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- `dqrng` updates (see #96); - be more careful setting seeds in tests; - restored some previously failing tests; - misc formatting/cleanup.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -12,8 +12,8 @@ Description: Provides GIS and map utilities, plus additional modeling tools for | |
| URL: | ||
| https://spades-tools.predictiveecology.org, | ||
| https://github.com/PredictiveEcology/SpaDES.tools | ||
| Date: 2024-04-25 | ||
| Version: 2.0.6.9000 | ||
| Date: 2024-05-13 | ||
| Version: 2.0.6.9001 | ||
| Authors@R: c( | ||
| person("Eliot J B", "McIntire", , "[email protected]", role = c("aut"), | ||
| comment = c(ORCID = "0000-0002-6914-8316")), | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,11 +1,13 @@ | ||
| rastDF <- data.frame(pkg = c("raster", "terra"), | ||
| class = c("Raster", "SpatRaster"), | ||
| read = c("raster::raster", "terra::rast"), | ||
| stack = c("raster::stack", "terra::rast"), | ||
| stackClass = c("RasterStack", "SpatRaster"), | ||
| extent = c("raster::extent", "terra::ext")) | ||
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| needTerraAndRaster <- function(envir = parent.frame()) { | ||
| rastDF <- data.frame( | ||
| pkg = c("raster", "terra"), | ||
| class = c("Raster", "SpatRaster"), | ||
| read = c("raster::raster", "terra::rast"), | ||
| stack = c("raster::stack", "terra::rast"), | ||
| stackClass = c("RasterStack", "SpatRaster"), | ||
| extent = c("raster::extent", "terra::ext") | ||
| ) | ||
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| if (!requireNamespace("raster", quietly = TRUE)) { | ||
| rastDF <- rastDF[rastDF$pkg == "terra", ] | ||
| } | ||
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@@ -18,17 +20,12 @@ needTerraAndRaster <- function(envir = parent.frame()) { | |
| # optsAsk in this environment, | ||
| # loads and libraries indicated plus testthat, | ||
| # sets options("reproducible.ask" = FALSE) if ask = FALSE | ||
| testInit <- function(libraries = character(), ask = FALSE, verbose, | ||
| tmpFileExt = "", | ||
| opts = NULL, needGoogleDriveAuth = FALSE | ||
| ) { | ||
| testInit <- function(libraries = character(), ask = FALSE, verbose, tmpFileExt = "", opts = NULL) { | ||
| data.table::setDTthreads(2) | ||
| reproducible::set.randomseed() | ||
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| pf <- parent.frame() | ||
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| if (isTRUE(needGoogleDriveAuth)) | ||
| libraries <- c(libraries) | ||
| if (length(libraries)) { | ||
| libraries <- unique(libraries) | ||
| loadedAlready <- vapply(libraries, function(pkg) | ||
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@@ -44,56 +41,35 @@ testInit <- function(libraries = character(), ask = FALSE, verbose, | |
| } | ||
| } | ||
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| # skip_gauth <- identical(Sys.getenv("SKIP_GAUTH"), "true") # only set in setup.R for covr | ||
| # if (isTRUE(needGoogleDriveAuth) ) { | ||
| # if (!skip_gauth) { | ||
| # if (interactive()) { | ||
| # if (!googledrive::drive_has_token()) { | ||
| # getAuth <- FALSE | ||
| # if (is.null(getOption("gargle_oauth_email"))) { | ||
| # possLocalCache <- "c:/Eliot/.secret" | ||
| # cache <- if (file.exists(possLocalCache)) | ||
| # possLocalCache else TRUE | ||
| # switch(Sys.info()["user"], | ||
| # emcintir = {options(gargle_oauth_email = "[email protected]", | ||
| # gargle_oauth_cache = cache)}, | ||
| # NULL) | ||
| # } | ||
| # if (is.null(getOption("gargle_oauth_email"))) { | ||
| # if (.isRstudioServer()) { | ||
| # .requireNamespace("httr", stopOnFALSE = TRUE) | ||
| # options(httr_oob_default = TRUE) | ||
| # } | ||
| # } | ||
| # getAuth <- TRUE | ||
| # if (isTRUE(getAuth)) | ||
| # googledrive::drive_auth() | ||
| # } | ||
| # } | ||
| # } | ||
| # skip_if_no_token() | ||
| # } | ||
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| out <- list() | ||
| withr::local_options("reproducible.ask" = ask, .local_envir = pf) | ||
| # withr::local_options("spades.debug" = debug, .local_envir = pf) | ||
| # withr::local_options("spades.moduleCodeChecks" = smcc, .local_envir = pf) | ||
| withr::local_options("spades.recoveryMode" = FALSE, .local_envir = pf) | ||
| withr::local_options("reproducible.verbose" = FALSE, .local_envir = pf) | ||
| withr::local_options("spades.useRequire" = FALSE, .local_envir = pf) | ||
| withr::local_options("spades.sessionInfo" = FALSE, .local_envir = pf) | ||
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| if (!missing(verbose)) | ||
| ## set default options for tests | ||
| withr::local_options(list( | ||
| reproducible.ask = ask, | ||
| reproducible.verbose = FALSE, | ||
| # spades.debug = debug, | ||
| # spades.moduleCodeChecks = smcc, | ||
| spades.sessionInfo = FALSE, | ||
| spades.recoveryMode = FALSE, | ||
| spades.useRequire = FALSE | ||
| ), .local_envir = pf) | ||
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| if (!missing(verbose)) { | ||
| withr::local_options("reproducible.verbose" = verbose, .local_envir = pf) | ||
| if (!is.null(opts)) | ||
| } | ||
| if (!is.null(opts)) { | ||
| withr::local_options(opts, .local_envir = pf) | ||
| tmpdir <- reproducible::normPath(withr::local_tempdir(tmpdir = reproducible::tempdir2(), .local_envir = pf)) | ||
| tmpCache <- reproducible::normPath(withr::local_tempdir(tmpdir = tmpdir, .local_envir = pf)) | ||
| } | ||
| tmpdir <- withr::local_tempdir(tmpdir = reproducible::tempdir2(), .local_envir = pf) |> | ||
| reproducible::normPath() | ||
| tmpCache <- withr::local_tempdir(tmpdir = tmpdir, .local_envir = pf) |> | ||
| reproducible::normPath() | ||
| if (isTRUE(any(nzchar(tmpFileExt)))) { | ||
| dotStart <- startsWith(tmpFileExt, ".") | ||
| if (any(!dotStart)) | ||
| tmpFileExt[!dotStart] <- paste0(".", tmpFileExt) | ||
| out$tmpfile <- reproducible::normPath(withr::local_tempfile(tmpdir = tmpdir, fileext = tmpFileExt)) | ||
| out$tmpfile <- withr::local_tempfile(tmpdir = tmpdir, fileext = tmpFileExt) |> | ||
| reproducible::normPath() | ||
| } | ||
| withr::local_dir(tmpdir, .local_envir = pf) | ||
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