From c76ba6fb1e2ca3661fe0deabebe4ecc53af7a5b5 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Tue, 3 Sep 2024 20:19:52 -0700 Subject: [PATCH 01/17] relicense PEcAn.DB as BSD3 with agreement of all contributors --- CHANGELOG.md | 2 +- base/db/LICENSE | 32 ++----------------- base/db/NEWS.md | 2 ++ base/db/R/assign.treatments.R | 10 ------ base/db/R/check.lists.R | 10 ------ base/db/R/covariate.functions.R | 9 ------ base/db/R/dbfiles.R | 9 ------ base/db/R/derive.trait.R | 10 ------ base/db/R/derive.traits.R | 10 ------ base/db/R/fetch.stats2se.R | 10 ------ base/db/R/get.trait.data.R | 10 ------ base/db/R/get.trait.data.pft.R | 10 ------ base/db/R/pft.add.spp.R | 8 ----- base/db/R/query.data.R | 10 ------ base/db/R/query.pft.R | 9 ------ base/db/R/query.prior.R | 9 ------ base/db/R/query.trait.data.R | 10 ------ base/db/R/query.traits.R | 9 ------ base/db/R/query.yields.R | 10 ------ base/db/R/symmetric_setdiff.R | 9 ------ base/db/R/take.samples.R | 10 ------ base/db/R/utils_db.R | 8 ----- base/db/tests/testthat.R | 8 ----- base/db/tests/testthat/test.contents_sanity.R | 8 ----- base/db/tests/testthat/test.db.utils.R | 8 ----- base/db/tests/testthat/test.derive.traits.R | 9 ------ base/db/tests/testthat/test.query.base.R | 8 ----- 27 files changed, 6 insertions(+), 251 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3ecce03b442..22204ce6604 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,7 +15,7 @@ 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` + * Base packages `PEcAn.all`, `PEcAn.DB`, 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/db/LICENSE b/base/db/LICENSE index 9e38c2dc685..09ef35a60b4 100644 --- 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 index fec3739e5f0..5d008066052 100644 --- 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 index d75f6b20b3a..3779d327676 100644 --- 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 index 18e7c8b3840..cc131ca59ed 100644 --- 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 index 31c93009ee9..c40e3ca5a05 100644 --- 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 index e0f9556779b..4214c06837b 100644 --- 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 index 7abc5b9cc64..01264b25e5e 100644 --- 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 index c5b8be9e7ec..cb8265149ab 100644 --- 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 index 7425399f3c3..d0bad8ae465 100644 --- 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 index f181856639c..b307da08c0b 100644 --- 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 index 5556930d449..a2af9c5215a 100644 --- 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 index ce8cf1c3b10..0193aae9c5a 100644 --- 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 index bed236305af..73ca64a7b81 100644 --- 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 index 3a4b231953f..1c45f215622 100644 --- 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 index 736565641f7..6c078dd8aa4 100644 --- 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 index 3162372f0f5..e55b781ab9b 100644 --- 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 index 5b4dab14c68..0d7f54815a1 100644 --- 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 index 4f07ef01b74..dfaef5956dc 100644 --- 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 index 1056ec0b5fd..9f8b2f146dd 100644 --- 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 index aa755a7e45e..06507a2cfba 100644 --- 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 diff --git a/base/db/R/utils_db.R b/base/db/R/utils_db.R index 938b504e294..f59a9c3c2fe 100644 --- a/base/db/R/utils_db.R +++ b/base/db/R/utils_db.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 -#------------------------------------------------------------------------------- .db.utils <- new.env() .db.utils$created <- 0 diff --git a/base/db/tests/testthat.R b/base/db/tests/testthat.R index d2515cd48b8..03f6b840cbf 100644 --- a/base/db/tests/testthat.R +++ b/base/db/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.DB) diff --git a/base/db/tests/testthat/test.contents_sanity.R b/base/db/tests/testthat/test.contents_sanity.R index 6b1ad0eee85..9a11d2bb7ae 100644 --- a/base/db/tests/testthat/test.contents_sanity.R +++ b/base/db/tests/testthat/test.contents_sanity.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("Basic Sanity tests for PEcAn functions that query BETYdb") test_that("append.covariates appends managements to yields",{ con <- check_db_test() diff --git a/base/db/tests/testthat/test.db.utils.R b/base/db/tests/testthat/test.db.utils.R index 85e4b17a661..7d8839357e2 100644 --- a/base/db/tests/testthat/test.db.utils.R +++ b/base/db/tests/testthat/test.db.utils.