MAgPIE release 4.8.0

.Rprofile

@@ -36,7 +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(packageVersion("piamenv"),
-             error = function(e) package_version("0.0")) < package_version("0.3.4")) {
+if (tryCatch(utils::packageVersion("piamenv") < "0.3.4", error = function(error) TRUE)) {
   renv::install("piamenv", prompt = FALSE)
 }

.githooks/pre-commit

@@ -7,26 +7,28 @@ if (tryCatch(utils::packageVersion("gms") < gmsRequiredVersion, error = function
 }
 
 message("Checking files for tabs... ", appendLF = FALSE)
-gms::checkNoTabs(pattern = "\\.(R|Rprofile|gms|cfg|bib)$", excludeFolders = c("output", "renv", ".git"))
+gms::checkNoTabs(pattern = "\\.(R|Rprofile|gms|cfg|bib)$",
+                 excludeFolders = c("output", "renv", ".git"))
 message("done.")
 
-# run codeCheck
-invisible(gms::codeCheck(strict = TRUE))
-message("")
+stagedFiles <- system("git diff --cached --name-only", intern = TRUE)
+
+# run codeCheck only if .gms file is staged
+if (any(endsWith(stagedFiles, ".gms"))) {
+  invisible(gms::codeCheck(strict = TRUE))
+  message("")
+}
 
 
 # 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")
-}
+maxFilesize <- 250 # kB
 
-maxfilesize(250)
+files <- union(system("git ls-tree -r HEAD --name-only", intern = TRUE), stagedFiles)
+out <- data.frame(files = files, size = round(file.size(files) / 1024, 2))
+out <- out[!is.na(out$size), ]
+out <- out[out$size > maxFilesize, ]
+if (nrow(out) > 0) {
+  stop(nrow(out), " files with size > ", maxFilesize, "kB detected: \n",
+       paste0(out$files, " (", out$size, "kB)", collapse = "\n"))
+}
+message("All files are smaller than ", maxFilesize, "kB\n")

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "MAgPIE - An Open Source land-use modeling framework",
-  "version": "4.7.3",
+  "version": "4.8.0",
   "creators": [
     {
       "name": "Dietrich, Jan Philipp",
@@ -99,6 +99,11 @@
       "affiliation": "Potsdam Institute for Climate Impact Research",
       "orcid": "0000-0003-0328-4750"
     },
+    {
+      "name": "Steinhauser, Jan",
+      "affiliation": "Potsdam Institute for Climate Impact Research",
+      "orcid": "0000-0002-5989-6855"
+    },
     {
       "name": "Lotze-Campen, Hermann",
       "affiliation": "Potsdam Institute for Climate Impact Research",
@@ -110,9 +115,9 @@
       "orcid": "0000-0001-9500-1986"
     }
   ],
-  "keywords": ["landuse", "modeling", "nlp", "partial equilibrium"],
+  "keywords": ["landuse", "modeling", "model", "nlp", "partial equilibrium"],
   "license": {
     "id": "AGPL-3.0-or-later"
   },
-  "publication_date": "2024-04-12"
+  "publication_date": "2024-06-10"
 }

CHANGELOG.md

@@ -1,10 +1,71 @@
-
 # Changelog
 
 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/).
 
