Merge pull request #1925 from LaviniaBaumstark/REMIND_release3p4p0

remind release 3.4.0

Author: LaviniaBaumstark

.Rprofile

@@ -3,26 +3,28 @@ local({
 # for some reason this also has implications for symlinking into the global cache
 Sys.setenv(RENV_PATHS_LIBRARY = "renv/library")
 
-# remind's renv integration previously relied on renv.lock, but now it should generally not be used anymore
-# this can safely be removed in January 2024
-if (file.exists("renv.lock") && file.exists("README.md") && !file.exists("renv/old_renv.lock")) {
-  file.rename("renv.lock", "renv/old_renv.lock")
-  message("moved legacy renv.lock to renv/old_renv.lock")
-}
-
 # do not check if library and renv.lock are in sync, because normally renv.lock does not exist
 options(renv.config.synchronized.check = FALSE)
 
-source("renv/activate.R")
+# always set the renv project to the current directory
+Sys.setenv("RENV_PROJECT" = getwd())
 
 # when increasing renvVersion first commit new version's activate script and
-# put that commit's hash into the download.file call below
+# put that commit's hash into the git checkout call below
 renvVersion <- "1.0.7"
+
+# reset renv/activate.R to match renv 1.0.7
+gitRoot <- system2("git", c("rev-parse", "--show-toplevel"), stdout = TRUE)
+if (Sys.getenv("RESET_RENV_ACTIVATE_SCRIPT", unset = "TRUE") == "TRUE" &&
+      normalizePath(gitRoot) == normalizePath(".")) {
+  system2("git", c("checkout", "b83bb1811ff08d8ee5ba8e834af5dd0080d10e66", "--", "renv/activate.R"))
+}
+
+source("renv/activate.R")
+
 if (packageVersion("renv") != renvVersion) {
   renvLockExisted <- file.exists(renv::paths$lockfile())
   renv::install(paste0("renv@", renvVersion))
-  message("Downloading 'renv/activate.R' of renv version 1.0.7")
-  download.file("https://raw.githubusercontent.com/remindmodel/remind/b83bb1811ff08d8ee5ba8e834af5dd0080d10e66/renv/activate.R", "renv/activate.R")
   if (!renvLockExisted) {
     unlink(renv::paths$lockfile())
   }
@@ -36,30 +38,10 @@ if (!"https://rse.pik-potsdam.de/r/packages" %in% getOption("repos")) {
 if (isTRUE(rownames(installed.packages(priority = "NA")) == "renv")) {
   message("R package dependencies are not installed in this renv, installing now...")
   renv::install("rmarkdown", prompt = FALSE) # rmarkdown is required to find dependencies in Rmd files
-  renv::hydrate() # auto-detect and install all dependencies
+  renv::hydrate(prompt = FALSE, report = FALSE) # auto-detect and install all dependencies
   message("Finished installing R package dependencies.")
 }
 
-# bootstrapping python venv, will only run once after remind is freshly cloned
-if (!dir.exists(".venv/")
-    && (Sys.which("python3") != ""
-        || (Sys.which("python.exe") != ""
-            && suppressWarnings(isTRUE(startsWith(system2("python.exe", "--version", stdout = TRUE), "Python 3")))
-           ))) {
-  message("Python venv is not available, setting up now...")
-  # use system python to set up venv
-  if (.Platform$OS.type == "windows") {
-    system2("python.exe", c("-mvenv", ".venv"))
-    pythonInVenv <- normalizePath(file.path(".venv", "Scripts", "python.exe"), mustWork = TRUE)
-  } else {
-    system2("python3", c("-mvenv", ".venv"))
-    pythonInVenv <- normalizePath(file.path(".venv", "bin", "python"), mustWork = TRUE)
-  }
-  # use venv python to install dependencies in venv
-  system2(pythonInVenv, c("-mpip", "install", "--upgrade", "pip", "wheel"))
-  system2(pythonInVenv, c("-mpip", "install", "-r", "requirements.txt"))
-}
-
 # Configure locations of REMIND input data
 # These can be located in directories on the local machine, remote directories,
 # or default directories on the cluster.
@@ -74,51 +56,12 @@ if (!dir.exists(".venv/")
 # REMIND_repos_dirs="C:\my\first\path;D:\my\second\path"
 remindReposDirs <- Sys.getenv("REMIND_repos_dirs")
 
-# for scp targets, you need to set three environment variables
-# on linux e.g. (separate multiple paths by semicolons)
-# REMIND_repos_scp="scp://cluster.pik-potsdam.de/p/projects/rd3mod/inputdata/output;scp://cluster.pik-potsdam.de/p/projects/remind/inputdata/CESparametersAndGDX"
-# REMIND_repos_scp_user="myusername"  # use your user name on the scp target, e.g. the cluster
-# REMIND_repos_scp_key="/home/myusername/.ssh/id_ed25519"  # path to your your ssh private key on your laptop
-# on windows e.g.
-# REMIND_repos_scp="scp://cluster.pik-potsdam.de/p/projects/rd3mod/inputdata/output;scp://cluster.pik-potsdam.de/p/projects/remind/inputdata/CESparametersAndGDX"
-# REMIND_repos_scp_user="myusername"  # use your user name on the scp target, e.g. the cluster
-# REMIND_repos_scp_key="C:\Users\myusername\.ssh\id_ed25519"  # path to your your ssh private key on your laptop
-remindReposSCP <- Sys.getenv("REMIND_repos_scp") # scp URL
-remindReposSCPUser <- Sys.getenv("REMIND_repos_scp_user")  # ssh user name
-remindReposSCPKey <- Sys.getenv("REMIND_repos_scp_key")  # ssh key path
-
-# unless specified otherwise, use cluster defaults
-use_cluster_defaults <- TRUE
-
 # add local directories, if any
 if ("" != remindReposDirs) {
-  directories <- unlist(strsplit(remindReposDirs, .Platform$path.sep,
-                                 fixed = TRUE))
+  directories <- unlist(strsplit(remindReposDirs, .Platform$path.sep, fixed = TRUE))
   directoriesList <- rep(list(NULL), length(directories))
   names(directoriesList) <- directories
-
   options(remind_repos = c(options("remind_repos")[[1]], directoriesList))
-  use_cluster_defaults <- FALSE
-}
-
-# add remote directories, if any remote directory and username and SSH key are set
-if ("" != remindReposSCP && "" != remindReposSCPUser && "" != remindReposSCPKey) {
-  SCPUrls <- unlist(strsplit(remindReposSCP, ";", fixed = TRUE))
-  config <- list(list(username = remindReposSCPUser, ssh_private_keyfile = remindReposSCPKey))
-  for (SCPUrl in SCPUrls) {
-    names(config) <- SCPUrl
-    options(remind_repos = c(options("remind_repos")[[1]], config))
-  }
-  use_cluster_defaults <- FALSE
-}
-
-# default to cluster directories
-if (use_cluster_defaults &&
-    all(file.exists(c("/p/projects/rd3mod/inputdata/output",
-                      "/p/projects/remind/inputdata/CESparametersAndGDX")))) {
-  options(remind_repos = list(
-    "/p/projects/rd3mod/inputdata/output" = NULL,
-    "/p/projects/remind/inputdata/CESparametersAndGDX" = NULL))
 }
 
 # Include local calibration results, if they exist, from either the main

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
     -   id: check-case-conflict
     -   id: check-json