Merge branch 'develop' into develop

.Rprofile

@@ -1,21 +1,24 @@
-# |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+# |  (C) 2008-2024 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: [email protected]
 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)
+}
 
-source("renv/activate.R")
+# 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
 
-renvVersion <- "0.16.0"
-if (packageVersion("renv") != renvVersion) {
-  renvLockExisted <- file.exists(renv::paths$lockfile())
-  renv::upgrade(version = renvVersion, reload = TRUE, prompt = FALSE)
-  if (!renvLockExisted) {
-    unlink(renv::paths$lockfile())
-  }
-}
+# 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"))
@@ -28,7 +31,7 @@ if (isTRUE(rownames(installed.packages(priority = "NA")) == "renv")) {
   message("Finished installing R package dependencies.")
 }
 
-# source global .Rprofile (very important to load user specific settings)
-if (file.exists("~/.Rprofile")) {
-  source("~/.Rprofile")
+# in case bootstrapping fails halfway, install piamenv and rely on requirement auto-fixing
+if (!requireNamespace("piamenv", quietly = TRUE)) {
+  renv::install("piamenv", prompt = FALSE)
 }

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "MAgPIE - An Open Source land-use modeling framework",
-  "version": "4.7.1dev",
+  "version": "4.7.2dev",
   "creators": [
     {
       "name": "Dietrich, Jan Philipp",
@@ -114,5 +114,5 @@
   "license": {
     "id": "AGPL-3.0-or-later"
   },
-  "publication_date": "2024-02-28"
+  "publication_date": "2024-04-02"
 }

CHANGELOG.md

@@ -4,18 +4,14 @@
 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/).
 
+
 ## [Unreleased]
 
 ### changed
-- **config** updated FSEC scenario config for revision and included new calibration file (after cost fix in preprocessing)
-- **70_livestock** if `c70_fac_req_regr` is set to `reg`: use of USDA/FAO values for historic factor requirements for livestock instead of using regression values and change of calibration year from 2005 to 2010 for regional factor requirements regression
-- **21_trade** Revision of trade module. Replaced `cfg$gms$s21_trade_bal_damper` in favour of `cfg$gms$k_import21`, which allows for additional imports to maintain feasibility
-- **58_peatland** Threshold in equations changed from 1e-10 to 1e-8 to avoid rare divisions by zero
-- - **44_biodiversity** update `bii_target realization` to take `f44_rr_layer` into account in `q44_bii`
-- **default.cfg** update additional data to rev4.49
+- **44_biodiversity** update `bii_target realization` to take `f44_rr_layer` into account in `q44_bii`
+- **default.cfg** update additional data to rev4.50
 
 ### added
-- **scripts** added a new validation_cell.R output script that generates a pdf with the comparison of magpie land use and crop type outputs with LUH and MAPSPAM historical data at cellular resolution.
 - **default.cfg** added cropland growth constraint `cfg$gms$s30_annual_max_growth` 
 - **default.cfg** added early afforestation constraint `cfg$gms$s32_max_aff_cell_2025` 
 - **default.cfg** added technical cost for missing BII increase `cfg$gms$s44_cost_bii_missing` 
@@ -24,16 +20,35 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 - **core** added `coup2110`timesteps
 - **15_food** added additional sigmoid food substition scenarios `sigmoid_75pc_25_50`, `sigmoid_50pc_25_50` and `sigmoid_25pc_25_50`
 - **30_crop** added regional cropland equation `q30_crop_reg` and presolve growth constraint
-- **32_forestry** added cluster-level new afforestation area constraint
+- **32_forestry** added cluster-level new afforestation area constraint for 2025
 - **60_bioenergy** added new realization `1st2ndgen_priced_feb24` to enable price-driven 2nd gen bioenergy production
 - **scripts** added automatic set writer for new bioenergy realization to `start_functions`
 - **scripts** added start scripts for the GENIE project
 - **scenario_config.csv** added preset for GENIE project
-- **config** added `.codeCheck` with additonal configuration when running `gms::codeCheck`
+
+### removed
+-
+
+### fixed
+-
+
+## [4.7.2] - 2024-04-02
+
+### changed
+- **21_trade** Revision of trade module. Replaced `cfg$gms$s21_trade_bal_damper` in favour of `cfg$gms$k_import21`, which allows for additional imports to maintain feasibility
+- **58_peatland** Threshold in equations changed from 1e-10 to 1e-8 to avoid rare divisions by zero
+- **70_livestock** if `c70_fac_req_regr` is set to `reg`: use of USDA/FAO values for historic factor requirements for livestock instead of using regression values and change of calibration year from 2005 to 2010 for regional factor requirements regression
+- **config** updated FSEC scenario config for revision and included new calibration file (after cost fix in preprocessing)
+- **scripts** modified output reporting for SEALS to account for forestry plantations
+
+### added
 - **30_crop** Improved representation of cropland requiring relocation in response to introducing semi-natural habitat at the 1 km level based on high-resolution satellite imagery.
+- **config** added `.codeCheck` with additonal configuration when running `gms::codeCheck`
+- **scripts** add additional BII reporting variables in FSDP_collect.R
+- **scripts** added a new validation_cell.R output script that generates a pdf with the comparison of magpie land use and crop type outputs with LUH and MAPSPAM historical data at cellular resolution.
 
