F ipcc2019

.Rbuildignore

@@ -0,0 +1,3 @@
+^renv$
+^renv\.lock$
+^.*\.zenodo.json$

.Rprofile

@@ -1,23 +1,33 @@
-# source global .Rprofile (very important to load user specific settings)
-# DO NOT EDIT THIS LINE!
-if(file.exists("~/.Rprofile")) source("~/.Rprofile")
+# |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+# |  authors, and contributors see CITATION.cff file. This file is part
+# |  of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of
+# |  AGPL-3.0, you are granted additional permissions described in the
+# |  MAgPIE License Exception, version 1.0 (see LICENSE file).
+# |  Contact: magpie@pik-potsdam.de
+Sys.setenv(RENV_PATHS_LIBRARY = "renv/library")
+
+source("renv/activate.R")
 
+if (!"https://rse.pik-potsdam.de/r/packages" %in% getOption("repos")) {
+  options(repos = c(getOption("repos"), pik = "https://rse.pik-potsdam.de/r/packages"))
+}
 
-# This profile can be used to link the model to a specified library snapshot
-# (e.g. if your model version is from an older date and does not work with the
-# newest libraries anymore) 
-# By default it is not active. Just uncomment the following lines and set the
-# snapshot path to a path of your choice
-# Please make also sure that in your config file this .Rprofile file is copied
-# to the model output folder. Otherwise, the run itself will again use the
-# default library set!
+# 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.")
+  }
+}
 
-# PLEASE NOTE: snapshots ending with '_R4' require R 4.1 (piam/1.24 and newer),
-# other snapshots require R 3.6 (piam/1.20)
-# snapshot <- "/p/projects/rd3mod/R/libraries/snapshots/2020_03_10"
-# if(file.exists(snapshot)) {
-#   cat("Setting libPaths to",snapshot,"\n")
-#   .libPaths(snapshot)
-# } else {
-#   cat("Could not find",snapshot,"\n")
-# }
+# source global .Rprofile (very important to load user specific settings)
+if (file.exists("~/.Rprofile")) {
+  source("~/.Rprofile")
+}

.github/workflows/test-code.yaml

@@ -9,41 +9,30 @@ on:
       - main
       - master
       - develop
-        
+
 name: check
 
 jobs:
   check:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
-
-      - name: Query dependencies
-        run: |
-          saveRDS("gms", ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+      - name: Remove .Rprofile
+        run: rm .Rprofile
 
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          extra-repositories: https://cloud.r-project.org https://rse.pik-potsdam.de/r/packages/
 
       - name: Install R dependencies
-        run: |
-          repos <- c("https://cloud.r-project.org","https://rse.pik-potsdam.de/r/packages/")
-          install.packages(c("remotes"), repos=repos)
-          remotes::install_cran("gms", repos=repos)
-        shell: Rscript {0}
-
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          packages: gms
+          extra-packages: gms
+
       - name: pre-commit Hook
         run: source(".githooks/pre-commit")
         shell: Rscript {0}
-
-

.gitignore

@@ -36,3 +36,5 @@ gamslice.txt
 
 #ignore lock file
 /.lock
+
+/renv.lock

.lintr

@@ -0,0 +1,2 @@
+linters: lucode2::lintrRules()
+encoding: "UTF-8"

.snapshot.Rprofile

@@ -0,0 +1,23 @@
+# source global .Rprofile (very important to load user specific settings)
+# DO NOT EDIT THIS LINE!
+if(file.exists("~/.Rprofile")) source("~/.Rprofile")
+
+
+# This profile can be used to link the model to a specified library snapshot
+# (e.g. if your model version is from an older date and does not work with the
+# newest libraries anymore).
+# By default it is not active. Just uncomment the following lines and set the
+# snapshot path to a path of your choice.
+# Please make also sure that in your config file this .Rprofile file is copied
+# to the model output folder. Otherwise, the run itself will again use the
+# default library set!
+
+# PLEASE NOTE: snapshots ending with '_R4' require R 4.1 (piam/1.24 and newer),
+# other snapshots require R 3.6 (piam/1.20)
+# snapshot <- "/p/projects/rd3mod/R/libraries/snapshots/2022_10_28_R4"
+# if(file.exists(snapshot)) {
+#   cat("Setting libPaths to",snapshot,"\n")
+#   .libPaths(snapshot, include.site = FALSE)
+# } else {
+#   cat("Could not find",snapshot,"\n")
+# }

