PecanProject · mdietze · Sep 4, 2024 · Sep 3, 2024 · Sep 3, 2024 · Sep 3, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,8 +14,8 @@ 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.
     * `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`
+    * 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`.
 

diff --git a/base/settings/LICENSE b/base/settings/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
diff --git a/base/settings/NEWS.md b/base/settings/NEWS.md
@@ -0,0 +1,15 @@
+# PEcAn.settings 1.8.0.9000
+
+* PEcAn.settings is now distributed under the BSD 3-clause license instead of the NCSA Open Source license.
+
+
+# PEcAn.settings 1.8.0
+
+* Bug fixes for ensemble runs.
+
+
+# PEcAn.settings 1.7.1
+
+* All changes in 1.7.1 and earlier were recorded in a single file for all of the
+  PEcAn packages; please see
+  https://github.com/PecanProject/pecan/blob/v1.7.1/CHANGELOG.md for details.
diff --git a/base/settings/R/SafeList.R b/base/settings/R/SafeList.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
-#-------------------------------------------------------------------------------
-
 #' Create a SafeList object
 #'
 #' `SafeList` is a wrapper class for the normal R list. It should behave

diff --git a/base/settings/R/Settings.R b/base/settings/R/Settings.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
-##-----------------------------------------------------------------------------
 #' Create a PEcAn Settings object
 #'
 #' @title Create a PEcAn Settings object

diff --git a/base/settings/R/addSecrets.R b/base/settings/R/addSecrets.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
-##-----------------------------------------------------------------------------
 #' Add secret information from ~/.pecan.xml
 #'
 #' Copies certains sections from ~/.pecan.xml to the settings. This allows

diff --git a/base/settings/R/check.all.settings.R b/base/settings/R/check.all.settings.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
-##-----------------------------------------------------------------------------
-
 #' check to see if inputs are specified - this should be part of the model code
 #' @title Check Inputs
 #' @param settings settings file

diff --git a/base/settings/R/clean.settings.R b/base/settings/R/clean.settings.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
-##-----------------------------------------------------------------------------
-
 #' Cleans PEcAn settings file
 #'
 #' This will try and clean the settings file so it is ready for

diff --git a/base/settings/R/fix.deprecated.settings.R b/base/settings/R/fix.deprecated.settings.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
-##-----------------------------------------------------------------------------
 #' Checks for and attempts to fix deprecated settings structure
 #'
 #' @title Fix Deprecated Settings

diff --git a/base/settings/R/read.settings.R b/base/settings/R/read.settings.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
-##-----------------------------------------------------------------------------
-
 #' Loads PEcAn settings file
 #'
 #' This will try and find the PEcAn settings file in the following order:

diff --git a/base/settings/R/update.settings.R b/base/settings/R/update.settings.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
-##-----------------------------------------------------------------------------
 #' Updates a pecan.xml file to match new layout. This will take care of the
 #' conversion to the latest pecan.xml file.
 #'

diff --git a/base/settings/tests/testthat.R b/base/settings/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.settings)
 

diff --git a/base/settings/tests/testthat/test.MultiSettings.class.R b/base/settings/tests/testthat/test.MultiSettings.class.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
-#------------------------------------------------------------------------------
 context("test MultiSettings class")
 
 

diff --git a/base/settings/tests/testthat/test.Safelist.class.R b/base/settings/tests/testthat/test.Safelist.class.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
-#------------------------------------------------------------------------------
 context("test SafeList class")
 
 test_that("SafeList constructors work as expected", {

diff --git a/base/settings/tests/testthat/test.Settings.class.R b/base/settings/tests/testthat/test.Settings.class.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
-#------------------------------------------------------------------------------
 context("test Settings class")
 
 test_that("Settings constructors work as expected", {

diff --git a/base/settings/tests/testthat/test.fix.deprecated.settings.R b/base/settings/tests/testthat/test.fix.deprecated.settings.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
-#----------------------------------------------------------------------------
 PEcAn.logger::logger.setQuitOnSevere(FALSE)
 PEcAn.logger::logger.setLevel("OFF")
 context("fix.deprecated.settings")

diff --git a/base/settings/tests/testthat/test.papply.R b/base/settings/tests/testthat/test.papply.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
-#------------------------------------------------------------------------------
 context("test papply")
 
 

diff --git a/base/settings/tests/testthat/test.read.settings.R b/base/settings/tests/testthat/test.read.settings.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
-#------------------------------------------------------------------------------
 context("tests for read.settings and related functions")
 
 PEcAn.logger::logger.setQuitOnSevere(FALSE)

diff --git a/shiny/SDAdashboard/LICENSE b/shiny/SDAdashboard/LICENSE
@@ -0,0 +1,11 @@
+Copyright (c) 2019-2024 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.