From 47b302b42332f4fdaad8931d27fd3d8deba093dc Mon Sep 17 00:00:00 2001 From: pvjeetze Date: Mon, 25 Mar 2024 11:04:42 +0100 Subject: [PATCH 01/16] slightly modified BII reporting in FSDP_collect & additional reporting for SEALS --- scripts/output/extra/reportMAgPIE2SEALS.R | 17 +++ scripts/output/projects/FSDP_collect.R | 8 +- scripts/start/BiosphereTest.R | 79 ++++++++++ scripts/start/SNV_tests.R | 83 +++++++++++ scripts/start/baseTestRuns.R | 170 ++++++++++++++++++++++ 5 files changed, 353 insertions(+), 4 deletions(-) create mode 100644 scripts/start/BiosphereTest.R create mode 100644 scripts/start/SNV_tests.R create mode 100644 scripts/start/baseTestRuns.R diff --git a/scripts/output/extra/reportMAgPIE2SEALS.R b/scripts/output/extra/reportMAgPIE2SEALS.R index 437b86a1d4..a334568712 100644 --- a/scripts/output/extra/reportMAgPIE2SEALS.R +++ b/scripts/output/extra/reportMAgPIE2SEALS.R @@ -14,6 +14,7 @@ # 1.00: first working version library(gms) +library(gdx) library(magpie4) message("Starting to report gridded MAgPIE land use for SEALS") @@ -32,9 +33,25 @@ message("Script started for output directory: ", outputdir) cfg <- gms::loadConfig(file.path(outputdir, "config.yml")) title <- cfg$title + # Restructure data to conform to SEALS reportLandUseForSEALS( magCellLand = "cell.land_0.5_share.mz", outFile = paste0("cell.land_0.5_SEALS_", title, ".nc"), dir = outputdir, selectyears = c(2020, 2030, 2040, 2050) ) + +# In case of reforestation using plantation growth curves set forestry to zero +# in order to calculated the difference in forest allocation between two SEALS runs +plantation <- readGDX(file.path(outputdir, "fulldata.gdx"), "s32_aff_plantation") + +if (plantation) { + land_hr <- read.magpie(file.path(outputdir, "cell.land_0.5_share.mz")) + land_hr[, , "forestry"] <- 0 + + reportLandUseForSEALS( + magCellLand = land_hr, + outFile = paste0("cell.land_0.5_SEALS_", title, "_noForestry.nc"), + dir = outputdir, selectyears = c(2020, 2030, 2040, 2050) + ) +} diff --git a/scripts/output/projects/FSDP_collect.R b/scripts/output/projects/FSDP_collect.R index 329b17edaa..12f2226a49 100644 --- a/scripts/output/projects/FSDP_collect.R +++ b/scripts/output/projects/FSDP_collect.R @@ -137,12 +137,12 @@ var_reg <- c(indicators_main, ### Validation "Biodiversity|Agricultural landscape intactness", "Biodiversity|Biodiversity hotspot intactness", - "Biodiversity|Biodiversity hotspot intactness (unitless)", "Biodiversity|BII in areas outside Biodiversity Hotspots, Intact Forest & Cropland Landscapes", "Biodiversity|Biodiversity Hotspot and Intact Forest Landscapes BII", "Biodiversity|Biodiversity Hotspot BII", + "Biodiversity|BII in 30x30 Landscapes", "Biodiversity|Cropland Landscapes BII", - "Key Biodiversity Area BII", + "Biodiversity|Key Biodiversity Area BII", "Biodiversity|Inverted Simpson crop area diversity index", "Population", "Income", @@ -472,7 +472,7 @@ var_reg <- c(indicators_main, "Resources|Nitrogen|Pollution|Surplus|+|Animal Waste Management", "Resources|Nitrogen|Pollution|Surplus|+|Non-agricultural land", "Resources|Water|Withdrawal|Agriculture", - + "Resources|Nitrogen|Cropland Budget|Soil Nitrogen Uptake Efficiency", "Emissions|CH4_GWP*AR6|Land", @@ -702,7 +702,7 @@ for (i in 1:length(outputdir)) { iso <- rbind(iso, a) } else missing <- c(missing,rep) } - + scen <- c("BAU", "FSDP", "SSP2fsdp") #scen <- c("ERROR") thisScen <- unlist(strsplit(cfg$title, "_"))[3] diff --git a/scripts/start/BiosphereTest.R b/scripts/start/BiosphereTest.R new file mode 100644 index 0000000000..33efe173ef --- /dev/null +++ b/scripts/start/BiosphereTest.R @@ -0,0 +1,79 @@ +# | (C) 2008-2021 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 + +# ---------------------------------------------------------- +# description: SNV test runs +# ---------------------------------------------------------- + +rev <- "rev1" + + +###################################### +#### Script to start a MAgPIE run #### +###################################### + +library(gms) +library(lucode2) +library(magclass) + +# Load start functions +source("scripts/start_functions.R") + +# ==================== +# Scenario runs +# ==================== + +prefix <- paste(rev, "BiosphereTest_CurrentDev", sep = "_") + +scenarios <- c( + "SSP2-REF", "SSP2-SNV20", + "SSP2-GSN", "SSP2-GSN-SNV20", + "SSP2-30by30", "SSP2-30by30-SNV20" +) + + for (scen in scenarios) { + actions <- unlist(strsplit(scen, "-")) + + source("config/default.cfg") + + cfg$results_folder <- "output/:title::date:" + + cfg$output <- c( + "output_check", "extra/disaggregation", "rds_report", + "extra/reportMAgPIE2SEALS", "projects/FSEC_cropDiversityGrid" + ) + + # sticky + cfg$gms$factor_costs <- "sticky_feb18" + + # crop realisation + cfg$gms$crop <- "endo_apr21" + cfg$gms$c30_marginal_land <- "q33_marginal" + + # SNV habitat defintion + cfg$gms$land_snv <- "secdforest, other" + + if (any(actions %in% c("SNV20"))) { + cfg$gms$s30_snv_shr <- 0.2 + cfg$gms$s30_snv_scenario_target <- 2050 + } + + if (any(actions %in% c("GSN"))) { + cfg$gms$c22_protect_scenario <- "GSN_HalfEarth" + cfg$gms$s22_conservation_target <- 2050 + } + + if (any(actions %in% c("30by30"))) { + cfg$gms$c22_protect_scenario <- "30by30" + cfg$gms$s22_conservation_target <- 2030 + } + + + cfg$title <- paste0(prefix, "_", scen) + start_run(cfg = cfg, codeCheck = FALSE) + } + diff --git a/scripts/start/SNV_tests.R b/scripts/start/SNV_tests.R new file mode 100644 index 0000000000..62b808e445 --- /dev/null +++ b/scripts/start/SNV_tests.R @@ -0,0 +1,83 @@ +# | (C) 2008-2021 Potsdam Institute for Climate Impact Research (PIK) +# | authors, and contributors see CITATION.cff file. This file is part +# | of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of +# | AGPL-3.0, you are granted additional permissions described in the +# | MAgPIE License Exception, version 1.0 (see LICENSE file). +# | Contact: magpie@pik-potsdam.de + +# ---------------------------------------------------------- +# description: SNV test runs +# ---------------------------------------------------------- + +rev <- "rev1" + + +###################################### +#### Script to start a MAgPIE run #### +###################################### + +library(gms) +library(lucode2) +library(magclass) + +# Load start functions +source("scripts/start_functions.R") + +# ==================== +# Scenario runs +# ==================== + +prefix <- paste(rev, "SNVTests_CurrentDev", sep = "_") + +scenarios <- c( + "default", "SNV10","SNV20","SNV30","SNV50" +) + + for (scen in scenarios) { + actions <- unlist(strsplit(scen, "-")) + + source("config/default.cfg") + + cfg$results_folder <- "output/:title::date:" + + cfg$output <- c( + "output_check", "extra/disaggregation", "rds_report", + "extra/reportMAgPIE2SEALS", "projects/FSEC_cropDiversityGrid" + ) + + # sticky + cfg$gms$factor_costs <- "sticky_feb18" + + # crop realisation + cfg$gms$crop <- "endo_apr21" + cfg$gms$c30_marginal_land <- "q33_marginal" + + # SNV habitat defintion + cfg$gms$land_snv <- "secdforest, other" + + + # permanent habitats + if (any(actions %in% c("SNV10"))) { + cfg$gms$s30_snv_shr <- 0.1 + cfg$gms$s30_snv_scenario_target <- 2030 + } + + if (any(actions %in% c("SNV20"))) { + cfg$gms$s30_snv_shr <- 0.2 + cfg$gms$s30_snv_scenario_target <- 2030 + } + + if (any(actions %in% c("SNV30"))) { + cfg$gms$s30_snv_shr <- 0.3 + cfg$gms$s30_snv_scenario_target <- 2030 + } + + if (any(actions %in% c("SNV50"))) { + cfg$gms$s30_snv_shr <- 0.5 + cfg$gms$s30_snv_scenario_target <- 2030 + } + + cfg$title <- paste0(prefix, "_", scen) + start_run(cfg = cfg, codeCheck = FALSE) + } + diff --git a/scripts/start/baseTestRuns.R b/scripts/start/baseTestRuns.R new file mode 100644 index 0000000000..ffadb243ec --- /dev/null +++ b/scripts/start/baseTestRuns.R @@ -0,0 +1,170 @@ +# | (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: magpie@pik-potsdam.de + +# ---------------------------------------------------------- +# description: Base test runs +# ---------------------------------------------------------- + +rev <- "rev1" + +###################################### +#### Script to start a MAgPIE run #### +###################################### + +library(gms) +library(lucode2) +library(magclass) + +# Load start functions +source("scripts/start_functions.R") + +# ==================== +# Calibration +# ==================== + +# source("config/default.cfg") + +# cfg$title <- "calib_run" +# cfg$output <- c("rds_report", "validation_short") + +# cfg$recalibrate <- FALSE +# cfg$recalibrate_landconversion_cost <- TRUE + +# # cc is new default +# cfg <- setScenario(cfg, "nocc_hist") + +# # crop penalty realisation +# cfg$gms$crop <- "endo_apr21" + +# # sticky +# cfg$gms$factor_costs <- "sticky_feb18" + +# # marginal land scenario +# cfg$gms$c30_marginal_land <- "q33_marginal" + +# start_run(cfg = cfg) +# calib_tgz <- magpie4::submitCalibration(paste(rev, "testRuns", sep = "_")) + +# ==================== +# Scenario runs +# ==================== + +prefix <- paste(rev, "3rdPaperTests", sep = "_") + +# scenarios <- c("SSP1", "SSP2", "SSP3", "SSP4", "SSP5", +# "SSP2-PB650-R", "SSP2-PB1050-R", +# "SSP2-PB650-P", "SSP2-PB1050-P") + +# scenarios <- c("SSP2-PB650-R", "SSP2-PB1050-R", +# "SSP2-PB650-P", "SSP2-PB1050-P") + +scenarios <- c("SSP2-PB650-Pmax-30by30", "SSP2-PB650-R-30by30", + "SSP2-PB650-Pmax-KBA", "SSP2-PB650-R-KBA", + "SSP2-PB650-Pmax-GSN_DSA", "SSP2-PB650-R-GSN_DSA", + "SSP2-PB650-Pmax-GSN_RarePhen", "SSP2-PB650-R-GSN_RarePhen", + "SSP2-PB650-Pmax-CCA", "SSP2-PB650-R-CCA", + "SSP2-PB650-Pmax-BH", "SSP2-PB650-R-BH") + + for (scen in scenarios) { + + scen <- unlist(strsplit(scen, "-")) + ssp <- scen[grepl("SSP", scen)] + + if(length(ssp) == 0){ + ssp <- "SSP2" + } + + source("config/default.cfg") + + cfg$results_folder <- "output/:title::date:" + + cfg$output <- c( + "output_check", "extra/disaggregation", "rds_report", + "extra/reportMAgPIE2SEALS", "projects/FSEC_cropDiversityGrid" + ) + + cfg$input <- c(regional = "rev4.96_h12_magpie.tgz", + cellular = "rev4.96_h12_fd712c0b_cellularmagpie_c200_MRI-ESM2-0-ssp370_lpjml-8e6c5eb1.tgz", + validation = "rev4.96_h12_validation.tgz", + additional = "additional_data_rev4.47.tgz", + # calibration = calib_tgz + calibration = "calibration_rev1_testRuns_10Jan24.tgz" + ) + + # Climate change switched off for these runs + cfg <- setScenario(cfg, "nocc_hist") + + # sticky + cfg$gms$factor_costs <- "sticky_feb18" + + # crop realisation + cfg$gms$crop <- "endo_apr21" + cfg$gms$c30_marginal_land <- "q33_marginal" + + # SNV habitat defintion + cfg$gms$land_snv <- "secdforest, other" + + cfg <- setScenario(cfg, c(ssp, "NPI")) + + if ("PB650" %in% scen) { + cfg <- setScenario(cfg, c(ssp, "NDC")) + cfg$gms$c56_pollutant_prices <- "R32M46-SSP2EU-PkBudg650" + cfg$gms$c56_emis_policy <- "redd+natveg_nosoil" + cfg$gms$c60_2ndgen_biodem <- "R32M46-SSP2EU-PkBudg650" + } + + if ("PB1050" %in% scen) { + cfg <- setScenario(cfg, c(ssp, "NDC")) + cfg$gms$c56_pollutant_prices <- "R32M46-SSP2EU-PkBudg1050" + cfg$gms$c56_emis_policy <- "redd+natveg_nosoil" + cfg$gms$c60_2ndgen_biodem <- "R32M46-SSP2EU-PkBudg1050" + } + + if ("P" %in% scen) { + cfg$gms$s32_aff_plantation <- 1 + cfg$gms$s32_aff_bii_coeff <- 1 + } + + if (all(c("PB1050", "Pmax") %in% scen)) { + cfg$gms$s32_aff_plantation <- 1 + cfg$gms$s32_aff_bii_coeff <- 1 + cfg$gms$s32_max_aff_area <- 300 + } + + if (all(c("PB650", "Pmax") %in% scen)) { + cfg$gms$s32_aff_plantation <- 1 + cfg$gms$s32_aff_bii_coeff <- 1 + cfg$gms$s32_max_aff_area <- 350 + } + + if ("30by30" %in% scen) { + cfg$gms$c22_protect_scenario <- "30by30" + } + + if ("KBA" %in% scen) { + cfg$gms$c22_protect_scenario <- "KBA" + } + + if ("GSN_RarePhen" %in% scen) { + cfg$gms$c22_protect_scenario <- "GSN_DSA" + } + + if ("30by30" %in% scen) { + cfg$gms$c22_protect_scenario <- "GSN_RarePhen" + } + + if ("CCA" %in% scen) { + cfg$gms$c22_protect_scenario <- "CCA" + } + + if ("BH" %in% scen) { + cfg$gms$c22_protect_scenario <- "BH" + } + + cfg$title <- paste0(prefix, "_", paste(scen, collapse = "-")) + start_run(cfg = cfg, codeCheck = FALSE) + } From 8679da0f11588e9802d3dae28944fcf784c43fef Mon Sep 17 00:00:00 2001 From: pvjeetze Date: Mon, 25 Mar 2024 11:07:33 +0100 Subject: [PATCH 02/16] removed extra scripts --- scripts/start/BiosphereTest.R | 79 ---------------- scripts/start/SNV_tests.R | 83 ----------------- scripts/start/baseTestRuns.R | 170 ---------------------------------- 3 files changed, 332 deletions(-) delete mode 100644 scripts/start/BiosphereTest.R delete mode 100644 scripts/start/SNV_tests.R delete mode 100644 scripts/start/baseTestRuns.R diff --git a/scripts/start/BiosphereTest.R b/scripts/start/BiosphereTest.R deleted file mode 100644 index 33efe173ef..0000000000 --- a/scripts/start/BiosphereTest.R +++ /dev/null @@ -1,79 +0,0 @@ -# | (C) 2008-2021 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 - -# ---------------------------------------------------------- -# description: SNV test runs -# ---------------------------------------------------------- - -rev <- "rev1" - - -###################################### -#### Script to start a MAgPIE run #### -###################################### - -library(gms) -library(lucode2) -library(magclass) - -# Load start functions -source("scripts/start_functions.R") - -# ==================== -# Scenario runs -# ==================== - -prefix <- paste(rev, "BiosphereTest_CurrentDev", sep = "_") - -scenarios <- c( - "SSP2-REF", "SSP2-SNV20", - "SSP2-GSN", "SSP2-GSN-SNV20", - "SSP2-30by30", "SSP2-30by30-SNV20" -) - - for (scen in scenarios) { - actions <- unlist(strsplit(scen, "-")) - - source("config/default.cfg") - - cfg$results_folder <- "output/:title::date:" - - cfg$output <- c( - "output_check", "extra/disaggregation", "rds_report", - "extra/reportMAgPIE2SEALS", "projects/FSEC_cropDiversityGrid" - ) - - # sticky - cfg$gms$factor_costs <- "sticky_feb18" - - # crop realisation - cfg$gms$crop <- "endo_apr21" - cfg$gms$c30_marginal_land <- "q33_marginal" - - # SNV habitat defintion - cfg$gms$land_snv <- "secdforest, other" - - if (any(actions %in% c("SNV20"))) { - cfg$gms$s30_snv_shr <- 0.2 - cfg$gms$s30_snv_scenario_target <- 2050 - } - - if (any(actions %in% c("GSN"))) { - cfg$gms$c22_protect_scenario <- "GSN_HalfEarth" - cfg$gms$s22_conservation_target <- 2050 - } - - if (any(actions %in% c("30by30"))) { - cfg$gms$c22_protect_scenario <- "30by30" - cfg$gms$s22_conservation_target <- 2030 - } - - - cfg$title <- paste0(prefix, "_", scen) - start_run(cfg = cfg, codeCheck = FALSE) - } - diff --git a/scripts/start/SNV_tests.R b/scripts/start/SNV_tests.R deleted file mode 100644 index 62b808e445..0000000000 --- a/scripts/start/SNV_tests.R +++ /dev/null @@ -1,83 +0,0 @@ -# | (C) 2008-2021 Potsdam Institute for Climate Impact Research (PIK) -# | authors, and contributors see CITATION.cff file. This file is part -# | of MAgPIE and licensed under AGPL-3.0-or-later. Under Section 7 of -# | AGPL-3.0, you are granted additional permissions described in the -# | MAgPIE License Exception, version 1.0 (see LICENSE file). -# | Contact: magpie@pik-potsdam.de - -# ---------------------------------------------------------- -# description: SNV test runs -# ---------------------------------------------------------- - -rev <- "rev1" - - -###################################### -#### Script to start a MAgPIE run #### -###################################### - -library(gms) -library(lucode2) -library(magclass) - -# Load start functions -source("scripts/start_functions.R") - -# ==================== -# Scenario runs -# ==================== - -prefix <- paste(rev, "SNVTests_CurrentDev", sep = "_") - -scenarios <- c( - "default", "SNV10","SNV20","SNV30","SNV50" -) - - for (scen in scenarios) { - actions <- unlist(strsplit(scen, "-")) - - source("config/default.cfg") - - cfg$results_folder <- "output/:title::date:" - - cfg$output <- c( - "output_check", "extra/disaggregation", "rds_report", - "extra/reportMAgPIE2SEALS", "projects/FSEC_cropDiversityGrid" - ) - - # sticky - cfg$gms$factor_costs <- "sticky_feb18" - - # crop realisation - cfg$gms$crop <- "endo_apr21" - cfg$gms$c30_marginal_land <- "q33_marginal" - - # SNV habitat defintion - cfg$gms$land_snv <- "secdforest, other" - - - # permanent habitats - if (any(actions %in% c("SNV10"))) { - cfg$gms$s30_snv_shr <- 0.1 - cfg$gms$s30_snv_scenario_target <- 2030 - } - - if (any(actions %in% c("SNV20"))) { - cfg$gms$s30_snv_shr <- 0.2 - cfg$gms$s30_snv_scenario_target <- 2030 - } - - if (any(actions %in% c("SNV30"))) { - cfg$gms$s30_snv_shr <- 0.3 - cfg$gms$s30_snv_scenario_target <- 2030 - } - - if (any(actions %in% c("SNV50"))) { - cfg$gms$s30_snv_shr <- 0.5 - cfg$gms$s30_snv_scenario_target <- 2030 - } - - cfg$title <- paste0(prefix, "_", scen) - start_run(cfg = cfg, codeCheck = FALSE) - } - diff --git a/scripts/start/baseTestRuns.R b/scripts/start/baseTestRuns.R deleted file mode 100644 index ffadb243ec..0000000000 --- a/scripts/start/baseTestRuns.R +++ /dev/null @@ -1,170 +0,0 @@ -# | (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: magpie@pik-potsdam.de - -# ---------------------------------------------------------- -# description: Base test runs -# ---------------------------------------------------------- - -rev <- "rev1" - -###################################### -#### Script to start a MAgPIE run #### -###################################### - -library(gms) -library(lucode2) -library(magclass) - -# Load start functions -source("scripts/start_functions.R") - -# ==================== -# Calibration -# ==================== - -# source("config/default.cfg") - -# cfg$title <- "calib_run" -# cfg$output <- c("rds_report", "validation_short") - -# cfg$recalibrate <- FALSE -# cfg$recalibrate_landconversion_cost <- TRUE - -# # cc is new default -# cfg <- setScenario(cfg, "nocc_hist") - -# # crop penalty realisation -# cfg$gms$crop <- "endo_apr21" - -# # sticky -# cfg$gms$factor_costs <- "sticky_feb18" - -# # marginal land scenario -# cfg$gms$c30_marginal_land <- "q33_marginal" - -# start_run(cfg = cfg) -# calib_tgz <- magpie4::submitCalibration(paste(rev, "testRuns", sep = "_")) - -# ==================== -# Scenario runs -# ==================== - -prefix <- paste(rev, "3rdPaperTests", sep = "_") - -# scenarios <- c("SSP1", "SSP2", "SSP3", "SSP4", "SSP5", -# "SSP2-PB650-R", "SSP2-PB1050-R", -# "SSP2-PB650-P", "SSP2-PB1050-P") - -# scenarios <- c("SSP2-PB650-R", "SSP2-PB1050-R", -# "SSP2-PB650-P", "SSP2-PB1050-P") - -scenarios <- c("SSP2-PB650-Pmax-30by30", "SSP2-PB650-R-30by30", - "SSP2-PB650-Pmax-KBA", "SSP2-PB650-R-KBA", - "SSP2-PB650-Pmax-GSN_DSA", "SSP2-PB650-R-GSN_DSA", - "SSP2-PB650-Pmax-GSN_RarePhen", "SSP2-PB650-R-GSN_RarePhen", - "SSP2-PB650-Pmax-CCA", "SSP2-PB650-R-CCA", - "SSP2-PB650-Pmax-BH", "SSP2-PB650-R-BH") - - for (scen in scenarios) { - - scen <- unlist(strsplit(scen, "-")) - ssp <- scen[grepl("SSP", scen)] - - if(length(ssp) == 0){ - ssp <- "SSP2" - } - - source("config/default.cfg") - - cfg$results_folder <- "output/:title::date:" - - cfg$output <- c( - "output_check", "extra/disaggregation", "rds_report", - "extra/reportMAgPIE2SEALS", "projects/FSEC_cropDiversityGrid" - ) - - cfg$input <- c(regional = "rev4.96_h12_magpie.tgz", - cellular = "rev4.96_h12_fd712c0b_cellularmagpie_c200_MRI-ESM2-0-ssp370_lpjml-8e6c5eb1.tgz", - validation = "rev4.96_h12_validation.tgz", - additional = "additional_data_rev4.47.tgz", - # calibration = calib_tgz - calibration = "calibration_rev1_testRuns_10Jan24.tgz" - ) - - # Climate change switched off for these runs - cfg <- setScenario(cfg, "nocc_hist") - - # sticky - cfg$gms$factor_costs <- "sticky_feb18" - - # crop realisation - cfg$gms$crop <- "endo_apr21" - cfg$gms$c30_marginal_land <- "q33_marginal" - - # SNV habitat defintion - cfg$gms$land_snv <- "secdforest, other" - - cfg <- setScenario(cfg, c(ssp, "NPI")) - - if ("PB650" %in% scen) { - cfg <- setScenario(cfg, c(ssp, "NDC")) - cfg$gms$c56_pollutant_prices <- "R32M46-SSP2EU-PkBudg650" - cfg$gms$c56_emis_policy <- "redd+natveg_nosoil" - cfg$gms$c60_2ndgen_biodem <- "R32M46-SSP2EU-PkBudg650" - } - - if ("PB1050" %in% scen) { - cfg <- setScenario(cfg, c(ssp, "NDC")) - cfg$gms$c56_pollutant_prices <- "R32M46-SSP2EU-PkBudg1050" - cfg$gms$c56_emis_policy <- "redd+natveg_nosoil" - cfg$gms$c60_2ndgen_biodem <- "R32M46-SSP2EU-PkBudg1050" - } - - if ("P" %in% scen) { - cfg$gms$s32_aff_plantation <- 1 - cfg$gms$s32_aff_bii_coeff <- 1 - } - - if (all(c("PB1050", "Pmax") %in% scen)) { - cfg$gms$s32_aff_plantation <- 1 - cfg$gms$s32_aff_bii_coeff <- 1 - cfg$gms$s32_max_aff_area <- 300 - } - - if (all(c("PB650", "Pmax") %in% scen)) { - cfg$gms$s32_aff_plantation <- 1 - cfg$gms$s32_aff_bii_coeff <- 1 - cfg$gms$s32_max_aff_area <- 350 - } - - if ("30by30" %in% scen) { - cfg$gms$c22_protect_scenario <- "30by30" - } - - if ("KBA" %in% scen) { - cfg$gms$c22_protect_scenario <- "KBA" - } - - if ("GSN_RarePhen" %in% scen) { - cfg$gms$c22_protect_scenario <- "GSN_DSA" - } - - if ("30by30" %in% scen) { - cfg$gms$c22_protect_scenario <- "GSN_RarePhen" - } - - if ("CCA" %in% scen) { - cfg$gms$c22_protect_scenario <- "CCA" - } - - if ("BH" %in% scen) { - cfg$gms$c22_protect_scenario <- "BH" - } - - cfg$title <- paste0(prefix, "_", paste(scen, collapse = "-")) - start_run(cfg = cfg, codeCheck = FALSE) - } From 96183c5bbd5c7a9b1da82ad12104a6ebbd46dc97 Mon Sep 17 00:00:00 2001 From: pvjeetze Date: Mon, 25 Mar 2024 11:14:28 +0100 Subject: [PATCH 03/16] changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7f744e0e1a..3dfbffae20 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,12 +7,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/). ## [Unreleased] ### changed +- **scripts** modified output reporting for SEALS to account for forestry plantations - **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 ### added +- **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. - **config** added `.codeCheck` with additonal configuration when running `gms::codeCheck` - **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. From a88e03cdf7bc144c3942d89f07d53ef83aaac99d Mon Sep 17 00:00:00 2001 From: Pascal Sauer Date: Thu, 28 Mar 2024 14:45:44 +0100 Subject: [PATCH 04/16] dont force renv 0.16.0, set renv.download.override on windows --- .Rprofile | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/.Rprofile b/.Rprofile index e8d4f1facc..d2f419f0cc 100644 --- a/.Rprofile +++ b/.Rprofile @@ -5,18 +5,15 @@ # | 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") { + # 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") -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()) - } -} - if (!"https://rse.pik-potsdam.de/r/packages" %in% getOption("repos")) { options(repos = c(getOption("repos"), pik = "https://rse.pik-potsdam.de/r/packages")) } From 0745bb84b351da92683bfb8c67cc639d33339809 Mon Sep 17 00:00:00 2001 From: Pascal Sauer Date: Thu, 28 Mar 2024 14:47:54 +0100 Subject: [PATCH 05/16] how to install v1 --- README.md | 88 +++++++++++++++++++++++++++++++++++++++++-------------- 1 file changed, 66 insertions(+), 22 deletions(-) diff --git a/README.md b/README.md index 787cd31368..e4f0319c6e 100644 --- a/README.md +++ b/README.md @@ -65,31 +65,75 @@ 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. +- we assume you know how to edit the PATH environment variable, just search for a tutorial online if unsure +- on Windows terminal = PowerShell +- commands formatted as `code` should generally be run in a terminal + +### gams >= 43.4.1 +- make sure you have a gams license incl. the CONOPT solver +- [download gams](https://www.gams.com/download) +- install gams + - [unix](https://www.gams.com/46/docs/UG_UNIX_INSTALL.html) + - [macOS](https://www.gams.com/46/docs/UG_MAC_INSTALL.html) + - [Windows](https://www.gams.com/46/docs/UG_WIN_INSTALL.html) + - add the gams path (like `C:\gams\46`) to your PATH + +### Windows only - winget / chocolatey +winget and chocolatey are package managers, they allow installing magpie requirements via a simple command. You only need one package manager, and you only need to run the install command for your package manager (either `winget install ...` or `choco install ...`, but not both). If neither package manager works you can fall back to downloading and running installers, but usually this requires additional steps after the installation like adding a path to the PATH environment variable. + +- check if `winget` is already installed by running `winget` in a terminal +- if missing install it as described [here](https://learn.microsoft.com/en-us/windows/package-manager/winget/#install-winget) +- alternative: [install chocolatey](https://chocolatey.org/install) + +### Windows only - git +- `winget install --id Git.Git -e --source winget` +- `choco install -y git` +- or [download](https://git-scm.com/download/win) and run installer + +### R >= 4.1.2 +- Ubuntu: `sudo apt install r-base` +- macOS: `brew install r` +- Windows + - `winget install posit.rig`, restart terminal, then `rig add release` + - `choco install -y rig`, restart terminal, then `rig add release` + - or [download](https://github.com/r-lib/rig/releases/tag/latest) and run installer + +### Windows only - Rtools +- `rig add rtools` +- or [download](https://cloud.r-project.org/bin/windows/Rtools/) and run installer, make sure your R and Rtools versions are the same + +### pandoc +- Ubuntu: `sudo apt install pandoc` +- macOS: `brew install pandoc` +- Windows: + - `winget install -e --id JohnMacFarlane.Pandoc` + - [download](https://pandoc.org/installing.html) and run installer (`choco install -y pandoc` did not work during testing) + +### TeX +- Windows: + - `winget install -e --id MiKTeX.MiKTeX` + - `choco install -y tinytex` + +### check setup is complete +- restart terminal +- `gams` should print many lines including "The installed license is valid." +- `git --version` +- `Rscript --version` +- `pandoc --version` + +### MAgPIE +```sh +git clone https://github.com/magpiemodel/magpie.git +cd magpie +Rscript start.R +``` +- choose "1" for a default run +- then select "1" for direct execution ## DOCKER To use Docker, copy your `gamslice.txt` From ffe86692b4c2fa95fda0ac27edfcf7af679fb07f Mon Sep 17 00:00:00 2001 From: Pascal Sauer Date: Thu, 28 Mar 2024 15:09:34 +0100 Subject: [PATCH 06/16] setup instructions restructure --- README.md | 106 +++++++++++++++++++++++++----------------------------- 1 file changed, 49 insertions(+), 57 deletions(-) diff --git a/README.md b/README.md index e4f0319c6e..1e22ed7383 100644 --- a/README.md +++ b/README.md @@ -70,54 +70,42 @@ The model is quite resource heavy and works best on machines with high CPU clock and memory. Recommended is a machine with at least 16GB of memory and a Core i7 CPU or similar. ## HOW TO INSTALL -- we assume you know how to edit the PATH environment variable, just search for a tutorial online if unsure -- on Windows terminal = PowerShell -- commands formatted as `code` should generally be run in a terminal - -### gams >= 43.4.1 -- make sure you have a gams license incl. the CONOPT solver -- [download gams](https://www.gams.com/download) -- install gams - - [unix](https://www.gams.com/46/docs/UG_UNIX_INSTALL.html) - - [macOS](https://www.gams.com/46/docs/UG_MAC_INSTALL.html) - - [Windows](https://www.gams.com/46/docs/UG_WIN_INSTALL.html) - - add the gams path (like `C:\gams\46`) to your PATH - -### Windows only - winget / chocolatey -winget and chocolatey are package managers, they allow installing magpie requirements via a simple command. You only need one package manager, and you only need to run the install command for your package manager (either `winget install ...` or `choco install ...