updating magpie

.Rbuildignore

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

.Rprofile

@@ -1,22 +1,25 @@
-# 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")
 
-# 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!
+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::hydrate() # auto-detect and install all dependencies
+  message("Finished installing R package dependencies.")
+}
 
-# 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")
+}

.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)

.github/pull_request_template.md

@@ -1,57 +1,53 @@
-## :bird: Purpose of this PR :bird:
+## :bird: Description of this PR :bird:
 
 - Briefly explain the purpose of this pull request
 
 ## :wrench: Checklist for PR creator :wrench:
 
-- [ ] Labeling pull request correctly [from the label list](https://github.com/magpiemodel/magpie/labels).
-
-* Low risk : Simple bugfixes (missing files, updated documentation, typos) or Start/output scripts
-* Medium risk : New realization / Changes to existing realization / Other changes which don't modify default.cfg
-* High risk : New input files (if cfg$input is changed in default.cfg) / Modification to core model (eg. changes in equations, calculations, introduction of new sets etc.) / Other changes in default.cfg
-
-- [ ] Providing additional information based on PR label
-
-* Low risk : No new model run needed.
-* Medium risk : Default run based on the current version of the fork from which PR is made
-* High risk
-  * Default run from the current develop branch
-  * Default run based on the current version of the fork from which PR is made
-
-- [ ] :chart_with_downwards_trend: Performance loss/gain from current default behavior :chart_with_upwards_trend:
-  * Current develop branch default : ** mins
-  * This PR's default :  ** mins
-
-- [ ] Added changes to `CHANGELOG.md`
-- [ ] Compilation check (model starts without compilation errors - use `gams main.gms action=c` in model folder for testing).
-- [ ] No hard coded numbers and cluster/country/region names.
-- [ ] The new code doesn't contain declared but unused parameters or variables.
-- [ ] Where relevant, In-code comments added including documentation comments.
-- [ ] Made sure that documentation created with [`goxygen`](https://github.com/pik-piam/goxygen) is okay (use `goxygen::goxygen()` for testing).
-- [ ] Changes to [`magpie4`](https://github.com/pik-piam/magpie4) R library for post processing of model output (ideally backward compatible).
-- [ ] Self-review of my own code.
-- [ ] For high risk runs: validation of major model indicators - Land-use, emissions, food prices, Tau.  %Delete this line in case it is not a high risk run%
-
-## :warning: Additional notes or warnings :warning:
-NA
-
-## :rotating_light: Checklist for RSE reviewer :rotating_light:
-
-- [ ] PR is labeled correctly.
-- [ ] `CHANGELOG` is updated correctly
-- [ ] No hard coded numbers and cluster/country/region names.
-- [ ] No unnecessary increase in module interfaces
-- [ ] All required updates in interfaces (if any) have been properly adressed in the module contracts
-- [ ] In-code comments and documentation comments are satisfactory.
-- [ ] model behavior/performance is satisfactory.
-- [ ] Requested changes (if any) were applied correctly
-
-## :rotating_light: Checklist for MAgPIE reviewer :rotating_light:
-
-- [ ] PR is labeled correctly.
-- [ ] `CHANGELOG` is updated correctly
-- [ ] No hard coded numbers and cluster/country/region names.
-- [ ] Changes to the model are scientifically sound
-- [ ] In-code comments and documentation comments are satisfactory.
-- [ ] model behavior/performance is satisfactory.
-- [ ] Requested changes (if any) were applied correctly
+- [ ] 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

@@ -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

@@ -26,9 +26,16 @@ 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"

.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": "4.3.4",
+  "version": "4.6.7",
   "creators": [
     {
       "name": "Dietrich, Jan Philipp",
@@ -65,10 +65,18 @@
       "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"
@@ -81,6 +89,11 @@
       "name": "Biewald, Anne",
       "affiliation": "Potsdam Institute for Climate Impact Research"
     },
+    {
+      "name": "Führlich, Pascal",
+      "affiliation": "Potsdam Institute for Climate Impact Research",
+      "orcid": "0000-0002-6856-8239"
+    },
     {
       "name": "Lotze-Campen, Hermann",
       "affiliation": "Potsdam Institute for Climate Impact Research",
@@ -96,5 +109,5 @@
   "license": {
     "id": "AGPL-3.0-or-later"
   },
-  "publication_date": "2021-04-30"
+  "publication_date": "2023-05-10"
 }