 
+## [4.8.0] - 2024-06-10
+
+### changed
+- **14_yields** revised timber yield calculations
+- **15_food, default.cfg and scenario_config.csv** changed fader setup and introduced new switches for specifying food substitution scenarios and exogeneous food intake scenarios
+- **22_land_conservation and default.cfg** Added options for baseline protection
+- **32_forestry** renamed interface `pm_demand_ext` to `pm_demand_forestry`
+- **32_forestry** revision and simplification of forestry implementation, renamed realization from `dynamic_feb21` to `dynamic_may24`.
+- **35_natveg**  `vm_land(j2,"forestry")` included in NPI/NDC constraint `q35_min_forest`
+- **35_natveg** replaced the realisation `dynamic_feb21` with realisation `pot_forest_may24`. The new realisation provides additional information on the potential forest area, which is now used to constrain forest and forestry expansion and recovery. The remaining area for forest establishment is provided to the forestry module via the new interface parameter `pcm_max_forest_est`.
+- **41_area_equipped_for_irrigation** updated (non-default) AEI data (from Mehta2022 to Mehta2024)
+- **52_carbon** Separate carbon densities for forest and other land. Before there was only a single carbon density for natural vegetation land.
+- **70_livestock** default.cfg and scenario_config.csv** changed fader setup and introduced new switches for specifying feed substitution with SCP scenarios
+- **80_optimization** Simplifed cycling through CONOPT4, CONOPT4 with OPTFILE, CONOPT4 without preprocessing and CONOPT3.
+- **default.cfg** changed default realization for 44_biodiversity to new realization `bii_target_apr24`
+- **default.cfg** defaults for `cfg$gms$sm_fix_SSP2`, `cfg$gms$sm_fix_cc` and other switches changed from 2020 to 2025
+- **default.cfg** Forestry sector included by default by using the `ForestryEndo` settings from `scenario_config.csv`: `s32_initial_distribution = 1`, `s32_demand_establishment = 1`, `s32_hvarea = 2`, `s35_secdf_distribution = 2`, `s35_hvarea = 2`, `s73_timber_demand_switch = 1`
+- **default.cfg** update additional data to rev4.50
+- **scripts** modified agmip_merge_report to use piamInterfaces
+- **scripts** start/test_runs.R added 2 more test runs from FSEC
+
+### added
+- **15_food** added additional sigmoid food substition scenarios `sigmoid_75pc_25_50`, `sigmoid_50pc_25_50` and `sigmoid_25pc_25_50`
+- **21_trade** Minimum trade margin for forestry products `s21_min_trade_margin_forestry`
+- **30_crop** added regional cropland equation `q30_crop_reg` and presolve growth constraint
+- **44_biodiversity** added new realization `bii_target_apr24`, taking into account `f44_rr_layer`
+- **60_bioenergy** added new realization `1st2ndgen_priced_feb24` to enable price-driven 2nd gen bioenergy production
+- **73_timber** added interface `im_timber_prod_cost`
+- **citation** added abstract
+- **core** added `coup2110`timesteps
+- **default.cfg** added cropland growth constraint `cfg$gms$s30_annual_max_growth`
+- **default.cfg** added settings for new price-driven bioenergy realization `1st2ndgen_priced_feb24`: `cfg$gms$s60_2ndgen_bioenergy_dem_min_post_fix`, `cfg$gms$c60_bioenergy_subsidy_fix_SSP2`, `s60_bioenergy_gj_price_1st`,
+- **default.cfg** added technical cost for missing BII increase `cfg$gms$s44_cost_bii_missing`
+- **default.cfg** cfg$gms$s80_secondsolve option for second solve statement with 0=off as default
+- **scenario_config.csv** added preset for GENIE project
+- **scripts** added "checkSummation" output script for consistency checking a report.mif
+- **scripts** added automatic set writer for new bioenergy realization to `start_functions`
+- **scripts** added start scripts for the GENIE project
+`s60_bioenergy_price_2nd`, `c60_price_implementation`
+
+### removed
+- **14_yields** removed interface `pm_timber_yield_initial`
+- **21_trade** removed interface `pm_selfsuff_ext`, removed `v21_manna_from_heaven`
+- **32_forestry** removed interface `pm_representative_rotation`
+- **35_natveg** removed growing stock calculation and calibration, which is no longer needed.
+- **62_material/16_demand** Removed double structure for forestry products. `pm_demand_foresty` is now used in `62_material`
+- **73_timber** removed interfaces `pm_demand_forestry_future` and `sm_wood_density`
+- **scripts** removed support for spam files in start_functions
+- **scripts/output/extra** removed scripts disaggregation_cropsplit and disaggregation_transitions
+
+### fixed
+- **14_yields** fix division by zero in preloop of managementcalib_aug19
+- **44_biodiversity** avoid division by zero
+- **58_peatland** Added balance variable to avoid random infeasibilites
+- **80_optimization** fixed a bug in nlp_apr17; cycling through CONOPT4, CONOPT4 without preprocessing and CONOPT3 was not working
+- **extra/disaggregation** fixed bug in disaggregation of land conservation related to switch from 59k to 67k that produced erroneous outputs
+- **scenario_config.csv** same revision for input files as in default.cfg
+- **scenario_fsec.csv** scenario settings
+- **scripts/start/test_runs.R** include all default output script, in particular disaggregation.R, which is needed for BII
+- **start/projects/fsec.R** scenario settings
+
+
 ## [4.7.3] - 2024-04-12
 