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("Testing utility functions") test_that("get.id works on some tables, and with different inputs", { diff --git a/base/db/tests/testthat/test.derive.traits.R b/base/db/tests/testthat/test.derive.traits.R index 4ba88caf3ed..b389b401f31 100644 --- a/base/db/tests/testthat/test.derive.traits.R +++ b/base/db/tests/testthat/test.derive.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 -#------------------------------------------------------------------------------- - test_that("derive.traits works",{ set.seed(0) input <- list(x = data.frame(mean = 1, stat = 1, n = 1)) diff --git a/base/db/tests/testthat/test.query.base.R b/base/db/tests/testthat/test.query.base.R index 43f60555bd2..301d10b7c90 100644 --- a/base/db/tests/testthat/test.query.base.R +++ b/base/db/tests/testthat/test.query.base.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 db.query") test_that("db.query can execute a trivial SQL statement and return results",{ From 3f4928fa018801d1dabff1d08ba271d4ea74dfc8 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 4 Sep 2024 00:12:50 -0700 Subject: [PATCH 02/17] relicense PEcAn.visualization as BSD3 with agreement of all contributors --- CHANGELOG.md | 2 +- base/visualization/LICENSE | 37 ++------------------ base/visualization/NEWS.md | 11 ++++++ base/visualization/R/plot_netcdf.R | 9 ----- base/visualization/R/plots.R | 9 ----- base/visualization/tests/testthat.R | 8 ----- base/visualization/tests/testthat/test.viz.R | 8 ----- 7 files changed, 15 insertions(+), 69 deletions(-) create mode 100644 base/visualization/NEWS.md diff --git a/CHANGELOG.md b/CHANGELOG.md index 22204ce6604..36203be8721 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,7 +15,7 @@ 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.DB`, PEcAn.QAQC`, `PEcAn.remote`, `PEcAn.settings`, and `PEcAn.workflow` + * Base packages `PEcAn.all`, `PEcAn.DB`, `PEcAn.QAQC`, `PEcAn.remote`, `PEcAn.settings`, `PEcAn.visualization`, 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/visualization/LICENSE b/base/visualization/LICENSE index 5a9e44128f1..09ef35a60b4 100644 --- a/base/visualization/LICENSE +++ b/base/visualization/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/visualization/NEWS.md b/base/visualization/NEWS.md new file mode 100644 index 00000000000..04eb05d89a1 --- /dev/null +++ b/base/visualization/NEWS.md @@ -0,0 +1,11 @@ +# PEcAn.visualization 1.8.0.9000 + +## License change +* PEcAn.visualization is now distributed under the BSD three-clause license instead of the NCSA Open Source license. + + +# PEcAn.visualization 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/visualization/R/plot_netcdf.R b/base/visualization/R/plot_netcdf.R index 1dcdcac74cd..451e4d89f7f 100644 --- a/base/visualization/R/plot_netcdf.R +++ b/base/visualization/R/plot_netcdf.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 -#------------------------------------------------------------------------------- - # ---------------------------------------------------------------------- # PRIVATE FUNCTIONS # ---------------------------------------------------------------------- diff --git a/base/visualization/R/plots.R b/base/visualization/R/plots.R index 85b6534142f..40bebb9510a 100644 --- a/base/visualization/R/plots.R +++ b/base/visualization/R/plots.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 -#------------------------------------------------------------------------------- - ##' Variable-width (diagonally cut) histogram ##' ##' When constructing a histogram, it is common to make all bars the same width. diff --git a/base/visualization/tests/testthat.R b/base/visualization/tests/testthat.R index d296184d0f0..461fd30776d 100644 --- a/base/visualization/tests/testthat.R +++ b/base/visualization/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.visualization) diff --git a/base/visualization/tests/testthat/test.viz.R b/base/visualization/tests/testthat/test.viz.R index 3dffbdd7ca8..d205843a58e 100644 --- a/base/visualization/tests/testthat/test.viz.R +++ b/base/visualization/tests/testthat/test.viz.