Merge branch 'develop' into GH-3910-arm64-traefik-docs

Author: infotroph

.github/workflows/integration-test.yml

@@ -8,7 +8,7 @@ on :
   - cron: '30 4 * * 4'    
 jobs:
   test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

CHANGELOG.md

@@ -22,11 +22,14 @@ For more information about this file see also [Keep a Changelog](http://keepacha
   *  `ca_compost_amendment` dataset with properties of 32 organic amendment materials for California agriculture (g/m2 and lbs/acre).
 - 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.
 
 ### Fixed
 - 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).
 
 ### Changed
+- 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.
 - With new `PEcAn.MA::meta_analysis_standalone` function, `PEcAn.MA::run.meta.analysis.pft` now saves all files all at once _after_ the complete meta-analysis runs (and only if it is successful, including prior and posterior checks), rather than saving intermediate objects (like "JAGS-ified" data) as they are created.

Makefile

@@ -106,7 +106,7 @@ depends = .doc/$(1) .install/$(1) .check/$(1) .test/$(1)
 
 ### Rules
 
-.PHONY: all install check test document clean shiny pkgdocs \
+.PHONY: all install check test document clean clean-src shiny pkgdocs \
             check_base check_models check_modules help
 
 all: install document
@@ -140,6 +140,12 @@ clean:
 		find "$$p" \( -name \*.mod -o -name \*.o -o -name \*.so \) -delete; \
 	done
 
+clean-src:
+	@echo "Removing compiled source artifacts..."
+	for p in $(SRCS_TO_CLEAN); do \
+		find "$$p" \( -name \*.mod -o -name \*.o -o -name \*.so \) -delete; \
+	done
+
 help:
 	@echo "Usage: make [target]"
 	@echo ""
@@ -167,6 +173,7 @@ help:
 	@echo "  book           Render the PEcAn bookdown documentation"
 	@echo "  pkgdocs        Build package documentation websites using pkgdown"
 	@echo "  clean          Remove build artifacts"
+	@echo "  clean-src      Remove compiled source artifacts (.o, .so, .mod) without full rebuild"
 	@echo "  help           Show this help message"
 
 ### Dependencies

README.md

@@ -3,6 +3,8 @@
 [![Slack](https://img.shields.io/badge/slack-join_chat-green.svg)](https://join.slack.com/t/pecanproject/shared_invite/enQtMzkyODUyMjQyNTgzLWEzOTM1ZjhmYWUxNzYwYzkxMWVlODAyZWQwYjliYzA0MDA0MjE4YmMyOTFhMjYyMjYzN2FjODE4N2Y4YWFhZmQ)
 [![DOI](https://zenodo.org/badge/4469/PecanProject/pecan.svg)](https://zenodo.org/badge/latestdoi/4469/PecanProject/pecan)
 
+> Due to spam we have disabled the automatic signup to slack. To access our slack space, please email kooper@illinois.edu to get an invite.
+
 ## Our Vision
 
 #### Ecosystem science, policy, and management informed by the best available data and models

base/settings/R/createMultisiteMultiSettings.r

@@ -117,8 +117,8 @@ getRunSettings <- function(templateSettings, siteId) {
   } else {
     site_info <- list(id = siteId)
   }
-  site_info$met.start <- startDate
-  site_info$met.end <- endDate
+  if (is.null(site_info$met.start)) site_info$met.start <- startDate
+  if (is.null(site_info$met.end)) site_info$met.end <- endDate
 
   return(list(
     site = site_info,

base/workflow/R/do_conversions.R

@@ -28,7 +28,7 @@ do_conversions <- function(settings, overwrite.met = FALSE, overwrite.fia = FALS
       next
     }
 
-    input.tag <- names(settings$run$input)[i]
+    input.tag <- names(settings$run$inputs)[i]
     PEcAn.logger::logger.info("PROCESSING: ",input.tag)
 
     # Check for existing file paths , skips if the file exists