Merge pull request #29 from yjunechoe/1.1.2

1.1.2
yjunechoe · Feb 18, 2024 · 03ca7ca · 03ca7ca
2 parents 67bb725 + 7a41d9a
commit 03ca7ca
Show file tree

Hide file tree

Showing 75 changed files with 178 additions and 147 deletions.
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 1.1.1
-Date: 2024-02-07 17:45:58 UTC
-SHA: c69f5c5308ae5c0c96d955d46d309231299f9c2f
+Version: 1.1.2
+Date: 2024-02-16 16:22:21 UTC
+SHA: 7e7dcf69b9d37cbd43f3b4ddb63916019f3bb32b
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: jlmerclusterperm
 Title: Cluster-Based Permutation Analysis for Densely Sampled Time Data
-Version: 1.1.1
+Version: 1.1.2
 Authors@R: 
     person("June", "Choe", , "jchoe001@gmail.com", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0002-0701-921X"))

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,10 @@
-# jlmerclusterperm 1.1.1
+# jlmerclusterperm 1.1.2
+
+- `jlmerclusterperm()` exposes a `cache_dir` argument for manually specifying the cache directory. This was added largely for the convenience of testing. The default value of `cache_dir = NULL` preserves old behavior.
+
+Fixes for CRAN:
+
+- Write cache to `tempdir()` for the purposes of running examples and tests.
 
 # jlmerclusterperm 1.1.1
 

diff --git a/R/aaa.R b/R/aaa.R
@@ -42,14 +42,17 @@ julia_setup_ok <- function() {
 #' Initial setup for the jlmerclusterperm package
 #'
 #' @param ... Ignored.
+#' @param cache_dir The location to write out package cache files (namely, Manifest.toml).
+#'   If `NULL` (default), attempts to write to the package's cache directory discovered via
+#'   `R_user_dir()` and falls back to `tempdir()`.
 #' @param restart Whether to set up a fresh Julia session, given that one is already running.
 #'   If `FALSE` and `jlmerclusterperm_setup()` has already been called, nothing happens.
 #' @param verbose Print progress and messages from Julia in the console
 #'
 #' @examplesIf julia_setup_ok()
 #' \donttest{
 #' options("jlmerclusterperm.nthreads" = 2)
-#' jlmerclusterperm_setup(verbose = FALSE)
+#' jlmerclusterperm_setup(cache_dir = tempdir(), verbose = FALSE)
 #'
 #' \dontshow{
 #' JuliaConnectoR::stopJulia()
@@ -58,22 +61,22 @@ julia_setup_ok <- function() {
 #'
 #' @export
 #' @return TRUE
-jlmerclusterperm_setup <- function(..., restart = TRUE, verbose = TRUE) {
+jlmerclusterperm_setup <- function(..., cache_dir = NULL, restart = TRUE, verbose = TRUE) {
   if (!JuliaConnectoR::juliaSetupOk()) cli::cli_abort("No Julia installation detected.")
   if (!julia_version_compatible()) cli::cli_abort("Julia version >=1.8 required.")
   if (restart || !is_setup()) {
     JuliaConnectoR::stopJulia()
-    setup_with_progress(verbose = verbose)
+    setup_with_progress(cache_dir = cache_dir, verbose = verbose)
     .jlmerclusterperm$is_setup <- TRUE
   } else {
     cli::cli_inform("Julia instance already running - skipping setup.")
   }
   invisible(TRUE)
 }
 
-setup_with_progress <- function(..., verbose = TRUE) {
+setup_with_progress <- function(..., cache_dir = NULL, verbose = TRUE) {
   start_with_threads(verbose = verbose)
-  set_projenv(verbose = verbose)
+  set_projenv(cache_dir = cache_dir, verbose = verbose)
   source_jl(verbose = verbose)
   define_globals()
   cleanup_jl()
@@ -96,19 +99,25 @@ start_with_threads <- function(..., max_threads = 7L, verbose = TRUE) {
   invisible(TRUE)
 }
 
