software.qmd

---
title: "Software"
description: |
  R packages and other software developed by the group
---

Reusable tools and packages developed by the group. See also our [ongoing projects](projects.qmd) and [publications](pubs.qmd).

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE, message = FALSE, warning = FALSE)
library(magrittr)

# Hide software not updated in this many months (set to NULL to disable)
stale_months <- 24
```

```{r load-team}
# Load team members and create lookup by GitHub username
team <- fs::dir_ls("_data/team", regexp = "\\w+\\-\\w+\\.yml") |>
  purrr::map(yaml::read_yaml)

team_by_github <- team %>%
  purrr::keep(~ !is.null(.x$github) && .x$github != "") %>%
  purrr::set_names(purrr::map_chr(., "github"))
```

```{r, results='asis'}
# Helper function to fetch package info from GitHub
fetch_package_info <- function(repo, team_by_github) {
  repo_info <- tryCatch(
    gh::gh("/repos/{repo}", repo = repo),
    error = function(err) list(
      name = basename(repo),
      description = "No description available",
      html_url = paste0("https://github.com/", repo),
      stargazers_count = 0,
      language = NA,
      pushed_at = NA
    )
  )

  contributors <- tryCatch(
    gh::gh("/repos/{repo}/contributors", repo = repo, per_page = 100),
    error = function(err) list()
  )

  team_contributors <- contributors %>%
    purrr::keep(~ .x$login %in% names(team_by_github)) %>%
    purrr::map(function(c) {
      tm <- team_by_github[[c$login]]
      list(
        name = tm$name,
        github = c$login,
        avatar_url = c$avatar_url
      )
    })

  list(
    Package = repo_info$name,
    description = repo_info$description %||% "No description available",
    github_url = repo_info$html_url,
    stars = repo_info$stargazers_count %||% 0,
    language = repo_info$language,
    updated = if (!is.null(repo_info$pushed_at)) substr(repo_info$pushed_at, 1, 10) else NA,
    team_contributors = team_contributors
  )
}

# Get packages from r-universe
pkg_descriptions <- jsonlite::fromJSON("https://epiforecasts.r-universe.dev/api/packages")
extra_metadata <- jsonlite::read_json("https://github.com/epiforecasts/universe/raw/main/packages.json") %>%
  dplyr::bind_rows() %>%
  dplyr::mutate(
    Package = package,
    display_website = display_website & !is.na(display_website),
    .keep = "unused"
  )

universe_packages <- pkg_descriptions %>%
  dplyr::left_join(extra_metadata, by = "Package") %>%
  dplyr::filter(display_website) %>%
  split(rownames(.)) %>%
  purrr::map(unlist) %>%
  purrr::map(function(e) {
    repo <- paste0(e[["_owner"]], "/", e[["Package"]])
    fetch_package_info(repo, team_by_github)
  })

# Get extra packages from YAML
extras <- yaml::read_yaml("_data/software-extras.yml")
extra_packages <- purrr::map(extras, function(e) {
  fetch_package_info(e$repo, team_by_github)
})

# Combine, filter stale, and sort by stars
all_packages <- c(universe_packages, extra_packages) %>%
  purrr::keep(~ !is.null(.x)) %>%
  purrr::keep(~ {
    if (is.null(stale_months) || is.na(.x$updated)) return(TRUE)
    as.Date(.x$updated) > Sys.Date() - (stale_months * 30)
  }) %>%
  { .[order(purrr::map_dbl(., "stars"), decreasing = TRUE)] }

# Render each package
all_packages %>%
  purrr::map_chr(function(e) {
    contributors_section <- ""
    if (length(e$team_contributors) > 0) {
      contributor_items <- purrr::map_chr(e$team_contributors, function(c) {
        sprintf(
          '<a href="https://github.com/%s" title="%s"><img src="%s" alt="%s" width="32" height="32"></a>',
          c$github, c$name, c$avatar_url, c$name
        )
      })
      contributors_section <- paste(contributor_items, collapse = " ")
    }

    knitr::knit_expand(
      "_software-item.Rmd",
      Package = e$Package,
      description = e$description,
      github_url = e$github_url,
      language = e$language %||% "",
      updated = e$updated %||% "",
      contributors_section = contributors_section
    )
  }) %>%
  { knitr::knit_child(text = unlist(.), quiet = TRUE) } %>%
  cat(sep = "\n")
```