Merge branch 'develop' into fix/3882-sa-median-manifest-lookup

Author: infotroph

.gitignore

@@ -81,6 +81,7 @@ tests/BC*
 compile_on_geo.sh
 documentation/tutorials/*/*.html
 pecan.Rproj
+.rcookies
 shiny/BenchmarkReport/*
 # Installation files from make
 .install/

CHANGELOG.md

@@ -9,6 +9,10 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 ## Unreleased
 
 ### Added
+- New function `PEcAn.utils::netcdf2df()` flattens all dims and vars of a netCDF into a dataframe,
+    with units attached as an attribute.
+- New package `PEcAn.RothC` runs the RothC soil carbon model.
+- Added `inst/ilamb/` pipeline in PEcAn.benchmark to convert downscaled SDA reanalysis GeoTIFFs into ILAMB-compatible CF netCDF for carbon-cycle benchmarking (#4019).
 - Added PEcAn.PEPRMT model, including a demo run with example data
 - Add `format_try_for_ma()` and `try_trait_mapping()` to `PEcAn.data.remote` to convert trait data from the external TRY database into the tabular format required by the PEcAn meta-analysis module (#3717).
 - Add function `qsub_sda()` for submitting SDA batch jobs by splitting a large number of sites into multiple small groups of sites (#3634).
@@ -23,13 +27,17 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 - Added lookup functions to `PEcAn.data.land`: `look_up_ca_n_rate()` and `look_up_ca_compost_amendment()` for querying crop-specific fertilization and compost data.
 - PEcAn.SIPNET gains support for SIPNET v2, whose features includes management events, nitrogen cycle tracking, explicit N2O and methane fluxes, runtime setting of feature flags, and changes to the parameter set (now 73 parameters). SIPNET v1 is still fully supported, but workarounds for bugs in the legacy `sipnet.unk` version have been removed.
 - Added `PEcAn.data.land::to_co2e()` for converting SOC change, CH4, and N2O to CO2-equivalent emissions using IPCC Global Warming Potential values.
+- Added `PEcAn.data.land::event_parquet_to_json` for generating PEcAn `event.json` files from well-formatted event parquet files, with support for ensembles of events.
 
 ### Fixed
+- Removed unused `grid2netcdf()` from `PEcAn.data.remote` and fixed R CMD check reference notes for `download.LandTrendr.AGB()` (#2758).
 - Fixed broken pecanproject.github.io, pecan.gitbooks.io, and other outdated documentation links across book_source, tutorials, models, modules, web, and shiny files (#3710).
 - Added note to DEV-INTRO.md documenting Traefik workaround for Apple Silicon (ARM64) Macs: use `traefik:v2.11` with `platform: linux/arm64` to fix 404 errors (#3910)
 - Fixed `web/08-finished.php`: show database info instead of "Still running" when workflow folder doesn't exist locally (#3501).
+- `PEcAn.utils::transformstats()`: corrected the LSD-to-SE conversion. The previous implementation included an extra `sqrt(n)` factor, causing SE estimates derived from LSD to appear `sqrt(n)` times smaller than they should be, non-conservatively over-weighting those observations in meta-analysis. (#3998)
 
 ### Changed
+- `PEcAn.uncertainty::get.parameter.samples()`: replaced the `save_to_disk` flag (from #3860) with an `outdir` argument (default `settings$outdir`) controlling whether `samples.Rdata` is written; `outdir = NULL` skips the save. Existing callers are unaffected (@omkarrr2533, #4016)
 - Updated Docker architecture documentation to match current docker-compose.yml: removed portainer/minio/thredds, added rstudio/api sections, updated service lists and volumes (#3268).
 - Improved PEcAn.SIPNET documentation including README, model description, and current installation instructions (@Eshaan-byte; #3703, #3705).
 - `assign.treatments` has been renamed to `assign_treatments` and moved from `PEcAn.utils` to `PEcAn.MA` since that's the only place where it's used.
@@ -45,7 +53,6 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 - Management events specified via `events.json` are now required to specify a crop code for each planting event, so that models can know when to restart with a different PFT (#3828, #3836).
 
 
-
 ## [1.10.0] - 2026-01-06
 
 ### Added

CITATION.cff

@@ -129,6 +129,7 @@ authors:
     affiliation: National Institute of Technology, Tiruchirappalli
   - given-names: Om Kapale
     affiliation: Chatrapati Shahu Maharaj CSCOE, Maharashtra
+  - given-names: Tejas Dahiya
 
 
 preferred-citation:

Makefile

@@ -69,8 +69,12 @@ recurse_dir = $(foreach d, $(wildcard $1*), $(call recurse_dir, $d/) $d)
 # For output from recurse_dir this removes all dirs, but in other cases beware.
 drop_parents = $(filter-out $(patsubst %/,%,$(dir $1)), $1)
 
-# Generates a list of regular files at any depth inside its argument
-files_in_dir = $(call drop_parents, $(call recurse_dir, $1))
+# Generates a list of regular files at any depth inside its argument,
+# excluding those in any `docs` folder
+files_in_dir = $(filter-out \
+  ${1}/docs/%, \
+  $(call drop_parents, $(call recurse_dir,$1)))
+
 
 # Git hash + clean status for this directory
 git_rev = $(shell \
@@ -118,9 +122,8 @@ check_modules: $(BASE_I) $(MODULES_C)
 
 document: $(ALL_PKGS_D) .doc/base/all
 
-pkgdocs:
+pkgdocs: $(ALL_PKGS_D) .doc/base/all
 	Rscript scripts/build_pkgdown.R $(ALL_PKGS) base/all || exit 1
-	
 
 install: $(ALL_PKGS_I) .install/base/all
 check: $(ALL_PKGS_C) .check/base/all

base/db/DESCRIPTION

@@ -80,5 +80,5 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.3
 X-schema.org-keywords: PEcAn, database
+RoxygenNote: 7.3.3

base/db/NAMESPACE

@@ -33,6 +33,7 @@ export(get.trait.data)
 export(get.trait.data.pft)
 export(get_postgres_envvars)
 export(get_run_ids)
+export(get_trait_data_pft)
 export(get_users)
 export(get_var_names)
 export(get_workflow_ids)

base/db/NEWS.md

@@ -1,5 +1,11 @@
 # PEcAn.DB 1.8.2
 
+## Fixed
+
+* `arrhenius.scaling.traits()`: previously returned `NULL` when no temperature covariates were found, crashing `query.trait.data()` with `argument is of length zero`. The function now drops rows that lack a measurement temperature covariate and emits a `logger.warn()` with the row count. If no observations have any temperature covariate, an empty data frame (zero rows, same columns) is returned. The `missing.temp` argument is retained for backward compatibility but is no longer applied.
+* `filter_sunleaf_traits()`: returned `NULL` instead of `data` unchanged when no `canopy_layer` covariate was found. Now returns the input data frame unmodified in that case, consistent with the more standardised measurement protocol for sun-leaf traits.
+* `query.trait.data()`: the `warning()` call for missing trait data was placed after `return(NA)` and therefore never fired. Moved before the return and changed to `logger.warn()` for consistency with the rest of the codebase.
+
 * Refactored `convert.input()` internals into smaller, and hopefully more testable, chunks. No user-visible changes expected.
 * Roxygen cleanup.
 

base/db/R/covariate.functions.R

@@ -53,37 +53,57 @@ query.covariates <- function(trait.ids, con = NULL, ...){
 ##--------------------------------------------------------------------------------------------------#
 ##' Apply Arrhenius scaling to 25 degC for temperature-dependent traits
 ##'
+##' Rows whose measurement temperature covariate is missing are dropped with a
+##' warning rather than silently assigned a default temperature.  If no
+##' temperature covariate is recorded for any observation the function returns
+##' an empty data frame (zero rows, same columns as \code{data}).
+##'
 ##' @param data data frame of data to scale, as returned by query.data()
 ##' @param covariates data frame of covariates, as returned by query.covariates().
-##'   Note that data with no matching covariates will be unchanged.
 ##' @param temp.covariates names of covariates used to adjust for temperature;
 ##'   if length > 1, order matters (first will be used preferentially)
-##' @param new.temp the reference temperature for the scaled traits. Curerntly 25 degC
-##' @param missing.temp the temperature assumed for traits with no covariate found. Curerntly 25 degC
+##' @param new.temp the reference temperature for the scaled traits. Currently 25 degC
+##' @param missing.temp no longer used; kept for backward compatibility only
 ##' @author Carl Davidson, David LeBauer, Ryan Kelly
 arrhenius.scaling.traits <- function(data, covariates, temp.covariates, new.temp = 25, missing.temp = 25){
   # Select covariates that match temp.covariates
-  covariates <- covariates[covariates$name %in% temp.covariates,]
-  
-  if(nrow(covariates)>0) {
+  covariates <- covariates[covariates$name %in% temp.covariates, ]
+
+  if (nrow(covariates) > 0) {
     # Sort covariates in order of priority
     covariates <- do.call(rbind,
-                          lapply(temp.covariates, function(temp.covariate) covariates[covariates$name == temp.covariate, ])
+                          lapply(temp.covariates, function(tc) covariates[covariates$name == tc, ])
     )
-    
+
     data <- append.covariate(data, 'temp', covariates)
-    
-    # Assign default value for traits with no covariates
-    data$temp[is.na(data$temp)] <- missing.temp
-    
+
+    # Drop rows that have no temperature covariate recorded
+    n_missing <- sum(is.na(data$temp))
+    if (n_missing > 0) {
+      PEcAn.logger::logger.warn(
+        n_missing, "row(s) of trait data dropped due to missing temperature covariate."
+      )
+      data <- data[!is.na(data$temp), ]
+    }
+
+    # Remove temporary covariate column before returning if nothing survived
+    if (nrow(data) == 0) {
+      return(data[, colnames(data) != 'temp', drop = FALSE])
+    }
+
     # Scale traits
-    data$mean <- PEcAn.utils::arrhenius.scaling(observed.value = data$mean, old.temp = data$temp, new.temp=new.temp)
-    data$stat <- PEcAn.utils::arrhenius.scaling(observed.value = data$stat, old.temp = data$temp, new.temp=new.temp)
-    
-    #remove temporary covariate column.
-    data<-data[,colnames(data)!='temp']
+    data$mean <- PEcAn.utils::arrhenius.scaling(observed.value = data$mean, old.temp = data$temp, new.temp = new.temp)
+    data$stat  <- PEcAn.utils::arrhenius.scaling(observed.value = data$stat,  old.temp = data$temp, new.temp = new.temp)
+
+    # Remove temporary covariate column
+    data <- data[, colnames(data) != 'temp', drop = FALSE]
   } else {
-    data <- NULL
+    # No temperature covariates found for any observation; drop all rows.
+    n_rows <- nrow(data)
+    PEcAn.logger::logger.warn(
+      n_rows, "row(s) of trait data dropped: no temperature covariate found for any observation."
+    )
+    data <- data[0, , drop = FALSE]
   }
   return(data)
 }
@@ -108,7 +128,7 @@ filter_sunleaf_traits <- function(data, covariates){
     # remove temporary covariate column
     data <- data[,colnames(data)!='canopy_layer']
   } else {
-    data <- NULL
+    # No canopy_layer covariate found; return data unchanged rather than NULL.
   }
   return(data)
 }