-set_projenv <- function(..., verbose = TRUE) {
+set_projenv <- function(..., cache_dir = NULL, verbose = TRUE) {
   if (verbose) cli::cli_progress_step("Activating package environment")
-  pkgdir <- system.file("julia/", package = "jlmerclusterperm")
-  cachedir <- R_user_dir("jlmerclusterperm", which = "cache")
-  userdir <- if (dir.exists(dirname(cachedir))) cachedir else tempdir()
+  userdir <- if (!is.null(cache_dir)) {
+    cache_dir
+  } else {
+    pkg_cache_dir <- R_user_dir("jlmerclusterperm", which = "cache")
+    if (dir.exists(dirname(pkg_cache_dir))) pkg_cache_dir else tempdir()
+  }
   projdir <- file.path(userdir, "julia")
   manifest <- file.path(projdir, "Manifest.toml")
-  manifest_cached <- file.exists(manifest) && (parse_julia_version(readLines(manifest)[3]) == julia_version())
+  manifest_cached <- file.exists(manifest) &&
+    (julia_version() == parse_julia_version(readLines(manifest)[3]))
   if (!dir.exists(userdir)) {
     dir.create(userdir)
-  } else if (!manifest_cached) {
-    unlink(dir(userdir, full.names = TRUE), recursive = TRUE)
   }
+  if (!manifest_cached) {
+    unlink(manifest)
+  }
+  pkgdir <- system.file("julia/", package = "jlmerclusterperm")
   file.copy(from = pkgdir, to = userdir, recursive = TRUE)
   JuliaConnectoR::juliaCall("cd", projdir)
   JuliaConnectoR::juliaEval("using Pkg")

diff --git a/R/calculate_pvalue.R b/R/calculate_pvalue.R
@@ -12,7 +12,7 @@
 #' \donttest{
 #' \dontshow{
 #' options("jlmerclusterperm.nthreads" = 2)
-#' jlmerclusterperm_setup(verbose = FALSE)
+#' jlmerclusterperm_setup(cache_dir = tempdir(), verbose = FALSE)
 #' julia_progress(show = FALSE)
 #' }
 #'

diff --git a/R/clusterpermute.R b/R/clusterpermute.R
@@ -13,7 +13,7 @@
 #' \donttest{
 #' \dontshow{
 #' options("jlmerclusterperm.nthreads" = 2)
-#' jlmerclusterperm_setup(verbose = FALSE)
+#' jlmerclusterperm_setup(cache_dir = tempdir(), verbose = FALSE)
 #' julia_progress(show = FALSE)
 #' }
 #'

diff --git a/R/compute_timewise_statistics.R b/R/compute_timewise_statistics.R
@@ -17,7 +17,7 @@
 #' \donttest{
 #' \dontshow{
 #' options("jlmerclusterperm.nthreads" = 2)
-#' jlmerclusterperm_setup(verbose = FALSE)
+#' jlmerclusterperm_setup(cache_dir = tempdir(), verbose = FALSE)
 #' julia_progress(show = FALSE)
 #' }
 #'

diff --git a/R/extract_clusters.R b/R/extract_clusters.R
@@ -16,7 +16,7 @@
 #' \donttest{
 #' \dontshow{
 #' options("jlmerclusterperm.nthreads" = 2)
-#' jlmerclusterperm_setup(verbose = FALSE)
+#' jlmerclusterperm_setup(cache_dir = tempdir(), verbose = FALSE)
 #' julia_progress(show = FALSE)
 #' }
 #'
@@ -83,7 +83,7 @@ extract_empirical_clusters <- function(empirical_statistics, threshold, binned =
 #' \donttest{
 #' \dontshow{
 #' options("jlmerclusterperm.nthreads" = 2)
-#' jlmerclusterperm_setup(verbose = FALSE)
+#' jlmerclusterperm_setup(cache_dir = tempdir(), verbose = FALSE)
 #' julia_progress(show = FALSE)
 #' }
 #'

diff --git a/R/interop-utils.R b/R/interop-utils.R
@@ -11,7 +11,7 @@ JuliaConnectoR::stopJulia
 #' \donttest{
 #' \dontshow{
 #' options("jlmerclusterperm.nthreads" = 2)
-#' jlmerclusterperm_setup(verbose = FALSE)
+#' jlmerclusterperm_setup(cache_dir = tempdir(), verbose = FALSE)
 #' }
 #'
 #' # Show current progress options

