Merge pull request #3 from magpiemodel/develop

Develop

.gitignore

@@ -20,13 +20,7 @@ magpie_calib.*
 .Rhistory
 
 #ignore documentation folder
-/doc/*/
-/doc/*.pdf
-/doc/*.rds
-/doc/*.tex
-/doc/*.aux
-/doc/*.log
-/doc/*.gz
+/doc/
 
 #ignore run specific files and folders
 /225*/

.travis.yml

@@ -3,14 +3,13 @@
 language: R
 repos:
   CRAN: https://cloud.r-project.org
-  PIK:  https://rse.pik-potsdam.de/r/packages/
 cache: packages
 latex: false
 pandoc: false
 sudo: false
-r_packages: lucode
 install:
-  - echo "This echo is required as travis would otherwise complain a non-existing DESCRIPTION file (it just requires some entry under "install")!"
+  - Rscript -e "if(!requireNamespace('devtools')) install.packages('devtools')"
+  - Rscript -e "if(!requireNamespace('lucode')) devtools::install_github('pik-piam/lucode')"
 script:
   - Rscript -e "null <- lucode::codeCheck(strict=TRUE)"
 

CHANGELOG.md

@@ -0,0 +1,62 @@
+
+# Changelog
+
+All notable changes to this project will be documented in this file.
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### added
+
+
+### changed
+ - **modules** modular structure updated from version 1 to version 2
+
+
+ ### fixed
+
+
+
+## [4.1.0] - 2019-05-02
+
+This release version is focussed on consistency between the MAgPIE setup and the [REMIND model] and result of a validation exercise of the coupled REMIND-MAgPIE system.
+
+### added
+ - **80_optimization** added support for GAMS version 26.x.x
+ - **scripts** added new start and output scripts
+ - **license** added exception to the applied AGPL license to clarify handling of required GAMS environment, solver libraries and R libraries
+
+### changed
+ - **56_ghg_policy** apply reduction factor on CO2 price to account for potential negative side effects; lowers the economic incentive for CO2 emission reduction (avoided deforestation) and afforestation
+ - **56_ghg_policy** non-linar phase-in of GHG prices over 20 year period
+ - **56_ghg_policy** multiply GHG prices with development state to account for institutional requirements needed for implementing a GHG pricing scheme
+ - **40_transport** introduced transport costs for monogastric livestock products
+ - **NPI/NDC scripts** added forest protection policy for Brazilian Atlantic Forest in default NDC and NPI scenarios
+ - **NPI/NDC scripts** harmonized the starting year of the NDC policies 2020.
+ - **interpolation scripts** changed output files to seven magpie land use types, added additional cropsplit script for more detailed cropland output
+ - **15_food** clean-up and cosmetic changes (correction of comments, parameter names, structure of code); update BMI share calculations with the values of the last consistent MAgPIE/food-demand-model iteration
+
+### fixed
+ - **42_water_demand** bugfix environmental flow policy harmonization for historic period
+ - **57_maccs** correction of cost calculation; Conversion from USD per ton C to USD per ton N and USD per ton CH4 was missing.
+ - **71_diagg_lvst** adjusted monogastric disaggregation for more flexiblity to avoid infeasibilities with EFPs (see 42_water_demand)
+ - **15_food** correction regarding the convergence measure of the iterative execution of the food demand model and MAgPIE; correction accounting for unusual time step length in body height calculations; body height regression parameters updated
+
+## [4.0.1] - 2018-10-05
+
+### fixed
+ - **FABLE** adapted FABLE-specific configuration so that it works with MAgPIE 4.0
+
+
+## [4.0.0] - 2018-10-04
+
+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/v4.1.0...develop
+[4.1.0]: https://github.com/magpiemodel/magpie/compare/v4.0.1...v4.1.0
+[4.0.1]: https://github.com/magpiemodel/magpie/compare/v4.0...v4.0.1
+[4.0.0]: https://github.com/magpiemodel/magpie/releases/tag/v4.0
+
+[REMIND model]: https://www.pik-potsdam.de/research/transformation-pathways/models/remind

CITATION.cff

@@ -76,8 +76,8 @@ authors:
     email: popp@pik-potsdam.de
 
 title: MAgPIE - An Open Source land-use modeling framework
-version: 4.0.1-dev
-date-released: 2018-10-05
+version: 4.2dev
+date-released: 2019-05-02
 repository-code: https://github.com/magpiemodel/magpie
 keywords:
   - landuse

LICENSE

@@ -1,14 +1,45 @@
 
-							 NOTES
+                           MAgPIE NOTES
 
-Besides distribution and software-as-a-service applications the source code
-should also be made available in the events of model based publications or
-model-based consulting.
+Following the principles of good scientific practice it is recommended
+to make the source code available in the events of model based publications
+or model-based consulting.
 
 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**).
 
