Merge branch 'wrap-module'

.Rbuildignore

@@ -17,3 +17,5 @@
 ^doc$
 ^Meta$
 ^inst/julia/Manifest.toml$
+^inst/julia/JlmerClusterPerm/Manifest.toml$
+^format/

.github/workflows/julia-style.yaml

@@ -0,0 +1,34 @@
+name: Julia-Style
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+on:
+  push:
+    branches:
+      - 'main'
+    tags: '*'
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+jobs:
+  format-check:
+    name: Style Enforcement (Julia ${{ matrix.julia-version }} - ${{ github.event_name }})
+    # Run on push's or non-draft PRs
+    if: (github.event_name == 'push') || (github.event.pull_request.draft == false)
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        julia-version: [1.8]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+      - uses: actions/checkout@v1
+      - name: Instantiate `format` environment and format
+        run: |
+          julia --project=format -e 'using Pkg; Pkg.instantiate(); Pkg.resolve()'
+          julia --project=format 'format/run.jl'
+      - uses: reviewdog/action-suggester@v1
+        if: github.event_name == 'pull_request'
+        with:
+          tool_name: JuliaFormatter
+          fail_on_error: true

.github/workflows/style.yaml → .github/workflows/r-style.yaml

@@ -4,7 +4,7 @@ on:
   push:
     paths: ["**.[rR]", "**.[qrR]md", "**.[rR]markdown", "**.[rR]nw", "**.[rR]profile"]
 
-name: Style
+name: R-Style
 
 jobs:
   style:

.gitignore

@@ -4,6 +4,8 @@
 .httr-oauth
 .DS_Store
 inst/julia/Manifest.toml
+inst/julia/JlmerClusterPerm/Manifest.toml
+format/Manifest.toml$
 ^CRAN-SUBMISSION$
 inst/doc
 /doc/

R/aaa.R

@@ -64,6 +64,7 @@ setup_with_progress <- function(..., verbose = TRUE) {
   start_with_threads(verbose = verbose)
   set_projenv(verbose = verbose)
   source_jl(verbose = verbose)
+  invisible(TRUE)
 }
 
 start_with_threads <- function(..., max_threads = 7, verbose = TRUE) {
@@ -79,6 +80,7 @@ start_with_threads <- function(..., max_threads = 7, verbose = TRUE) {
     suppressMessages(JuliaConnectoR::startJuliaServer())
   }
   .jlmerclusterperm$opts$nthreads <- nthreads
+  invisible(TRUE)
 }
 
 set_projenv <- function(..., verbose = TRUE) {
@@ -88,44 +90,41 @@ set_projenv <- function(..., verbose = TRUE) {
   JuliaConnectoR::juliaCall("cd", pkgdir)
   JuliaConnectoR::juliaEval("using Pkg")
   JuliaConnectoR::juliaEval('Pkg.activate(".", io = devnull)')
+  JuliaConnectoR::juliaEval('Pkg.develop(path = "JlmerClusterPerm", io = devnull)')
   JuliaConnectoR::juliaEval("Pkg.instantiate()") # io = devnull
   JuliaConnectoR::juliaEval("Pkg.resolve(io = devnull)")
   JuliaConnectoR::juliaCall("cd", getwd())
-  JuliaConnectoR::juliaEval(paste0("pg_width = ", max(1L, cli::console_width() - 44L)))
-  JuliaConnectoR::juliaEval("pg_io = stderr")
-  JuliaConnectoR::juliaEval(paste0("using Random123; const rng = Threefry2x((", seed, ", 20))"))
   .jlmerclusterperm$opts$seed <- seed
   .jlmerclusterperm$opts$pkgdir <- pkgdir
+  define_globals()
+  invisible(TRUE)
+}
+
+define_globals <- function(...) {
+  JuliaConnectoR::juliaEval(sprintf(
+    "pg = Dict(:width => %i, :io => stderr);
+    using Random123;
+    const rng = Threefry2x((%i, 20));",
+    max(1L, cli::console_width() - 44L),
+    as.integer(.jlmerclusterperm$opts$seed)
+  ))
+  .jlmerclusterperm$get_jl_opts <- function(x) {
+    list(JuliaConnectoR::juliaEval("(pg = pg, rng = rng)"))
+  }
+  invisible(TRUE)
 }
 
