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index.Rmd
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index.Rmd
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---
title: rOpenSci News Digest, February 2022
author:
- Maëlle Salmon
date: '2022-02-18'
slug: ropensci-news-digest-february-2022
categories: []
tags:
- newsletter
description: Community manager job ad, co-working sessions, R Journal commentary, new packages and package news
output:
html_document:
keep_md: yes
params:
last_newsletter: '2022-01-21'
---
```{r setup, include=FALSE}
library("magrittr")
library("rlang")
last_newsletter <- anytime::anytime(params$last_newsletter)
knitr::opts_chunk$set(echo = FALSE)
url <- sprintf(
"/blog/%s/%s/%s/%s",
lubridate::year(rmarkdown::yaml_front_matter(knitr::current_input())$date),
stringr::str_pad(lubridate::month(rmarkdown::yaml_front_matter(knitr::current_input())$date), 2, "0", side = "left"),
stringr::str_pad(lubridate::day(rmarkdown::yaml_front_matter(knitr::current_input())$date), 2, "0", side = "left"),
rmarkdown::yaml_front_matter(knitr::current_input())$slug
)
english <- function(x) {
as.character(english::english(x))
}
nice_string <- function(...) {
glue::glue_collapse(..., sep = ", ", last = ", and ")
}
```
<!-- Before sending DELETE THE INDEX_CACHE and re-knit! -->
Dear rOpenSci friends, it's time for our monthly news roundup!
<!-- blabla -->
You can read this post [on our blog](`r url`).
Now let's dive into the activity at and around rOpenSci!
## rOpenSci HQ
### rOpenSci is hiring its next Community Manager!
* Come be part of making our great community even better;
* Help start a new program promoting diverse leadership in open source;
* Join a remote, flexible, global, friendly community and team!
More details [in the job ad](/careers/community-manager-2022/).
### Next coworking sessions
Join us for social coworking & office hours monthly on 1st Tuesdays! Hosted by Steffi LaZerte and various community hosts. Everyone welcome. No RSVP needed. Consult our [Events](/events) page to find your local time and how to join.
Our next sessions are:
* [Tuesday, 01 March 2022, 9 AM North American Pacific / 17:00 UTC](/events/coworking-2022-03/) "Changing package maintainers", *Hosted by Steffi LaZerte and Hannah Owens*
- Cowork on a project of your choice;
- Take this time to ensure your packages are understandable to potential collaborators (or future maintainers);
- Or ask our community host, Hannah Owens, about her experience taking over maintenance of the rOpenSci spocc package.
* [Tuesday, 05 April 2022 9 AM Australian Western / 1:00 UTC ](/events/coworking-2022-04/) "Making figures sparkle" *Hosted by Steffi LaZerte and Nick Tierney*
* Cowork on a project of your choice;
* Work on some figures to make them glitter;
* Or ask our community host, Nick Tierney (author of data visualization packages including rOpenSci package [visdat](https://docs.ropensci.org/visdat/)) for some tips to make your figures sparkle!
Find out about more [events](/events).
### Suggested reading
[Maëlle Salmon](/author/maëlle-salmon/) (Research Software Engineer with rOpenSci) and [Karthik Ram](/author/karthik-ram/) (rOpenSci executive director) authored a commentary ["The R Developer Community Does Have a Strong Software Engineering Culture"](https://journal.r-project.org/archive/2021/RJ-2021-110/index.html) in the latest issue of The R Journal edited by Di Cook,
as a response to the discussion paper ["Software Engineering and R Programming: A Call for Research"](https://journal.r-project.org/archive/2021/RJ-2021-108/index.html) by [Melina Vidoni](author/melina-vidoni/) (who's an Associate editor of rOpenSci Software Peer Review).
Ready for more? Two other interesting reads are the commentaries ["We Need Trustworthy R Packages"](https://journal.r-project.org/archive/2021/RJ-2021-109/index.html) by [Will Landau](/author/will-landau/) (who maintains rOpenSci packages [targets](https://docs.ropensci.org/targets/) and [drake](https://docs.ropensci.org/drake/)), and ["The R Quest: from Users to Developers"](https://journal.r-project.org/archive/2021/RJ-2021-111/index.html) by Simon Urbanek.
