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index.Rmd
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index.Rmd
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---
title: 'rOpenSci News Digest, August 2023'
author: 'The rOpenSci Team'
date: '2023-08-25'
tags:
- newsletter
slug: news-august-2023
description: Open Call for Champions program, community call in Spanish and English, coworking
params:
last_newsletter: "2023-07-21"
---
```{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
### Open Call for rOpenSci Champions Program Applications!
Still open: [our call](/blog/2023/07/14/call-champions-program/) for the second cohort of Champions and Mentors for the rOpenSci Champions Program 🎉 !
This 12-month-long program will continue to support our goal of identifying, recognizing, and rewarding passionate community members who help the community grow and improve. The activities include [cohort-based training](/blog/2023/08/04/champions-program-training/), project development, and personal mentorship.
This program focuses on people who belong to groups that are historically and systematically excluded from the open software and research software communities and who are interested in contributing to rOpenSci and the broader open source and research software communities.
You can apply to be a [champion](https://airtable.com/shrAsYlSXU0coJ5Ld) or a [mentor](https://airtable.com/shrlrLdQbb4wphosK) until **September 4th**.
Want to hear more from the protagonists?
In these videos (in [English](https://vimeo.com/848537831) and [Spanish](https://vimeo.com/854320485)) our champions and mentors tell us what it's like to be part of the program.
More information on eligibility, timeline, curriculum, application process, etc. is [on the program webpage](/champions/).
### Our first community call in Spanish (and English too)!
As global movements, Open Source and Open Science face language-based exclusion as most resources are in English. This affects scientists and research software engineers working in R, particularly those who don’t have English as their first language.
rOpenSci multilingual efforts aim to lower access barriers, democratize quality resources, and increase the possibilities of contributing to open software and science. We successfully piloted our Spanish-language peer review and the localization to Spanish of our comprehensive guide to software development, with Portuguese translation underway.
[Maëlle Salmon](/author/ma%C3%ABlle-salmon/), [Paola Corrales](/author/pao-corrales/), and [Elio Campitelli](/author/elio-campitelli/), will share the rOpenSci Multilingual project details on this call. Maëlle will present the R packages that allow us to have our content in several languages. Then Elio and Paola will share the translation workflow and show the Translation Guide written to document the process.
- [**Multilingual Publishing**: Tuesday, 21 November 2023 12:00 UTC](/commcalls/nov2023-multilingual/).
- [**Proyecto Multilingüe**: Thursday, 23 November 2023 12:00 UTC](/commcalls/nov2023-multilenguaje/).
### Community call recording: Mentoring & Training Program for Scientific Open Source Champions
[Video and resources](/commcalls/july2023-championprogram/).
Champions programs are designed to identify, recognize, and reward emerging leaders within a community. The [rOpenSci Champions Program](/champions/) is part of a series of activities and projects we are carrying out to ensure our research software serves everyone in our communities, which means that it needs to be sustainable and open, and built by and for all groups.
On this [call](/commcalls/july2023-championprogram/) _Beatriz Milz_, _Victor Ordu_ and _Carolina Pradier_ shared their experience of being rOpenSci mentors and champions.
### Coworking
Read [all about coworking](/blog/2023/06/21/coworking/) in our recent [post](/blog/2023/06/21/coworking/)!
Join us for social coworking & office hours monthly on first 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.
- Tuesday, September 5th, 09:00 Australia Western (01:00 UTC), [" AI in/for R"](/events/coworking-2023-09/) *Hosted by [Joel Nitta](/author/joel-nitta/) and [Steffi LaZerte](/author/steffi-lazerte/)*
- Explore how R can inform/perform AI as well as how AI can inform/perform R.
- Cowork independently on work related to R.
- ~~**Note** October coworking is cancelled (see you in November!)~~ **Nope, it's back on!** Stay tuned for coworking Tuesday, October 3rd, 14h00 Europe Central (12:00 UTC), Theme TBA
And remember, you can always cowork independently on work related to R, work on packages that tend to be neglected, or work on what ever you need to get done!
