PecanProject · mdietze · Sep 8, 2024 · Sep 4, 2024 · Sep 4, 2024 · Sep 4, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,10 +15,10 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 
 - 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.
     * `apps/api`
-    * Shiny apps `dbsync`, `Data-Ingest`, `Elicitation`, `ForecastingDashboard`, `global-sensitivity`, `Pecan.depend`, and `SDAdashboard`
-    * Base packages `PEcAn.all`, `PEcAn.QAQC`, `PEcAn.remote`, `PEcAn.settings`, and `PEcAn.workflow`
-    * 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`.
+    * Shiny apps `dbsync`, `BenchmarkReport`, `Data-Ingest`, `Elicitation`, `ForecastingDashboard`, `global-sensitivity`, `Pecan.depend`, `SDAdashboard`, and `ViewMet`
+    * Base packages `PEcAn.all`, `PEcAn.DB`, `PEcAn.QAQC`, `PEcAn.remote`, `PEcAn.settings`, `PEcAn.visualization`, and `PEcAn.workflow`
+    * Model packages `PEcAn.BASGRA`, `PEcAn.CLM45`, `PEcAn.DALEC`, `PEcAn.dvmdostem`, `PEcAn.FATES`, `PEcAn.GDAY`, `PEcAn.JULES`, `PEcAn.LDNDC`, `PEcAn.LINKAGES`, `PEcAn.LPJGUESS`, `PEcAn.MAAT`, `PEcAn.MAESPA`, `PEcAn.PRELES`, `PEcAn.SIBCASA`, `PEcAn.SIPNET`, `PEcAn.STICS`, and the new model package template.
+    * Modules `PEcAn.allometry`, `PEcAn.assim.batch`, `PEcAn.data.mining`, `PEcAn.emulator`, `PEcAn.MA`, `PEcAn.photosynthesis`, `PEcAn.priors`, and `PEcAn.RTM`.
 
 ### Removed
 

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,39 @@
-## This is the master copy of the PEcAn License
+All portions of the PEcAn project not marked otherwise are distributed under the BSD 3-clause license:
 
-University of Illinois/NCSA Open Source License
+Copyright (c) 2012-2024 Pecan Project
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+may be used to endorse or promote products derived from this software without
+specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+
+
+----------------------------------
+
+
+Portions of the PEcAn project are distributed under the University of Illinois/NCSA Open Source License:
 
 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -36,33 +69,3 @@ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
 
 --------------------
-
-
-Portions of the PEcAn project are distributed under the BSD 3-clause license:
-
-Copyright (c) 2024 Pecan Project
-
-Redistribution and use in source and binary forms, with or without modification,
-are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
-list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright notice,
-this list of conditions and the following disclaimer in the documentation
-and/or other materials provided with the distribution.
-
-3. Neither the name of the copyright holder nor the names of its contributors
-may be used to endorse or promote products derived from this software without
-specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/base/db/LICENSE b/base/db/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
diff --git a/base/db/NEWS.md b/base/db/NEWS.md
@@ -1,5 +1,7 @@
 # PEcAn.DB 1.8.0.9000
 
+## License change
+* PEcAn.DB is now distributed under the BSD three-clause license instead of the NCSA Open Source license.
 
 
 # PEcAn.DB 1.8.0

diff --git a/base/db/R/assign.treatments.R b/base/db/R/assign.treatments.R
@@ -1,13 +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
-#-------------------------------------------------------------------------------
-
-##-----------------------------------------------------------------------------#
 ##' Change treatments to sequential integers
 ##'
 ##' Assigns all control treatments the same value, then assigns unique treatments

diff --git a/base/db/R/check.lists.R b/base/db/R/check.lists.R
@@ -1,13 +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
-#-------------------------------------------------------------------------------
-
-##--------------------------------------------------------------------------------------------------#
 ##' Check two lists. Identical does not work since one can be loaded
 ##' from the database and the other from a CSV file.
 ##'

diff --git a/base/db/R/covariate.functions.R b/base/db/R/covariate.functions.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
-#-------------------------------------------------------------------------------
-
 ######################## COVARIATE FUNCTIONS #################################
 
