Merge pull request magpiemodel#534 from pfuehrlich-pik/develop

magpie release 4.6.4

.Rprofile

@@ -14,17 +14,9 @@ if (!"https://rse.pik-potsdam.de/r/packages" %in% getOption("repos")) {
 
 # bootstrapping, will only run once after this repo is freshly cloned
 if (isTRUE(rownames(installed.packages(priority = "NA")) == "renv")) {
-  if (file.exists("DESCRIPTION") && !identical(readLines("DESCRIPTION"), readLines("DEPENDENCIES"))) {
-    warning("Unexpected DESCRIPTION file found, try removing it. Will not install dependencies.")
-  } else {
-    message("R package dependencies are not installed in this renv, installing now...")
-    renv::install("yaml", prompt = FALSE) # yaml is required to find dependencies in Rmd files
-    # renv will only consider a file called DESCRIPTION, so rename DEPENDENCIES
-    file.copy("DEPENDENCIES", "DESCRIPTION")
-    renv::hydrate() # auto-detect and install all dependencies
-    file.remove("DESCRIPTION")
-    message("Finished installing R package dependencies.")
-  }
+  message("R package dependencies are not installed in this renv, installing now...")
+  renv::hydrate() # auto-detect and install all dependencies
+  message("Finished installing R package dependencies.")
 }
 
 # source global .Rprofile (very important to load user specific settings)

.githooks/pre-commit

@@ -1,23 +1,32 @@
 #!/usr/bin/env Rscript
 
-if(!requireNamespace("gms", quietly = TRUE)) install.packages("gms", repos = c("https://rse.pik-potsdam.de/r/packages/", "https://cloud.r-project.org"))
+gmsRequiredVersion <- "0.24.1"
+if (tryCatch(utils::packageVersion("gms") < gmsRequiredVersion, error = function(error) TRUE)) {
+  message("gms >= ", gmsRequiredVersion, " is required, installing now...")
+  install.packages("gms")
+}
+
+message("Checking files for tabs... ", appendLF = FALSE)
+gms::checkNoTabs(pattern = "\\.(R|Rprofile|gms|cfg|bib)$", excludeFolders = c("output", "renv", ".git"))
+message("done.")
 
 # run codeCheck
-null <- gms::codeCheck(strict=TRUE)
+invisible(gms::codeCheck(strict = TRUE))
 message("")
 
-# make sure that files are not too big
 
-maxfilesize <- function(max=512) {
-  files <- union(system("git ls-tree -r HEAD --name-only", intern=TRUE),
-                 system("git diff --cached --name-only", intern=TRUE))
-  out <- data.frame(files=files,size=round(file.size(files)/1024,2))
-  out <- out[!is.na(out$size),]
-  out <- out[out$size > max,]
-  if(nrow(out)>0) {
-    stop(nrow(out), " files with size > ",max,"kB detected: \n",paste0(out$files," (", out$size, "kB)", collapse = "\n"))
+# make sure that files are not too big
+maxfilesize <- function(max) {
+  files <- union(system("git ls-tree -r HEAD --name-only", intern = TRUE),
+                 system("git diff --cached --name-only", intern = TRUE))
+  out <- data.frame(files = files, size = round(file.size(files) / 1024, 2))
+  out <- out[!is.na(out$size), ]
+  out <- out[out$size > max, ]
+  if (nrow(out) > 0) {
+    stop(nrow(out), " files with size > ", max, "kB detected: \n",
+         paste0(out$files, " (", out$size, "kB)", collapse = "\n"))
   }
-  message("All files are smaller than ",max,"kB\n")
+  message("All files are smaller than ", max, "kB\n")
 }
 
 maxfilesize(250)

.gitignore

@@ -38,3 +38,4 @@ gamslice.txt
 /.lock
 
 /renv.lock
+.Rproj.user

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "MAgPIE - An Open Source land-use modeling framework",
-  "version": "4.6.3",
+  "version": "4.6.4",
   "creators": [
     {
       "name": "Dietrich, Jan Philipp",
@@ -109,5 +109,5 @@
   "license": {
     "id": "AGPL-3.0-or-later"
   },
-  "publication_date": "2023-01-19"
+  "publication_date": "2023-02-22"
 }

