Merge branch 'develop' into gsoc/convert-input

CHANGELOG.md

@@ -16,10 +16,11 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 
 ### Changed
 - The following components have changed their licensing. With approval of all their contributors, we now provide them under a BSD 3-clause license rather than the previously used NCSA Open Source license. As a reminder, we intend to relicense the entire system and this list will expand as we gather permission from the relevant copyright owners.
-    * Shiny apps `dbsync`, `Data-Ingest`, `Elicitation`, and `global-sensitivity`
+    * `apps/api`
+    * Shiny apps `dbsync`, `Data-Ingest`, `Elicitation`, `ForecastingDashboard`, `global-sensitivity`, and `Pecan.depend`
     * Base packages `PEcAn.all`, `PEcAn.QAQC`, `PEcAn.remote`, and `PEcAn.workflow`
-    * Model packages `PEcAn.LDNDC`, `PEcAn.SIBCASA`, and `PEcAn.STICS`
-    * Module `PEcAn.data.mining`
+    * Model packages `PEcAn.BASGRA`, `PEcAn.dvmdostem`, `PEcAn.FATES`, `PEcAn.GDAY`, `PEcAn.LDNDC`, `PEcAn.MAAT`, `PEcAn.MAESPA`, `PEcAn.SIBCASA`, `PEcAn.STICS`, and the new model package template.
+    * Modules `PEcAn.data.mining`, `PEcAn.emulator`, amd `PEcAn.RTM`.
 
 ### Removed
 

apps/api/pecanapi-spec.yml

@@ -18,8 +18,8 @@ info:
   contact:
     email: "[email protected]"
   license:
-    name: University of Illinois/NCSA Open Source License
-    url: https://opensource.org/licenses/NCSA
+    name: BSD-3
+    url: https://opensource.org/license/bsd-3-clause
 externalDocs:
   description: Find out more about PEcAn Project
   url: https://pecanproject.github.io/

models/basgra/LICENSE

@@ -1,34 +1,3 @@
-## This is the master copy of the PEcAn License
-
-University of Illinois/NCSA Open Source License
-
-Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
-
-PEcAn project
-www.pecanproject.org
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the 
-"Software"), to deal with the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-- Redistributions of source code must retain the above copyright
-  notice, this list of conditions and the following disclaimers.
-- Redistributions in binary form must reproduce the above copyright
-  notice, this list of conditions and the following disclaimers in the
-  documentation and/or other materials provided with the distribution.
-- Neither the names of University of Illinois, NCSA, nor the names
-  of its contributors may be used to endorse or promote products
-  derived from this Software without specific prior written permission.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
-IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR
-ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF 
-CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
-
+YEAR: 2024
+COPYRIGHT HOLDER: PEcAn Project
+ORGANIZATION: PEcAn Project, authors affiliations

models/basgra/NEWS.md

@@ -0,0 +1,7 @@
+# PEcAn.BASGRA 1.8.0.9000
+
+## License change
+* PEcAn.BASGRA is now distributed under the BSD three-clause license instead of the NCSA Open Source license.
+
+## Added
+* Added a `NEWS.md` file to track changes to the package. Prior to this point changes are tracked in the main CHANGELOG for the PEcAn repository.

models/basgra/R/write.config.BASGRA.R

@@ -1,12 +1,3 @@
-#-------------------------------------------------------------------------------
-# Copyright (c) 2012 University of Illinois, NCSA.
-# All rights reserved. This program and the accompanying materials
-# are made available under the terms of the 
-# University of Illinois/NCSA Open Source License
-# which accompanies this distribution, and is available at
-# http://opensource.ncsa.illinois.edu/license.html
-#-------------------------------------------------------------------------------
-
 ##-------------------------------------------------------------------------------------------------#
 ##' Writes a BASGRA config file.
 ##'

models/basgra/tests/testthat.R

@@ -1,11 +1,3 @@
-#-------------------------------------------------------------------------------
-# Copyright (c) 2012 University of Illinois, NCSA.
-# All rights reserved. This program and the accompanying materials
-# are made available under the terms of the 
-# University of Illinois/NCSA Open Source License
-# which accompanies this distribution, and is available at
-# http://opensource.ncsa.illinois.edu/license.html
-#-------------------------------------------------------------------------------
 library(testthat)
 library(PEcAn.utils)
 

models/dvmdostem/LICENSE

@@ -1,34 +1,3 @@
-## This is the master copy of the PEcAn License
-
-University of Illinois/NCSA Open Source License
-
-Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
-
-PEcAn project
-www.pecanproject.org
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the 
-"Software"), to deal with the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-- Redistributions of source code must retain the above copyright
-  notice, this list of conditions and the following disclaimers.
-- Redistributions in binary form must reproduce the above copyright
-  notice, this list of conditions and the following disclaimers in the
-  documentation and/or other materials provided with the distribution.
-- Neither the names of University of Illinois, NCSA, nor the names
-  of its contributors may be used to endorse or promote products
-  derived from this Software without specific prior written permission.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
-IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR
-ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF 
-CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
-
+YEAR: 2024
+COPYRIGHT HOLDER: PEcAn Project
+ORGANIZATION: PEcAn Project, authors affiliations

models/dvmdostem/NEWS.md

@@ -0,0 +1,7 @@
+# PEcAn.dvmdostem 1.7.3.9000
+
+## License change
+* PEcAn.dvmdostem is now distributed under the BSD three-clause license instead of the NCSA Open Source license.
+
+## Added
+* Added a `NEWS.md` file to track changes to the package. Prior to this point changes are tracked in the main CHANGELOG for the PEcAn repository.