 ### removed
-- **core**    removed no longer needed set `si` Suitability classes
+- **core** removed no longer needed set `si` Suitability classes
 
 ### fixed
 - **52_carbon** i52_land_carbon_sink was not identical before 2020 for different RCPs. Fixed by setting to RCPBU until the year defined in sm_fix_cc.
@@ -857,7 +872,8 @@ 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/v4.7.1...develop
+[Unreleased]: https://github.com/magpiemodel/magpie/compare/v4.7.2...develop
+[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
 [4.7.0]: https://github.com/magpiemodel/magpie/compare/v4.6.11...v4.7.0
 [4.6.11]: https://github.com/magpiemodel/magpie/compare/v4.6.10...v4.6.11

CITATION.cff

@@ -137,8 +137,8 @@ authors:
     email: [email protected]
 
 title: MAgPIE - An Open Source land-use modeling framework
-version: 4.7.1dev
-date-released: 2024-02-28
+version: 4.7.2dev
+date-released: 2024-04-02
 repository-code: https://github.com/magpiemodel/magpie
 keywords:
   - landuse

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 4.7.1 can be found at
-https://rse.pik-potsdam.de/doc/magpie/4.7.1/
+The model documentation for version 4.7.2 can be found at
+https://rse.pik-potsdam.de/doc/magpie/4.7.2/
 
 A most recent version of the documentation can also be extracted from the
 model source code via the R package goxygen
@@ -65,31 +65,69 @@ When using a modified version of **MAgPIE** which is not identical to versions
 in the official main repository at https://github.com/magpiemodel add a suffix
 to the name to allow distinguishing versions (format **MAgPIE-suffix**).
 
-## SYSTEM REQUIREMENTS
+## HARDWARE REQUIREMENTS
 The model is quite resource heavy and works best on machines with high CPU clock
-and memory. Recommended is a machine with Windows, MacOS or Linux, with at least
-16GB of memory and a Core i7 CPU or similar.
+and memory. Recommended is a machine with at least 16GB of memory and a Core i7 CPU or similar.
 
