Improve tests

taxonomicallyinformedannotation · Jul 3, 2024 · d1d2cfb · d1d2cfb
1 parent 9af7d88
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diff --git a/R/install_latest_version.R b/R/install_latest_version.R
@@ -2,132 +2,28 @@
 #'
 #' @description This function installs the latest version
 #'
-#' @param test Flag for test
-#'
 #' @return NULL
 #'
 #' @export
 #'
 #' @examples NULL
-install_latest_version <- function(test = FALSE) {
+install_latest_version <- function() {
   options(repos = c(CRAN = "https://cloud.r-project.org"))
   if (Sys.info()[["sysname"]] == "Windows") {
     message("You should install RTools if not already done")
   }
   if (Sys.info()[["sysname"]] == "Linux") {
     system(command = "sudo apt install libcurl4-openssl-dev")
   }
-  if (!requireNamespace("pak", quietly = TRUE)) {
-    lib <- Sys.getenv("R_LIBS_SITE")
-    if (lib == "") {
-      lib <- file.path(dirname(.Library), "site-library")
-      cat(sprintf("R_LIBS_SITE=%s\n", lib), append = TRUE)
-      cat(sprintf("R_LIB_FOR_PAK=%s\n", lib), append = TRUE)
-
-      message("Setting R_LIBS_SITE to ", lib)
-    } else {
-      message("R_LIBS_SITE is already set to ", lib)
-      cat(sprintf(
-        "R_LIB_FOR_PAK=%s\n",
-        strsplit(lib, .Platform$path.sep)[[1]][[1]]
-      ), append = TRUE)
-    }
-    install.packages(
-      "pak",
-      repos = sprintf(
-        "https://r-lib.github.io/p/pak/stable/%s/%s/%s",
-        .Platform$pkgType,
-        R.Version()$os,
-        R.Version()$arch
-      )
-    )
+  if (!requireNamespace("devtools")) {
+    install.packages("devtools")
   }
   ref <- ifelse(
     test = Sys.getenv("BRANCH_NAME") != "",
     yes = Sys.getenv("BRANCH_NAME"),
     no = "main"
   )
-  pak::pak_cleanup(force = TRUE)
-  pak::pak_update()
-  if (!requireNamespace(c("timaR"), quietly = TRUE)) {
-    message("Installing for the first time...")
-    local_version <- "myFirstInstallTrickToWork"
-  } else {
-    local_version <- pak::pkg_status("timaR")$version[1]
-  }
-  # TODO not ideal
-  remote_version <- readLines(
-    "https://raw.githubusercontent.com/taxonomicallyinformedannotation/tima-r/main/DESCRIPTION"
-  )[[3]] |>
-    gsub(
-      pattern = "Version: ",
-      replacement = "",
-      fixed = TRUE
-    )
-  if ((local_version == remote_version) && (test == FALSE)) {
-    message(
-      "You already have the latest version (",
-      local_version,
-      ") skipping"
-    )
-  } else {
-    pak::pak_update()
-    pak::pak(ask = FALSE, upgrade = TRUE)
-    # Try installing the local version first
-    success <- tryCatch(
-      {
-        message("Installing local version")
-        pak::pkg_install(
-          pkg = ".",
-          ask = FALSE,
-          upgrade = FALSE
-        )
-        return(test == FALSE)
-      },
-      error = function(e) {
-        return(FALSE)
-      }
-    )
-    # If local version installation fails, try the URL from DESCRIPTION file
-    if (!success) {
-      success <- tryCatch(
-        {
-          message("Installing local version from URL")
-          pak::pkg_install(
-            pkg = desc::desc_get_urls()[[1]],
-            ask = FALSE,
-            upgrade = FALSE
-          )
-          return(test == FALSE)
-        },
-        error = function(e) {
-          return(FALSE)
-        }
-      )
-    }
-    # If URL installation fails, try installing the remote version from GitHub
-    if (!success) {
-      success <- tryCatch(
-        {
-          message("Installing remote version")
-          pak::pkg_install(
-            pkg = "taxonomicallyinformedannotation/tima-r",
-            ask = FALSE,
-            upgrade = FALSE
-          )
-          return(test == FALSE)
-        },
-        error = function(e) {
-          message("Install failed")
-          return(FALSE)
-        }
-      )
-    }
-    # Final message if all attempts fail
-    if (!success) {
-      message("All installation attempts failed")
-    }
-  }
+  devtools::install_github(repo = paste0("taxonomicallyinformedannotation/tima-r@", ref))
   cache <- fs::path_home(".tima")
   message("Creating cache at ", cache)
   fs::dir_create(path = cache)

diff --git a/codemeta.json b/codemeta.json
@@ -578,7 +578,7 @@
     "SystemRequirements": null
   },
   "keywords": ["metaboliteannotation", "chemotaxonomy", "scoringsystem", "naturalproducts", "computationalmetabolomics", "taxonomicdistance", "specializedmetabolome"],
-  "fileSize": "4379.43KB",
+  "fileSize": "4376.027KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

diff --git a/man/install_latest_version.Rd b/man/install_latest_version.Rd
diff --git a/tests/testthat/test-functions.R b/tests/testthat/test-functions.R
@@ -2,7 +2,8 @@ library(testthat)
 ## need to do all in one because of outputs needed in the same temp dir
 ## use fixtures instead in the future
 test_that(desc = "Test functions", code = {
-  install_latest_version(test = TRUE)
+  install_latest_version()
+  setwd(fs::path_home(".tima"))
   ## Prepare parameters
   paths <- parse_yaml_paths()
   params <- get_params(step = "prepare_params")
@@ -662,6 +663,3 @@ test_that(desc = "Test functions", code = {
 
   succeed()
 })
-
-## See https://github.com/markfairbanks/tidytable/issues/269
-.datatable.aware <- TRUE