## Software :package:
### New packages
```{r new-packages, cache = TRUE}
cran_unquote <- function(string) {
gsub("\\'(.*?)\\'", "\\1", string)
}
tidy_package <- function(entry) {
tibble::tibble(
package = entry$name,
description = cran_unquote(entry$description),
details = cran_unquote(entry$details),
on_cran = entry$on_cran,
on_bioc = entry$on_bioc,
onboarding = entry$onboarding,
url = entry$url,
maintainer = entry$maintainer # use desc for more info
)
}
registry <- "https://raw.githubusercontent.com/ropensci/roregistry/gh-pages/registry.json" %>%
jsonlite::read_json() %>%
purrr::pluck("packages") %>%
purrr::map_df(tidy_package)
since <- lubridate::as_date(last_newsletter) - 1
until <- lubridate::as_date(last_newsletter) + 1
commits <- gh::gh(
"GET /repos/{owner}/{repo}/commits",
owner = "ropensci",
repo = "roregistry",
since = sprintf(
"%s-%s-%sT00:00:00Z",
lubridate::year(since),
stringr::str_pad(lubridate::month(since), 2, "0", side = "left"),
stringr::str_pad(lubridate::day(since), 2, "0", side = "left")
),
until = sprintf(
"%s-%s-%sT00:00:00Z",
lubridate::year(until),
stringr::str_pad(lubridate::month(until), 2, "0", side = "left"),
stringr::str_pad(lubridate::day(until), 2, "0", side = "left")
)
)
empty <- TRUE
i <- length(commits)
while (empty == TRUE) {
old <- "https://raw.githubusercontent.com/ropensci/roregistry/%s/packages.json" %>%
sprintf(commits[[i]]$sha) %>%
jsonlite::read_json() %>%
purrr::map_df(function(x) tibble::tibble(package = x$package, url = x$url, branch = x$branch))
i <- i - 1
if (nrow(old) > 100) {
empty <- FALSE
}
}
old <- dplyr::filter(
old,
!grepl("ropenscilabs\\/", url),
!grepl("ropensci-archive\\/", url)
)
new <- dplyr::filter(
registry,
!package %in% old$package,
!grepl("ropenscilabs\\/", url),
!grepl("ropensci-archive\\/", url)
)
```
The following `r if(nrow(new)>1) english(nrow(new))` package`r if(nrow(new)>1) "s"` recently became a part of our software suite:
```{r, results='asis', cache = TRUE}
packages <- split(new, seq(nrow(new)))
present_one <- function(package) {
url_parts <- urltools::url_parse(package$url)
desc_link <- gh::gh(
"/repos/{owner}/{repo}/contents/{path}",
owner = strsplit(url_parts$path, "\\/")[[1]][1],
repo = strsplit(url_parts$path, "\\/")[[1]][2],
path = "DESCRIPTION"
) %>%
purrr::pluck("download_url")
withr::with_tempfile(
"tf", {
download.file(desc_link, tf)
desc <<- desc::desc(file = tf)
}
)
# as in pkgdown
authors <- unclass(desc$get_authors())
aut <- purrr::keep(authors, function(x) {any( x$role %in% "aut") && all(x$role != "cre") })
aut <- purrr::map_chr(aut, function(x) paste(x$given, x$family))
rev <- purrr::keep(authors, function(x) {any( x$role %in% "rev") && all(x$role != "cre") })
rev <- purrr::map_chr(rev, function(x) paste(x$given, x$family))
maintainer <- purrr::keep(authors, function(x) {any( x$role %in% "cre") })
maintainer <- paste(c(maintainer[[1]]$given, maintainer[[1]]$family), collapse = " ")
author_string <- sprintf("developed by %s", maintainer)
if (length(aut) > 0) {
author_string <- paste0(author_string, sprintf(" together with %s", nice_string(aut)))
}
string <- sprintf(
"[%s](https://docs.ropensci.org/%s), %s: %s. ",
package$package,
package$package,
author_string,
stringr::str_remove(stringr::str_squish(package$details), "\\.$")
)
if (package$on_cran) {
string <- paste0(
string,
sprintf(
" It is available on [CRAN]( https://CRAN.R-project.org/package=%s). ",
package$package
)
)
}
if (package$on_bioc) {
string <- paste0(
string, sprintf(
" It is available on [Bioconductor](https://bioconductor.org/packages/%s/). ",
package$package
)
)
}
if (nzchar(package$onboarding)) {
string <- paste0(string, sprintf("It has been [reviewed](%s)", package$onboarding))
if (length(rev) > 0) {
string <- paste0(string, sprintf(" by %s.", nice_string(rev)))
} else {
string <- paste0(string, ".")