models/dvmdostem/R/model2netcdf.dvmdostem.R

@@ -1,11 +1,3 @@
-#-------------------------------------------------------------------------------
-# Copyright (c) 2016 NCSA.
-# All rights reserved. This program and the accompanying materials
-# are made available under the terms of the 
-# University of Illinois/NCSA Open Source License
-# which accompanies this distribution, and is available at
-# http://opensource.ncsa.illinois.edu/license.html
-#-------------------------------------------------------------------------------
 library(lubridate)
 
 ##-------------------------------------------------------------------------------------------------#

models/dvmdostem/R/write.config.dvmdostem.R

@@ -1,12 +1,4 @@
-#-------------------------------------------------------------------------------
-# Copyright (c) 2012 University of Illinois, NCSA.
-# All rights reserved. This program and the accompanying materials
-# are made available under the terms of the
-# University of Illinois/NCSA Open Source License
-# which accompanies this distribution, and is available at
-# http://opensource.ncsa.illinois.edu/license.html
-#-------------------------------------------------------------------------------
-##------------------------------------------------------------------------------------------------#
+
 ##' Setup the output variables that dvmdostem will generate and PEcAn will analyze.
 ##' This function handles the interplay between output variables and output spec file.
 ##' There are custom tags in the <model> section of the pecan xml file for dvmdostem

models/dvmdostem/tests/testthat.R

@@ -1,11 +1,3 @@
-#-------------------------------------------------------------------------------
-# Copyright (c) 2012 University of Illinois, NCSA.
-# All rights reserved. This program and the accompanying materials
-# are made available under the terms of the 
-# University of Illinois/NCSA Open Source License
-# which accompanies this distribution, and is available at
-# http://opensource.ncsa.illinois.edu/license.html
-#-------------------------------------------------------------------------------
 library(testthat)
 library(PEcAn.utils)
 

models/fates/LICENSE

@@ -1,29 +1,3 @@
-University of Illinois/NCSA Open Source License
-
-Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the 
-"Software"), to deal with the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-- Redistributions of source code must retain the above copyright
-  notice, this list of conditions and the following disclaimers.
-- Redistributions in binary form must reproduce the above copyright
-  notice, this list of conditions and the following disclaimers in the
-  documentation and/or other materials provided with the distribution.
-- Neither the names of University of Illinois, NCSA, nor the names
-  of its contributors may be used to endorse or promote products
-  derived from this Software without specific prior written permission.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
-IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR
-ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF 
-CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
-
+YEAR: 2024
+COPYRIGHT HOLDER: PEcAn Project
+ORGANIZATION: PEcAn Project, authors affiliations

models/fates/NEWS.md

@@ -0,0 +1,7 @@
+# PEcAn.FATES 1.7.3.9000
+
+## License change
+* PEcAn.FATES is now distributed under the BSD three-clause license instead of the NCSA Open Source license.
+
+## Added
+* Added a `NEWS.md` file to track changes to the package. Prior to this point changes are tracked in the main CHANGELOG for the PEcAn repository.

models/fates/R/met2model.FATES.R

@@ -1,11 +1,3 @@
-#-------------------------------------------------------------------------------
-# Copyright (c) 2016 NCSA.
-# All rights reserved. This program and the accompanying materials
-# are made available under the terms of the 
-# University of Illinois/NCSA Open Source License
-# which accompanies this distribution, and is available at
-# http://opensource.ncsa.illinois.edu/license.html
-#-------------------------------------------------------------------------------
 
 # R Code to convert NetCDF CF met files into NetCDF FATES met files.
 

models/fates/R/model2netcdf.FATES.R

@@ -1,11 +1,3 @@
-#-------------------------------------------------------------------------------
-# Copyright (c) 2016 NCSA.
-# All rights reserved. This program and the accompanying materials
-# are made available under the terms of the 
-# University of Illinois/NCSA Open Source License
-# which accompanies this distribution, and is available at
-# http://opensource.ncsa.illinois.edu/license.html
-#-------------------------------------------------------------------------------
 
 ##' @name model2netcdf.FATES
 ##' @title Code to convert FATES netcdf output into into CF standard

models/fates/R/recurse.create.R

@@ -1,11 +1,3 @@
-#-------------------------------------------------------------------------------
-# Copyright (c) 2016 NCSA.
-# All rights reserved. This program and the accompanying materials
-# are made available under the terms of the 
-# University of Illinois/NCSA Open Source License
-# which accompanies this distribution, and is available at
-# http://opensource.ncsa.illinois.edu/license.html
-#-------------------------------------------------------------------------------
 