+--------------------------------------------------------------------------------
+
+                       MAgPIE LICENSE EXCEPTION
+                             Version 1.0
+
+This MAgPIE Exception ("Exception") is an additional permission under
+section 7 of the GNU Affero General Public License, version 3 (AGPL-3.0). It
+applies to a given file that bears a notice placed by the copyright holder
+of the file stating that the file is governed by AGPL-3.0 along with this
+Exception.
+
+Grant of Additional Permissions.
+
+1.
+In the event that you are required by any provision of the AGPL-3.0 to
+provide or make available the Corresponding Source of the Program as defined
+under section 1 of the AGPL-3.0, you are exempt from this obligation to the
+extent that the definition of Corresponding Source would also cover solver
+libraries or other components of the General Algebraic Modeling System
+(GAMS) required to run the Program.
+
+2.
+In the event that you convey the Program and the Program is linked with
+libraries written for the R software environment ("R Libraries"), you are
+not required to license these R Libraries under the AGPL-3-0 (or a
+compatible license), provided the R Libraries are licensed under a Free and
+Open Source license ("FOSS License"). A FOSS license is a license that meets
+both the Open Source Definition of the Open Source Initaitive and the Free
+Software Definition of the Free Software Foundation in its respective most
+current form.
+
 --------------------------------------------------------------------------------
 
                     GNU AFFERO GENERAL PUBLIC LICENSE

README.md

@@ -4,22 +4,25 @@
 
 ## WHAT IS MAGPIE?
 The *Model of Agricultural Production and its Impact on the Environment* (MAgPIE)
-is a modular open source framework for modeling global land-systems, which is 
-coupled to the grid-based dynamic vegetation model LPJmL, with a spatial resolution 
-of 0.5°x0.5°. It takes regional economic conditions such as demand for agricultural 
-commodities, technological development and production costs as well as spatially 
-explicit data on potential crop yields, land and water constraints (from LPJmL) into 
-account. Based on these, the model derives specific land use patterns, yields and 
-total costs of agricultural production for each grid cell. The objective function of 
-the land use model is to minimize total cost of production for a given amount of 
-regional food and bioenergy demand. Regional food energy demand is defined for an 
-exogenously given population in 10 food energy categories, based on regional diets. 
-Future trends in food demand are derived from a cross-country regression analysis, 
+is a modular open source framework for modeling global land-systems, which is
+coupled to the grid-based dynamic vegetation model LPJmL, with a spatial resolution
+of 0.5°x0.5°. It takes regional economic conditions such as demand for agricultural
+commodities, technological development and production costs as well as spatially
+explicit data on potential crop yields, land and water constraints (from LPJmL) into
+account. Based on these, the model derives specific land use patterns, yields and
+total costs of agricultural production for each grid cell. The objective function of
+the land use model is to minimize total cost of production for a given amount of
+regional food and bioenergy demand. Regional food energy demand is defined for an
+exogenously given population in 10 food energy categories, based on regional diets.
+Future trends in food demand are derived from a cross-country regression analysis,
 based on future scenarios on GDP and population growth.
 
 ## DOCUMENTATION
-The model documentation for version 4 can be found at
-https://rse.pik-potsdam.de/doc/magpie/version4/
+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 4.1 can be found at
+https://rse.pik-potsdam.de/doc/magpie/4.1/
 
 A most recent version of the documentation can also be extracted from the
 model source code via the R package goxygen
@@ -34,20 +37,23 @@ The Coding Etiquette explains also the used name conventions and other
 structural characteristics.
 
 ## COPYRIGHT
-Copyright 2008-2018 Potsdam Institute for Climate Impact Research (PIK)
+Copyright 2008-2019 Potsdam Institute for Climate Impact Research (PIK)
 
 ## LICENSE
 This program is free software: you can redistribute it and/or modify
 it under the terms of the **GNU Affero General Public License** as published by
 the Free Software Foundation, **version 3** of the License or later. You should
 have received a copy of the GNU Affero General Public License along with this
 program. See the LICENSE file in the root directory. If not, see
-http://www.gnu.org/licenses/
+https://www.gnu.org/licenses/agpl.txt
+
+Under Section 7 of AGPL-3.0, you are granted additional permissions described
+in the MAgPIE License Exception, version 1.0 (see LICENSE file).
 
 ## NOTES
-Besides distribution and software-as-a-service applications the source code
-should also be made available in the events of model based publications or
-model-based consulting.
+Following the principles of good scientific practice it is recommended
+to make the source code available in the events of model based publications
+or model-based consulting.
 
 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
@@ -120,7 +126,7 @@ pkgs <- c("ggplot2",
           "lusweave",
           "luscale",
           "goxygen",
-		  "luplot")
+          "luplot")
 install.packages(pkgs)
 ```
 For post-processing model outputs *Latex* is required