Skip to content

Commit 5f451a5

Browse files
gvegayonclaude
gvegayon
and
claude
authored
docs: make citation guidance unmissable and fix CITATION metadata (#50)
- **Corrected the JOSS issue number: 39 → 42.** (39 is fmcmc's; slurmR is 4(42), 1493.) - Replaced the leading `citation(auto = meta)` so the JOSS paper is the *first* entry — the auto-generated boilerplate was appearing above it. Adds a How to cite note to the README, vignettes and ?slurmR, plus a startup message, and adds the CRAN DOI. Co-authored-by: Claude Opus 5 <noreply@anthropic.com>
1 parent df891c4 commit 5f451a5

7 files changed

Lines changed: 77 additions & 13 deletions

File tree

‎R/slurmR.R‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -45,6 +45,9 @@ NULL
4545

4646

4747
.onAttach <- function(libname, pkgname) {
48+
packageStartupMessage(
49+
"Using slurmR in your research? Please cite it: citation(\"slurmR\")"
50+
)
4851

4952
packageStartupMessage(
5053
"slurmR default option for `tmp_path` (used to store auxiliar files) set to:\n ", opts_slurmR$get_tmp_path(),

‎README.Rmd‎

Lines changed: 10 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -28,6 +28,16 @@ knitr::opts_chunk$set(
2828

2929
# slurmR: A Lightweight Wrapper for Slurm <img src="man/figures/logo.png" height="180px" align="right"/>
3030

31+
32+
<!-- how-to-cite -->
33+
> [!NOTE]
34+
> **How to cite slurmR.** If you use **slurmR** in published work, please cite it:
35+
>
36+
> Vega Yon GG, Marjoram P (2019). slurmR: A lightweight wrapper for HPC with Slurm. *Journal of Open Source Software*, 4(42), 1493. doi:[10.21105/joss.01493](https://doi.org/10.21105/joss.01493)
37+
>
38+
> Run `citation("slurmR")` in R for the BibTeX entry.
39+
<!-- how-to-cite -->
40+
3141
Slurm Workload Manager is a popular HPC cluster job scheduler found in many of the top 500 supercomputers. The `slurmR` R package provides an R wrapper to it that matches the parallel package's syntax, this is, just like `parallel` provides the `parLapply`, `clusterMap`, `parSapply`, etc., `slurmR` provides `Slurm_lapply`, `Slurm_Map`, `Slurm_sapply`, etc.
3242

3343
While there are other alternatives such as `future.batchtools`, `batchtools`, `clustermq`, and `rslurm`, this R package has the following goals:

‎README.md‎

Lines changed: 10 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -15,6 +15,16 @@ Epidemiology](https://raw.githubusercontent.com/USCbiostats/badges/master/tommy-
1515

1616
# slurmR: A Lightweight Wrapper for Slurm <img src="man/figures/logo.png" height="180px" align="right"/>
1717

18+
19+
<!-- how-to-cite -->
20+
> [!NOTE]
21+
> **How to cite slurmR.** If you use **slurmR** in published work, please cite it:
22+
>
23+
> Vega Yon GG, Marjoram P (2019). slurmR: A lightweight wrapper for HPC with Slurm. *Journal of Open Source Software*, 4(42), 1493. doi:[10.21105/joss.01493](https://doi.org/10.21105/joss.01493)
24+
>
25+
> Run `citation("slurmR")` in R for the BibTeX entry.
26+
<!-- how-to-cite -->
27+
1828
Slurm Workload Manager is a popular HPC cluster job scheduler found in
1929
many of the top 500 supercomputers. The `slurmR` R package provides an R
2030
wrapper to it that matches the parallel package’s syntax, this is, just

‎inst/CITATION‎

Lines changed: 39 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -1,22 +1,48 @@
1-
citation(auto = meta)
1+
# Year resolution: CRAN sets Date/Publication on the installed package; fall
2+
# back to DESCRIPTION's Date, then to the current year, so the package entry
3+
# never renders as "(????)".
4+
year <- if (!is.null(meta$`Date/Publication`)) {
5+
substr(meta$`Date/Publication`, 1, 4)
6+
} else if (!is.null(meta$Date)) {
7+
substr(meta$Date, 1, 4)
8+
} else {
9+
format(Sys.Date(), "%Y")
10+
}
11+
note <- sprintf("R package version %s", meta$Version)
212

313
bibentry(
414
bibtype = "Article",
5-
title = "slurmR: A lightweight wrapper for HPC with Slurm",
6-
author = c(
7-
person("George", "Vega Yon", email = "g.vegayon@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3171-0844")),
8-
person("Paul", "Marjoram", email = "pmarjora@usc.edu", role = c("ctb", "ths"), comment = c(ORCID = "0000-0003-0824-7449"))
15+
title = "slurmR: A lightweight wrapper for HPC with Slurm",
16+
author = c(
17+
person("George", "Vega Yon", comment = c(ORCID = "0000-0002-3171-0844")),
18+
person("Paul", "Marjoram", comment = c(ORCID = "0000-0003-0824-7449"))
919
),
10-
journal = "The Journal of Open Source Software",
11-
year = 2019,
12-
month = "jul",
13-
volume = 4,
14-
number = 39,
20+
journal = "Journal of Open Source Software",
21+
year = "2019",
22+
month = "oct",
23+
volume = "4",
24+
number = "42",
25+
pages = "1493",
1526
doi = "10.21105/joss.01493",
1627
url = "https://doi.org/10.21105/joss.01493",
1728
textVersion = paste(
18-
"Vega Yon et al., (2019). slurmR: A lightweight wrapper for HPC",
19-
"with Slurm. Journal of Open Source Software, 4(39), 1493,",
29+
"Vega Yon GG, Marjoram P (2019). slurmR: A lightweight wrapper for HPC",
30+
"with Slurm. Journal of Open Source Software, 4(42), 1493.",
2031
"https://doi.org/10.21105/joss.01493"
21-
)
32+
),
33+
header = "To cite slurmR in publications use:"
34+
)
35+
36+
bibentry(
37+
bibtype = "Manual",
38+
title = "{{slurmR: A Lightweight Wrapper for 'Slurm'}}",
39+
author = c(
40+
person("George", "Vega Yon", comment = c(ORCID = "0000-0002-3171-0844")),
41+
person("Paul", "Marjoram", comment = c(ORCID = "0000-0003-0824-7449"))
42+
),
43+
year = year,
44+
note = note,
45+
url = "https://github.com/USCbiostats/slurmR",
46+
doi = "10.32614/CRAN.package.slurmR",
47+
header = "And the R package itself:"
2248
)

‎vignettes/debugging-re-submission.Rmd‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -9,6 +9,11 @@ vignette: >
99
%\VignetteEncoding{UTF-8}
1010
---
1111

12+
<!-- how-to-cite -->
13+
> **How to cite.** If you use **slurmR** in published work, please cite it — run
14+
> `citation("slurmR")` in R for the full entry.
15+
<!-- how-to-cite -->
16+
1217
# Introduction
1318

1419
Want it or not, a lot of times jobs fail. In such cases, it could be hard to

‎vignettes/getting-started.Rmd‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -13,6 +13,11 @@ vignette: >
1313
%\VignetteEncoding{UTF-8}
1414
---
1515

16+
<!-- how-to-cite -->
17+
> **How to cite.** If you use **slurmR** in published work, please cite it — run
18+
> `citation("slurmR")` in R for the full entry.
19+
<!-- how-to-cite -->
20+
1621
# The slurmR R package
1722

1823
The `slurmR` package provides wrappers and tools for integrating R with the

‎vignettes/working-with-slurm.Rmd‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -9,6 +9,11 @@ vignette: >
99
%\VignetteEncoding{UTF-8}
1010
---
1111

12+
<!-- how-to-cite -->
13+
> **How to cite.** If you use **slurmR** in published work, please cite it — run
14+
> `citation("slurmR")` in R for the full entry.
15+
<!-- how-to-cite -->
16+
1217
```{r setup, include = FALSE}
1318
knitr::opts_chunk$set(
1419
collapse = TRUE,

0 commit comments

Comments
 (0)