feat: Enable package installation from GitHub, Bioconductor and local…

… directory.

R/dependencies.R

@@ -21,6 +21,22 @@ write_dependencies <- function(deps) {
   writeLines(deps, "dependencies.R")
 }
 
+extract_package_name <- function(package) {
+  if (grepl("@", package)) package <- strsplit(package, "@")[[1]][1]
+  if (grepl("bioc::", package)) return(strsplit(package, "::")[[1]][2])
+
+  if (grepl("/", package)) {
+    package_splited <- strsplit(package, "/")[[1]]
+    return(package_splited[length(package_splited)])
+  }
+
+  package
+}
+
+extract_packages_names <- function(packages) {
+  purrr::map_chr(packages, extract_package_name)
+}
+
 # nolint start: line_length_linter
 #' Manage dependencies
 #'
@@ -58,7 +74,8 @@ NULL
 pkg_install <- function(packages) {
   stopifnot(is.character(packages))
   renv::install(packages)
-  write_dependencies(c(packages, read_dependencies()))
+  packages_names <- extract_packages_names(packages)
+  write_dependencies(c(packages_names, read_dependencies()))
   renv::snapshot()
   invisible()
 }
@@ -68,7 +85,8 @@ pkg_install <- function(packages) {
 pkg_remove <- function(packages) {
   stopifnot(is.character(packages))
   renv::remove(packages)
-  write_dependencies(setdiff(read_dependencies(), packages))
+  packages_names <- extract_packages_names(packages)
+  write_dependencies(setdiff(read_dependencies(), packages_names))
   renv::snapshot()
   invisible()
 }

tests/testthat/test-dependencies.R

@@ -0,0 +1,28 @@
+describe("extract_package_name", {
+  it("returns the package name intact when using only the package name", {
+    expect_equal(extract_package_name("shiny"), "shiny")
+  })
+
+  it("returns the package name intact when using the package name and version", {
+    expect_equal(extract_package_name("shiny@1.6.0"), "shiny")
+  })
+
+  it("returns the package name when installing a package from GitHub", {
+    expect_equal(extract_package_name("r-lib/httr"), "httr")
+    expect_equal(extract_package_name("r-lib/testthat@c67018fa4970"), "testthat")
+  })
+
+  it("returns the package name when installing a package from a local path", {
+    expect_equal(extract_package_name("~/path/to/package"), "package")
+  })
+
+  it("returns the package name when installing a package from Bioconductor", {
+    expect_equal(extract_package_name("bioc::Biobase"), "Biobase")
+  })
+})
+
+describe("extract_packages_names", {
+  it("returns a vector of package names when installing multiple packages", {
+    expect_equal(extract_packages_names(c("shiny", "dplyr")), c("shiny", "dplyr"))
+  })
+})