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("Testing Visualization") From 6d0428c3f4674a321e78815b6a9e1e3e2933fb55 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 4 Sep 2024 00:23:49 -0700 Subject: [PATCH 03/17] relicense PEcAn.allometry as BSD3 with agreement of all contributors --- CHANGELOG.md | 2 +- modules/allometry/LICENSE | 32 +++----------------------- modules/allometry/NEWS.md | 10 ++++++++ modules/allometry/R/AllomAve.R | 8 ------- modules/allometry/R/allom.BayesFit.R | 8 ------- modules/allometry/R/allom.predict.R | 8 ------- modules/allometry/R/query.allom.data.R | 8 ------- modules/allometry/R/read.allom.data.R | 8 ------- modules/allometry/tests/testthat.R | 8 ------- 9 files changed, 14 insertions(+), 78 deletions(-) create mode 100644 modules/allometry/NEWS.md diff --git a/CHANGELOG.md b/CHANGELOG.md index 36203be8721..95e933e97f0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,7 +17,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha * Shiny apps `dbsync`, `Data-Ingest`, `Elicitation`, `ForecastingDashboard`, `global-sensitivity`, `Pecan.depend`, and `SDAdashboard` * Base packages `PEcAn.all`, `PEcAn.DB`, `PEcAn.QAQC`, `PEcAn.remote`, `PEcAn.settings`, `PEcAn.visualization`, 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`. + * Modules `PEcAn.allometry`, PEcAn.data.mining`, `PEcAn.emulator`, amd `PEcAn.RTM`. ### Removed diff --git a/modules/allometry/LICENSE b/modules/allometry/LICENSE index 9e38c2dc685..09ef35a60b4 100644 --- a/modules/allometry/LICENSE +++ b/modules/allometry/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/modules/allometry/NEWS.md b/modules/allometry/NEWS.md new file mode 100644 index 00000000000..d0bcb027c0d --- /dev/null +++ b/modules/allometry/NEWS.md @@ -0,0 +1,10 @@ +# PEcAn.allometry 1.7.2.9000 + +## License change +* PEcAn.allometry is now distributed under the BSD three-clause license instead of the NCSA Open Source license. + + +# PEcAn.allometry 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/modules/allometry/R/AllomAve.R b/modules/allometry/R/AllomAve.R index af297be4d7c..357da3edb19 100644 --- a/modules/allometry/R/AllomAve.R +++ b/modules/allometry/R/AllomAve.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 -#------------------------------------------------------------------------------- #' AllomAve #' diff --git a/modules/allometry/R/allom.BayesFit.R b/modules/allometry/R/allom.BayesFit.R index 7ddc1011ac2..91e92022435 100644 --- a/modules/allometry/R/allom.BayesFit.R +++ b/modules/allometry/R/allom.BayesFit.R @@ -1,11 +1,3 @@ -#------------------------------------------------------------------------------- -# Copyright (c) 2015 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 -#------------------------------------------------------------------------------- #' allom.BayesFit #' diff --git a/modules/allometry/R/allom.predict.R b/modules/allometry/R/allom.predict.R index 2423fc283db..ea94f83526f 100644 --- a/modules/allometry/R/allom.predict.R +++ b/modules/allometry/R/allom.predict.R @@ -1,11 +1,3 @@ -#------------------------------------------------------------------------------- -# Copyright (c) 2015 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 -#------------------------------------------------------------------------------- #' allom.predict #' diff --git a/modules/allometry/R/query.allom.data.R b/modules/allometry/R/query.allom.data.R index 8234e0b2dfd..26eb0ed8aac 100644 --- a/modules/allometry/R/query.allom.data.R +++ b/modules/allometry/R/query.allom.data.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 -#------------------------------------------------------------------------------- #' query.allom.data #' diff --git a/modules/allometry/R/read.allom.data.R b/modules/allometry/R/read.allom.data.R index 09c560d1c63..8b48962a9dc 100644 --- a/modules/allometry/R/read.allom.data.R +++ b/modules/allometry/R/read.allom.data.R @@ -1,11 +1,3 @@ -#------------------------------------------------------------------------------- -# Copyright (c) 2015 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 -#------------------------------------------------------------------------------- #' read.allom.data #' diff --git a/modules/allometry/tests/testthat.R b/modules/allometry/tests/testthat.R index a775e051786..4194358dc88 100644 --- a/modules/allometry/tests/testthat.R +++ b/modules/allometry/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) From 76d303972b9fe37ffd2961ee2e2128e722158af6 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 4 Sep 2024 00:30:39 -0700 Subject: [PATCH 04/17] relicense PEcAn.assim.batch as BSD3 with agreement of all contributors --- modules/assim.batch/LICENSE | 32 +++----------------------------- modules/assim.batch/NEWS.md | 2 ++ 2 files changed, 5 insertions(+), 29 deletions(-) diff --git a/modules/assim.batch/LICENSE