Merge pull request #177 from Moore-Institute-4-Plastic-Pollution-Res/…

…main

add fixes to webr

.github/workflows/deploy-cran-repo.yml → .github/workflows/deploy.yml

@@ -5,7 +5,7 @@ on:
     # Only build on main or master branch
     branches: [main, master]
   # Or when triggered manually
-  workflow_dispatch: {}
+  workflow_dispatch:
 
 name: Build and deploy wasm R package repository
 

DESCRIPTION

@@ -1,4 +1,4 @@
-Package: OpenSpecy
+Package: OpenSpecyWebr
 Type: Package
 Title: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
 Version: 1.1.0
@@ -80,7 +80,6 @@ Imports:
     data.table,
     jsonlite,
     yaml,
-    osfr,
     caTools,
     hyperSpec,
     mmand,
@@ -94,15 +93,11 @@ Suggests:
     knitr,
     rmarkdown,
     testthat (>= 3.1.9),
-    aws.s3, 
-    loggit,
-    config, 
     shinyjs, 
     shinyWidgets,
     bs4Dash,
     dplyr, 
     DT,
-    mongolite, 
     ggplot2
 RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -61,8 +61,6 @@ S3method(restrict_range,OpenSpecy)
 S3method(restrict_range,default)
 S3method(sample_spec,OpenSpecy)
 S3method(sample_spec,default)
-S3method(share_spec,OpenSpecy)
-S3method(share_spec,default)
 S3method(sig_noise,OpenSpecy)
 S3method(sig_noise,default)
 S3method(smooth_intens,OpenSpecy)
@@ -95,7 +93,6 @@ export(fill_spec)
 export(filter_spec)
 export(flatten_range)
 export(gen_grid)
-export(get_lib)
 export(get_metadata)
 export(heatmap_spec)
 export(human_ts)
@@ -130,7 +127,6 @@ export(restrict_range)
 export(rm_lib)
 export(run_app)
 export(sample_spec)
-export(share_spec)
 export(sig_noise)
 export(smooth_intens)
 export(spec_res)
@@ -172,9 +168,6 @@ importFrom(mmand,closing)
 importFrom(mmand,components)
 importFrom(mmand,gaussianSmooth)
 importFrom(mmand,shapeKernel)
-importFrom(osfr,osf_download)
-importFrom(osfr,osf_ls_files)
-importFrom(osfr,osf_retrieve_node)
 importFrom(plotly,add_markers)
 importFrom(plotly,add_trace)
 importFrom(plotly,layout)
@@ -202,10 +195,7 @@ importFrom(utils,head)
 importFrom(utils,installed.packages)
 importFrom(utils,modifyList)
 importFrom(utils,packageVersion)
-importFrom(utils,read.csv)
 importFrom(utils,read.table)
-importFrom(utils,sessionInfo)
 importFrom(utils,unzip)
-importFrom(utils,write.csv)
 importFrom(yaml,read_yaml)
 importFrom(yaml,write_yaml)

R/as_OpenSpecy.R

@@ -148,6 +148,7 @@
 #' \code{\link{read_spec}()} for reading \code{OpenSpecy} objects.
 #'
 #' @importFrom data.table as.data.table
+#' @importFrom digest digest
 #' @export
 as_OpenSpecy <- function(x, ...) {
   UseMethod("as_OpenSpecy")

R/io_spec.R

@@ -8,8 +8,6 @@
 #'
 #' @param x an object of class \code{\link{OpenSpecy}}.
 #' @param file file path to be read from or written to.
-#' @param share defaults to \code{NULL}; needed to share spectra with the
-#' Open Specy community; see \code{\link{share_spec}()} for details.
 #' @param method optional; function to be used as a custom reader or writer.
 #' Defaults to the appropriate function based on the file extension.
 #' @param digits number of significant digits to use when formatting numeric
@@ -110,7 +108,7 @@ write_spec.OpenSpecy <- function(x, file, method = NULL,
 #' @rdname io_spec
 #'
 #' @export
-read_spec <- function(file, share = NULL, method = NULL, ...) {
+read_spec <- function(file, method = NULL, ...) {
   if (is.null(method)) {
     if (grepl("(\\.yaml$)|(\\.yml$)", file, ignore.case = T)) {
       yml <- read_yaml(file = file, ...)
@@ -147,8 +145,6 @@ read_spec <- function(file, share = NULL, method = NULL, ...) {
     os$metadata$file_name <- basename(file)
   }
 
-  if (!is.null(share)) share_spec(os, file = file, share = share)
-
   return(os)
 }
 

R/manage_lib.R

@@ -180,32 +180,6 @@ check_lib <- function(type = c("derivative", "nobaseline", "raw", "mediod",
   invisible()
 }
 
-#' @rdname manage_lib
-#'
-#' @importFrom utils read.csv
-#' @importFrom osfr osf_retrieve_node osf_ls_files osf_download
-#'
-#' @export
-get_lib <- function(type = c("derivative", "nobaseline", "raw", "mediod",
-                             "model"),
-                    path = "system", node = "x7dpz", conflicts = "overwrite",
-                    ...) {
-  lp <- ifelse(path == "system",
-               system.file("extdata", package = "OpenSpecy"),
-               path)
-
-  osf <- osf_retrieve_node(node) |>
-    osf_ls_files(pattern = ".rds", n_max = Inf)
-
-  message("Fetching Open Specy reference libraries from OSF ...")
-    osf |> subset(grepl(
-      paste0("(", paste(type, collapse = "|"), ").rds"),
-      osf$name)) |>
-      osf_download(path = lp, conflicts = conflicts, progress = TRUE, ...)
-
-  message("Use 'load_lib()' to load the library")
-}
-
 #' @rdname manage_lib
 #'
 #' @export

R/read_envi.R

@@ -13,8 +13,6 @@
 #' standard deviations for the \code{gaussianSmooth} function from the
 #' \code{mmand} package to describe how spectral smoothing occurs on each dimension.
 #' The first two dimensions are x and y, the third is the wavenumbers.
-#' @param share defaults to \code{NULL}; needed to share spectra with the
-#' Open Specy community; see \code{\link{share_spec}()} for details.
 #' @param metadata a named list of the metadata; see
 #' \code{\link{as_OpenSpecy}()} for details.
 #' @param \ldots further arguments passed to the submethods.
@@ -45,7 +43,7 @@
 #' @importFrom caTools read.ENVI
 #' @importFrom mmand gaussianSmooth
 #' @export
-read_envi <- function(file, header = NULL, spectral_smooth = F, sigma = c(1,1,1), share = NULL,
+read_envi <- function(file, header = NULL, spectral_smooth = F, sigma = c(1,1,1),
                       metadata = list(
                         file_name = basename(file),
                         user_name = NULL,
@@ -118,8 +116,6 @@ read_envi <- function(file, header = NULL, spectral_smooth = F, sigma = c(1,1,1)
                      coords = dt[, 1:2] |> unique(),
                      session_id = T)
 
-  if (!is.null(share)) share_spec(os, file = file, share = share)
-
   return(os)
 }