## Software :package:
```{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$package,
!grepl("ropenscilabs\\/", url),
!grepl("ropensci-archive\\/", url)
)
```
### New versions
```{r news, cache=TRUE}
registry <- dplyr::filter(
registry,
!grepl("ropenscilabs\\/", url),
!grepl("ropensci-archive\\/", url)
)
registry <- registry %>%
dplyr::rowwise() %>%
dplyr::mutate(
owner = strsplit(urltools::path(url), "/")[[1]][1],
repo = strsplit(urltools::path(url), "/")[[1]][2]
) %>%
dplyr::filter(
!is.na(owner)
)
packages <- split(registry, seq(nrow(registry)))
packages <- packages[purrr::map_chr(packages, "package") != "commonmark"]
get_release <- function(repo) {
info <- gh::gh(
"GET /repos/{owner}/{repo}/releases",
owner = repo$owner,
repo = repo$repo,
per_page = 3
)
info <- info[!purrr::map_lgl(info, "draft")]
if(length(info) == 0 || anytime::anytime(info[[1]]$published_at) < last_newsletter) {
return(NULL)
}
tibble::tibble(
package = repo$package,
version = info[[1]]$tag_name,
url = info[[1]]$html_url,
description = repo$description
)
}
packages[purrr::map_chr(packages, "package") == "gert"][[1]]$owner <- "r-lib"
packages[purrr::map_chr(packages, "package") == "gert"][[1]]$repo <- "gert"
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)$yaml
yaml <- glue::glue_collapse(yaml, sep = "\n")
yaml <- yaml::yaml.load(yaml)
language <- function(path) {
name <- fs::path_ext_remove(fs::path_file(path))
if (grepl("\\.[a-z][a-z]", name)) {
sub(".*\\.", "", name)
} else {
"en"
}
}
meta <- tibble::tibble(
date = anytime::anydate(yaml$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$tags,
socialImg = yaml$socialImg %||% "",
socialAlt = yaml$socialAlt %||% "",
description = stringr::str_squish(yaml$description %||% ""),
newsletter = "newsletter" %in% yaml$tags,
slug = yaml$slug,
dir = fs::path_dir(path),
language = language(path)
)
post_url <- if (meta[["language"]] == "en") {
sprintf(
"/blog/%s/%s/%s/%s",
lubridate::year(meta$date),
stringr::str_pad(lubridate::month(meta$date), 2, "0", side = "left"),
stringr::str_pad(lubridate::day(meta$date), 2, "0", side = "left"),
meta$slug
)
} else {
sprintf(
"/%s/blog/%s/%s/%s/%s",
meta[["language"]],
lubridate::year(meta$date),
stringr::str_pad(lubridate::month(meta$date), 2, "0", side = "left"),
stringr::str_pad(lubridate::day(meta$date), 2, "0", side = "left"),
meta$slug
)
}
meta$url <- post_url
meta
}
paths <- fs::dir_ls("..", recurse = TRUE, glob = "*.md")
paths <- paths[!paths %in% c("../_index.md", "../2021-02-03-targets/raw_data_source.md",
"../2021-02-03-targets/README.md")]
posts <- purrr::map_df(paths, parse_one_post)
posts <- dplyr::filter(posts, date >= as.Date(last_newsletter), !newsletter)
posts <- split(posts, posts[["dir"]])
format_post <- function(dir) {
main_language <- if (any(dir[["language"]] == "en")) {
"en"
} else {
dir[["language"]][[1]]
}
post <- dir[which(dir[["language"]] == main_language),]
string <- sprintf("* [%s](%s) by %s", post$title, post$url, post$author)
if (post$description != "") {
string <- paste0(string, ". ", sub("\\?$", "", sub("\\!$", "", sub("\\.$", "", post$description), ".")), ".")
} else {
string <- paste0(string, ".")