`, but not both). If neither package manager works you can fall back to downloading and running installers, but usually this requires additional steps after the installation like adding a path to the PATH environment variable. - -- check if `winget` is already installed by running `winget` in a terminal -- if missing install it as described [here](https://learn.microsoft.com/en-us/windows/package-manager/winget/#install-winget) -- alternative: [install chocolatey](https://chocolatey.org/install) - -### Windows only - git -- `winget install --id Git.Git -e --source winget` -- `choco install -y git` -- or [download](https://git-scm.com/download/win) and run installer - -### R >= 4.1.2 -- Ubuntu: `sudo apt install r-base` -- macOS: `brew install r` -- Windows - - `winget install posit.rig`, restart terminal, then `rig add release` - - `choco install -y rig`, restart terminal, then `rig add release` - - or [download](https://github.com/r-lib/rig/releases/tag/latest) and run installer - -### Windows only - Rtools -- `rig add rtools` -- or [download](https://cloud.r-project.org/bin/windows/Rtools/) and run installer, make sure your R and Rtools versions are the same - -### pandoc -- Ubuntu: `sudo apt install pandoc` -- macOS: `brew install pandoc` -- Windows: - - `winget install -e --id JohnMacFarlane.Pandoc` - - [download](https://pandoc.org/installing.html) and run installer (`choco install -y pandoc` did not work during testing) - -### TeX -- Windows: - - `winget install -e --id MiKTeX.MiKTeX` - - `choco install -y tinytex` +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. [install pandoc](https://pandoc.org/installing.html) +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 @@ -125,15 +113,19 @@ winget and chocolatey are package managers, they allow installing magpie require - `git --version` - `Rscript --version` - `pandoc --version` - -### MAgPIE -```sh -git clone https://github.com/magpiemodel/magpie.git -cd magpie -Rscript start.R -``` -- choose "1" for a default run -- then select "1" for direct execution +- `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 only: this will install all required R packages (takes a while) +1. choose "1" for a default run +1. then select "1" for direct execution ## DOCKER To use Docker, copy your `gamslice.txt` From 2824b0945ec6156bc38cd89fa6d26658957d0e8e Mon Sep 17 00:00:00 2001 From: Pascal Sauer <156898545+pascal-sauer@users.noreply.github.com> Date: Thu, 28 Mar 2024 15:15:12 +0100 Subject: [PATCH 07/16] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 1e22ed7383..3e0eb48981 100644 --- a/README.md +++ b/README.md @@ -101,7 +101,7 @@ version and added to the PATH environment variable, so MAgPIE can use them. #### 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. [install pandoc](https://pandoc.org/installing.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 From 5f7c1a223df7d854661690060f1ce80c4fa4e579 Mon Sep 17 00:00:00 2001 From: Pascal Sauer <156898545+pascal-sauer@users.noreply.github.com> Date: Thu, 28 Mar 2024 15:18:37 +0100 Subject: [PATCH 08/16] Update README.md --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index 3e0eb48981..d3c9366d16 100644 --- a/README.md +++ b/README.md @@ -122,8 +122,7 @@ PATH environment variable. Search for a tutorial online if you are unsure how to ### 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 only: this will install all required R packages (takes a while) +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 From 66ee2d65213cb526f87198c662d521eb7fdaaa8b Mon Sep 17 00:00:00 2001 From: Pascal Sauer <156898545+pascal-sauer@users.noreply.github.com> Date: Thu, 28 Mar 2024 15:26:11 +0100 Subject: [PATCH 09/16] Update README.md --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index d3c9366d16..3132b3be89 100644 --- a/README.md +++ b/README.md @@ -126,6 +126,9 @@ PATH environment variable. Search for a tutorial online if you are unsure how to 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` into the MAgPIE main directory, and build the magpie image using the command From 856b5aa19468d8fb88dde542d69278876153518e Mon Sep 17 00:00:00 2001 From: Pascal Sauer Date: Thu, 28 Mar 2024 15:47:50 +0100 Subject: [PATCH 10/16] upgrade to renv 1.0.5 --- .Rprofile | 5 +- renv/activate.R | 467 ++++++++++++++++++++++++++++++++++-------------- 2 files changed, 341 insertions(+), 131 deletions(-) diff --git a/.Rprofile b/.Rprofile index d2f419f0cc..7fbeb85143 100644 --- a/.Rprofile +++ b/.Rprofile @@ -6,12 +6,15 @@ # | Contact: magpie@pik-potsdam.de Sys.setenv(RENV_PATHS_LIBRARY = "renv/library") if (Sys.info()[["sysname"]] == "Windows") { - # use R's default download function to prevent + # 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) } +# do not check if library and renv.lock are in sync, because renv.lock does not exist +options(renv.config.synchronized.check = FALSE) + source("renv/activate.R") if (!"https://rse.pik-potsdam.de/r/packages" %in% getOption("repos")) { diff --git a/renv/activate.R b/renv/activate.R index 019b5a6693..9b2e7f1841 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,11 +2,27 @@ local({ # the requested version of renv - version <- "0.16.0" + version <- "1.0.5" + attr(version, "sha") <- NULL # the project directory project <- getwd() + # use start-up diagnostics if enabled + diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") + if (diagnostics) { + start <- Sys.time() + profile <- tempfile("renv-startup-", fileext = ".Rprof") + utils::Rprof(profile) + on.exit({ + utils::Rprof(NULL) + elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) + writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) + writeLines(sprintf("- Profile: %s", profile)) + print(utils::summaryRprof(profile)) + }, add = TRUE) + } + # figure out whether the autoloader is enabled enabled <- local({ @@ -15,6 +31,14 @@ local({ if (!is.null(override)) return(override) + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + # next, check environment variables # TODO: prefer using the configuration one in the future envvars <- c( @@ -34,9 +58,22 @@ local({ }) - if (!enabled) + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + return(FALSE) + } + # avoid recursion if (identical(getOption("renv.autoloader.running"), TRUE)) { warning("ignoring recursive attempt to run renv autoloader") @@ -60,21 +97,75 @@ local({ # load bootstrap tools `%||%` <- function(x, y) { - if (is.environment(x) || length(x)) x else y + if (is.null(x)) y else x + } + + catf <- function(fmt, ..., appendLF = TRUE) { + + quiet <- getOption("renv.bootstrap.quiet", default = FALSE) + if (quiet) + return(invisible()) + + msg <- sprintf(fmt, ...) + cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") + + invisible(msg) + + } + + header <- function(label, + ..., + prefix = "#", + suffix = "-", + n = min(getOption("width"), 78)) + { + label <- sprintf(label, ...) + n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L) + if (n <= 0) + return(paste(prefix, label)) + + tail <- paste(rep.int(suffix, n), collapse = "") + paste0(prefix, " ", label, " ", tail) + + } + + startswith <- function(string, prefix) { + substring(string, 1, nchar(prefix)) == prefix } bootstrap <- function(version, library) { + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + # attempt to download renv - tarball <- tryCatch(renv_bootstrap_download(version), error = identity) - if (inherits(tarball, "error")) - stop("failed to download renv ", version) + catf("- Downloading renv ... ", appendLF = FALSE) + withCallingHandlers( + tarball <- renv_bootstrap_download(version), + error = function(err) { + catf("FAILED") + stop("failed to download:\n", conditionMessage(err)) + } + ) + catf("OK") + on.exit(unlink(tarball), add = TRUE) # now attempt to install - status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity) - if (inherits(status, "error")) - stop("failed to install renv ", version) + catf("- Installing renv ... ", appendLF = FALSE) + withCallingHandlers( + status <- renv_bootstrap_install(version, tarball, library), + error = function(err) { + catf("FAILED") + stop("failed to install:\n", conditionMessage(err)) + } + ) + catf("OK") + # add empty line to break up bootstrapping from normal output + catf("") + + return(invisible()) } renv_bootstrap_tests_running <- function() { @@ -83,28 +174,32 @@ local({ renv_bootstrap_repos <- function() { + # get CRAN repository + cran <- getOption("renv.repos.cran", "https://cloud.r-project.org") + # check for repos override repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) - if (!is.na(repos)) + if (!is.na(repos)) { + + # check for RSPM; if set, use a fallback repository for renv + rspm <- Sys.getenv("RSPM", unset = NA) + if (identical(rspm, repos)) + repos <- c(RSPM = rspm, CRAN = cran) + return(repos) + } + # check for lockfile repositories repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) if (!inherits(repos, "error") && length(repos)) return(repos) - # if we're testing, re-use the test repositories - if (renv_bootstrap_tests_running()) - return(getOption("renv.tests.repos")) - # retrieve current repos repos <- getOption("repos") # ensure @CRAN@ entries are resolved - repos[repos == "@CRAN@"] <- getOption( - "renv.repos.cran", - "https://cloud.r-project.org" - ) + repos[repos == "@CRAN@"] <- cran # add in renv.bootstrap.repos if set default <- c(FALLBACK = "https://cloud.r-project.org") @@ -143,33 +238,34 @@ local({ renv_bootstrap_download <- function(version) { - # if the renv version number has 4 components, assume it must - # be retrieved via github - nv <- numeric_version(version) - components <- unclass(nv)[[1]] - - # if this appears to be a development version of 'renv', we'll - # try to restore from github - dev <- length(components) == 4L - - # begin collecting different methods for finding renv - methods <- c( - renv_bootstrap_download_tarball, - if (dev) - renv_bootstrap_download_github - else c( - renv_bootstrap_download_cran_latest, - renv_bootstrap_download_cran_archive + sha <- attr(version, "sha", exact = TRUE) + + methods <- if (!is.null(sha)) { + + # attempting to bootstrap a development version of renv + c( + function() renv_bootstrap_download_tarball(sha), + function() renv_bootstrap_download_github(sha) + ) + + } else { + + # attempting to bootstrap a release version of renv + c( + function() renv_bootstrap_download_tarball(version), + function() renv_bootstrap_download_cran_latest(version), + function() renv_bootstrap_download_cran_archive(version) ) - ) + + } for (method in methods) { - path <- tryCatch(method(version), error = identity) + path <- tryCatch(method(), error = identity) if (is.character(path) && file.exists(path)) return(path) } - stop("failed to download renv ", version) + stop("All download methods failed") } @@ -233,8 +329,6 @@ local({ type <- spec$type repos <- spec$repos - message("* Downloading renv ", version, " ... ", appendLF = FALSE) - baseurl <- utils::contrib.url(repos = repos, type = type) ext <- if (identical(type, "source")) ".tar.gz" @@ -251,13 +345,10 @@ local({ condition = identity ) - if (inherits(status, "condition")) { - message("FAILED") + if (inherits(status, "condition")) return(FALSE) - } # report success and return - message("OK (downloaded ", type, ")") destfile } @@ -314,8 +405,6 @@ local({ urls <- file.path(repos, "src/contrib/Archive/renv", name) destfile <- file.path(tempdir(), name) - message("* Downloading renv ", version, " ... ", appendLF = FALSE) - for (url in urls) { status <- tryCatch( @@ -323,14 +412,11 @@ local({ condition = identity ) - if (identical(status, 0L)) { - message("OK") + if (identical(status, 0L)) return(destfile) - } } - message("FAILED") return(FALSE) } @@ -344,8 +430,7 @@ local({ return() # allow directories - info <- file.info(tarball, extra_cols = FALSE) - if (identical(info$isdir, TRUE)) { + if (dir.exists(tarball)) { name <- sprintf("renv_%s.tar.gz", version) tarball <- file.path(tarball, name) } @@ -354,7 +439,7 @@ local({ if (!file.exists(tarball)) { # let the user know we weren't able to honour their request - fmt <- "* RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." + fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." msg <- sprintf(fmt, tarball) warning(msg) @@ -363,10 +448,7 @@ local({ } - fmt <- "* Bootstrapping with tarball at path '%s'." - msg <- sprintf(fmt, tarball) - message(msg) - + catf("- Using local tarball '%s'.", tarball) tarball } @@ -393,8 +475,6 @@ local({ on.exit(do.call(base::options, saved), add = TRUE) } - message("* Downloading renv ", version, " from GitHub ... ", appendLF = FALSE) - url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) name <- sprintf("renv_%s.tar.gz", version) destfile <- file.path(tempdir(), name) @@ -404,26 +484,105 @@ local({ condition = identity ) - if (!identical(status, 0L)) { - message("FAILED") + if (!identical(status, 0L)) return(FALSE) - } - message("OK") + renv_bootstrap_download_augment(destfile) + return(destfile) } + # Add Sha to DESCRIPTION. This is stop gap until #890, after which we + # can use renv::install() to fully capture metadata. + renv_bootstrap_download_augment <- function(destfile) { + sha <- renv_bootstrap_git_extract_sha1_tar(destfile) + if (is.null(sha)) { + return() + } + + # Untar + tempdir <- tempfile("renv-github-") + on.exit(unlink(tempdir, recursive = TRUE), add = TRUE) + untar(destfile, exdir = tempdir) + pkgdir <- dir(tempdir, full.names = TRUE)[[1]] + + # Modify description + desc_path <- file.path(pkgdir, "DESCRIPTION") + desc_lines <- readLines(desc_path) + remotes_fields <- c( + "RemoteType: github", + "RemoteHost: api.github.com", + "RemoteRepo: renv", + "RemoteUsername: rstudio", + "RemotePkgRef: rstudio/renv", + paste("RemoteRef: ", sha), + paste("RemoteSha: ", sha) + ) + writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path) + + # Re-tar + local({ + old <- setwd(tempdir) + on.exit(setwd(old), add = TRUE) + + tar(destfile, compression = "gzip") + }) + invisible() + } + + # Extract the commit hash from a git archive. Git archives include the SHA1 + # hash as the comment field of the tarball pax extended header + # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html) + # For GitHub archives this should be the first header after the default one + # (512 byte) header. + renv_bootstrap_git_extract_sha1_tar <- function(bundle) { + + # open the bundle for reading + # We use gzcon for everything because (from ?gzcon) + # > Reading from a connection which does not supply a 'gzip' magic + # > header is equivalent to reading from the original connection + conn <- gzcon(file(bundle, open = "rb", raw = TRUE)) + on.exit(close(conn)) + + # The default pax header is 512 bytes long and the first pax extended header + # with the comment should be 51 bytes long + # `52 comment=` (11 chars) + 40 byte SHA1 hash + len <- 0x200 + 0x33 + res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len]) + + if (grepl("^52 comment=", res)) { + sub("52 comment=", "", res) + } else { + NULL + } + } + renv_bootstrap_install <- function(version, tarball, library) { # attempt to install it into project library - message("* Installing renv ", version, " ... ", appendLF = FALSE) dir.create(library, showWarnings = FALSE, recursive = TRUE) + output <- renv_bootstrap_install_impl(library, tarball) + + # check for successful install + status <- attr(output, "status") + if (is.null(status) || identical(status, 0L)) + return(status) + + # an error occurred; report it + header <- "installation of renv failed" + lines <- paste(rep.int("=", nchar(header)), collapse = "") + text <- paste(c(header, lines, output), collapse = "\n") + stop(text) + + } + + renv_bootstrap_install_impl <- function(library, tarball) { # invoke using system2 so we can capture and report output bin <- R.home("bin") exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" - r <- file.path(bin, exe) + R <- file.path(bin, exe) args <- c( "--vanilla", "CMD", "INSTALL", "--no-multiarch", @@ -431,19 +590,7 @@ local({ shQuote(path.expand(tarball)) ) - output <- system2(r, args, stdout = TRUE, stderr = TRUE) - message("Done!") - - # check for successful install - status <- attr(output, "status") - if (is.numeric(status) && !identical(status, 0L)) { - header <- "Error installing renv:" - lines <- paste(rep.int("=", nchar(header)), collapse = "") - text <- c(header, lines, output) - writeLines(text, con = stderr()) - } - - status + system2(R, args, stdout = TRUE, stderr = TRUE) } @@ -653,34 +800,62 @@ local({ } - renv_bootstrap_validate_version <- function(version) { + renv_bootstrap_validate_version <- function(version, description = NULL) { - loadedversion <- utils::packageDescription("renv", fields = "Version") - if (version == loadedversion) - return(TRUE) + # resolve description file + # + # avoid passing lib.loc to `packageDescription()` below, since R will + # use the loaded version of the package by default anyhow. note that + # this function should only be called after 'renv' is loaded + # https://github.com/rstudio/renv/issues/1625 + description <- description %||% packageDescription("renv") - # assume four-component versions are from GitHub; three-component - # versions are from CRAN - components <- strsplit(loadedversion, "[.-]")[[1]] - remote <- if (length(components) == 4L) - paste("rstudio/renv", loadedversion, sep = "@") + # check whether requested version 'version' matches loaded version of renv + sha <- attr(version, "sha", exact = TRUE) + valid <- if (!is.null(sha)) + renv_bootstrap_validate_version_dev(sha, description) else - paste("renv", loadedversion, sep = "@") + renv_bootstrap_validate_version_release(version, description) + + if (valid) + return(TRUE) + + # the loaded version of renv doesn't match the requested version; + # give the user instructions on how to proceed + remote <- if (!is.null(description[["RemoteSha"]])) { + paste("rstudio/renv", description[["RemoteSha"]], sep = "@") + } else { + paste("renv", description[["Version"]], sep = "@") + } + + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = description[["RemoteSha"]] + ) fmt <- paste( "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.", - "Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.", - "Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.", + "- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.", + "- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.", sep = "\n" ) - - msg <- sprintf(fmt, loadedversion, version, remote) - warning(msg, call. = FALSE) + catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) FALSE } + renv_bootstrap_validate_version_dev <- function(version, description) { + expected <- description[["RemoteSha"]] + is.character(expected) && startswith(expected, version) + } + + renv_bootstrap_validate_version_release <- function(version, description) { + expected <- description[["Version"]] + is.character(expected) && identical(expected, version) + } + renv_bootstrap_hash_text <- function(text) { hashfile <- tempfile("renv-hash-") @@ -700,6 +875,12 @@ local({ # warn if the version of renv loaded does not match renv_bootstrap_validate_version(version) + # execute renv load hooks, if any + hooks <- getHook("renv::autoload") + for (hook in hooks) + if (is.function(hook)) + tryCatch(hook(), error = warnify) + # load the project renv::load(project) @@ -839,26 +1020,78 @@ local({ } + renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { + sha <- sha %||% attr(version, "sha", exact = TRUE) + parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = "") + } + + renv_bootstrap_exec <- function(project, libpath, version) { + if (!renv_bootstrap_load(project, libpath, version)) + renv_bootstrap_run(version, libpath) + } + + renv_bootstrap_run <- function(version, libpath) { + + # perform bootstrap + bootstrap(version, libpath) + + # exit