Merge pull request #726 from jdrtommey/develop

MAgPIE release 4.8.2

.Rprofile

@@ -36,6 +36,6 @@ if (isTRUE(rownames(installed.packages(priority = "NA")) == "renv")) {
 }
 
 # in case bootstrapping fails halfway, install piamenv and rely on requirement auto-fixing
-if (tryCatch(utils::packageVersion("piamenv") < "0.3.4", error = function(error) TRUE)) {
-  renv::install("piamenv", prompt = FALSE)
+if (tryCatch(utils::packageVersion("piamenv") < "0.5.5", error = function(error) TRUE)) {
+  renv::install("piamenv", type = getOption("pkgType"), prompt = FALSE)
 }

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "MAgPIE - An Open Source land-use modeling framework",
-  "version": "4.8.1",
+  "version": "4.8.2",
   "creators": [
     {
       "name": "Dietrich, Jan Philipp",
@@ -104,6 +104,10 @@
       "affiliation": "Potsdam Institute for Climate Impact Research",
       "orcid": "0000-0002-5989-6855"
     },
+    {
+      "name": "Hötten, David",
+      "affiliation": "Potsdam Institute for Climate Impact Research"
+    },
     {
       "name": "Lotze-Campen, Hermann",
       "affiliation": "Potsdam Institute for Climate Impact Research",
@@ -119,5 +123,5 @@
   "license": {
     "id": "AGPL-3.0-or-later"
   },
-  "publication_date": "2024-06-19"
+  "publication_date": "2024-09-24"
 }

CHANGELOG.md

@@ -4,12 +4,59 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
 
+## [4.8.2] - 2024-09-24
+
+### changed
+- **15_food** revision of MP/SCP implementation for milk and meat alternatives. Added demand for fat and sugar as ingredients for MP-based milk alternatives. Added optional demand for fat as ingredient for MP-based meat alternatives.
+- **21_trade** refactor equations for enhanced readablility and improve documentation
+- **29_cropland** added option for linear and sigmoidal faders
+- **32_forestry** Interfaces `vm_landexpansion_forestry` and `vm_landreduction_forestry` have been corrected by harvested and replanted timber plantation area
+- **58_peatland** variable `v58_scalingFactorExp` converted into parameter `p58_scalingFactorExp` to avoid infeasibilites. `p58_scalingFactorRed` has been revised.
+- **80_optimization** abort GAMS in case of execution errors, added threads = 1 as default to avoid infeasibilites and Flg_NoDefc = TRUE as option
+- **config** `cfg$gms$land_snv`changed from "secdforest, forestry, past, other" to "secdforest, other"
+- **config** additional data update additional_data_rev4.53.tgz
+- **config** default settings for 58_peatland revised
+- **config** initial treecover on cropland starts from zero
+- **config** split scenario_config into project-specific configs
+- **config** Submissions with high memory requirements now get 16 CPUs and 80GB of memory to account for the new specifications of PIK's new HPC 'Foote'. `maxMem` was renamed to `highMem`, because 80GB of memory does not correspond to the maximum available memory of a compute node.
+- **config** The default realization for the 38_factor_costs module was switched to `sticky_feb18`. In this realization, capital stocks and their depreciation are tracked, giving some inertia to random relocation of production, improving high resolution outputs.
+- **script** replaced gdx package with gdx2 package calls
+- **script** scripts/start_functions.R decide individually for demand and price whether they are read from a REMIND report.
+- **script** updated EATLancet project start scripts
+- **scripts** `.nc` files are no longer created by default after disaggregation
+- **scripts** output/extra/highres.R use default 13_tc realization
+- **scripts** rewrite of merge_report.R based on rds files and rbind, which allows for more flexibility when merging reports. Avoid inconsistent use of "GLO" instead of "World" in report.rds files.
+
+
+### added
+- **42_water_demand** added water abstraction type dimension for non-ag uses
+- **56_ghg_policy** added optional temporal and regional fader for GHG emission pricing policy
+- **70_livestock** added realization `fbask_jan16_sticky`
+- **config** added `scenario_config_year_fix.csv` for choosing until when parameters are fixed to SSP2 values
+- **cropland** added option for discarding initial treecover on cropland
+- **script** added output script for conversion of validation.mif file into validation.rds
+- **script** check of variables needed in piamInterfaces in report_rds.R
+- **script** for downscaling to 0.25 deg using LUH2v2h as reference via mrdownscale
+- **scripts** added out of bounds check as output script
+- **scripts** added output report `EU_report.R` that uses `EU_report.Rmd`
+- **scripts** added output script converting all grid-level .mz files to .nc (netCDF)
+- **scripts** added script for automatic submission of SEALS allocation runs `./extra/runSEALSallocation.R`
+- **scripts** added start script for 'Healthly Landscapes' paper `paper_healthyLscps.R`
+
+
+### fixed
+- **15_food** fixing parameter declaration of i15_processed_kcal_structure_iso
+- **35_natveg** bugfix secdforest and other land restoration to avoid double-counting of restoration in equation `q29_land_snv`
+- **80_optimization** bugfix for variables levels not obeying the bounds in nlp_par, `conopt` changed to `conopt3`
+- **scripts** fixing an error in start.R and output.R which occurred if more than one slurm job was submitted at the same time.
+
+
 ## [4.8.1] - 2024-06-19
 