b/modules/assim.batch/LICENSE index 9e38c2dc685..09ef35a60b4 100644 --- a/modules/assim.batch/LICENSE +++ b/modules/assim.batch/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/modules/assim.batch/NEWS.md b/modules/assim.batch/NEWS.md index d1c0b35b72c..2e34eecf11e 100644 --- a/modules/assim.batch/NEWS.md +++ b/modules/assim.batch/NEWS.md @@ -1,5 +1,7 @@ # PEcAn.assim.batch 1.8.0.9000 +## License change +* PEcAn.assim.batch is now distributed under the BSD three-clause license instead of the NCSA Open Source license. # PEcAn.assim.batch 1.8.0 From df35aae89e846c926a0bcce2b527ff4c80a43473 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 4 Sep 2024 01:51:22 -0700 Subject: [PATCH 05/17] relicense PEcAn.MA as BSD3 with agreement of all contributors --- CHANGELOG.md | 2 +- modules/meta.analysis/LICENSE | 32 ++----------------- modules/meta.analysis/NEWS.md | 9 ++++++ modules/meta.analysis/R/approx.posterior.R | 9 ------ modules/meta.analysis/R/jagify.R | 9 ------ modules/meta.analysis/R/meta.analysis.R | 9 ------ .../meta.analysis/R/meta.analysis.summary.R | 9 ------ .../R/meta.analysis.write.model.R | 9 ------ modules/meta.analysis/R/rename_jags_columns.R | 10 ------ modules/meta.analysis/R/run.meta.analysis.R | 8 ----- modules/meta.analysis/R/single.MA.R | 8 ----- modules/meta.analysis/tests/testthat.R | 8 ----- .../tests/testthat/test.approx.posterior.R | 8 ----- 13 files changed, 13 insertions(+), 117 deletions(-) create mode 100644 modules/meta.analysis/NEWS.md diff --git a/CHANGELOG.md b/CHANGELOG.md index 95e933e97f0..dcb5052489b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,7 +17,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha * Shiny apps `dbsync`, `Data-Ingest`, `Elicitation`, `ForecastingDashboard`, `global-sensitivity`, `Pecan.depend`, and `SDAdashboard` * Base packages `PEcAn.all`, `PEcAn.DB`, `PEcAn.QAQC`, `PEcAn.remote`, `PEcAn.settings`, `PEcAn.visualization`, 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.allometry`, PEcAn.data.mining`, `PEcAn.emulator`, amd `PEcAn.RTM`. + * Modules `PEcAn.allometry`, `PEcAn.assim.batch`, `PEcAn.data.mining`, `PEcAn.emulator`, `PEcAn.MA`, and `PEcAn.RTM`. ### Removed diff --git a/modules/meta.analysis/LICENSE b/modules/meta.analysis/LICENSE index 9e38c2dc685..09ef35a60b4 100644 --- a/modules/meta.analysis/LICENSE +++ b/modules/meta.analysis/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/modules/meta.analysis/NEWS.md b/modules/meta.analysis/NEWS.md new file mode 100644 index 00000000000..1967a5fd637 --- /dev/null +++ b/modules/meta.analysis/NEWS.md @@ -0,0 +1,9 @@ +# PEcAn.MA 1.7.3.9000 + +## License change +* PEcAn.MA is now distributed under the BSD three-clause license instead of the NCSA Open Source license. + + +# PEcAn.MA 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/modules/meta.analysis/R/approx.posterior.R b/modules/meta.analysis/R/approx.posterior.R index ca66f183b4f..cb856c6d0d5 100644 --- a/modules/meta.analysis/R/approx.posterior.R +++ b/modules/meta.analysis/R/approx.posterior.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 -#------------------------------------------------------------------------------- - ##' Approximate the posterior MCMC with a closed form pdf ##' ##' returns priors where posterior MCMC are missing diff --git a/modules/meta.analysis/R/jagify.R b/modules/meta.analysis/R/jagify.R index 70a0bb84c0e..1f80121d31d 100644 --- a/modules/meta.analysis/R/jagify.R +++ b/modules/meta.analysis/R/jagify.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 -#------------------------------------------------------------------------------- - ##' ##' Convert queried data to format required by JAGS meta-analysis model ##' diff --git a/modules/meta.analysis/R/meta.analysis.R b/modules/meta.analysis/R/meta.analysis.R index e150b1f5687..dfae26db4fa 100644 --- a/modules/meta.analysis/R/meta.analysis.R +++ b/modules/meta.analysis/R/meta.analysis.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 -#------------------------------------------------------------------------------- - ##' Trait Meta-analysis ##' ##' Runs hierarchical meta-analysis of plant trait data diff --git a/modules/meta.analysis/R/meta.analysis.summary.R b/modules/meta.analysis/R/meta.analysis.summary.R index 62cbf6faf13..7e28c29ce7b 100644 --- a/modules/meta.analysis/R/meta.analysis.summary.R +++ b/modules/meta.analysis/R/meta.analysis.summary.