 ##--------------------------------------------------------------------------------------------------#

diff --git a/base/db/R/dbfiles.R b/base/db/R/dbfiles.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
-#-------------------------------------------------------------------------------
-
 ##' Function to insert a file into the dbfiles table as an input
 ##'
 ##' This will write into the dbfiles, inputs, machines and formats the required

diff --git a/base/db/R/derive.trait.R b/base/db/R/derive.trait.R
@@ -1,13 +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
-#-------------------------------------------------------------------------------
-
-##--------------------------------------------------------------------------------------------------#
 ##'
 ##' Performs an arithmetic function, FUN, over a series of traits and returns
 ##' the result as a derived trait.

diff --git a/base/db/R/derive.traits.R b/base/db/R/derive.traits.R
@@ -1,13 +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
-#-------------------------------------------------------------------------------
-
-##--------------------------------------------------------------------------------------------------#
 ##' Equivalent to derive.trait(), but operates over a series of trait datasets,
 ##' as opposed to individual trait rows. See \code{\link{derive.trait}}; for more information.
 ##'

diff --git a/base/db/R/fetch.stats2se.R b/base/db/R/fetch.stats2se.R
@@ -1,13 +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
-#-------------------------------------------------------------------------------
-
-##--------------------------------------------------------------------------------------------------#
 ##' Queries data from the trait database and transforms statistics to SE
 ##'
 ##' Performs query and then uses \code{transformstats} to convert miscellaneous statistical summaries

diff --git a/base/db/R/get.trait.data.R b/base/db/R/get.trait.data.R
@@ -1,13 +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
-#-------------------------------------------------------------------------------
-
-##--------------------------------------------------------------------------------------------------#
 ##' Get trait data from the database.
 ##'
 ##' This will use the following items from settings:

diff --git a/base/db/R/get.trait.data.pft.R b/base/db/R/get.trait.data.pft.R
@@ -1,13 +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
-#-------------------------------------------------------------------------------
-
-##--------------------------------------------------------------------------------------------------#
 ##' Get trait data from the database for a single PFT
 ##'
 ##' @details `pft` should be a list containing at least `name` and `outdir`, and optionally `posteriorid` and `constants`. BEWARE: All existing files in `outir` will be deleted!

diff --git a/base/db/R/pft.add.spp.R b/base/db/R/pft.add.spp.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
-#-------------------------------------------------------------------------------
 ## M. Dietze
 ##' adds a list of species to a pft based on USDA Plants acronyms
 ##'

diff --git a/base/db/R/query.data.R b/base/db/R/query.data.R
@@ -1,13 +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
-#-------------------------------------------------------------------------------
-
-##--------------------------------------------------------------------------------------------------#
 ##' Function to query data from database for specific species and convert stat to SE
 ##'
 ##' @name query.data

diff --git a/base/db/R/query.pft.R b/base/db/R/query.pft.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
-#-------------------------------------------------------------------------------
-#--------------------------------------------------------------------------------------------------#
 ##'  select plant id's associated with pft
 ##'
 ##' @title Query species given pft name

diff --git a/base/db/R/query.prior.R b/base/db/R/query.prior.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
-#-------------------------------------------------------------------------------
-#--------------------------------------------------------------------------------------------------#
 ##' Query Priors
 ##'
 ##' Query priors associated with a plant functional type and a set of traits.

diff --git a/base/db/R/query.trait.data.R b/base/db/R/query.trait.data.R
@@ -1,13 +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
-#-------------------------------------------------------------------------------
-
-##--------------------------------------------------------------------------------------------------#
 ##' Extract trait data from database
 ##'
 ##' Extracts data from database for a given trait and set of species,

diff --git a/base/db/R/query.traits.R b/base/db/R/query.traits.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
-#-------------------------------------------------------------------------------
-#------------------------------------------------------------------------------#
 ##' Query available trait data associated with a given pft and a list of traits
 ##'
 ##' @name query.traits

diff --git a/base/db/R/query.yields.R b/base/db/R/query.yields.R
@@ -1,13 +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
-#-------------------------------------------------------------------------------
-
-##--------------------------------------------------------------------------------------------------#
 ##' Function to query yields data from database for specific species and convert stat to SE
 ##'
 ##' @name query.yields

diff --git a/base/db/R/symmetric_setdiff.R b/base/db/R/symmetric_setdiff.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
-#-------------------------------------------------------------------------------
-
 #' Symmetric set difference of two data frames
 #'
 #' @param x,y `data.frame`s to compare

diff --git a/base/db/R/take.samples.R b/base/db/R/take.samples.R
@@ -1,13 +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
-#-------------------------------------------------------------------------------
-
-##-----------------------------------------------------------------------------#
 ##' sample from normal distribution, given summary stats
 ##'
 ##' @name take.samples