 ##' @name recurse.create
 ##' @title recurse.create

models/fates/R/write.configs.FATES.R

@@ -1,13 +1,3 @@
-#-------------------------------------------------------------------------------
-# Copyright (c) 2016 NCSA.
-# All rights reserved. This program and the accompanying materials
-# are made available under the terms of the 
-# University of Illinois/NCSA Open Source License
-# which accompanies this distribution, and is available at
-# http://opensource.ncsa.illinois.edu/license.html
-#-------------------------------------------------------------------------------
-
-##-------------------------------------------------------------------------------------------------#
 ##' Writes config files for use with FATES.
 ##'
 ##' @name write.config.FATES
@@ -19,7 +9,6 @@
 ##' @return none
 ##' @export
 ##' @author Mike Dietze, Shawn Serbin
-##-------------------------------------------------------------------------------------------------#
 write.config.FATES <- function(defaults, trait.values, settings, run.id){
 
    ## site information

models/fates/tests/testthat.R

@@ -1,11 +1,3 @@
-#-------------------------------------------------------------------------------
-# Copyright (c) 2012 University of Illinois, NCSA.
-# All rights reserved. This program and the accompanying materials
-# are made available under the terms of the 
-# University of Illinois/NCSA Open Source License
-# which accompanies this distribution, and is available at
-# http://opensource.ncsa.illinois.edu/license.html
-#-------------------------------------------------------------------------------
 library(testthat)
 library(PEcAn.utils)
 

models/gday/LICENSE

@@ -1,33 +1,3 @@
-## This is the master copy of the PEcAn License
-
-University of Illinois/NCSA Open Source License
-
-Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
-
-PEcAn project
-www.pecanproject.org
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal with the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-- Redistributions of source code must retain the above copyright
-  notice, this list of conditions and the following disclaimers.
-- Redistributions in binary form must reproduce the above copyright
-  notice, this list of conditions and the following disclaimers in the
-  documentation and/or other materials provided with the distribution.
-- Neither the names of University of Illinois, NCSA, nor the names
-  of its contributors may be used to endorse or promote products
-  derived from this Software without specific prior written permission.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
-IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR
-ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF
-CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
+YEAR: 2024
+COPYRIGHT HOLDER: PEcAn Project
+ORGANIZATION: PEcAn Project, authors affiliations

models/gday/NEWS.md

@@ -0,0 +1,7 @@
+# PEcAn.GDAY 1.7.3.9000
+
+## License change
+* PEcAn.GDAY is now distributed under the BSD three-clause license instead of the NCSA Open Source license.
+
+## Added
+* Added a `NEWS.md` file to track changes to the package. Prior to this point changes are tracked in the main CHANGELOG for the PEcAn repository.

models/gday/R/met2model.GDAY.R

@@ -1,12 +1,3 @@
-#-------------------------------------------------------------------------------
-# Copyright (c) 2015 Boston University, NCSA.
-# All rights reserved. This program and the accompanying materials
-# are made available under the terms of the
-# NCSA Open Source License
-# which accompanies this distribution, and is available at
-# http://opensource.ncsa.illinois.edu/license.html
-#-------------------------------------------------------------------------------
-
 # R Code to convert NetCDF CF met files into GDAY met files
 
 ## If files already exist in 'Outfolder', the default function is NOT to overwrite them and only

models/gday/R/model2netcdf.GDAY.R

@@ -1,13 +1,3 @@
-#-------------------------------------------------------------------------------
-# Copyright (c) 2015 Boston University, NCSA.
-# All rights reserved. This program and the accompanying materials
-# are made available under the terms of the
-# NCSA Open Source License
-# which accompanies this distribution, and is available at
-# http://opensource.ncsa.illinois.edu/license.html
-#-------------------------------------------------------------------------------
-
-#------------------------------------------------------------------------------#
 ##' Convert GDAY output to netCDF
 ##'
 ##' Converts all output contained in a folder to netCDF.

models/gday/R/write.config.GDAY.R

@@ -1,13 +1,3 @@
-#-------------------------------------------------------------------------------
-# Copyright (c) 2015 Boston University, NCSA.
-# All rights reserved. This program and the accompanying materials
-# are made available under the terms of the
-# NCSA Open Source License
-# which accompanies this distribution, and is available at
-# http://opensource.ncsa.illinois.edu/license.html
-#-------------------------------------------------------------------------------
-
-##-------------------------------------------------------------------------------------------------#
 ##' Writes a config file for GDAY
 ##'
 ##' Requires a pft xml object, a list of trait values for a single model run,

models/gday/tests/testthat.R

@@ -1,11 +1,3 @@
-#-------------------------------------------------------------------------------
-# Copyright (c) 2012 University of Illinois, NCSA.
-# All rights reserved. This program and the accompanying materials
-# are made available under the terms of the
-# University of Illinois/NCSA Open Source License
-# which accompanies this distribution, and is available at
-# http://opensource.ncsa.illinois.edu/license.html
-#-------------------------------------------------------------------------------
 library(testthat)
 library(PEcAn.utils)