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 -#------------------------------------------------------------------------------- - ##' Generate summary statistics and diagnostics for PEcAn meta.analysis ##' ##' @param mcmc.object JAGS mcmc output from \code{\link{pecan.ma}} diff --git a/modules/meta.analysis/R/meta.analysis.write.model.R b/modules/meta.analysis/R/meta.analysis.write.model.R index f8b49350454..db3a6e03ba5 100644 --- a/modules/meta.analysis/R/meta.analysis.write.model.R +++ b/modules/meta.analysis/R/meta.analysis.write.model.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 -#------------------------------------------------------------------------------- - ##' Convert template ma.model.template.R to a JAGS model. ##' ##' Writes a meta-analysis model based on available data and prior specification. diff --git a/modules/meta.analysis/R/rename_jags_columns.R b/modules/meta.analysis/R/rename_jags_columns.R index 43d22ef7b0e..dd6676c307f 100644 --- a/modules/meta.analysis/R/rename_jags_columns.R +++ b/modules/meta.analysis/R/rename_jags_columns.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 -#------------------------------------------------------------------------------- - -##-----------------------------------------------------------------------------# ##' Renames the variables within output data frame trait.data ##' ##' @param data data frame to with variables to rename diff --git a/modules/meta.analysis/R/run.meta.analysis.R b/modules/meta.analysis/R/run.meta.analysis.R index 65afcdf61bd..360d3453a0a 100644 --- a/modules/meta.analysis/R/run.meta.analysis.R +++ b/modules/meta.analysis/R/run.meta.analysis.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 -#------------------------------------------------------------------------------- run.meta.analysis.pft <- function(pft, iterations, random = TRUE, threshold = 1.2, dbfiles, dbcon, use_ghs = TRUE, update = FALSE) { # check to see if get.trait was executed diff --git a/modules/meta.analysis/R/single.MA.R b/modules/meta.analysis/R/single.MA.R index 836e6ae8b79..89377fcb039 100644 --- a/modules/meta.analysis/R/single.MA.R +++ b/modules/meta.analysis/R/single.MA.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 -#------------------------------------------------------------------------------- ##' Individual Meta-analysis ##' diff --git a/modules/meta.analysis/tests/testthat.R b/modules/meta.analysis/tests/testthat.R index c2dcd0f0512..1681958672a 100644 --- a/modules/meta.analysis/tests/testthat.R +++ b/modules/meta.analysis/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.MA) diff --git a/modules/meta.analysis/tests/testthat/test.approx.posterior.R b/modules/meta.analysis/tests/testthat/test.approx.posterior.R index 51499ef662d..5be5ee4153b 100644 --- a/modules/meta.analysis/tests/testthat/test.approx.posterior.R +++ b/modules/meta.analysis/tests/testthat/test.approx.posterior.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 approx.posterior function") load("data/trait.mcmc.RData") From 85a254f29f8fdc1ee540cd1f0ebd5be3627d1bdb Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 4 Sep 2024 02:11:19 -0700 Subject: [PATCH 06/17] relicense PEcAn.photosynthesis as BSD3 with agreement of all contributors --- CHANGELOG.md | 2 +- modules/photosynthesis/LICENSE | 35 +++------------------------------- modules/photosynthesis/NEWS.md | 2 ++ 3 files changed, 6 insertions(+), 33 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index dcb5052489b..ae8bdfffded 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,7 +17,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha * Shiny apps `dbsync`, `Data-Ingest`, `Elicitation`, `ForecastingDashboard`, `global-sensitivity`, `Pecan.depend`, and `SDAdashboard` * Base packages `PEcAn.all`, `PEcAn.DB`, `PEcAn.QAQC`, `PEcAn.remote`, `PEcAn.settings`, `PEcAn.visualization`, 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.allometry`, `PEcAn.assim.batch`, `PEcAn.data.mining`, `PEcAn.emulator`, `PEcAn.MA`, and `PEcAn.RTM`. + * Modules `PEcAn.allometry`, `PEcAn.assim.batch`, `PEcAn.data.mining`, `PEcAn.emulator`, `PEcAn.MA`, `PEcAn.photosynthesis`, and `PEcAn.RTM`. ### Removed diff --git a/modules/photosynthesis/LICENSE b/modules/photosynthesis/LICENSE index 487f189dfcd..09ef35a60b4 100644 --- a/modules/photosynthesis/LICENSE +++ b/modules/photosynthesis/LICENSE @@ -1,32 +1,3 @@ -## This is the master copy of the PEcAn License - -University of Illinois/NCSA Open Source License - -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/modules/photosynthesis/NEWS.md b/modules/photosynthesis/NEWS.md index c324fb63283..e3786699302 100644 --- a/modules/photosynthesis/NEWS.md +++ b/modules/photosynthesis/NEWS.md @@ -1,5 +1,7 @@ # PEcAn.photosynthesis 1.7.3.9000 +## License change +* PEcAn.photosynthesis is now distributed under the BSD three-clause license instead of the NCSA Open Source license. # PEcAn.photosynthesis 1.7.3 From a5d0a16f8d906d1a18e550994ed107705de2ecad Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 4 Sep 2024 02:16:04 -0700 Subject: [PATCH 07/17] relicense PEcAn.priors as BSD3 with agreement of all contributors --- CHANGELOG.md | 2 +- modules/priors/LICENSE | 37 +++------------------------------ modules/priors/NEWS.md | 10 +++++++++ modules/priors/R/priors.R | 10 --------- modules/priors/tests/testthat.R | 8 ------- 5 files changed, 14 insertions(+), 53 deletions(-) create mode 100644 modules/priors/NEWS.md diff --git a/CHANGELOG.md b/CHANGELOG.md index ae8bdfffded..5659959adb4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,7 +17,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha * Shiny apps `dbsync`, `Data-Ingest`, `Elicitation`, `ForecastingDashboard`, `global-sensitivity`, `Pecan.depend`, and `SDAdashboard` * Base packages `PEcAn.all`, `PEcAn.DB`, `PEcAn.QAQC`, `PEcAn.remote`, `PEcAn.settings`, `PEcAn.visualization`, 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.allometry`, `PEcAn.assim.batch`, `PEcAn.data.mining`, `PEcAn.emulator`, `PEcAn.MA`, `PEcAn.photosynthesis`, and `PEcAn.RTM`. + * Modules `PEcAn.allometry`, `PEcAn.assim.batch`, `PEcAn.data.mining`, `PEcAn.emulator`, `PEcAn.MA`, `PEcAn.photosynthesis`, `PEcAn.priors`, and `PEcAn.RTM`. ### Removed diff --git a/modules/priors/LICENSE b/modules/priors/LICENSE index 5a9e44128f1..09ef35a60b4 100644 --- a/modules/priors/LICENSE +++ b/modules/priors/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/modules/priors/NEWS.md b/modules/priors/NEWS.md new file mode 100644 index 00000000000..43373f15666 --- /dev/null +++ b/modules/priors/NEWS.md @@ -0,0 +1,10 @@ +# PEcAn.priors 1.7.3.9000 + +## License change +* PEcAn.priors is now distributed under the BSD three-clause license instead of the NCSA Open Source license. + + +# PEcAn.priors 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/modules/priors/R/priors.R b/modules/priors/R/priors.R index 406b31cad6b..e1414aa1deb 100644 --- a/modules/priors/R/priors.R +++ b/modules/priors/R/priors.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 -#------------------------------------------------------------------------------- - -#--------------------------------------------------------------------------------------------------# ##' Fit a distribution to data ##' ##' @title Fit distribution to data diff --git a/modules/priors/tests/testthat.R b/modules/priors/tests/testthat.R index 594bfe02e9d..a78a81228a7 100644 --- a/modules/priors/tests/testthat.R +++ b/modules/priors/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) PEcAn.logger::logger.setQuitOnSevere(FALSE) From 28fc4c8be1d51880c73dddca993fdb088edb5293 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 4 Sep 2024 10:50:20 -0700 Subject: [PATCH 08/17] relicense PEcAn.CLM45 as BSD3 with agreement of all contributors --- CHANGELOG.md | 2 +- models/clm45/LICENSE | 32 +++------------------------- models/clm45/NEWS.md | 10 +++++++++ models/clm45/R/met2model.CLM45.R | 9 -------- models/clm45/R/model2netcdf.CLM45.R | 8 ------- models/clm45/R/write.configs.CLM45.R | 9 -------- models/clm45/tests/testthat.R | 8 ------- 7 files changed, 14 insertions(+), 64 deletions(-) create mode 100644 models/clm45/NEWS.md diff --git a/CHANGELOG.md b/CHANGELOG.md index 5659959adb4..b1f53d14d0a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,7 +16,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha * `apps/api` * Shiny apps `dbsync`, `Data-Ingest`, `Elicitation`, `ForecastingDashboard`, `global-sensitivity`, `Pecan.depend`, and `SDAdashboard` * Base packages `PEcAn.all`, `PEcAn.DB`, `PEcAn.QAQC`, `PEcAn.remote`, `PEcAn.settings`, `PEcAn.visualization`, 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. + * Model packages `PEcAn.BASGRA`, `PEcAn.CLM45`, PEcAn.dvmdostem`, `PEcAn.FATES`, `PEcAn.GDAY`, `PEcAn.LDNDC`, `PEcAn.MAAT`, `PEcAn.MAESPA`, `PEcAn.SIBCASA`, `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/models/clm45/LICENSE b/models/clm45/LICENSE index 9e38c2dc685..09ef35a60b4 100644 --- a/models/clm45/LICENSE +++ b/models/clm45/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/models/clm45/NEWS.md b/models/clm45/NEWS.md new file mode 100644 index 00000000000..72171423795 --- /dev/null +++ b/models/clm45/NEWS.md @@ -0,0 +1,10 @@ +# PEcAn.CLM45 1.7.3.9000 + +## License change +* PEcAn.CLM45 is now distributed under