Exported LazyH5

dipterix · Jan 9, 2025 · 34dda1c · 34dda1c
1 parent d7ee145
commit 34dda1c
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Showing 5 changed files with 38 additions and 38 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ieegio
 Title: File IO for Intracranial Electroencephalography
-Version: 0.0.2.9008
+Version: 0.0.2.9009
 Language: en-US
 Encoding: UTF-8
 Authors@R: 
@@ -27,6 +27,7 @@ Imports:
     fst (>= 0.9.0),
     gifti (>= 0.8.0),
     grDevices,
+    hdf5r,
     jsonlite,
     oro.nifti,
     R.matlab (>= 3.7.0),
@@ -35,7 +36,6 @@ Imports:
     rpyANTs (>= 0.0.3),
     stringr,
     utils,
-    hdf5r,
     yaml
 Suggests: 
     reticulate,

diff --git a/NAMESPACE b/NAMESPACE
@@ -54,6 +54,7 @@ S3method(print,ieegio_get_channel)
 S3method(print,ieegio_surface)
 S3method(print,ieegio_volume)
 S3method(print,nwb.proxy)
+export(LazyH5)
 export(as_ieegio_volume)
 export(burn_volume)
 export(ieegio_sample_data)

diff --git a/R/aaa.R b/R/aaa.R
@@ -136,28 +136,6 @@ ensure_r_package <- function(pkg, ...) {
   stop("R package `", pkg, "` is missing. Please manually install them in interactive mode.")
 }
 
-ensure_py_package <- function(pkg, method = c("pip", "conda"), ...) {
-  if(!file.exists(rpymat::env_path())) {
-    if(package_installed("ravemanager")) {
-      ravemanager <- asNamespace("ravemanager")
-      ravemanager$configure_python()
-    } else {
-      rpyANTs::install_ants()
-    }
-  }
-  pkg_list <- rpymat::list_pkgs()
-  if(pkg %in% pkg_list$package) {
-    return(invisible())
-  }
-  method <- match.arg(method)
-  if (method == "pip") {
-    rpymat::add_packages(pkg, pip = TRUE)
-  } else {
-    rpymat::add_packages(pkg)
-  }
-  return(invisible())
-}
-
 ensure_package <- function(pkg, ..., lang = c("r", "python"), need_interactive = TRUE) {
   lang <- match.arg(lang)
   if(need_interactive && !interactive()) {

diff --git a/R/hdf5-class.R b/R/hdf5-class.R
@@ -88,6 +88,7 @@ h5FileValid <- function(filename){
 
 #' @title Lazy 'HDF5' file loader
 #' @description provides hybrid data structure for 'HDF5' file
+#' @export
 LazyH5 <- R6::R6Class(
   classname = 'LazyH5',
   portable = TRUE,
@@ -218,6 +219,13 @@ LazyH5 <- R6::R6Class(
                 storage.mode(x) <- "double"
               }
             },
+            "character" = {
+              x <- as.character(x)
+            },
+            "string" = {
+              x <- as.character(x)
+              ctype <- "character"
+            },
             {
               storage.mode(x) <- ctype
             }
@@ -285,7 +293,7 @@ LazyH5 <- R6::R6Class(
               if(!ptr$path_valid(path = nm)){
                 ptr <- ptr$create_group(i)
                 if(!self$quiet){
-                  cat('{private$file} => {nm} (Group Created)\n')
+                  cat(sprintf('%s => %s (Group Created)\n', private$file, nm))
                 }
               }else{
                 ptr <- ptr[[i]]
@@ -297,13 +305,13 @@ LazyH5 <- R6::R6Class(
             if(ptr$path_valid(path = nm)){
               # dataset exists, unlink first
               if(!self$quiet){
-                cat('{private$file} => {private$name} (Dataset Removed)\n')
+                cat(sprintf('%s => %s (Dataset Removed)\n', private$file, nm))
               }
               ptr$link_delete(nm)
             }
             # new create
             if(!self$quiet){
-              cat('{private$file} => {private$name} (Dataset Created)\n')
+              cat(sprintf('%s => %s (Dataset Created)\n', private$file, nm))
             }
             if(missing(robj)){
               robj <- NA

diff --git a/R/py-setup.R b/R/py-setup.R
@@ -86,18 +86,31 @@ validate_python <- function(verbose = TRUE) {
   )
 })
 
-ensure_py_package <- function(packages, python_ver = "auto", ...) {
-  if(!dir.exists(rpymat::env_path())) {
-    standalone <- !file.exists(rpymat::conda_bin())
-    rpymat::configure_conda(python_ver = python_ver, force = TRUE, standalone = standalone)
-  }
-  rpymat::ensure_rpymat(verbose = FALSE)
-  installed_pkgs_tbl <- rpymat::list_pkgs()
-  packages <- packages[!packages %in% installed_pkgs_tbl$package]
-  if(length(packages)) {
-    rpymat::add_packages(packages, ...)
+ensure_py_package <- local({
+
+  installed_pkgs_tbl <- NULL
+
+  function(packages, python_ver = "auto", ...) {
+    if(!dir.exists(rpymat::env_path())) {
+      standalone <- !file.exists(rpymat::conda_bin())
+      rpymat::configure_conda(python_ver = python_ver, force = TRUE, standalone = standalone)
+    }
+    rpymat::ensure_rpymat(verbose = FALSE)
+
+    if(is.null(installed_pkgs_tbl) || !is.data.frame(installed_pkgs_tbl) || !all(packages %in% installed_pkgs_tbl$package)) {
+      installed_pkgs_tbl <<- rpymat::list_pkgs()
+    }
+
+    packages <- packages[!packages %in% installed_pkgs_tbl$package]
+
+    if(length(packages)) {
+      rpymat::add_packages(packages, ...)
+      installed_pkgs_tbl <<- rpymat::list_pkgs()
+    }
+
+    invisible()
   }
-}
+})
 
 import_py_module <- function(name, package = name, convert = FALSE) {
   rpymat::ensure_rpymat(verbose = FALSE, cache = TRUE)