diff --git a/R/jlmer.R b/R/jlmer.R
@@ -14,7 +14,7 @@
 #' \donttest{
 #' \dontshow{
 #' options("jlmerclusterperm.nthreads" = 2)
-#' jlmerclusterperm_setup(verbose = FALSE)
+#' jlmerclusterperm_setup(cache_dir = tempdir(), verbose = FALSE)
 #' julia_progress(show = FALSE)
 #' }
 #'
@@ -57,7 +57,7 @@ to_jlmer <- function(formula, data, family = c("gaussian", "binomial"), jlmer_sp
 #' \donttest{
 #' \dontshow{
 #' options("jlmerclusterperm.nthreads" = 2)
-#' jlmerclusterperm_setup(verbose = FALSE)
+#' jlmerclusterperm_setup(cache_dir = tempdir(), verbose = FALSE)
 #' julia_progress(show = FALSE)
 #' }
 #'

diff --git a/R/julia_rng.R b/R/julia_rng.R
@@ -5,7 +5,7 @@
 #' \donttest{
 #' \dontshow{
 #' options("jlmerclusterperm.nthreads" = 2)
-#' jlmerclusterperm_setup(verbose = FALSE)
+#' jlmerclusterperm_setup(cache_dir = tempdir(), verbose = FALSE)
 #' julia_progress(show = FALSE)
 #' }
 #'

diff --git a/R/permute.R b/R/permute.R
@@ -9,7 +9,7 @@
 #' \donttest{
 #' \dontshow{
 #' options("jlmerclusterperm.nthreads" = 2)
-#' jlmerclusterperm_setup(verbose = FALSE)
+#' jlmerclusterperm_setup(cache_dir = tempdir(), verbose = FALSE)
 #' julia_progress(show = FALSE)
 #' }
 #'

diff --git a/R/permute_timewise_statistics.R b/R/permute_timewise_statistics.R
@@ -10,7 +10,7 @@
 #' \donttest{
 #' \dontshow{
 #' options("jlmerclusterperm.nthreads" = 2)
-#' jlmerclusterperm_setup(verbose = FALSE)
+#' jlmerclusterperm_setup(cache_dir = tempdir(), verbose = FALSE)
 #' julia_progress(show = FALSE)
 #' }
 #'

diff --git a/R/threshold_search.R b/R/threshold_search.R
@@ -10,7 +10,7 @@
 #' \donttest{
 #' \dontshow{
 #' options("jlmerclusterperm.nthreads" = 2)
-#' jlmerclusterperm_setup(verbose = FALSE)
+#' jlmerclusterperm_setup(cache_dir = tempdir(), verbose = FALSE)
 #' julia_progress(show = FALSE)
 #' }
 #'

diff --git a/R/tidy.R b/R/tidy.R
@@ -14,7 +14,7 @@ generics::tidy
 #' \donttest{
 #' \dontshow{
 #' options("jlmerclusterperm.nthreads" = 2)
-#' jlmerclusterperm_setup(verbose = FALSE)
+#' jlmerclusterperm_setup(cache_dir = tempdir(), verbose = FALSE)
 #' julia_progress(show = FALSE)
 #' }
 #'
@@ -99,7 +99,7 @@ tidy.jlmer_mod <- function(x, effects = c("var_model", "ran_pars", "fixed"), ...
 #' \donttest{
 #' \dontshow{
 #' options("jlmerclusterperm.nthreads" = 2)
-#' jlmerclusterperm_setup(verbose = FALSE)
+#' jlmerclusterperm_setup(cache_dir = tempdir(), verbose = FALSE)
 #' julia_progress(show = FALSE)
 #' }
 #'

diff --git a/README.md b/README.md
@@ -273,7 +273,7 @@ following as you see fit.
 To cite jlmerclusterperm:
 
 - Choe, J. (2023). jlmerclusterperm: Cluster-Based Permutation Analysis
-  for Densely Sampled Time Data. R package version 1.1.1.
+  for Densely Sampled Time Data. R package version 1.1.2.
   <https://cran.r-project.org/package=jlmerclusterperm>.
 
 To cite the cluster-based permutation test:

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,3 +1,7 @@
+Fixes for CRAN:
+
+* Write cache to `tempdir()` for the purposes of running examples and tests.
+
 ## R CMD check results
 
 0 errors | 0 warnings | 0 notes
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/Garrison-et-al-2020.html b/docs/articles/Garrison-et-al-2020.html
diff --git a/docs/articles/Geller-et-al-2020.html b/docs/articles/Geller-et-al-2020.html