 ## HOW TO INSTALL
-MAgPIE requires *GAMS* (https://www.gams.com/) including licenses for the
-solvers *CONOPT* and (optionally) *CPLEX* for its core calculations. As the model
-benefits significantly of recent improvements in *GAMS* and *CONOPT4* it is
-recommended to work with the most recent versions of both.
-Please make sure that the GAMS installation path is added to the PATH variable
-of the system.
-
-In addition *R* (https://www.r-project.org/) is required for pre- and
-postprocessing and run management (needs to be added to the PATH variable
-as well).
-
-Several R packages are required to run MAgPIE. Under Windows you first need to install
-Rtools (https://cran.r-project.org/bin/windows/Rtools/) and to add it to the PATH
-variable. When running R from the MAgPIE folder for the first time all
-required packages are automatically installed into an isolated,
-project specific R package environment (renv).
-For post-processing model outputs *Latex* is required
-(https://www.latex-project.org/get/). To be seen by the model it also needs to
-added to the PATH variable of your system.
+Commands formatted as `code` should generally be run in a terminal (PowerShell on Windows).
+
+### List of Requirements
+- license for gams incl. CONOPT solver
+- gams >= 43.4.1
+- git >= 2.16.1
+- R >= 4.1.2 (+ matching Rtools on Windows)
+- pandoc >= 2.14.2
+- TeX >= 3.14159265
+
+### OS specific setup
+Choose your operating system and follow the instructions there. You can also
+install requirements differently (e.g. using only installers on Windows), in
+the end it is only important that all requirements are installed in a suitable
+version and added to the PATH environment variable, so MAgPIE can use them.
+
+#### Ubuntu
+1. make sure you have a gams license incl. the CONOPT solver
+1. [install gams](https://www.gams.com/46/docs/UG_UNIX_INSTALL.html)
+1. install git, R, and pandoc with `sudo apt install git r-base pandoc`
+1. install TinyTeX with `Rscript -e 'install.packages("tinytex"); tinytex::install_tinytex()'`
+
+#### macOS
+1. make sure you have a gams license incl. the CONOPT solver
+1. [install gams](https://www.gams.com/46/docs/UG_MAC_INSTALL.html)
+1. install git, R, and pandoc with `brew install git r pandoc`
+1. install TinyTeX with `Rscript -e 'install.packages("tinytex"); tinytex::install_tinytex()'`
+
+#### Windows
+1. make sure you have a gams license incl. the CONOPT solver
+1. [install gams](https://www.gams.com/46/docs/UG_WIN_INSTALL.html)
+1. [download .msi pandoc file](https://github.com/jgm/pandoc/releases/latest) and run installer (`choco install pandoc` did not work in testing)
+1. [install chocolatey](https://chocolatey.org/install)
+1. install git, rig (R installer), and tinytex with `choco install -y git rig tinytex`
+1. restart terminal
+1. install R and Rtools with `rig add release; rig add rtools`
+
+### check setup is complete
+- restart terminal
+- `gams` should print many lines including "The installed license is valid."
+- `git --version`
+- `Rscript --version`
+- `pandoc --version`
+- `tex --version`
+
+If any of these are not found: Find the path to that executable
+(gams/git/Rscript/pandoc/tex, on Windows ending in '.exe') and add it to your
+PATH environment variable. Search for a tutorial online if you are unsure how to do that.
+
+### download and run MAgPIE
+1. download MAgPIE with `git clone https://github.com/magpiemodel/magpie.git`
+1. go into the MAgPIE folder `cd magpie`
+1. start a MAgPIE run with `Rscript start.R`, first time: installs all required R packages (takes a while)
+1. choose "1" for a default run
+1. then select "1" for direct execution
+
+### troubleshooting
+Please check [this discussion](https://github.com/magpiemodel/magpie/discussions/650) for known problems and solutions and to report new problems you encounter while setting up MAgPIE.
 
 ## DOCKER
 To use Docker, copy your `gamslice.txt`
@@ -188,7 +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/4.7.1/#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/4.7.2/#how-to-cite) in the model documentation for information how to cite the model.
 
 ## AUTHORS
 See list of authors in CITATION.cff

config/default.cfg

@@ -1,4 +1,4 @@
-# |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+# |  (C) 2008-2024 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

core/calculations.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 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

core/declarations.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 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

core/load_gdx.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 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

core/macros.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 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

core/sets.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 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

main.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 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

modules/09_drivers/aug17/declarations.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 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

modules/09_drivers/aug17/input.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 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

modules/09_drivers/aug17/preloop.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 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

modules/09_drivers/aug17/realization.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 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

modules/09_drivers/aug17/sets.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 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

modules/09_drivers/module.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 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

modules/10_land/landmatrix_dec18/declarations.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 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

modules/10_land/landmatrix_dec18/equations.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 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

modules/10_land/landmatrix_dec18/input.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 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

modules/10_land/landmatrix_dec18/postsolve.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 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

modules/10_land/landmatrix_dec18/preloop.gms

@@ -1,4 +1,4 @@
-*** |  (C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)
+*** |  (C) 2008-2024 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