forked from remindmodel/remind
-
Notifications
You must be signed in to change notification settings - Fork 0
/
.Rprofile
143 lines (122 loc) · 6.33 KB
/
.Rprofile
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
local({
# setting RENV_PATHS_LIBRARY ensures packages are installed into renv/library
# 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)
# 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 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$lockfile())
renv::install(paste0("renv@", renvVersion))
if (!renvLockExisted) {
unlink(renv::paths$lockfile())
}
}
if (!"https://rse.pik-potsdam.de/r/packages" %in% getOption("repos")) {
options(repos = c(getOption("repos"), pik = "https://rse.pik-potsdam.de/r/packages"))
}
# bootstrapping, will only run once after remind is freshly cloned
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(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.
# To use these, set the environment variable in your ~/.bashrc file in your home
# direcotry (on linux) or in the system environment variables dialog (on windows):
# local directories
# e.g.
# on Linux (separate multiple paths by colons)
# REMIND_repos_dirs="/my/first/path:/my/second/path"
# on Windows (separate multiple paths by semicolons)
# 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))
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
# directory or output directories.
path <- file.path(
c('.', file.path('..', '..')),
'calibration_results', '.Rprofile_calibration_results')
path <- head(path[file.exists(path)], 1)
if (!rlang::is_empty(path))
source(path)
})