early if we're just testing bootstrap + if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) + return(TRUE) + + # try again to load + if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { + return(renv::load(project = getwd())) + } + + # failed to download or load renv; warn the user + msg <- c( + "Failed to find an renv installation: the project will not be loaded.", + "Use `renv::activate()` to re-initialize the project." + ) + + warning(paste(msg, collapse = "\n"), call. = FALSE) + + } renv_json_read <- function(file = NULL, text = NULL) { + jlerr <- NULL + # if jsonlite is loaded, use that instead - if ("jsonlite" %in% loadedNamespaces()) - renv_json_read_jsonlite(file, text) + if ("jsonlite" %in% loadedNamespaces()) { + + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + jlerr <- json + + } + + # otherwise, fall back to the default JSON reader + json <- tryCatch(renv_json_read_default(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + # report an error + if (!is.null(jlerr)) + stop(jlerr) else - renv_json_read_default(file, text) + stop(json) } renv_json_read_jsonlite <- function(file = NULL, text = NULL) { - text <- paste(text %||% read(file), collapse = "\n") + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") jsonlite::fromJSON(txt = text, simplifyVector = FALSE) } renv_json_read_default <- function(file = NULL, text = NULL) { # find strings in the JSON - text <- paste(text %||% read(file), collapse = "\n") + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' locs <- gregexpr(pattern, text, perl = TRUE)[[1]] @@ -906,14 +1139,14 @@ local({ map <- as.list(map) # remap strings in object - remapped <- renv_json_remap(json, map) + remapped <- renv_json_read_remap(json, map) # evaluate eval(remapped, envir = baseenv()) } - renv_json_remap <- function(json, map) { + renv_json_read_remap <- function(json, map) { # fix names if (!is.null(names(json))) { @@ -940,7 +1173,7 @@ local({ # recurse if (is.recursive(json)) { for (i in seq_along(json)) { - json[i] <- list(renv_json_remap(json[[i]], map)) + json[i] <- list(renv_json_read_remap(json[[i]], map)) } } @@ -960,35 +1193,9 @@ local({ # construct full libpath libpath <- file.path(root, prefix) - # attempt to load - if (renv_bootstrap_load(project, libpath, version)) - return(TRUE) - - # load failed; inform user we're about to bootstrap - prefix <- paste("# Bootstrapping renv", version) - postfix <- paste(rep.int("-", 77L - nchar(prefix)), collapse = "") - header <- paste(prefix, postfix) - message(header) - - # perform bootstrap - bootstrap(version, libpath) - - # exit early if we're just testing bootstrap - if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) - return(TRUE) - - # try again to load - if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { - message("* Successfully installed and loaded renv ", version, ".") - return(renv::load()) - } - - # failed to download or load renv; warn the user - msg <- c( - "Failed to find an renv installation: the project will not be loaded.", - "Use `renv::activate()` to re-initialize the project." - ) + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) - warning(paste(msg, collapse = "\n"), call. = FALSE) + invisible() }) From 8591beea87bde679d7f7a4d917d9046bd2d9bd37 Mon Sep 17 00:00:00 2001 From: Jan Philipp Dietrich Date: Thu, 28 Mar 2024 16:04:37 +0100 Subject: [PATCH 11/16] added compatibility of master to recent gms package release --- .codeCheck | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 .codeCheck diff --git a/.codeCheck b/.codeCheck new file mode 100644 index 0000000000..0c2f270989 --- /dev/null +++ b/.codeCheck @@ -0,0 +1,6 @@ +capitalExclusionList: + - land + - iso + - type + - age + - k From 394b295369eec99e396d390dbc60a1c1f6812c5f Mon Sep 17 00:00:00 2001 From: Pascal Sauer Date: Thu, 28 Mar 2024 16:11:41 +0100 Subject: [PATCH 12/16] always install piamenv --- .Rprofile | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.Rprofile b/.Rprofile index 7fbeb85143..fe15cca3cb 100644 --- a/.Rprofile +++ b/.Rprofile @@ -28,6 +28,10 @@ if (isTRUE(rownames(installed.packages(priority = "NA")) == "renv")) { message("Finished installing R package dependencies.") } +if (!requireNamespace("piamenv", quietly = TRUE)) { + renv::install("piamenv", prompt = FALSE) +} + # source global .Rprofile (very important to load user specific settings) if (file.exists("~/.Rprofile")) { source("~/.Rprofile") From fc81609673dd2618dc1f780716c5658f3d19866f Mon Sep 17 00:00:00 2001 From: Pascal Sauer Date: Tue, 2 Apr 2024 11:17:35 +0200 Subject: [PATCH 13/16] .Rprofile tweaks --- .Rprofile | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/.Rprofile b/.Rprofile index fe15cca3cb..f797a57bca 100644 --- a/.Rprofile +++ b/.Rprofile @@ -12,8 +12,11 @@ if (Sys.info()[["sysname"]] == "Windows") { options(renv.download.override = utils::download.file) } -# do not check if library and renv.lock are in sync, because renv.lock does not exist -options(renv.config.synchronized.check = FALSE) +# 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 + +# the text "renvVersion" is required for a check in a coupling script, will be removed soon source("renv/activate.R") @@ -28,11 +31,7 @@ if (isTRUE(rownames(installed.packages(priority = "NA")) == "renv")) { message("Finished installing R package dependencies.") } +# in case bootstrapping fails halfway, install piamenv and rely on requirement auto-fixing if (!requireNamespace("piamenv", quietly = TRUE)) { renv::install("piamenv", prompt = FALSE) } - -# source global .Rprofile (very important to load user specific settings) -if (file.exists("~/.Rprofile")) { - source("~/.Rprofile") -} From 081bd0422fe251060d19fcf0353c7fe477017c43 Mon Sep 17 00:00:00 2001 From: Pascal Sauer Date: Tue, 2 Apr 2024 11:20:39 +0200 Subject: [PATCH 14/16] copyright 2024 --- .Rprofile | 2 +- config/default.cfg | 2 +- core/calculations.gms | 2 +- core/declarations.gms | 2 +- core/load_gdx.gms | 2 +- core/macros.gms | 2 +- core/sets.gms | 2 +- main.gms | 2 +- modules/09_drivers/aug17/declarations.gms | 2 +- modules/09_drivers/aug17/input.gms | 2 +- modules/09_drivers/aug17/preloop.gms | 2 +- modules/09_drivers/aug17/realization.gms | 2 +- modules/09_drivers/aug17/sets.gms | 2 +- modules/09_drivers/module.gms | 2 +- modules/10_land/landmatrix_dec18/declarations.gms | 2 +- modules/10_land/landmatrix_dec18/equations.gms | 2 +- modules/10_land/landmatrix_dec18/input.gms | 2 +- modules/10_land/landmatrix_dec18/postsolve.gms | 2 +- modules/10_land/landmatrix_dec18/preloop.gms | 2 +- modules/10_land/landmatrix_dec18/presolve.gms 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scripts/start/extra/emulator.R | 2 +- scripts/start/extra/input_REMIND.R | 2 +- scripts/start/extra/irrig_dep_test.R | 2 +- scripts/start/extra/publish_data.R | 2 +- scripts/start/extra/recalibrate_FSEC.R | 2 +- scripts/start/extra/recalibrate_default.R | 2 +- scripts/start/extra/recalibrate_realizations.R | 2 +- scripts/start/extra/test_maccs.R | 2 +- scripts/start/extra/test_n.R | 2 +- scripts/start/forestry.R | 2 +- scripts/start/projects/TAUhistfree.R | 2 +- scripts/start/projects/aff_bgp.R | 2 +- scripts/start/projects/duallayer.R | 2 +- scripts/start/projects/fable_india.R | 2 +- scripts/start/projects/forestry.R | 2 +- scripts/start/projects/forestry_co2.R | 2 +- scripts/start/projects/gmd-2021-76.R | 2 +- scripts/start/projects/paper_ClimNat.R | 2 +- scripts/start/projects/paper_fooddemand_standalone.R | 2 +- scripts/start/projects/paper_grassland.R | 2 +- scripts/start/projects/paper_peatland.R | 2 +- scripts/start/projects/paper_scp.R | 2 +- scripts/start/projects/project_BEST.R | 2 +- scripts/start/projects/project_EAT2p0.R | 2 +- scripts/start/projects/project_FSEC_Scenarios.R | 2 +- scripts/start/projects/project_GCS.R | 2 +- scripts/start/projects/project_LAMACLIMA_WP4.R | 2 +- scripts/start/projects/project_SHAPE.R | 2 +- scripts/start/projects/project_agmip.R | 2 +- scripts/start/projects/project_coacch.R | 2 +- scripts/start/projects/project_coacch_lpjml5.R | 2 +- scripts/start/projects/project_inms2.R | 2 +- scripts/start/projects/project_sim4nexus.R | 2 +- scripts/start/projects/project_sustag.R | 2 +- scripts/start/projects/rcTest_default.R | 2 +- scripts/start/projects/sticky.R | 2 +- scripts/start/projects/test_bii.R | 2 +- scripts/start/projects/test_country.R | 2 +- scripts/start/projects/test_diets.R | 2 +- scripts/start/projects/test_rotations.R | 2 +- scripts/start/test_runs.R | 2 +- scripts/start_functions.R | 2 +- standalone/demand_model.gms | 2 +- standalone/template.gms | 2 +- start.R | 2 +- 696 files changed, 697 insertions(+), 697 deletions(-) diff --git a/.Rprofile b/.Rprofile index f797a57bca..9924bee02a 100644 --- a/.Rprofile +++ b/.Rprofile @@ -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 diff --git a/config/default.cfg b/config/default.cfg index ef7007e6a3..e336490046 100644 --- a/config/default.cfg +++ b/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. 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Under Section 7 of *** | AGPL-3.0, you are granted additional permissions described in the diff --git a/modules/71_disagg_lvst/off/presolve.gms b/modules/71_disagg_lvst/off/presolve.gms index 1724f1af5f..8cca56fa92 100644 --- a/modules/71_disagg_lvst/off/presolve.gms +++ b/modules/71_disagg_lvst/off/presolve.