}
if (post$socialImg != "") {
img_file <- fs::path_file(post$socialImg)
download.file(sprintf("https://ropensci.org/%s", post$socialImg), 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$socialAlt)
)
}
other_langs <- dir[which(dir[["language"]] != main_language),]
other_langs <- split(other_langs, sort(as.numeric(rownames(other_langs))))
if (length(other_langs) > 0) {
other_langs_text <- purrr::map_chr(
other_langs,
~ sprintf("<a href='%s' lang='%s'>%s (%s)</a>", .x[["url"]], .x[["language"]], .x[["title"]], .x[["language"]])
) %>%
toString
other_langs_text <- sprintf("Other languages: %s.", other_langs_text)
string <- sprintf("%s %s", string, other_langs_text)
}
string
}
```
```{r, results='asis'}
software_review <- posts[purrr::map_lgl(posts, ~any(.x[["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, ~any(.x[["other"]]))]
if (length(others) > 0) {
cat(
paste0(
purrr::map_chr(others, format_post),
collapse = "\n\n"
)
)
cat("\n\n")
}
tech_notes <- posts[purrr::map_lgl(posts, ~any(.x[["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")
}
```
## Call for maintainers
If you're interested in maintaining any of the R packages below, you might enjoy reading our blog post [What Does It Mean to Maintain a Package?](/blog/2023/02/07/what-does-it-mean-to-maintain-a-package/) (or listening to its discussion on the [R Weekly highlights podcast](https://rweekly.fireside.fm/111) hosted by Eric Nantz and Mike Thomas)!
- **[rvertnet](https://cran.r-project.org/web/packages/rvertnet/index.html)**, Retrieve, map and summarize data from the VertNet.org archives (<https://vertnet.org/>). Functions allow searching by many parameters, including taxonomic names, places, and dates. In addition, there is an interface for conducting spatially delimited searches, and another for requesting large datasets via email. [Issue for volunteering](https://github.com/ropensci-archive/rvertnet/issues/71).
- **[natserv](https://cran.r-project.org/web/packages/natserv/index.html)**. Interface to NatureServe (<https://www.natureserve.org/>). Includes methods to get data, image metadata, search taxonomic names, and make maps. [Issue for volunteering](https://github.com/ropensci-archive/natserv/issues/29).
### Call for comaintainers
Refer to our somewhat [recent blog post](/blog/2022/10/17/maintain-or-co-maintain-an-ropensci-package/#packages-looking-for-co-maintainers) to identify other packages where help is especially wished for!
See also our [help wanted page](/help-wanted/) -- before opening a PR, we recommend asking in the issue whether help is still needed.
## Package development corner
Some useful tips for R package developers. :eyes:
### Register a package author in DESCRIPTION in one function call...
with [`desc::desc_add_author_gh()`](https://desc.r-lib.org/reference/desc_add_author_gh.html)!
For instance, `desc::desc_add_author_gh("maelle", role = "aut")`.
You can also register _yourself_ with [`desc::desc_add_me()`](https://desc.r-lib.org/reference/desc_add_me.html).
These functions are great tools to implement our advice ["Be generous with attributions"](https://devguide.ropensci.org/collaboration.html#attributions).
### Hadley Wickham's newsletter "Tidy design principles"
Hadley Wickham started a [free newsletter](https://tidydesign.substack.com/) to share his "semi-regular thoughts on writing good R code", as part of work on his [new book](https://design.tidyverse.org/).
### Broken `@docType` package documentation
If you got an email from CRAN about a broken `@docType` package documentation (package-level manual page), you might want to read this
[roxygen2 GitHub issue](https://github.com/r-lib/roxygen2/issues/1491).
[Example fix](https://github.com/ropensci/rnaturalearth/commit/7191a22b8277a31caeef944fcbe78367ebdfeca5).
rOpenSci dev guide recommends having a package-level manual page.
You can create it by running [`usethis::use_package_doc()`](https://usethis.r-lib.org/reference/use_package_doc.html).
## 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 [Mastodon account](https://hachyderm.io/@rOpenSci).