 ### changed
@@ -23,6 +84,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 - **56_ghg_policy** added NDC scenarios
 - **60_bioenergy** added NDC scenarios
 - **scripts** start script for EAT2p0 Deep Dive project
+
 ### fixed
 - **15_food** Small number rather 0 in condition checking calorie balancing
 - **34_urban** `static` realization was not working because `vm_carbon_stock` was referenced without the set `stockType`
@@ -871,7 +933,8 @@ 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/v4.7.3...develop
+[Unreleased]: https://github.com/magpiemodel/magpie/compare/v4.8.0...develop
+[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
 [4.7.2]: https://github.com/magpiemodel/magpie/compare/v4.7.1...v4.7.2
 [4.7.1]: https://github.com/magpiemodel/magpie/compare/v4.7.0...v4.7.1

CITATION.cff

@@ -1,5 +1,6 @@
 cff-version: 1.0.3
 message: If you use this model, please cite it as below.
+type: software
 authors:
   - family-names: Dietrich
     given-names: Jan Philipp
@@ -118,6 +119,12 @@ authors:
     affiliation: "Potsdam Institute for Climate Impact Research"
     email: [email protected]
 
+  - family-names: Steinhauser
+    given-names: Jan
+    orcid: https://orcid.org/0000-0002-5989-6855
+    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
@@ -131,12 +138,26 @@ authors:
     email: [email protected]
 
 title: MAgPIE - An Open Source land-use modeling framework
-version: 4.7.3
-date-released: 2024-04-12
+abstract: The *Model of Agricultural Production and its Impact on the Environment* (MAgPIE)
+  is a modular open source framework for modeling global land-systems, which is
+  coupled to the grid-based dynamic vegetation model LPJmL, with a spatial resolution
+  of 0.5degx0.5deg. It takes regional economic conditions such as demand for agricultural
+  commodities, technological development and production costs as well as spatially
+  explicit data on potential crop yields, land and water constraints (from LPJmL) into
+  account. Based on these, the model derives specific land use patterns, yields and
+  total costs of agricultural production for each grid cell. The objective function of
+  the land use model is to minimize total cost of production for a given amount of
+  regional food and bioenergy demand. Regional food energy demand is defined for an
+  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: 4.8.0
+date-released: 2024-06-10
 repository-code: https://github.com/magpiemodel/magpie
 keywords:
   - landuse
   - modeling
+  - model
   - nlp
   - partial equilibrium
 doi: 10.5281/zenodo.1418752

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 4.7.3 can be found at
-https://rse.pik-potsdam.de/doc/magpie/4.7.3/
+The model documentation for version 4.8.0 can be found at
+https://rse.pik-potsdam.de/doc/magpie/4.8.0/
 
 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/4.7.3/#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/4.8.0/#how-to-cite) in the model documentation for information how to cite the model.
 
 ## AUTHORS
 See list of authors in CITATION.cff