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 diff --git a/modules/71_disagg_lvst/off/realization.gms b/modules/71_disagg_lvst/off/realization.gms index 4494ad794a..056a9267d5 100644 --- a/modules/71_disagg_lvst/off/realization.gms +++ b/modules/71_disagg_lvst/off/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 diff --git a/modules/73_timber/default/declarations.gms b/modules/73_timber/default/declarations.gms index ae6352f39f..fc431387df 100644 --- a/modules/73_timber/default/declarations.gms +++ b/modules/73_timber/default/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 diff --git a/modules/73_timber/default/equations.gms b/modules/73_timber/default/equations.gms index 06a0a86b36..d78bdb9177 100644 --- a/modules/73_timber/default/equations.gms +++ b/modules/73_timber/default/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 diff --git a/modules/73_timber/default/input.gms b/modules/73_timber/default/input.gms index 254d4a3aa2..c484cb178f 100644 --- a/modules/73_timber/default/input.gms +++ b/modules/73_timber/default/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 diff --git a/modules/73_timber/default/postsolve.gms b/modules/73_timber/default/postsolve.gms index 460db7e6d7..4ab5390f4b 100644 --- a/modules/73_timber/default/postsolve.gms +++ b/modules/73_timber/default/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 diff --git a/modules/73_timber/default/preloop.gms b/modules/73_timber/default/preloop.gms index 4437e845c6..1d1af6183c 100644 --- a/modules/73_timber/default/preloop.gms +++ b/modules/73_timber/default/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 diff --git a/modules/73_timber/default/presolve.gms b/modules/73_timber/default/presolve.gms index 0d48f6f028..0637bd7719 100644 --- a/modules/73_timber/default/presolve.gms +++ b/modules/73_timber/default/presolve.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 diff --git a/modules/73_timber/default/realization.gms b/modules/73_timber/default/realization.gms index 54b2e821a3..3e091e309d 100644 --- a/modules/73_timber/default/realization.gms +++ b/modules/73_timber/default/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 diff --git a/modules/73_timber/default/scaling.gms b/modules/73_timber/default/scaling.gms index ec3e8d2cac..4741722426 100644 --- a/modules/73_timber/default/scaling.gms +++ b/modules/73_timber/default/scaling.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 diff --git a/modules/73_timber/default/sets.gms b/modules/73_timber/default/sets.gms index bf07c22198..e1c6037786 100644 --- a/modules/73_timber/default/sets.gms +++ b/modules/73_timber/default/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 diff --git a/modules/73_timber/module.gms b/modules/73_timber/module.gms index 87fe568c32..6da09b4853 100644 --- a/modules/73_timber/module.gms +++ b/modules/73_timber/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 diff --git a/modules/80_optimization/lp_nlp_apr17/declarations.gms b/modules/80_optimization/lp_nlp_apr17/declarations.gms index eca6e5ec3c..0411e24104 100644 --- a/modules/80_optimization/lp_nlp_apr17/declarations.gms +++ b/modules/80_optimization/lp_nlp_apr17/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 diff --git a/modules/80_optimization/lp_nlp_apr17/input.gms b/modules/80_optimization/lp_nlp_apr17/input.gms index 5b7f1d4edd..5b21b43fb8 100644 --- a/modules/80_optimization/lp_nlp_apr17/input.gms +++ b/modules/80_optimization/lp_nlp_apr17/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 diff --git a/modules/80_optimization/lp_nlp_apr17/realization.gms b/modules/80_optimization/lp_nlp_apr17/realization.gms index 0b0008e1c4..667da31736 100644 --- a/modules/80_optimization/lp_nlp_apr17/realization.gms +++ b/modules/80_optimization/lp_nlp_apr17/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 diff --git a/modules/80_optimization/lp_nlp_apr17/solve.gms b/modules/80_optimization/lp_nlp_apr17/solve.gms index 672c4bfa31..697e9266a2 100644 --- a/modules/80_optimization/lp_nlp_apr17/solve.gms +++ b/modules/80_optimization/lp_nlp_apr17/solve.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 diff --git a/modules/80_optimization/module.gms b/modules/80_optimization/module.gms index cff00726b0..0f4941f399 100644 --- a/modules/80_optimization/module.gms +++ b/modules/80_optimization/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 diff --git a/modules/80_optimization/nlp_apr17/declarations.gms b/modules/80_optimization/nlp_apr17/declarations.gms index 6ee52314f8..bdd0c53998 100644 --- a/modules/80_optimization/nlp_apr17/declarations.gms +++ b/modules/80_optimization/nlp_apr17/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 diff --git a/modules/80_optimization/nlp_apr17/input.gms b/modules/80_optimization/nlp_apr17/input.gms index f2e369af2a..f41c3e4508 100644 --- a/modules/80_optimization/nlp_apr17/input.gms +++ b/modules/80_optimization/nlp_apr17/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 diff --git a/modules/80_optimization/nlp_apr17/realization.gms b/modules/80_optimization/nlp_apr17/realization.gms index e45364d549..33d93e0156 100644 --- a/modules/80_optimization/nlp_apr17/realization.gms +++ b/modules/80_optimization/nlp_apr17/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 diff --git a/modules/80_optimization/nlp_apr17/solve.gms b/modules/80_optimization/nlp_apr17/solve.gms index 7c971b1493..cc6e94e947 100644 --- a/modules/80_optimization/nlp_apr17/solve.gms +++ b/modules/80_optimization/nlp_apr17/solve.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 diff --git a/modules/80_optimization/nlp_par/declarations.gms b/modules/80_optimization/nlp_par/declarations.gms index fbf5ded274..567c8b9468 100644 --- a/modules/80_optimization/nlp_par/declarations.gms +++ b/modules/80_optimization/nlp_par/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 diff --git a/modules/80_optimization/nlp_par/input.gms b/modules/80_optimization/nlp_par/input.gms index 00370ae459..c08ecb087b 100644 --- a/modules/80_optimization/nlp_par/input.gms +++ b/modules/80_optimization/nlp_par/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 diff --git a/modules/80_optimization/nlp_par/realization.gms b/modules/80_optimization/nlp_par/realization.gms index 251d6d87d3..acf7a1e2a7 100644 --- a/modules/80_optimization/nlp_par/realization.gms +++ b/modules/80_optimization/nlp_par/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 diff --git a/modules/80_optimization/nlp_par/solve.gms b/modules/80_optimization/nlp_par/solve.gms index 0b8fe4e232..9d8cc1b784 100644 --- a/modules/80_optimization/nlp_par/solve.gms +++ b/modules/80_optimization/nlp_par/solve.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 diff --git a/modules/include.gms b/modules/include.gms index 0729ba1b54..32b37ac6ae 100644 --- a/modules/include.gms +++ b/modules/include.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 diff --git a/output.R b/output.R index 440b6d65d5..a503204356 100644 --- a/output.R +++ b/output.R @@ -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 diff --git a/scripts/calibration/calc_calib.R b/scripts/calibration/calc_calib.R index 9ffd6773e7..76ec96c28b 100644 --- a/scripts/calibration/calc_calib.R +++ b/scripts/calibration/calc_calib.R @@ -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 diff --git a/scripts/calibration/landconversion_cost.R b/scripts/calibration/landconversion_cost.R index a149101479..7dfdd074eb 100644 --- a/scripts/calibration/landconversion_cost.R +++ b/scripts/calibration/landconversion_cost.R @@ -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 diff --git a/scripts/downloader/inputdelete.cfg b/scripts/downloader/inputdelete.cfg index 9d2fc65ce9..869190bda4 100644 --- a/scripts/downloader/inputdelete.cfg +++ b/scripts/downloader/inputdelete.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 diff --git a/scripts/insertheader/insertheader.R b/scripts/insertheader/insertheader.R index 9753476410..a739931056 100644 --- a/scripts/insertheader/insertheader.R +++ b/scripts/insertheader/insertheader.R @@ -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 @@ -6,7 +6,7 @@ # | Contact: magpie@pik-potsdam.de insertheader <- function(maindir=".", - header=c("(C) 2008-2023 Potsdam Institute for Climate Impact Research (PIK)", + header=c("(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", diff --git a/scripts/npi_ndc/start_npi_ndc.R b/scripts/npi_ndc/start_npi_ndc.R index 38cbabf597..9b4681768b 100644 --- a/scripts/npi_ndc/start_npi_ndc.R +++ b/scripts/npi_ndc/start_npi_ndc.R @@ -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 diff --git a/scripts/output/comparison_validation.R b/scripts/output/comparison_validation.R index 68dc26672d..b49a32b1b2 100644 --- a/scripts/output/comparison_validation.R +++ b/scripts/output/comparison_validation.R @@ -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 diff --git a/scripts/output/deprecated/disaggregation_cropsplit.R b/scripts/output/deprecated/disaggregation_cropsplit.R index f4e92ba427..d2bcc54fef 100644 --- a/scripts/output/deprecated/disaggregation_cropsplit.R +++ b/scripts/output/deprecated/disaggregation_cropsplit.R @@ -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 diff --git a/scripts/output/deprecated/disaggregation_transitions.R b/scripts/output/deprecated/disaggregation_transitions.R index d062d47fcb..5c0e40f611 100644 --- a/scripts/output/deprecated/disaggregation_transitions.R +++ b/scripts/output/deprecated/disaggregation_transitions.R @@ -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 diff --git a/scripts/output/extra/ForestChangeCluster.R b/scripts/output/extra/ForestChangeCluster.R index 152e989f9f..7046e42c73 100644 --- a/scripts/output/extra/ForestChangeCluster.R +++ b/scripts/output/extra/ForestChangeCluster.R @@ -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 diff --git a/scripts/output/extra/aff_area.R b/scripts/output/extra/aff_area.R index e52798f9b7..ad1a408efd 100644 --- a/scripts/output/extra/aff_area.R +++ b/scripts/output/extra/aff_area.R @@ -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 diff --git a/scripts/output/extra/disaggregation.R b/scripts/output/extra/disaggregation.R index 9c4b2736db..769ee3f95c 100644 --- a/scripts/output/extra/disaggregation.R +++ b/scripts/output/extra/disaggregation.R @@ -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 diff --git a/scripts/output/extra/disaggregation_LUH2.R b/scripts/output/extra/disaggregation_LUH2.R index dcbfa210b8..2d43a52d00 100644 --- a/scripts/output/extra/disaggregation_LUH2.R +++ b/scripts/output/extra/disaggregation_LUH2.R @@ -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. 