 ### changed
 - **29_ageclass** module 29_ageclass has been renamed to 28_ageclass to make space for `29_cropland` just before `30_croparea`
 - **30_crop** module `30_crop` renamed to `30_croparea`, which now only accounts for crop area.
-- **30_crop** Semi-Natural Vegetation (SNV) implementation has been moved from `30_crop` to `29_cropland` 
+- **30_crop** Semi-Natural Vegetation (SNV) implementation has been moved from `30_crop` to `29_cropland`
 - **30_crop** the previous `30_crop/endo_apr21` realization has been moved to `30_croparea/simple_apr24`
 - **30_crop** the two realizations `penalty_apr22` and `rotation_apr22` have been merged into a single `30_croparea/detail_apr24` realization
 - **default.cfg** update additional data to rev4.51
@@ -962,7 +1009,8 @@ 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/v4.8.1...develop
+[Unreleased]: https://github.com/magpiemodel/magpie/compare/v4.8.2...develop
+[4.8.2]: https://github.com/magpiemodel/magpie/compare/v4.8.1...v4.8.2
 [4.8.1]: https://github.com/magpiemodel/magpie/compare/v4.8.0...v4.8.1
 [4.8.0]: https://github.com/magpiemodel/magpie/compare/v4.7.3...v4.8.0
 [4.7.3]: https://github.com/magpiemodel/magpie/compare/v4.7.2...v4.7.3

CITATION.cff

@@ -125,6 +125,11 @@ authors:
     affiliation: "Potsdam Institute for Climate Impact Research"
     email: [email protected]
 
+  - family-names: Hötten
+    given-names: David
+    affiliation: "Potsdam Institute for Climate Impact Research"
+    email: [email protected]
+
   - family-names: Lotze-Campen
     given-names: Hermann
     orcid: https://orcid.org/0000-0002-0003-5508
@@ -151,8 +156,8 @@ abstract: The *Model of Agricultural Production and its Impact on the Environmen
   exogenously given population in 10 food energy categories, based on regional diets.
   Future trends in food demand are derived from a cross-country regression analysis,
   based on future scenarios on GDP and population growth.
-version: 4.8.1
-date-released: 2024-06-19
+version: 4.8.2
+date-released: 2024-09-24
 repository-code: https://github.com/magpiemodel/magpie
 keywords:
   - landuse

DESCRIPTION

@@ -8,8 +8,7 @@ Imports:
     curl,
     data.table,
     dplyr,
-    gdx,
-    gdxrrw,
+    gdx2,
     ggplot2,
     ggrepel,
     gms (>= 0.24.0),
@@ -22,13 +21,15 @@ Imports:
     m4fsdp,
     madrat,
     magclass (>= 6.14.0),
-    magpie4 (>= 2.3.10),
+    magpie4 (>= 2.12.6),
     MagpieNCGains,
     magpiesets,
     mip,
     mrcommons,
     patchwork,
-    piamenv (>= 0.3.4),
+    piamenv (>= 0.5.5),
+    piamInterfaces (>= 0.20.7),
+    piamutils,
     quitte,
     raster,
     remulator,
@@ -39,6 +40,7 @@ Imports:
 Suggests:
     goxygen,
     languageserver,
+    mrdownscale (>= 0.23.0),
     qgraph,
     shinyresults,
     XML

Makefile

@@ -21,7 +21,7 @@ update-renv: ## Upgrade all pik-piam packages in your renv to the respective
 
 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()'
+	Rscript -e 'renv::update(); piamenv::archiveRenv()'
 
 archive-renv: ## Write renv.lock to archive.
 	Rscript -e 'piamenv::archiveRenv()'

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 4.8.1 can be found at
-https://rse.pik-potsdam.de/doc/magpie/4.8.1/
+The model documentation for version 4.8.2 can be found at
+https://rse.pik-potsdam.de/doc/magpie/4.8.2/
 
 A most recent version of the documentation can also be extracted from the
 model source code via the R package goxygen
@@ -226,7 +226,7 @@ [email protected]
 Please contact [email protected]
 
 ## CITATION
-See file CITATION.cff or the [How-to-Cite section](https://rse.pik-potsdam.de/doc/magpie/4.8.1/#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/4.8.2/#how-to-cite) in the model documentation for information how to cite the model.
 
 ## AUTHORS
 See list of authors in CITATION.cff