the BSD three-clause license instead of the NCSA Open Source license. + + +# PEcAn.CLM45 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/models/clm45/R/met2model.CLM45.R b/models/clm45/R/met2model.CLM45.R index 60dda63ca0f..f8759922a13 100644 --- a/models/clm45/R/met2model.CLM45.R +++ b/models/clm45/R/met2model.CLM45.R @@ -1,12 +1,3 @@ -#------------------------------------------------------------------------------- -# Copyright (c) 2015 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 CLM met files. ##' met2model wrapper for CLM45 diff --git a/models/clm45/R/model2netcdf.CLM45.R b/models/clm45/R/model2netcdf.CLM45.R index 6f028bf4768..ec98d75e13a 100644 --- a/models/clm45/R/model2netcdf.CLM45.R +++ b/models/clm45/R/model2netcdf.CLM45.R @@ -1,11 +1,3 @@ -## ------------------------------------------------------------------------------- -## Copyright (c) 2015 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.CLM45 ##' @title Code to convert CLM45 netcdf output into into CF standard diff --git a/models/clm45/R/write.configs.CLM45.R b/models/clm45/R/write.configs.CLM45.R index 205e733537e..7c4c6a88b33 100644 --- a/models/clm45/R/write.configs.CLM45.R +++ b/models/clm45/R/write.configs.CLM45.R @@ -1,12 +1,3 @@ -##------------------------------------------------------------------------------ -##Copyright (c) 2015 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 the Community Land Model model. ##' ##' @name write.config.CLM45 diff --git a/models/clm45/tests/testthat.R b/models/clm45/tests/testthat.R index 2582bc74de6..bd9de84301b 100644 --- a/models/clm45/tests/testthat.R +++ b/models/clm45/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) From 7e6eae550aea8dd51826c50883026ad9d77d3c49 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 4 Sep 2024 11:04:32 -0700 Subject: [PATCH 09/17] relicense PEcAn.DALEC as BSD3 with agreement of all contributors --- CHANGELOG.md | 2 +- models/dalec/DESCRIPTION | 3 ++- models/dalec/LICENSE | 37 +++------------------------- models/dalec/NEWS.md | 10 ++++++++ models/dalec/R/met2model.DALEC.R | 9 ------- models/dalec/R/model2netcdf.DALEC.R | 10 -------- models/dalec/R/write.configs.dalec.R | 9 ------- 7 files changed, 16 insertions(+), 64 deletions(-) create mode 100644 models/dalec/NEWS.md diff --git a/CHANGELOG.md b/CHANGELOG.md index b1f53d14d0a..48c3ed33dad 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,7 +16,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha * `apps/api` * Shiny apps `dbsync`, `Data-Ingest`, `Elicitation`, `ForecastingDashboard`, `global-sensitivity`, `Pecan.depend`, and `SDAdashboard` * Base packages `PEcAn.all`, `PEcAn.DB`, `PEcAn.QAQC`, `PEcAn.remote`, `PEcAn.settings`, `PEcAn.visualization`, and `PEcAn.workflow` - * Model packages `PEcAn.BASGRA`, `PEcAn.CLM45`, PEcAn.dvmdostem`, `PEcAn.FATES`, `PEcAn.GDAY`, `PEcAn.LDNDC`, `PEcAn.MAAT`, `PEcAn.MAESPA`, `PEcAn.SIBCASA`, `PEcAn.STICS`, and the new model package template. + * Model packages `PEcAn.BASGRA`, `PEcAn.CLM45`, `PEcAn.DALEC`, `PEcAn.dvmdostem`, `PEcAn.FATES`, `PEcAn.GDAY`, `PEcAn.LDNDC`, `PEcAn.MAAT`, `PEcAn.MAESPA`, `PEcAn.SIBCASA`, `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/models/dalec/DESCRIPTION b/models/dalec/DESCRIPTION index 3dacc2cb3fc..a73bd635c4d 100644 --- a/models/dalec/DESCRIPTION +++ b/models/dalec/DESCRIPTION @@ -5,7 +5,8 @@ Version: 1.7.3.9000 Authors@R: c(person("Mike", "Dietze", role = c("aut", "cre"), email = "dietze@bu.edu"), person("Tristan", "Quaife", role = c("aut")), - person("University of Illinois, NCSA", role = c("cph"))) + person("University of Illinois, NCSA", role = c("cph")), + person("Boston University", role = c("cph"))) Author: Mike Dietze, Tristain Quaife Maintainer: Mike Dietze Description: This module provides functions to link DALEC to PEcAn. diff --git a/models/dalec/LICENSE b/models/dalec/LICENSE index 5a9e44128f1..09ef35a60b4 100644 --- a/models/dalec/LICENSE +++ b/models/dalec/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/models/dalec/NEWS.md b/models/dalec/NEWS.md new file mode 100644 index 00000000000..cd70e8ae222 --- /dev/null +++ b/models/dalec/NEWS.md @@ -0,0 +1,10 @@ +# PEcAn.DALEC 1.7.3.9000 + +## License change +* PEcAn.DALEC is now distributed under the BSD three-clause license instead of the NCSA Open Source license. + + +# PEcAn.DALEC 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/models/dalec/R/met2model.DALEC.R b/models/dalec/R/met2model.DALEC.R index 242bfe61110..8658471f972 100644 --- a/models/dalec/R/met2model.DALEC.R +++ b/models/dalec/R/met2model.DALEC.