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "MAgPIE - An Open Source land-use modeling framework",
-  "version": "4.6.1dev",
+  "version": "4.6.2dev",
   "creators": [
     {
       "name": "Dietrich, Jan Philipp",
@@ -109,5 +109,5 @@
   "license": {
     "id": "AGPL-3.0-or-later"
   },
-  "publication_date": "2022-12-13"
+  "publication_date": "2023-01-12"
 }

CHANGELOG.md

@@ -5,17 +5,22 @@ 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/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+
 ## [Unreleased]
 
 ### changed
-- **36_employment** include labor costs from MACCs in employment
-- **57_maccs** split costs into labor and capital
-- **38_factor_cots** renamed `p36_cost_shares` to `pm_cost_share_crops`
-- **config** scenario_fsec.csv update
-- **scripts** FSDP_collect FSDP_process fsec.R updates
+- **config** update input data to rev4.79
+- **config** and **38_factor_costs** changed name of `s38_fix_capital_need` to `s38_startyear_labor_substitution`
+- **config** added `s38_target_labor_share`, `s38_targetyear_labor_share` and `s38_target_fulfillment` to define labor share target scnarios
+- **38_factor_costs** changed name of set `req` to `factors` (also used in 11_costs, 57_maccs, 70_livestock)
+- **38_factos_costs** sticky_labor realization: included option to set a labor share target
+- **15_food** changed `anthro_iso_jun22` realisation such that results in case of `exo_diet = 1/0` and `exo_waste = 1/0` are identical until 2020
+- **62_material** Bioplastic demand identical in all scenarios until 2020
 
 ### added
-- **scripts** added output script that generates a short mif containing only variables relevant for the REMIND coupling
+- **scripts** added start script which starts an empty model just regenerating a previous run
+- **31_past** added additional limitation (single climate scenario input) for **grasslands_apr22**
+- **59_som** added new **cellpool_jan23** realization with updated 2019 IPCC guidelines values
 
 ### removed
 -
@@ -24,6 +29,23 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 -
 
 
+## [4.6.2] - 2023-01-12
+
+### changed
+- **36_employment** include labor costs from MACCs in employment
+- **38_factor_cots** renamed `p36_cost_shares` to `pm_cost_share_crops`
+- **57_maccs** split costs into labor and capital
+- **config** scenario_fsec.csv update
+- **config** updated SHAPE SDP scenarios in scenario_config.csv
+- **scripts** FSDP_collect FSDP_process fsec.R updates
+
+### added
+- **renv** MAgPIE now runs in an isolated, stable, reproducible R package environment
+- **scripts** added output script that generates a short mif containing only variables relevant for the REMIND coupling
+- **scripts** added output script that generates subnational validation outputs for fable_India projects
+- **setup** required R packages are automatically installed
+
+
 ## [4.6.1] - 2022-12-13
 
 ### changed
@@ -54,6 +76,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - **config** changed default value for s56_limit_ch4_n2o_price from 1000 to 4000 for consistency with c57_macc_version = "PBL_2022"
 - **scripts** rewrite of land conversion cost calibration script `landconversion_cost.R`
 
+
 ## [4.6.0] - 2022-11-09
 
 ### changed
@@ -222,6 +245,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - **scripts** fixed configuration error in FSEC output scripts, FSEC_dietaryIndicators.R and FSEC_environmentalPollutants.R
 - **scripts** scripts/start/extra/emulator.R  Throw an error if no file can be found to take the GHG prices from
 
+
 ## [4.4.0] - 2021-12-13
 
 ### changed
@@ -312,6 +336,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - **73_timber** plausible cost for balance variable in case of s73_timber_demand_switch = 0 to avoid cost distortion
 - **56_ghg_policy** choose the correct scenario for fixing the GHG prices until sm_fix_SSP2
 
+
 ## [4.3.5] - 2021-09-02
 
 ### changed
@@ -380,6 +405,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - - **15_food** single-cell protein substitution scenarios included in intersolve.gms.
 - **20_processing** The "mixed" scenario for single-cell protein production (c20_scp_type) was not working as expected. The corresponding code in 20_processing has been updated.
 