CHANGELOG.md

@@ -6,6 +6,46 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 
+## [4.6.4] - 2023-02-22
+
+### changed
+- **15_food** Interpret EAT-Lancet guidelines not as target but as lower/upper limits
+- **config** changed order of output scripts. Some functions in rds_report require gridded outputs.
+- **config** input data revision to rev4.81 for trade margin bugfix
+- **config** scenario_fsec.csv updated input data tgz
+- **config** scenario_fsec.csv updated to new biodiversity scenario
+- **scripts** fsec.R and project_FSEC_Scenarios.R include capitalSubst and landscapeElements scenarios
+- **scripts** highres.R changed default resolution to c1000
+- **scripts** recalibrate.R and recalibrate_realization were modified to always use best_calib for the yield calibration.
+- **scripts** updated FSEC scenario start and output scripts
+- **scripts** when manually running output scripts for multiple runs the lockfile is only created once
+- **sticky_labor** changed labor cost share constraint from regional to cellular level
+- **sticky_labor** renamed equation `q38_labor_capital_ratio` to `q38_labor_share_target`
+
+### added
+- **15_food** half_overweight scenario added
+- **21_trade** New Bilateral trade realization selfsuff_reduced_bilat22 for bilateral trade within selffsuff constraints
+- **32_forestry** added switch `s32_aff_prot` for protection of afforested areas (0=until end of planning horizon 1=forever)
+- **56_ghg_policy** added two scenarios for GHG emission pricing and options for afforestation
+- **config** added options for afforestation assumptions and updated additional data to 4.38
+- **config** added setting cfg$keep_restarts which controls whether restart files should be kept after a run finished
+- **config** changed default for `s_use_gdx` from 2 to 0
+- **scripts** added restart points after each time step from which the model can now be restarted if the simulation aborts at some point
+- **scripts** added SLURM dayMax submission type for standby QOS
+- **sticky_labor** `nl_fix`, `nl_relax` and `nl_release` added
+
+### removed
+- **42_water_demand** removed fm_multicropping factor because of fallow inconsistency
+
+### fixed
+- **14_yields** nl_fix updated to current equation
+- **32_forestry** pm_land_conservation(t,j,"secdforest","restore") now accounts for the rotation length in timber plantations to avoid infeasibilities
+- **44_biodiversity** added regional layer `i` in `bii_target` realisation to make it compatible with the high-resolution parallel optimization output script
+- **59_som** division by zero prevented by if condition
+- **scripts** fixed a bug where renvs for high resolution runs were missing some packages
+- **scripts** fixed in the calc_calib.R script the saving of calib_factors used in each iteration to ensure that they correspond to the divergence reported. Changed divergence from zero to NA for those iterations where calib_factors are above the limit. The best_calib selection criterion was changed from selecting the factors of the iteration with the lowest standard deviation to the selection, for each region, of the factor of the iteration with the lowest divergence. Also, factors from the first iteration are now not considered, and if two different factors had the same divergence for a region, the one of the latest iteration is picked.
+
+
 ## [4.6.3] - 2023-01-19
 
 ### changed
@@ -612,7 +652,8 @@ This release version is focussed on consistency between the MAgPIE setup and the
 First open source release of the framework. See [MAgPIE 4.0 paper](https://doi.org/10.5194/gmd-12-1299-2019) for more information.
 