 source_jl <- function(..., verbose = TRUE) {
   jl_pkgs <- readLines(file.path(.jlmerclusterperm$opts$pkgdir, "load-pkgs.jl"))
-  jl_scripts <- list.files(.jlmerclusterperm$opts$pkgdir, pattern = "\\d{2}-.*\\.jl$", full.names = TRUE)
-  load_steps <- c(jl_pkgs, jl_scripts)
   i <- 1L
-  if (verbose) cli::cli_progress_step("Running package setup scripts ({i}/{length(load_steps)})")
-  for (i in seq_along(load_steps)) {
+  if (verbose) cli::cli_progress_step("Running package setup scripts ({i}/{length(jl_pkgs) + 1})")
+  for (i in (seq_along(jl_pkgs) + 1)) {
     if (verbose) cli::cli_progress_update()
-    jl_load <- load_steps[i]
-    if (grepl("^using ", jl_load)) {
-      JuliaConnectoR::juliaEval(jl_load)
+    if (i <= length(jl_pkgs)) {
+      JuliaConnectoR::juliaEval(jl_pkgs[i])
     } else {
-      JuliaConnectoR::juliaCall("include", jl_load)
+      .jlmerclusterperm$jl <- JuliaConnectoR::juliaImport("JlmerClusterPerm")
     }
   }
-  exported_fns <- c(
-    "jlmer", "compute_timewise_statistics",
-    "extract_clusters", "permute_timewise_statistics",
-    "guess_shuffle_as", "permute_by_predictor"
-  )
-  for (jl_fn in exported_fns) {
-    .jlmerclusterperm[[jl_fn]] <- JuliaConnectoR::juliaFun(jl_fn)
-  }
-  .jlmerclusterperm$exported_fns <- exported_fns
+  invisible(TRUE)
 }
-
-#' @keywords internal
-dev_source <- function() { # nocov start
-  .jlmerclusterperm$opts$pkgdir <- system.file("julia/", package = "jlmerclusterperm")
-  source_jl()
-} # nocov end

R/compute_timewise_statistics.R

@@ -69,8 +69,8 @@ compute_timewise_statistics <- function(jlmer_spec, family = c("gaussian", "bino
 
 
   out <- JuliaConnectoR::juliaGet(do.call(
-    .jlmerclusterperm$compute_timewise_statistics,
-    c(args, term_groups$jl, statistic, is_mem, opts)
+    .jlmerclusterperm$jl$compute_timewise_statistics,
+    c(args, term_groups$jl, statistic, is_mem, .jlmerclusterperm$get_jl_opts(), opts)
   ))
 
   alert_diagnostics(jlmer_spec, out)

R/extract_clusters.R

@@ -57,7 +57,7 @@ extract_empirical_clusters <- function(empirical_statistics, threshold, binned =
   empirical_statistics <- apply_threshold(empirical_statistics, statistic, threshold)
   predictors <- rownames(empirical_statistics)
   n <- as.integer(max(min(top_n, ncol(empirical_statistics)), 1))
-  largest_clusters <- .jlmerclusterperm$extract_clusters(empirical_statistics, binned, n)
+  largest_clusters <- .jlmerclusterperm$jl$extract_clusters(empirical_statistics, binned, n)
   cluster_dfs <- df_from_DF(largest_clusters)
   empirical_clusters <- split(cluster_dfs[, -5], predictors[cluster_dfs$id])[predictors]
   empirical_clusters <- lapply(empirical_clusters, function(cluster_df) {
@@ -125,7 +125,7 @@ extract_null_cluster_dists <- function(null_statistics, threshold, binned = FALS
   null_statistics <- apply_threshold(null_statistics, statistic, threshold)
   null_cluster_dists <- apply(null_statistics, 3, function(t_matrix) {
     t_matrix <- t_matrix[!is.nan(rowSums(t_matrix)), ]
-    largest_clusters <- df_from_DF(.jlmerclusterperm$extract_clusters(t_matrix, binned, 1L))
+    largest_clusters <- df_from_DF(.jlmerclusterperm$jl$extract_clusters(t_matrix, binned, 1L))
   }, simplify = FALSE)
   structure(null_cluster_dists,
     class = "null_cluster_dists",

R/interop-utils.R

@@ -40,19 +40,19 @@ julia_progress <- function(show, width) {
   show_missing <- missing(show)
   both_missing <- show_missing && missing(width)
   opts_is_list <- !show_missing && is.list(show) && identical(names(show), c("show", "width"))
-  old_opts <- JuliaConnectoR::juliaGet(JuliaConnectoR::juliaEval("(show = !(pg_io isa Base.DevNull), width = pg_width)"))
+  old_opts <- JuliaConnectoR::juliaGet(JuliaConnectoR::juliaEval("(show = pg[:io] != devnull, width = pg[:width])"))
   if (!show_missing) {
     if (opts_is_list) {
       width <- show$width
       show <- show$show
     }
-    JuliaConnectoR::juliaEval(paste0("pg_io = ", if (show) "stderr" else "devnull"))
+    JuliaConnectoR::juliaEval(paste0("pg[:io] = ", if (show) "stderr" else "devnull"))
   }
   if (!missing(width)) {
     if (width == "auto") {
       width <- max(1L, cli::console_width() - 44L)
     }
-    JuliaConnectoR::juliaEval(paste0("pg_width = ", width))
+    JuliaConnectoR::juliaEval(paste0("pg[:width] = ", width))
   }
   out <- strip_JLTYPE(old_opts)
   if (both_missing) {

R/jlmer.R

@@ -84,7 +84,7 @@ jlmer <- function(jlmer_spec, family = c("gaussian", "binomial"), ..., progress
   family <- match.arg(family)
   args <- prep_for_jlmer(jlmer_spec, family = family, ...)[-3]
 
-  mod <- do.call(.jlmerclusterperm$jlmer, c(args, jlmer_spec$meta$is_mem, progress = progress, ...))
+  mod <- do.call(.jlmerclusterperm$jl$jlmer, c(args, jlmer_spec$meta$is_mem, progress = progress, ...))
   structure(mod, class = c("jlmer_mod", class(mod)))
 }
 

R/permute.R

@@ -68,7 +68,7 @@ permute_by_predictor <- function(jlmer_spec, predictors, predictor_type = c("gue
   time <- jlmer_spec$meta$time
   predictor_type <- match.arg(predictor_type)
   if (predictor_type == "guess") {
-    predictor_type <- .jlmerclusterperm$guess_shuffle_as(df_jl, predictors, subject, trial)
+    predictor_type <- .jlmerclusterperm$jl$guess_shuffle_as(df_jl, predictors, subject, trial)
     cli::cli_alert_info("Guessed {.arg predictor_type} to be {.val {predictor_type}}")
   }
   predictor_group <- Filter(function(x) any(predictors %in% x), jlmer_spec$meta$term_groups)
@@ -81,7 +81,9 @@ permute_by_predictor <- function(jlmer_spec, predictors, predictor_type = c("gue
     }
     predictors <- predictor_group
   }
-  shuffled <- df_from_DF(.jlmerclusterperm$permute_by_predictor(df_jl, predictor_type, predictors, subject, trial, as.integer(n)))
+  shuffled <- df_from_DF(.jlmerclusterperm$jl$permute_by_predictor(
+    df_jl, predictor_type, predictors, subject, trial, as.integer(n), .jlmerclusterperm$get_jl_opts()[[1]]
+  ))
   class(shuffled) <- class(df)
   shuffled
 }

R/permute_timewise_statistics.R

@@ -70,16 +70,11 @@ permute_timewise_statistics <- function(jlmer_spec, family = c("gaussian", "bino
   }
 
   out <- JuliaConnectoR::juliaGet(do.call(
-    .jlmerclusterperm$permute_timewise_statistics,
-    c(args, nsim, participant_col, trial_col, term_groups$jl, predictors_subset, statistic, is_mem, opts)
+    .jlmerclusterperm$jl$permute_timewise_statistics,
+    c(args, nsim, participant_col, trial_col, term_groups$jl,
+      predictors_subset, statistic, is_mem, .jlmerclusterperm$get_jl_opts(), opts)
   ))
 
-  # shuffle_predictor_groups <- Filter(function(x) !identical(x, "(Intercept)"), jlmer_spec$meta$term_groups)
-  # counter_states <- split(out$counter_states, rep(names(shuffle_predictor_groups), each = nsim))
-  # counter_states[] <- lapply(names(counter_states), function(x) {
-  #   list(predictors = shuffle_predictor_groups[[x]], counter = counter_states[[x]])
-  # })
-
   dimnames(out$z_array) <- list(
     Sim = as.factor(zero_pad(1:nsim)),
     Time = sort(unique(jlmer_spec$data[[jlmer_spec$meta$time]])),

R/threshold_search.R

@@ -29,7 +29,8 @@
 #' null_statistics <- permute_timewise_statistics(spec, nsim = 100)
 #'
 #' # Test cluster mass/probability under different threshold values
-#' walk_threshold_steps(empirical_statistics, null_statistics, steps = 1:3)
+#' walk_threshold_steps(empirical_statistics, null_statistics, steps = 1:3,
+#'                      progress = FALSE)
 #'
 #' \dontshow{
 #' JuliaConnectoR::stopJulia()