Develop

.Rbuildignore

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

.Rprofile

@@ -1,16 +1,42 @@
-# source global .Rprofile (very important to load user specific settings)
-# DO NOT EDIT THIS LINE!
-if(file.exists("~/.Rprofile")) source("~/.Rprofile")
+# |  (C) 2008-2025 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")
+if (Sys.info()[["sysname"]] == "Windows") {
+  # make renv use R's default download function to prevent
+  # curl: (35) schannel: next InitializeSecurityContext failed: Unknown error
+  # (0x80092012) - The revocation function was unable to check revocation for the certificate.
+  options(renv.download.override = utils::download.file)
+}
 
-# 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!
+# do not check if library and renv.lock are in sync, because normally renv.lock does not exist
+options(renv.config.synchronized.check = FALSE,
+        renv.config.user.profile = TRUE) # load user specific settings from ~/.Rprofile
 
-# snapshot <- "/p/projects/rd3mod/R/libraries/snapshots/dec2016"
-# if(file.exists(snapshot)) .libPaths(snapshot)
+# the text "renvVersion" is required for a check in a coupling script, will be removed soon
 
+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"))
+}
+
+# bootstrapping, will only run once after this repo is freshly cloned
+if (isTRUE(rownames(installed.packages(priority = "NA")) == "renv")) {
+  message("R package dependencies are not installed in this renv, installing now...")
+  renv::install("rmarkdown", prompt = FALSE) # rmarkdown is required to find dependencies in Rmd files
+  renv::hydrate(prompt = FALSE, report = FALSE) # auto-detect and install all dependencies
+  message("Finished installing R package dependencies.")
+  if (!("upstream" %in% gert::git_remote_list()$name)) {
+    gert::git_remote_add("https://github.com/magpiemodel/magpie.git", "upstream")
+    message("Added upstream git remote pointing to magpiemodel/magpie.")
+  }
+}
+
+# in case bootstrapping fails halfway, install piamenv and rely on requirement auto-fixing
+if (tryCatch(utils::packageVersion("piamenv") < "0.5.5", error = function(error) TRUE)) {
+  renv::install("piamenv", prompt = FALSE)
+}

.codeCheck

@@ -0,0 +1,6 @@
+capitalExclusionList:
+  - land
+  - iso
+  - type
+  - age
+  - k

.gitattributes

@@ -0,0 +1,3 @@
+# Handle line endings automatically for files detected as text
+# and leave all files detected as binary untouched.
+* text=auto

.githooks/pre-commit

@@ -0,0 +1,35 @@
+#!/usr/bin/env Rscript
+
+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)$",
+                 excludeFolders = c("output", "renv", ".git"))
+message("done.")
+
+stagedFiles <- system("git diff --cached --name-only", intern = TRUE)
+
+# run codeCheck only if .gms file is staged
+if (any(endsWith(stagedFiles, ".gms"))) {
+  invisible(gms::codeCheck(strict = TRUE))
+  message("")
+}
+
+
+# make sure that files are not too big
+maxFilesize <- 250 # kB
+exemptFromLimit <- "^renv/archive/[0-9\\.]+_renv\\.lock$"
+
+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 & !grepl(exemptFromLimit, out$files), ]
+if (nrow(out) > 0) {
+  stop(nrow(out), " files with size > ", maxFilesize, "kB detected: \n",
+       paste0(out$files, " (", out$size, "kB)", collapse = "\n"))
+}
+message("All files are smaller than ", maxFilesize, "kB\n")

