Merge branch 'develop' into quarto-ensemble-sensivity

Author: AritraDey-Dev

CHANGELOG.md

@@ -3,7 +3,14 @@ All notable changes are kept in this file. All changes made should be added to t
 `Unreleased`. Once a new release is made this file will be updated to create a new `Unreleased`
 section for the next release.
 
-For more information about this file see also [Keep a Changelog](http://keepachangelog.com/) .
+	For more information about this file see also [Keep a Changelog](http://keepachangelog.com/) .
+
+## Unreleased
+
+### Added
+
+* Add function `clip_and_save_raster_file()` for subsetting rasters to match a polygon of interest (#3537).
+
 
 ## [1.9.0] - 2025-05-25
 
@@ -16,6 +23,9 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 - Added automated pkgdown documentation for all PEcAn packages (@divine7022, #3482): 
   - Compiled pages are live at https://pecanproject.github.io/package-documentation and inside Docker at `pecan.localhost/pkgdocs/`, and these are automatically updated each time a PR to the source packages is merged.
   - You can compile all pkgdown pages locally at any time with `make pkgdocs`.
+- Included all relevant carbon pools (`ROOT_BIOMASS`, `AG_BIOMASS`, `SOIL_STOCK`, `LIT_BIOMASS`) in BADM-based IC extraction; excluded non-pool variables like `SOIL_CHEM`.
+- Added explicit support for `LIT_BIOMASS` to fully utilize **BADM** biomass capabilities.
+- Added `test-IC_BADM_Utilities.R` to validate BADM initial condition extraction and processing
 - The ERA5 NC extraction function can now handle multi-site instead of one.
 - New Quarto notebook tutorial for PEcAn uncertainty analysis (`documentation/tutorials/Demo_02_Uncertainty_Analysis/uncertainty.qmd`) (#3570)
   - Complete workflow demonstration for ensemble and sensitivity analysis using PEcAn's programmatic interface
@@ -24,6 +34,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha
   - Model result visualization with run ID identification and ensemble analysis capabilities
   - Session information for reproducibility and clear documentation of PEcAn's uncertainty analysis outputs
 - Added function for merging images from the same tiling system (MODIS, GLANCE, ICESat-2, HLS, etc.).
+- Added function for converting images towards the GDAL-supported formats (H5, NetCDF, HDF4, GeoTIFF, etc .).
 
 ### Fixed
 - api to correctly use x_var from request in plotResults #3528
@@ -34,6 +45,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 - updated github action to build docker images
 - PEcAn.SIPNET now accepts relative paths in its input XML (#3418). Previously all files referenced in the autogenerated `job.sh` needed to be specified as absolute paths.
 - R version 4.4 installs Python 3.12 which wants to leverage os managed packages instead, install python3-pika using apt.
+- Fixed a bugs and BADM now process both single-site and multi-site settings, detecting the input structure and processing each site independently to generate the correct number of ensemble members per site.
 
 ### Changed
 

base/logger/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: PEcAn.logger
 Title: Logger Functions for 'PEcAn'
-Version: 1.8.3
+Version: 1.8.4
 Authors@R: c(person("Rob", "Kooper", role = c("aut", "cre"),
                      email = "[email protected]"),
              person("Alexey", "Shiklomanov", role = c("aut"),

base/logger/NEWS.md

@@ -1,3 +1,8 @@
+# PEcAn.logger 1.8.4 (unreleased)
+
+- All `logger.set*` functions now invisibly return the previously set value. This can be handy for restoring settings after a temporary change.
+- Multipart logger messages passed in `...` now get a more robust conversion to string before concatenating, hopefully giving nicer results for nontext objects such as dates and lists.
+
 # PEcAn.logger 1.8.3
 
 - Maintenance release with no user-visible changes.

base/logger/R/logger.R

@@ -4,12 +4,12 @@
 .utils.logger$stderr <- TRUE
 .utils.logger$quit <- FALSE
 .utils.logger$level <- 0
-.utils.logger$width <- ifelse(getOption("width") < 10, 
-                              getOption("width"), 
+.utils.logger$width <- ifelse(getOption("width") < 10,
+                              getOption("width"),
                               getOption("width") - 5)
 
 ##' Prints a debug message.
-##' 
+##'
 ##' This function will print a debug message.
 ##'
 ##' @param msg the message that should be printed.
@@ -26,7 +26,7 @@ logger.debug <- function(msg, ...) {
 
 
 ##' Prints an informational message.
-##' 
+##'
 ##' This function will print an informational message.
 ##'
 ##' @param msg the message that should be printed.
@@ -43,7 +43,7 @@ logger.info <- function(msg, ...) {
 
 
 ##' Prints a warning message.
-##' 
+##'
 ##' This function will print a warning message.
 ##'
 ##' @param msg the message that should be printed.
@@ -60,7 +60,7 @@ logger.warn <- function(msg, ...) {
 
 
 ##' Prints an error message.
-##' 
+##'
 ##' This function will print an error message.
 ##'
 ##' @param msg the message that should be printed.
@@ -76,14 +76,13 @@ logger.error <- function(msg, ...) {
 } # logger.error
 