}
}
paste("+", string)
}
text <- purrr::map_chr(
packages,
present_one
)
cat(paste0(text, collapse = "\n\n"))
```
Discover [more packages](/packages), read more about [Software Peer Review](/software-review).
### New versions
```{r news, cache=TRUE}
registry <- dplyr::filter(
registry,
!grepl("ropenscilabs\\/", url),
!grepl("ropensci-archive\\/", url)
)
registry <- registry %>%
dplyr::rowwise() %>%
dplyr::mutate(
owner = strsplit(urltools::path(url), "/")[[1]][1],
repo = strsplit(urltools::path(url), "/")[[1]][2]
) %>%
dplyr::filter(
!is.na(owner)
)
packages <- split(registry, seq(nrow(registry)))
get_release <- function(repo) {
info <- gh::gh(
"GET /repos/{owner}/{repo}/releases",
owner = repo$owner,
repo = repo$repo,
per_page = 3,
description = repo$description
)
info <- info[!purrr::map_lgl(info, "draft")]
if(length(info) == 0 || anytime::anytime(info[[1]]$published_at) < last_newsletter) {
return(NULL)
}
tibble::tibble(
package = repo$package,
version = info[[1]]$tag_name,
url = info[[1]]$html_url,
description = repo$description
)
}
releases <- purrr::map_df(
packages,
get_release
)
releases <- split(releases, seq(nrow(releases)))
format_release <- function(release) {
sprintf(
'[%s](https://docs.ropensci.org/%s "%s") ([`%s`](%s))',
release$package,
release$package,
release$description,
release$version,
release$url
)
}
all_releases <- purrr::map_chr(releases, format_release)
text <- nice_string(all_releases)
```
The following `r if (length(releases) > 1) english(length(releases))` package`r if (length(releases) > 1) "s"` `r if (length(releases) > 1) "have" else "has"` had an update since the last newsletter: `r text`.
## Software Peer Review
```{r software-review, results='asis'}
# from pkgdown https://github.com/r-lib/pkgdown/blob/1ca166905f1b019ed4af9642617ea09fa2b8fc17/R/utils.r#L176
get_description <- function(body) {
lines <- strsplit(body, "\n")[[1]]
name <- stringr::str_squish(sub("Package:", "", lines[grepl("^Package", lines)][1]))
description <- stringr::str_squish(sub("Title:", "", lines[grepl("^Title", lines)][1]))
description <- cran_unquote(sub("\\.$", "", description))
list(name = name, description = description)
}
get_user_text <- function(issue) {
info <- gh::gh("GET /users/{username}", username = issue$user$login)
name <- info$name %||% issue$user$login
url <- if (nzchar(info$blog)) info$blog else info$html_url
if (!grepl("^https?:", url)) url <- paste0("http://", url)
sprintf("[%s](%s)", name, url)
}
tidy_issue <- function(issue) {
labels <- purrr::map_chr(issue$labels, "name")
label <- labels[grepl("[0-9]\\/.*", labels)][1]
df <- tibble::tibble(
label = label,
name = get_description(issue$body)$name,
description = get_description(issue$body)$description,
title = issue$title,
holding = "holding" %in% purrr::map_chr(issue$labels, "name"),
others = toString(purrr::map_chr(issue$labels, "name")),
closed_at = issue$closed_at %||% NA,
url = issue$html_url,
user = get_user_text(issue),
stats = dplyr::if_else("stats" %in% purrr::map_chr(issue$labels, "name"), " (Stats).", "")
)
dplyr::rowwise(df) %>%
dplyr::mutate(text = sprintf(" * [%s](%s), %s. Submitted by %s. %s", name, url, description, user, stats))
}
get_issues <- function(label, state) {
issues <- gh::gh(
"GET /repos/{owner}/{repo}/issues",
owner = "ropensci",
repo = "software-review",
state = state,
labels = label
)
purrr::map_df(issues, tidy_issue)
}
active_issues <- purrr::map_df(
c("1/editor-checks","2/seeking-reviewer(s)","3/reviewer(s)-assigned","4/review(s)-in-awaiting-changes","5/awaiting-reviewer(s)-response","6/approved"),
get_issues,
state = "open"
)
closed_issues <- get_issues(state = "closed", label ="6/approved")
ok_date <- function(date) {
if (is.na(date)) {
return(TRUE)
}
anytime::anytime(date) >= last_newsletter
}
closed_issues <- dplyr::rowwise(closed_issues) %>%
dplyr::filter(ok_date(closed_at))
issues <- dplyr::bind_rows(active_issues, closed_issues)
no_holding <- sum(issues$holding)
issues <- dplyr::filter(issues, !holding)
text <- sprintf("There are %s recently closed and active submissions", english(nrow(issues)))
if (no_holding > 0) {
text <- paste0(
text,
sprintf(
" and %s submission%s on hold.",
no_holding,
if (no_holding > 1) "s" else ""
)
)
} else {
text <- paste0(text, ".")