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/pull_request_template.md

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+## :bird: Description of this PR :bird:
+
+- Briefly explain the purpose of this pull request
+
+## :wrench: Checklist for PR creator :wrench:
+
+- [ ] Label pull request [from the label list](https://github.com/magpiemodel/magpie/labels).
+  - **Low risk**: Simple bugfixes (missing files, updated documentation, typos) or changes  in start or output scripts
+  - **Medium risk**: Uncritical changes in the model core (e.g. moderate modifications in non-default realizations)
+  - **High risk**: Critical changes in model core or default settings (e.g. changing a model default or adjusting a core mechanic in the model)
+
+- [ ] Self-review own code
+  - No hard coded numbers and cluster/country/region names.
+  - The new code doesn't contain declared but unused parameters or variables.
+  - [`magpie4`](https://github.com/pik-piam/magpie4) R library has been updated accordingly and backwards compatible where necessary.
+  - `scenario_config.csv` has been updated accordingly (important if `default.cfg` has been updated)
+
+- [ ] Document changes 
+  - Add changes to `CHANGELOG.md`
+  - Where relevant, put In-code documentation comments
+  - Properly address updates in interfaces in the module documentations
+  - run [`goxygen::goxygen()`](https://github.com/pik-piam/goxygen) and verify the modified code is properly documented
+
+- [ ] Perform test runs
+  - **Low risk**: 
+    - Run a compilation check via `Rscript start.R --> "compilation check"`
+  - **Medium risk**: 
+    - Run test runs via `Rscript start.R --> "test runs"`
+    - Check logs for errors/warnings
+  - **High risk**:
+    - Run test runs via `Rscript start.R --> "test runs"`
+    - Check logs for errors/warnings
+    - Default run from the PR target branch for comparison
+    - Provide relevant comparison plots (land-use, emissions, food prices, land-use intensity,...)
+
+### :chart_with_downwards_trend: Performance changes :chart_with_upwards_trend:
+
+  - Current develop branch default : ** mins
+  - This PR's default :  ** mins
+
+## :rotating_light: Checklist for reviewer :rotating_light:
+
+- PR is labeled correctly
+- Code changes look reasonable
+  - No hard coded numbers and cluster/country/region names.
+  - No unnecessary increase in module interfaces
+  - model behavior/performance is satisfactory.
+- Changes are properly documented
+  - `CHANGELOG` is updated correctly
+  - Updates in interfaces have been properly addressed in the module documentations
+  - In-code documentation looks appropriate
+- [ ] content review done (at least 1)
+- [ ] RSE review done (at least 1)

.github/workflows/test-code.yaml

@@ -0,0 +1,33 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+      - develop
+  pull_request:
+    branches:
+      - main
+      - master
+      - develop
+
+name: check
+
+jobs:
+  check:
+    runs-on: ubuntu-22.04
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Remove .Rprofile
+        run: rm .Rprofile
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+          extra-repositories: "https://rse.pik-potsdam.de/r/packages"
+
+      - name: pre-commit Hook
+        run: source(".githooks/pre-commit")
+        shell: Rscript {0}

.gitignore

@@ -5,6 +5,7 @@ magpie_calib.*
 
 #ignore input files
 *.cs*
+!/data-changelog.csv
 *.mz
 *.rds
 /input/
@@ -13,6 +14,7 @@ magpie_calib.*
 *.gdx
 *.rda
 *.opt
+*.op2
 *.lst
 /output/
 
@@ -24,6 +26,17 @@ magpie_calib.*
 
 #ignore run specific files and folders
 /225*/
+/run_details/
+/logs/
 *.out
 /scripts/npi_ndc/npi_ndc_overview.txt
 Rplots.pdf
+
+#ignore GAMS license
+gamslice.txt
+
+#ignore lock file
+/.lock
+
+/renv.lock
+.Rproj.user