 
-##' Prints an severe message and stops execution.
-##' 
+##' Prints a severe message and stops execution.
+##'
 ##' This function will print a message and stop execution of the code. This
 ##' should only be used if the application should terminate.
-##' 
-##' set \code{\link{logger.setQuitOnSevere}(FALSE)} to avoid terminating
-##' the session. This is set by default to TRUE if interactive or running
-##' inside Rstudio.
+##'
+##' Set \code{\link{logger.setQuitOnSevere}(FALSE)} to avoid terminating
+##' the session. The default is to not quit if running interactively.
 ##'
 ##' @param msg the message that should be printed.
 ##' @param ... any additional text that should be printed.
@@ -96,13 +95,13 @@ logger.error <- function(msg, ...) {
 ##' }
 logger.severe <- function(msg, ..., wrap = TRUE) {
   logger.message("SEVERE", msg, ...)
-  
+
   # run option
   error <- getOption("error")
   if (!is.null(error)) {
     eval(error)
   }
-  
+
   # quit if not interactive, otherwise use stop
   if (.utils.logger$quit) {
     quit(save = "no", status = 1)
@@ -113,11 +112,13 @@ logger.severe <- function(msg, ..., wrap = TRUE) {
 
 
 ##' Prints a message at a certain log level.
-##' 
-##' This function will print a message. This is the function that is responsible for
-##' the actual printing of the message.
 ##'
-##' This is a place holder and will be later filled in with a more complex logging set
+##' This function will print a message. This is the function that is responsible
+##' for the actual printing of the message.
+##'
+##' This is a place holder and will be later filled in with a more complex
+##' logging set
+##'
 ##' @param level the level of the message (DEBUG, INFO, WARN, ERROR)
 ##' @param msg the message that should be printed.
 ##' @param ... any additional text that should be printed.
@@ -138,24 +139,28 @@ logger.message <- function(level, msg, ..., wrap = TRUE) {
     if (length(func) == 0) {
       func <- "console"
     }
-    
+
     stamp.text <- sprintf("%s %-6s [%s] :", Sys.time(), level, func)
-    long.msg <- stringi::stri_trans_general(paste(c(msg, ...), collapse = " "), "latin-ascii")
+    args <- sapply(list(...), FUN = toString)
+    long.msg <- stringi::stri_trans_general(
+      paste(c(msg, args), collapse = " "),
+      "latin-ascii"
+    )
     if (nchar(long.msg) > 20 && wrap) {
-      new.msg <- paste("\n", strwrap(long.msg, width = .utils.logger$width, 
+      new.msg <- paste("\n", strwrap(long.msg, width = .utils.logger$width,
                                      indent = 2, exdent = 2), collapse = " ")
     } else {
       new.msg <- long.msg
     }
     text <- paste(stamp.text, new.msg, "\n")
-    
+
     if (.utils.logger$console) {
       if (.utils.logger$stderr) {
         cat(text, file = stderr())
       } else {
         cat(text, file = stdout())
       }
-      
+
     }
     if (!is.na(.utils.logger$filename)) {
       cat(text, file = .utils.logger$filename, append = TRUE)
@@ -165,35 +170,56 @@ logger.message <- function(level, msg, ..., wrap = TRUE) {
 
 
 ##' Configure logging level.
-##' 
+##'
 ##' This will configure the logger level. This allows to turn DEBUG, INFO,
-##' WARN and ERROR messages on and off.
+##' WARN, ERROR, and SEVERE messages on and off.
+##'
+##' Note that this controls _printing_ of messages and does not change other behavior.
+##' In particular, suppressing SEVERE by setting the level to "OFF" does not prevent
+##' logger.severe() from signaling an error (and terminating the program if 
+##' `logger.setQuitOnSevere(TRUE)`).
+##'
+##' @param level the level of the message. One of "ALL", "DEBUG", "INFO", "WARN",
+##' "ERROR", "SEVERE", or "OFF".
 ##'
-##' @param level the level of the message (ALL, DEBUG, INFO, WARN, ERROR, OFF)
 ##' @export
 ##' @return When logger level is set, the previous level is returned invisibly.
 ##'   This can be passed to `logger.setLevel()` to restore the previous level.
 ##' @author Rob Kooper
 ##' @examples
 ##' \dontrun{
 ##' logger.setLevel('DEBUG')
+##' 
+##' # Temporarily turn logger off
+##' old_logger_level <- logger.setLevel("OFF")
+##'   # code here
+##' logger.setLevel(old_logger_level)
 ##' }
 logger.setLevel <- function(level) {
   original_level <- logger.getLevel()
   .utils.logger$level <- logger.getLevelNumber(level)
+
   invisible(original_level)
 } # logger.setLevel
 