}
count_label <- function(label) {
no <- snakecase::to_sentence_case(english(sum(issues$label == label, na.rm = TRUE)))
url <- paste0("https://github.com/ropensci/software-review/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc+label%3A", label)
sprintf("* %s at ['%s'](%s):\n\n %s", no, label, url, paste0(issues$text[!is.na(issues$label)][ issues$label == label], collapse = "\n\n"))
}
cat(text)
cat(
paste0(
" Issues are at different stages: \n\n",
paste0(
purrr::map_chr(sort(unique(issues$label[!is.na(issues$label)]), decreasing = TRUE), count_label),
collapse = "\n\n"
)
)
)
```
Find out more about [Software Peer Review](/software-review) and how to get involved.
## On the blog
<!-- Do not forget to rebase your branch! -->
```{r blog}
parse_one_post <- function(path){
lines <- suppressWarnings(readLines(path, encoding = "UTF-8"))
yaml <- blogdown:::split_yaml_body(lines)$yaml
yaml <- glue::glue_collapse(yaml, sep = "\n")
yaml <- yaml::yaml.load(yaml)
meta <- tibble::tibble(
date = anytime::anydate(yaml$date),
author = nice_string(yaml$author),
title = yaml$title,
software_peer_review = "Software Peer Review" %in% yaml$tags,
tech_note = "tech notes" %in% yaml$tags && !"Software Peer Review" %in% yaml$tags,
other = !"tech notes" %in% yaml$tags && !"Software Peer Review" %in% yaml$tags,
twitterImg = yaml$twitterImg %||% "",
twitterAlt = yaml$twitterAlt %||% "",
description = yaml$description %||% "",
newsletter = "newsletter" %in% yaml$tags,
slug = yaml$slug
)
meta
}
paths <- fs::dir_ls("..", recurse = TRUE, glob = "*.md")
paths <- paths[!paths %in% c("../_index.md", "../2021-02-03-targets/raw_data_source.md",
"../2021-02-03-targets/README.md")]
posts <- purrr::map_df(paths, parse_one_post)
posts <- dplyr::filter(posts, date >= as.Date(last_newsletter), !newsletter)
posts <- split(posts, seq(nrow(posts)))
format_post <- function(post) {
url <- sprintf(
"/blog/%s/%s/%s/%s",
lubridate::year(post$date),
stringr::str_pad(lubridate::month(post$date), 2, "0", side = "left"),
stringr::str_pad(lubridate::day(post$date), 2, "0", side = "left"),
post$slug
)
string <- sprintf("* [%s](%s) by %s", post$title, url, post$author)
if (post$description != "") {
string <- paste0(string, ". ", sub("\\?$", "", sub("\\!$", "", sub("\\.$", "", post$description), ".")), ".")
} else {
string <- paste0(string, ".")
}
if (post$twitterImg != "") {
img_file <- fs::path_file(post$twitterImg)
download.file(sprintf("https://ropensci.org/%s", post$twitterImg), img_file)
img_file %>% magick::image_read() %>% magick::image_scale("400x") %>% magick::image_write(img_file)
string <- paste0(
string,
sprintf('{{< figure src="%s" alt="%s" width="400" >}}\n\n', img_file, post$twitterAlt)
)
}
string
}
```
```{r, results='asis'}
software_review <- posts[purrr::map_lgl(posts, "software_peer_review")]
if (length(software_review) > 0) {
cat("### Software Review\n\n")
cat(
paste0(
purrr::map_chr(software_review, format_post),
collapse = "\n\n"
)
)
cat("\n\n")
}
others <- posts[purrr::map_lgl(posts, "other")]
if (length(others) > 0) {
if (length(others) != length(posts)) cat("### Other topics\n\n")
cat(
paste0(
purrr::map_chr(others, format_post),
collapse = "\n\n"
)
)
cat("\n\n")
}
tech_notes <- posts[purrr::map_lgl(posts, "tech_note")]
if (length(tech_notes) > 0) {
cat("\n\n")
cat("### Tech Notes\n\n")
cat(
paste0(
purrr::map_chr(tech_notes, format_post),
collapse = "\n\n"
)
)
cat("\n\n")
}
```
## Use cases
```{r usecases, eval=TRUE}
# rerun get_use_cases.R at the same time
usecases <- jsonlite::read_json("../../../data/usecases/usecases.json")
get_one_case <- function(usecase) {
tibble::tibble(
title = usecase$title,
reporter = usecase$reporter,
url = usecase$url,
image = usecase$image,
date = anytime::anydate(usecase$date)
)
}
usecases <- purrr::map_df(usecases, get_one_case)
usecases <- dplyr::filter(usecases, date >= as.Date(last_newsletter))
usecases <- split(usecases, seq(nrow(usecases)))
```
`r snakecase::to_sentence_case(english(length(usecases)))` use cases of our packages and resources have been reported since we sent the last newsletter.