.lintr

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

.zenodo.json

@@ -0,0 +1,131 @@
+{
+  "title": "MAgPIE - An Open Source land-use modeling framework",
+  "version": "4.13.0dev",
+  "creators": [
+    {
+      "name": "Dietrich, Jan Philipp",
+      "affiliation": "Potsdam Institute for Climate Impact Research",
+      "orcid": "0000-0002-4309-6431"
+    },
+    {
+      "name": "Bodirsky, Benjamin Leon",
+      "affiliation": "Potsdam Institute for Climate Impact Research",
+      "orcid": "0000-0002-8242-6712"
+    },
+    {
+      "name": "Weindl, Isabelle",
+      "affiliation": "Potsdam Institute for Climate Impact Research"
+    },
+    {
+      "name": "Humpenöder, Florian",
+      "affiliation": "Potsdam Institute for Climate Impact Research",
+      "orcid": "0000-0003-2927-9407"
+    },
+    {
+      "name": "Stevanovic, Miodrag",
+      "affiliation": "Potsdam Institute for Climate Impact Research"
+    },
+    {
+      "name": "Kreidenweis, Ulrich",
+      "affiliation": "Potsdam Institute for Climate Impact Research"
+    },
+    {
+      "name": "Wang, Xiaoxi",
+      "affiliation": "Potsdam Institute for Climate Impact Research"
+    },
+    {
+      "name": "Karstens, Kristine",
+      "affiliation": "Potsdam Institute for Climate Impact Research"
+    },
+    {
+      "name": "Mishra, Abhijeet",
+      "affiliation": "Potsdam Institute for Climate Impact Research",
+      "orcid": "0000-0002-8287-9922"
+    },
+    {
+      "name": "Beier, Felicitas Dorothea",
+      "affiliation": "Potsdam Institute for Climate Impact Research"
+    },
+    {
+      "name": "Molina Bacca, Edna Johanna",
+      "affiliation": "Potsdam Institute for Climate Impact Research",
+      "orcid": "0000-0001-6530-1849"
+    },
+    {
+      "name": "von Jeetze, Patrick",
+      "affiliation": "Potsdam Institute for Climate Impact Research",
+      "orcid": "0000-0002-1197-4412"
+    },
+    {
+      "name": "Windisch, Michael",
+      "affiliation": "Potsdam Institute for Climate Impact Research"
+    },
+    {
+      "name": "Crawford, Michael Scott",
+      "affiliation": "Potsdam Institute for Climate Impact Research",
+      "orcid": "0000-0003-1282-400X"
+    },
+    {
+      "name": "Leip, Debbora",
+      "affiliation": "Potsdam Institute for Climate Impact Research"
+    },
+    {
+      "name": "Klein, David",
+      "affiliation": "Potsdam Institute for Climate Impact Research"
+    },
+    {
+      "name": "Singh, Vartika",
+      "affiliation": "Potsdam Institute for Climate Impact Research"
+    },
+    {
+      "name": "Ambrósio, Geanderson",
+      "affiliation": "Potsdam Institute for Climate Impact Research"
+    },
+    {
+      "name": "Araujo, Ewerton",
+      "affiliation": "Potsdam Institute for Climate Impact Research"
+    },
+    {
+      "name": "Biewald, Anne",
+      "affiliation": "Potsdam Institute for Climate Impact Research"
+    },
+    {
+      "name": "Sauer, Pascal",
+      "affiliation": "Potsdam Institute for Climate Impact Research",
+      "orcid": "0000-0002-6856-8239"
+    },
+    {
+      "name": "Köberle, Alexandre",
+      "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": "Hötten, David",
+      "affiliation": "Potsdam Institute for Climate Impact Research"
+    },
+    {
+      "name": "Schröter, Georg",
+      "affiliation": "Potsdam Institute for Climate Impact Research"
+    },
+    {
+      "name": "Lotze-Campen, Hermann",
+      "affiliation": "Potsdam Institute for Climate Impact Research",
+      "orcid": "0000-0002-0003-5508"
+    },
+    {
+      "name": "Popp, Alexander",
+      "affiliation": "Potsdam Institute for Climate Impact Research",
+      "orcid": "0000-0001-9500-1986"
+    }
+  ],
+  "keywords": ["landuse", "modeling", "model", "nlp", "partial equilibrium"],
+  "license": {
+    "id": "AGPL-3.0-or-later"
+  },
+  "publication_date": "2025-10-23"
+}