 
 ## Given the string representation this will return the numeric value
-## DEBUG = 10
-## INFO  = 20
-## WARN  = 30
-## ERROR = 40
-## ALL   = 99
 ##
-##@return level the level of the message
-##@author Rob Kooper
+## Supported levels
+##   ALL    = 0
+##   DEBUG  = 10
+##   INFO   = 20
+##   WARN   = 30
+##   ERROR  = 40
+##   SEVERE = 50
+##   OFF    = 60
+##
+## SEVERE is treated as more serious than ERROR,
+## and will terminate the session if `logger.setQuitOnSevere(TRUE)`
+## or call stop() otherwise
+##
+## @return level the level of the message
+## @author Rob Kooper
 logger.getLevelNumber <- function(level) {
   if (toupper(level) == "ALL") {
     return(0)
@@ -206,7 +232,7 @@ logger.getLevelNumber <- function(level) {
   } else if (toupper(level) == "ERROR") {
     return(40)
   } else if (toupper(level) == "SEVERE") {
-    return(40)
+    return(50)
   } else if (toupper(level) == "OFF") {
     return(60)
   } else {
@@ -217,10 +243,15 @@ logger.getLevelNumber <- function(level) {
 
 
 ##' Get configured logging level.
+##'
+##' This will return the current level configured of the logging messages.
 ##' 
-##' This will return the current level configured of the logging messages
+##' Note that `logger.setLevel()` invisibly returns current level, so 
+##' `logger.getLevel()` is not required to restore the level after a 
+##' temporary change.
 ##'
-##' @return level the level of the message (ALL, DEBUG, INFO, WARN, ERROR, OFF)
+##' @return A string giving the lowest message level that will be reported, one of 
+##' "ALL", "DEBUG", "INFO", "WARN", "ERROR", "SEVERE", or "OFF".
 ##' @export
 ##' @author Rob Kooper
 ##' @examples
@@ -247,54 +278,70 @@ logger.getLevel <- function() {
 
 
 ##' Configure logging to console.
-##' 
+##'
 ##' Should the logging to be printed to the console or not.
 ##'
 ##' @param console set to true to print logging to console.
-##' @param stderr set to true (default) to use stderr instead of stdout for logging
+##' @param stderr set to true (default) to log to stderr instead of stdout
+##' @return Invisibly, a list of the previously set values of `console`
+##'   and `stderr`. This can be used to restore the previous settings after a
+##'   temporary change.
 ##' @export
 ##' @author Rob Kooper
 ##' @examples
 ##' \dontrun{
 ##' logger.setUseConsole(TRUE)
 ##' }
 logger.setUseConsole <- function(console, stderr = TRUE) {
+  old <- list(console = .utils.logger$console, stderr = .utils.logger$stderr)
   .utils.logger$console <- console
   .utils.logger$stderr <- stderr
+
+  invisible(old)
 } # logger.setUseConsole
 
 
 ##' Configure logging output filename.
-##' 
+##'
 ##' The name of the file where the logging information should be written to.
 ##'
-##' @param filename the file to send the log messages to (or NA to not write to file)
+##' @param filename the file to send the log messages to
+##'  (or NA to not write to file)
+##' @return Invisibly, the previously set filename.
+##'   This can be used to restore settings after a temporary change.
 ##' @export
 ##' @author Rob Kooper
 ##' @examples
 ##' \dontrun{
 ##' logger.setOutputFile('pecan.log')
 ##' }
 logger.setOutputFile <- function(filename) {
+  old <- .utils.logger$filename
   .utils.logger$filename <- filename
+
+  invisible(old)
 } # logger.setOutputFile
 
 
 ##' Configure whether severe should quit.
-##' 
-##' The default is for a non-interactive session to quit. Setting this to false is
-##' especially useful for running tests when placed in \code{inst/tests/test.<fn>.R}, 
-##' but is not passed from \code{tests/run.all.R}.
+##'
+##' The default is for a non-interactive session to quit.
+##' Setting this to false is especially useful for running tests.
 ##'
 ##' @param severeQuits should R quit on a severe error.
 ##' @export
+##' @return invisibly, the previous value of `severeQuits`.
+##'   This can be used to restore settings after a temporary change.
 ##' @author Rob Kooper
 ##' @examples
 ##' \dontrun{
 ##' logger.setQuitOnSevere(FALSE)
 ##' }
 logger.setQuitOnSevere <- function(severeQuits) {
+  old <- .utils.logger$quit
   .utils.logger$quit <- severeQuits
+
+  invisible(old)
 } # logger.setQuitOnSevere
 
 
@@ -304,12 +351,17 @@ logger.setQuitOnSevere <- function(severeQuits) {
 ##' wrap the line when printing a message at that many chars.
 ##'
 ##' @param width number of chars to print before wrapping to next line.
+##' @return Invisibly, the previously set width.
+##'   This can be used to restore settings after a temporary change.
 ##' @export
 ##' @author David LeBauer
 ##' @examples
 ##' \dontrun{
 ##' logger.setWidth(70)
 ##' }
 logger.setWidth <- function(width) {
+  old <- .utils.logger$width
   .utils.logger$width <- width
+
+  invisible(old)
 } # logger.setWidth