```{r usecases2, results='asis', eval=TRUE}
format_case <- function(usecase) {
string <- sprintf("* [%s](%s). Reported by %s.", sub("\\.$", "", usecase$title), usecase$url, usecase$reporter)
}
cat(
paste0(
purrr::map_chr(usecases, format_case),
collapse = "\n\n"
)
)
```
Explore [other use cases](/usecases) and [report your own](https://discuss.ropensci.org/c/usecases/10)!
## Package development corner
Some useful tips for R package developers. :eyes:
### Make the best out of your package logo
Have you designed (or commissioned) a beautiful logo for your package?
Use [`usethis::use_logo()`](https://usethis.r-lib.org/reference/use_logo.html) that will enforce a specific size and save it under `man/figures/logo.png`, as well as providing you with the Markdown code to insert your logo in your package repo README.
Why do this? This has two advantages:
* If you have a package-level doc (i.e. a manual page for `?package-name`), or create one via [`usethis::use_package_doc()`](https://usethis.r-lib.org/reference/use_package_doc.html), roxygen2 will automatically add the logo to that doc page. Type `?usethis` in your R console for an example.
* If you use [pkgdown BS5 templates](https://www.tidyverse.org/blog/2021/12/pkgdown-2-0-0/#bootstrap-5), which is the case if your package is part of rOpenSci suite, your package logo will appear on all pages, as well as in social media cards.
### Resources about testing
Some links about testing your package...
* When wondering what good tests look like (spoiler: they look obvious): [Why Good Developers Write Bad Unit Tests](https://mtlynch.io/good-developers-bad-tests/) (seen via [an issue in the R packages book repo](https://github.com/hadley/r-pkgs/issues/551)).
* When things go well in one testing context (say, `devtools::test()`) but not in another one (say, `devtools::check()`): [a conversation around usual suspects](https://github.com/hadley/r-pkgs/issues/483). One prevention strategy is to read and apply the advice in testthat [Test fixtures vignette](https://testthat.r-lib.org/articles/test-fixtures.html).
* When having to put helper code somewhere: [Helper code and files for your testthat tests](https://blog.r-hub.io/2020/11/18/testthat-utility-belt/).
* That interacts with a database: [dittodb by Jonathan Keane and Mauricio Vargas](https://docs.ropensci.org/dittodb/).
* That interacts with a web resource: [HTTP testing in R](https://books.ropensci.org/http-testing) (or the more recent [httptest2 package](https://enpiar.com/httptest2/) that is like httptest, but for [httr2](https://httr2.r-lib.org/)).
### The state of continuous integration (CI) for R packages
We no longer recommend using [Travis CI](https://ropensci.org/blog/2020/11/19/moving-away-travis/).
The development version of our dev guide has [updated advice on CI](https://devdevguide.netlify.app/ci.html).
If you adopt GitHub Actions,
* Have a look at the [changelog for r-lib/actions](https://github.com/r-lib/actions/releases) if these are the actions you use;
* Do not miss the tech note ["pkgcheck now available as a GitHub action!"](/blog/2022/02/01/pkgcheck-action/).
### Miscellaneous package building advice
See the tech note [A Blend of Package Build Failures](/blog/2022/01/31/package-build-failures/).
## Last words
Thanks for reading! If you want to get involved with rOpenSci, check out our [Contributing Guide](https://contributing.ropensci.org) that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or contribute in other ways like sharing use cases.
If you haven't subscribed to our newsletter yet, you can [do so via a form](/news/). Until it's time for our next newsletter, you can keep in touch with us via our [website](/) and [Twitter account](https://twitter.com/ropensci).