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Under Section 7 of # | AGPL-3.0, you are granted additional permissions described in the diff --git a/scripts/start/projects/project_FSEC_Scenarios.R b/scripts/start/projects/project_FSEC_Scenarios.R index c561f64530..8b5dbf1475 100644 --- a/scripts/start/projects/project_FSEC_Scenarios.R +++ b/scripts/start/projects/project_FSEC_Scenarios.R @@ -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 diff --git a/scripts/start/projects/project_GCS.R b/scripts/start/projects/project_GCS.R index 063a780201..a9bc2fff2e 100644 --- a/scripts/start/projects/project_GCS.R +++ b/scripts/start/projects/project_GCS.R @@ -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. 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Under Section 7 of # | AGPL-3.0, you are granted additional permissions described in the diff --git a/scripts/start/projects/project_agmip.R b/scripts/start/projects/project_agmip.R index 86202fd789..4ab9bc299b 100644 --- a/scripts/start/projects/project_agmip.R +++ b/scripts/start/projects/project_agmip.R @@ -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 diff --git a/scripts/start/projects/project_coacch.R b/scripts/start/projects/project_coacch.R index 76a79e10d1..7f6308483e 100644 --- a/scripts/start/projects/project_coacch.R +++ b/scripts/start/projects/project_coacch.R @@ -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 diff --git a/scripts/start/projects/project_coacch_lpjml5.R b/scripts/start/projects/project_coacch_lpjml5.R index be003d2855..1352c337cc 100644 --- a/scripts/start/projects/project_coacch_lpjml5.R +++ b/scripts/start/projects/project_coacch_lpjml5.R @@ -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 diff --git a/scripts/start/projects/project_inms2.R b/scripts/start/projects/project_inms2.R index 47971a3331..c192a79250 100644 --- a/scripts/start/projects/project_inms2.R +++ b/scripts/start/projects/project_inms2.R @@ -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 diff --git a/scripts/start/projects/project_sim4nexus.R b/scripts/start/projects/project_sim4nexus.R index e1349edc9c..c6ee4a9030 100644 --- a/scripts/start/projects/project_sim4nexus.R +++ b/scripts/start/projects/project_sim4nexus.R @@ -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 diff --git a/scripts/start/projects/project_sustag.R b/scripts/start/projects/project_sustag.R index 8242da4faf..7cd6410f55 100644 --- a/scripts/start/projects/project_sustag.R +++ b/scripts/start/projects/project_sustag.R @@ -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 diff --git a/scripts/start/projects/rcTest_default.R b/scripts/start/projects/rcTest_default.R index 0c58bc64c0..07b9ae68ec 100644 --- a/scripts/start/projects/rcTest_default.R +++ b/scripts/start/projects/rcTest_default.R @@ -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 diff --git a/scripts/start/projects/sticky.R b/scripts/start/projects/sticky.R index fdeb330f5e..a7c450e7b2 100644 --- a/scripts/start/projects/sticky.R +++ b/scripts/start/projects/sticky.R @@ -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 diff --git a/scripts/start/projects/test_bii.R b/scripts/start/projects/test_bii.R index bf35b38ce7..ffe3a09d57 100644 --- a/scripts/start/projects/test_bii.R +++ b/scripts/start/projects/test_bii.R @@ -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 diff --git a/scripts/start/projects/test_country.R b/scripts/start/projects/test_country.R index b3b86b59ee..2013ecbf0f 100644 --- a/scripts/start/projects/test_country.R +++ b/scripts/start/projects/test_country.R @@ -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 diff --git a/scripts/start/projects/test_diets.R b/scripts/start/projects/test_diets.R index 5b34d09103..ca4a1ffb29 100644 --- a/scripts/start/projects/test_diets.R +++ b/scripts/start/projects/test_diets.R @@ -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 diff --git a/scripts/start/projects/test_rotations.R b/scripts/start/projects/test_rotations.R index ca6ded54dd..60be6169e9 100644 --- a/scripts/start/projects/test_rotations.R +++ b/scripts/start/projects/test_rotations.R @@ -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 diff --git a/scripts/start/test_runs.R b/scripts/start/test_runs.R index 0a5f8c9204..93cfc01d17 100644 --- a/scripts/start/test_runs.R +++ b/scripts/start/test_runs.R @@ -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 diff --git a/scripts/start_functions.R b/scripts/start_functions.R index a6d47fe389..3c7044b445 100644 --- a/scripts/start_functions.R +++ b/scripts/start_functions.R @@ -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 diff --git a/standalone/demand_model.gms b/standalone/demand_model.gms index 9e336aad32..ec08f4e602 100644 --- a/standalone/demand_model.gms +++ b/standalone/demand_model.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 diff --git a/standalone/template.gms b/standalone/template.gms index 1fd74a3cd0..17f6fcb916 100644 --- a/standalone/template.gms +++ b/standalone/template.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 diff --git a/start.R b/start.R index 121986e4e7..4362fd8c0a 100644 --- a/start.R +++ b/start.R @@ -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 From ab37df1796e29abe15afb785334522aa5ecbea82 Mon Sep 17 00:00:00 2001 From: Pascal Sauer Date: Tue, 2 Apr 2024 13:58:28 +0200 Subject: [PATCH 15/16] release 4.7.2 --- .zenodo.json | 4 ++-- CHANGELOG.md | 17 +++++++++-------- CITATION.cff | 4 ++-- README.md | 6 +++--- 4 files changed, 16 insertions(+), 15 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index e4d2e90f7a..f426c80450 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -1,6 +1,6 @@ { "title": "MAgPIE - An Open Source land-use modeling framework", - "version": "4.7.1dev", + "version": "4.7.2", "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" } diff --git a/CHANGELOG.md b/CHANGELOG.md index 3dfbffae20..fb0f942c3b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,23 +4,23 @@ 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] +## [4.7.2] - 2024-04-02 ### changed -- **scripts** modified output reporting for SEALS to account for forestry plantations -- **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 +- **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. -- **config** added `.codeCheck` with additonal configuration when running `gms::codeCheck` -- **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. ### 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. @@ -844,7 +844,8 @@ 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 diff --git a/CITATION.cff b/CITATION.cff index 271e8173e4..fcdbdc8eee 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -131,8 +131,8 @@ authors: email: popp@pik-potsdam.de title: MAgPIE - An Open Source land-use modeling framework -version: 4.7.1dev -date-released: 2024-02-28 +version: 4.7.2 +date-released: 2024-04-02 repository-code: https://github.com/magpiemodel/magpie keywords: - landuse diff --git a/README.md b/README.md index 3132b3be89..c2bcd28745 100644 --- a/README.md +++ b/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 @@ -226,7 +226,7 @@ magpie@pik-potsdam.de Please contact magpie@pik-potsdam.de ## 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 From 413bc615738c2bdea01c4d7ef50fca49bdefe09a Mon Sep 17 00:00:00 2001 From: Pascal Sauer Date: Wed, 3 Apr 2024 10:37:49 +0200 Subject: [PATCH 16/16] merge master into develop --- .zenodo.json | 2 +- CHANGELOG.md | 15 +++++++++++++++ CITATION.cff | 2 +- 3 files changed, 17 insertions(+), 2 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index f426c80450..7b5aeeed0c 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -1,6 +1,6 @@ { "title": "MAgPIE - An Open Source land-use modeling framework", - "version": "4.7.2", + "version": "4.7.2dev", "creators": [ { "name": "Dietrich, Jan Philipp", diff --git a/CHANGELOG.md b/CHANGELOG.md index fb0f942c3b..5892061e44 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,21 @@ 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 +- + +### added +- + +### removed +- + +### fixed +- + ## [4.7.2] - 2024-04-02 ### changed diff --git a/CITATION.cff b/CITATION.cff index fcdbdc8eee..2514db68e0 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -131,7 +131,7 @@ authors: email: popp@pik-potsdam.de title: MAgPIE - An Open Source land-use modeling framework -version: 4.7.2 +version: 4.7.2dev date-released: 2024-04-02 repository-code: https://github.com/magpiemodel/magpie keywords: