jokergoo / getoptlong

Parse command-line arguments and simple variable interpolation

Activities on my repos (R packages, 2013-04-18 ~ 2022-12-10): (code for generating this plot: https://jokergoo.github.io/spiralize_vignettes/examples.html#github-commits)

code

library(spiralize)
library(grid)

repos = c("GlobalOptions", "GetoptLong", "circlize", "bsub", "pkgndep", "ComplexHeatmap", "EnrichedHeatmap", 
    "HilbertCurve", "gtrellis", "cola", "simplifyEnrichment", "InteractiveComplexHeatmap", "spiralize", "rGREAT", "simona")

df_all = data.frame(commits = numeric(0), date = character(0), repo = character(0))
for(r in repos) {
    # go to each repo folder
    setwd(paste0("~/project/development/", r))
    df = read.table(pipe("git log --date=short --pretty=format:%ad | sort | uniq -c"))
    colnames(df) = c("commits", "date")
    df$repo = r

    df_all = rbind(df_all, df)
}

df_all$date = as.Date(df_all$date)

start = min(df_all$date)
end = max(df_all$date)

d = start + seq(1, end - start + 1) - 1
n = numeric(length(d))
nl = lapply(repos, function(x) numeric(length(d)))
names(nl) = repos

for(i in seq_len(nrow(df_all))) {
    ind = as.double(difftime(df_all[i, "date"], start), "days") + 1
    n[ind] = n[ind] + df_all[i, "commits"]

    nl[[ df_all[i, "repo"] ]][ind] = nl[[ df_all[i, "repo"] ]][ind] + df_all[i, "commits"]
}

calc_pt_size = function(x) {
    pt_size = x
    pt_size[pt_size > 20] = 20
    pt_size[pt_size < 2 & pt_size > 0] = 2
    pt_size
}
xlim = range(d)

pl = list()
pl[[1]] = grid.grabExpr({
    spiral_initialize_by_time(xlim, verbose = FALSE, normalize_year = TRUE)
    spiral_track()
    spiral_points(d, 0.5, pch = 16, size = unit(calc_pt_size(n), "pt"))
    grid.text("All packages", x = 0, y = 1, just = c("left", "top"), gp = gpar(fontsize = 14))

    for(t in c("2013-01-01", "2014-01-01", "2015-01-01", "2016-01-01", "2017-01-01",
               "2018-01-01", "2019-01-01", "2020-01-01", "2021-01-01", "2022-01-01", "2023-01-01")) {
        spiral_text(t, 0.5, gsub("-\\d+-\\d+$", "", as.character(t)), gp = gpar(fontsize = 8), facing = "inside")
    }
})

for(i in order(sapply(nl, sum), decreasing = TRUE)) {
    pl[[ names(nl)[i] ]] = grid.grabExpr({
        spiral_initialize_by_time(xlim, verbose = FALSE, normalize_year = TRUE)
        spiral_track()
        spiral_points(d, 0.5, pch = 16, size = unit(calc_pt_size(nl[[i]]), "pt"))
        grid.text(names(nl)[i], x = 0, y = 1, just = c("left", "top"), gp = gpar(fontsize = 14))

        for(t in c("2013-01-01", "2014-01-01", "2015-01-01", "2016-01-01", "2017-01-01",
                   "2018-01-01", "2019-01-01", "2020-01-01", "2021-01-01", "2022-01-01", "2023-01-01")) {
            spiral_text(t, 0.5, gsub("-\\d+-\\d+$", "", as.character(t)), gp = gpar(fontsize = 8), facing = "inside")
        }
    })
}

library(cowplot)
png("~/test.png", 300*4*1.5, 300*4*1.5, res = 72*1.5)
plot_grid(plotlist = pl, ncol = 4)
dev.off()

getoptlong's Issues

Failed to install this R package in R-3.5.1

Hi,

The package we are developing is dependent on this GetoptLong package.
But we failed to install this package in R-3.5.1 when we were testing our package, and more than one device got this error.
Can you have a look and find the possible reason?

The Chinese characters in the code below mean 'There is no package called GetoptLong'

> install.packages("GetoptLong")
Warning message:
package ‘GetoptLong’ is not available (for R version 3.5.1) 
> library("GetoptLong")
Error in library("GetoptLong") : 不存在叫‘GetoptLong’这个名字的程辑包
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936  LC_CTYPE=Chinese (Simplified)_China.936    LC_MONETARY=Chinese (Simplified)_China.936
[4] LC_NUMERIC=C                               LC_TIME=Chinese (Simplified)_China.936    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_3.5.1      tools_3.5.1         remotes_2.1.1

Thank you so much!

verbose error!

library(GetoptLong)

cutoff = 0.05
GetoptLong(
    "number=i", "Number of items.",
    "cutoff=f", "Cutoff for filtering results.",
    "verbose!", "Print message."
)

Error in strsplit(argv_str, " ") : 非字符参数
Calls: GetoptLong -> negatable_logical_is_called -> strsplit
停止执行

add default in the help message

test shebang mode

support numeric_version() for setting versions

support position argument ?

verbose! does not work as expected

Not supported on solaris

Because I have no solaris machine to test.

foo! also needs a default

use space

GetoptLong("
Usage: Rscript foo.R [options]

  <count=i{2,}> This is a count. This is a count. This is a count.
  <#count> This is a count. This is a count.
  <number=f> This is a number. This is a number. This is a number.
  <#number> This is a number. This is a number.
", template_control = list(opt_width = c(count = 28, number = 28))
)

support --word1-word2

The object can be named as word1_word2

Implement argument parsing purely in R

how to use version opt and subcommands?

if opt desc is very long

Subcommand is possibly supported in the future?

Hi @jokergoo,

Thanks for developing this nice tool, I found it easy and elegant. I am writing some related scripts based on it. I am wondering subcommand is possibly implemented in the future?

Best,

Shixiang

condition in stop(github_error(request)): Bad credentials (401)

Hi jokergoo, when I try

devtools::install_github("jokergoo/GetoptLong")

on my R shell I get:

condition in stop(github_error(request)): Bad credentials (401)

• Traceback:

1. devtools::install_github("jokergoo/GetoptLong")
2. install_remotes(remotes, quiet = quiet, ...)
3. vapply(remotes, install_remote, ..., FUN.VALUE = logical(1))
4. FUN(X[[i]], ...)
5. remote_download(remote, quiet = quiet)
6. remote_download.github_remote(remote, quiet = quiet)
7. download_github(dest, src, auth)

Have you seen this error message before?
thanks
Alex

improve some messages from Getopt::Long

Reconstruct the package

Maybe each option is an object.

automatically guess

Usage: Rscript foo.R [options]

  <count=i{2,}> This is a count. This is a count. This is a count.
  <#count> This is a count. This is a count.
  <number=f> This is a number. This is a number. This is a number.
  <#number> This is a number. This is a number.
", template_control = [list](https://rdrr.io/r/base/list.html)(opt_width = [c](https://rdrr.io/r/base/c.html)(count = 28, number = 28))
)