+
 ## [4.3.3] - 2021-03-30
 
 ### added
@@ -439,6 +465,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - **32_forestry** Bugfixes for "ac_est" and carbon treshold afforestation; removed plantations from "vm_cdr_aff".
 - **core** bugfix m_fillmissingyears macro; was running over t before; now running over t_all_
 
+
 ## [4.3.1] - 2020-11-03
 
 ### added
@@ -477,6 +504,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
  - **35_natveg** Clearer calculations for harvested area for timber production.
  - **52_carbon** Fix to the Carbon densities received from LPJmL for timber plantations.
 
+
 ## [4.2.1] - 2020-05-15
 
 ### added
@@ -494,7 +522,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
  - **NPI/NDC policy calculations** revision of calculation method
 
 
-
 ## [4.2.0] - 2020-04-15
 
 This release version is focussed on consistency between the MAgPIE setup and the [REMIND model] and result of a validation exercise of the coupled (REMIND 2.1)-(MAgPIE 4.2) system.
@@ -575,6 +602,7 @@ This release version is focussed on consistency between the MAgPIE setup and the
  - **71_diagg_lvst** adjusted monogastric disaggregation for more flexiblity to avoid infeasibilities with EFPs (see 42_water_demand)
  - **15_food** correction regarding the convergence measure of the iterative execution of the food demand model and MAgPIE; correction accounting for unusual time step length in body height calculations; body height regression parameters updated
 
+
 ## [4.0.1] - 2018-10-05
 
 ### fixed
@@ -586,7 +614,8 @@ 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/v4.6.1...develop
+[Unreleased]: https://github.com/magpiemodel/magpie/compare/v4.6.2...develop
+[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
 [4.6.0]: https://github.com/magpiemodel/magpie/compare/v4.5.0...v4.6.0
 [4.5.0]: https://github.com/magpiemodel/magpie/compare/v4.4.0...v4.5.0

CITATION.cff

@@ -125,8 +125,8 @@ authors:
     email: popp@pik-potsdam.de
 
 title: MAgPIE - An Open Source land-use modeling framework
-version: 4.6.1dev
-date-released: 2022-12-13
+version: 4.6.2dev
+date-released: 2023-01-12
 repository-code: https://github.com/magpiemodel/magpie
 keywords:
   - landuse

DEPENDENCIES

@@ -0,0 +1,38 @@
+Package: magpiemodel
+Imports:
+    callr,
+    citation,
+    curl,
+    data.table,
+    dplyr,
+    gdx,
+    gdxrrw,
+    ggplot2,
+    ggrepel,
+    gms,
+    here,
+    iamc,
+    lucode2 (>= 0.36.0),
+    luplot,
+    luscale,
+    lusweave,
+    m4fsdp,
+    madrat,
+    magclass,
+    magpie4,
+    MagpieNCGains,
+    magpiesets,
+    mip,
+    mrcommons,
+    patchwork,
+    piamenv (>= 0.3.4),
+    quitte,
+    raster,
+    remulator,
+    renv,
+    stringr,
+    txtplot,
+    withr
+Suggests:
+    goxygen,
+    qgraph

Makefile

@@ -0,0 +1,40 @@
+.PHONY: help docs update-renv update-all-renv check check-fix
+.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")'
+
+help: ## Show this help.
+	@Rscript -e $(HELP_PARSING)
+
+docs: ## Generate/update model HTML documentation in the doc/ folder.
+	Rscript -e 'goxygen::goxygen(); warnings()'
+	@echo -e '\nOpen\ndoc/html/index.htm\nin your browser to view the generated documentation.'
+
+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
+                 ## to the respective latest release and write renv.lock to archive.
+	Rscript -e 'renv::update(exclude = "renv"); piamenv::archiveRenv()'
+
+archive-renv: ## Write renv.lock to archive.
+	Rscript -e 'piamenv::archiveRenv()'
+
+restore-renv: ## Restore renv to the state described in interactively
+              ## selected renv.lock from the archive or a run folder.
+	Rscript -e 'piamenv::restoreRenv()'
+
+check: ## Check if the GAMS code follows the coding etiquette
+       ## using gms::codeCheck.
+	Rscript -e 'invisible(gms::codeCheck(strict = TRUE))'
+
+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))'