 
-[Unreleased]: https://github.com/magpiemodel/magpie/compare/v4.6.3...develop
+[Unreleased]: https://github.com/magpiemodel/magpie/compare/v4.6.4...develop
+[4.6.4]: https://github.com/magpiemodel/magpie/compare/v4.6.3...v4.6.4
 [4.6.3]: https://github.com/magpiemodel/magpie/compare/v4.6.2...v4.6.3
 [4.6.2]: https://github.com/magpiemodel/magpie/compare/v4.6.1...v4.6.2
 [4.6.1]: https://github.com/magpiemodel/magpie/compare/v4.6.0...v4.6.1

CITATION.cff

@@ -125,8 +125,8 @@ authors:
     email: [email protected]
 
 title: MAgPIE - An Open Source land-use modeling framework
-version: 4.6.3
-date-released: 2023-01-19
+version: 4.6.4
+date-released: 2023-02-22
 repository-code: https://github.com/magpiemodel/magpie
 keywords:
   - landuse

DEPENDENCIES → DESCRIPTION

@@ -1,4 +1,7 @@
 Package: magpiemodel
+Description: Refer to README.md for a description of the MAgPIE model.
+    This file only lists dependencies and is called DESCRIPTION for
+    technical reasons.
 Imports:
     callr,
     citation,
@@ -9,7 +12,7 @@ Imports:
     gdxrrw,
     ggplot2,
     ggrepel,
-    gms,
+    gms (>= 0.24.0),
     here,
     iamc,
     lucode2 (>= 0.36.0),
@@ -35,4 +38,6 @@ Imports:
     withr
 Suggests:
     goxygen,
+    languageserver,
     qgraph
+Encoding: UTF-8

Makefile

@@ -1,12 +1,12 @@
-.PHONY: help docs update-renv update-all-renv check check-fix
+.PHONY: help docs update-renv update-renv-all archive-renv restore-renv check check-fix start output
 .DEFAULT_GOAL := help
 
 # extracts the help text and formats it nicely
 HELP_PARSING = 'm <- readLines("Makefile");\
 				m <- grep("\#\#", m, value=TRUE);\
 				command <- sub("^([^ ]*) *\#\#(.*)", "\\1", m);\
 				help <- sub("^([^ ]*) *\#\#(.*)", "\\2", m);\
-				cat(sprintf("%-8s%s", command, help), sep="\n")'
+				cat(sprintf("%-18s%s", command, help), sep="\n")'
 
 help: ## Show this help.
 	@Rscript -e $(HELP_PARSING)
@@ -19,7 +19,7 @@ update-renv: ## Upgrade all pik-piam packages in your renv to the respective
              ## latest release and write renv.lock to archive.
 	Rscript -e 'piamenv::updateRenv()'
 
-update-all-renv: ## Upgrade all packages (including CRAN packages) in your renv
+update-renv-all: ## Upgrade all packages (including CRAN packages) in your renv
                  ## to the respective latest release and write renv.lock to archive.
 	Rscript -e 'renv::update(exclude = "renv"); piamenv::archiveRenv()'
 
@@ -38,3 +38,9 @@ check-fix: ## Check if the GAMS code follows the coding etiquette
            ## and offer fixing any problems directly if possible
            ## using gms::codeCheck.
 	Rscript -e 'invisible(gms::codeCheck(strict = TRUE, interactive = TRUE))'
+
+start: ## Start a MAgPIE run.
+	Rscript start.R
+
+output: ## Run an output script.
+	Rscript output.R

README.md

@@ -24,8 +24,8 @@ https://www.pik-potsdam.de/research/projects/activities/land-use-modelling/magpi
 A framework description paper has been published in
 Geoscientific Model Development (GMD): https://doi.org/10.5194/gmd-12-1299-2019
 
-The model documentation for version 4.6.3 can be found at
-https://rse.pik-potsdam.de/doc/magpie/4.6.3/
+The model documentation for version 4.6.4 can be found at
+https://rse.pik-potsdam.de/doc/magpie/4.6.4/
 
 A most recent version of the documentation can also be extracted from the
 model source code via the R package goxygen
@@ -188,7 +188,7 @@ [email protected]
 Please contact [email protected]
 
 ## CITATION
-See file CITATION.cff or the [How-to-Cite section](https://rse.pik-potsdam.de/doc/magpie/4.6.3/#how-to-cite) in the model documentation for information how to cite the model.
+See file CITATION.cff or the [How-to-Cite section](https://rse.pik-potsdam.de/doc/magpie/4.6.4/#how-to-cite) in the model documentation for information how to cite the model.
 
 ## AUTHORS
 See list of authors in CITATION.cff