA-FIMS/FIMS/refs/heads/main/vignettes/fims-demo.Rmd',
output = 'fims_demo.R',
input = 'https://raw.githubusercontent.com/NOAA-FIMS/FIMS/refs/heads/main/vignettes/fims-demo.Rmd',
output = 'fims_demo.R',
documentation = 0
)

Expand Down Expand Up @@ -279,4 +279,4 @@ cat("\n```")

## 🙋 Need Help?

To report errors in this guide, please [open an issue](https://github.com/NOAA-FIMS/FIMS/issues) on GitHub.
To report errors in this guide, please [open an issue](https://github.com/NOAA-FIMS/FIMS/issues) on GitHub.
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