index.Rmd

---
title: rOpenSci News Digest, September 2021
author:
  - The rOpenSci Team
date: '2021-09-30'
slug: ropensci-news-digest-september-2021
categories: []
tags:
  - newsletter
description: First statistical software peer-review submission, website search, social co-working, new packages and package news
output:
  html_document:
    keep_md: yes
params:
  last_newsletter: '2021-08-31'
---

```{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))
}
```
<!-- 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

A first package was submitted to [rOpenSci Statistical Software Peer Review](/stat-software-review/), two months after its [opening](/blog/2021/07/23/ropensci-news-digest-july-2021/): the [tsbox package](https://github.com/ropensci/software-review/issues/464) by [Christoph Sax](https://github.com/christophsax). 
We are very excited, and thankful for the opportunity to hone our new software review tooling!

We've made it easier to browse our [website](/) by adding some basic search from the navbar.
The search isn't on the full content, but on page titles and descriptions. 
We hope it'll help you find what you're after!
Other ways to find an rOpenSci related thing you vaguely remember is by [asking us](https://contributing.ropensci.org/resources.html#channels), searching through [our website source](https://github.com/ropensci/roweb3/) or using your favourite search engine.

Our next Social Coworking and Office Hours is [Tuesday, October 5th, 9 AM Australian Western / 1:00 UTC](/events/coworking-2021-10/), and hosted by [Nicholas Tierney](/author/nicholas-tierney/).
Find out about [more events](/events).

## 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, eval=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(c(x$given, x$family), collapse = " "))
  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", toString(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 (package$package == "jagstargets"){ package$onboarding <- "https://github.com/ropensci/software-review/issues/425"}
  if (nzchar(package$onboarding)) {
    string <- paste0(string, sprintf("It has been [reviewed](%s)", package$onboarding))
    if (package$package == "jagstargets") {
      rev <- c(rev, " Ernest Guevarra")
    } 
    if (length(rev) > 0) {
      string <- paste0(string, sprintf(" by %s.", toString(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 <- toString(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 latest 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 [Statistical Software Peer Review](/stat-software-review/), including 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$date),
    author = toString(yaml$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$description), ".")), ".")
    if (post$title == "How to Use System Commands in your R Script or Package") {
      string <- sprintf("%s This post was featured in the [R Weekly Highlights podcast by Eric Nantz](https://share.fireside.fm/episode/87RSVeFz+YtoLm80R).", string)
    }
  } else {
    string <- paste0(string, ".")  
  }
  
  if (post$twitterImg != "") {
    img_file <- fs::path_file(post$twitterImg)
    download.file(sprintf("https://ropensci.org/%s", post$twitterImg), img_file)
    img_file %>% magick::image_read() %>% magick::image_scale("400x") %>% magick::image_write(img_file)
    string <- paste0(
      string,
      sprintf('\n\n{{< figure src="%s" alt="%s" width="400" >}}\n\n', img_file, post$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) {
  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}
# 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'}
format_case <- function(usecase) {
  string <- sprintf("* [%s](%s). Reported by %s.", sub("\\.$", "", usecase$title), usecase$url, usecase$reporter)
  string
}
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)!

## Call for maintainers

There's no open call for new maintainers at this point but you can refer to our [contributing guide](https://contributing.ropensci.org/) for finding ways to get involved!
As the maintainer of an rOpenSci package, feel free to contact us on Slack or email `info@ropensci.org` to get your call for maintainer featured in the next newsletter.

## Package development corner

Some useful tips for R package developers. :eyes:

Short anti-struggle list:

* Struggling to write [graceful](https://books.ropensci.org/http-testing/graceful.html) R package examples for CRAN?
Let's remind you of [`@examplesIf` in the latest `roxygen2`](https://roxygen2.r-lib.org/articles/rd.html#functions).

* Struggling with GitHub Actions and dependencies installed from an additional repository? (E.g. [an R-universe repository](/blog/2021/06/22/setup-runiverse/)?)
The r-lib setup-r action now has a [`extra-repositories` input](https://github.com/r-lib/actions/blob/8f28ffb1dc3d672a7d1beec9f4869f5d86168b10/setup-r/action.yml#L46).

* Struggling with encoding in particular a NOTE about UTF-8 strings? Read the [related thread on our forum](https://discuss.ropensci.org/t/note-on-utf-8-strings-by-goodpractice-gp/2165).

How to test code run by [callr](https://callr.r-lib.org/), while having tests contribute to code coverage?
[covr](https://covr.r-lib.org/) modifies the code through injecting tracing symbols and running as its own temporary and definitely self-contained process. 
Any processes external to this, which includes anything via callr, cannot be traced. 
This is an entirely standard condition of any code tracing algorithm. 
A good tip is to ensure everything inside a callr call is bundled as a simple function that can be tested in tests without the callr wrapper.

Another challenge for testing might be interactive behavior. 
For Shiny apps you might look into [shinytest](https://rstudio.github.io/shinytest/), for anything happening in the browser you might enjoy [chromote](https://rstudio.github.io/chromote/) or [crrri](https://rlesur.github.io/crrri/).
You can also resort to [mocking](https://blog.r-hub.io/2019/10/29/mocking/).
For code that's supposed to be only run in interactive sessions, you might use [rlang functions in particular the `rlang::is_interactive()`](https://rlang.r-lib.org/reference/is_interactive.html) in code and tests. 
You can look at the [targets testing suite for external processes](https://github.com/ropensci/targets/tree/main/tests/interactive) and [usethis manual tests](https://github.com/r-lib/usethis/tree/master/tests/manual).

Now about real testers, i.e. the users! :wink:
To help them use your package optimally, you have to write a nice interface, good docs (including system requirements), informative error messages, etc.
Have you also considered adding some sort of sitrep (situation report) function?
The devtools package has [`devtools::dev_sitrep()`](https://devtools.r-lib.org/reference/dev_sitrep.html) e.g. reports on the package development situation, with clear hints given if something is not quite right.
The usethis package has [`usethis::git_sitrep()`](https://usethis.r-lib.org/reference/git_sitrep.html) (using the gert package under the hood!), blogdown has [`blogdown::check_site()`](https://alison.netlify.app/ares-kind-tools/#114).
Good candidates for checks are common pain points, so finding them might require some sort of external perspective on your package.

## 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).