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 DALEC met files ## If files already exist in 'Outfolder', the default function is NOT to overwrite them and only diff --git a/models/dalec/R/model2netcdf.DALEC.R b/models/dalec/R/model2netcdf.DALEC.R index 71e7b9a9ef0..18be5fcb01f 100644 --- a/models/dalec/R/model2netcdf.DALEC.R +++ b/models/dalec/R/model2netcdf.DALEC.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 DALEC output to netCDF ##' ##' Converts all output contained in a folder to netCDF. diff --git a/models/dalec/R/write.configs.dalec.R b/models/dalec/R/write.configs.dalec.R index 21e481c242a..863e5fc1ecf 100644 --- a/models/dalec/R/write.configs.dalec.R +++ b/models/dalec/R/write.configs.dalec.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 -#------------------------------------------------------------------------------- - #--------------------------------------------------------------------------------------------------# # Template for functions to prepare and write out files model-specific configuration files for MA #--------------------------------------------------------------------------------------------------# From 837f963656d5ec9eaed95efac013fcac7bdb1182 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 4 Sep 2024 11:08:51 -0700 Subject: [PATCH 10/17] relicense PEcAn.JULES as BSD3 with agreement of all contributors --- CHANGELOG.md | 2 +- models/jules/LICENSE | 37 +++-------------------------- models/jules/NEWS.md | 10 ++++++++ models/jules/R/model2netcdf.JULES.R | 10 -------- models/jules/R/write.config.JULES.R | 10 -------- models/jules/tests/testthat.R | 8 ------- 6 files changed, 14 insertions(+), 63 deletions(-) create mode 100644 models/jules/NEWS.md diff --git a/CHANGELOG.md b/CHANGELOG.md index 48c3ed33dad..890e18f005a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,7 +16,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha * `apps/api` * Shiny apps `dbsync`, `Data-Ingest`, `Elicitation`, `ForecastingDashboard`, `global-sensitivity`, `Pecan.depend`, and `SDAdashboard` * 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.LDNDC`, `PEcAn.MAAT`, `PEcAn.MAESPA`, `PEcAn.SIBCASA`, `PEcAn.STICS`, and the new model package template. + * Model packages `PEcAn.BASGRA`, `PEcAn.CLM45`, `PEcAn.DALEC`, `PEcAn.dvmdostem`, `PEcAn.FATES`, `PEcAn.GDAY`, `PEcAn.JULES`, `PEcAn.LDNDC`, `PEcAn.MAAT`, `PEcAn.MAESPA`, `PEcAn.SIBCASA`, `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/models/jules/LICENSE b/models/jules/LICENSE index 5a9e44128f1..09ef35a60b4 100644 --- a/models/jules/LICENSE +++ b/models/jules/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/models/jules/NEWS.md b/models/jules/NEWS.md new file mode 100644 index 00000000000..3b5ab1d8d20 --- /dev/null +++ b/models/jules/NEWS.md @@ -0,0 +1,10 @@ +# PEcAn.JULES 1.7.3.9000 + +## License change +* PEcAn.JULES is now distributed under the BSD three-clause license instead of the NCSA Open Source license. + + +# PEcAn.JULES 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/models/jules/R/model2netcdf.JULES.R b/models/jules/R/model2netcdf.JULES.R index 6270cb6da0c..733bef29e1b 100755 --- a/models/jules/R/model2netcdf.JULES.R +++ b/models/jules/R/model2netcdf.JULES.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 -#------------------------------------------------------------------------------- - -##-------------------------------------------------------------------------------------------------# ##' Convert MODEL output into the PEcAn standard ##' ##' @name model2netcdf.JULES diff --git a/models/jules/R/write.config.JULES.R b/models/jules/R/write.config.JULES.R index f68cce831ac..1f01f7b60be 100644 --- a/models/jules/R/write.config.JULES.R +++ b/models/jules/R/write.config.JULES.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 -#------------------------------------------------------------------------------- - -##-------------------------------------------------------------------------------------------------# ##' Writes a JULES config file. ##' ##' Requires a pft xml object, a list of trait values for a single model run, diff --git a/models/jules/tests/testthat.R b/models/jules/tests/testthat.R index 060471e6cbb..ba6e49d00b7 100644 --- a/models/jules/tests/testthat.R +++ b/models/jules/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) From a9a32b7b6e526608b40578b8046e97813a30469d Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 4 Sep 2024 11:13:25 -0700 Subject: [PATCH 11/17] relicense PEcAn.LINKAGES as BSD3 with agreement of all contributors --- CHANGELOG.md | 2 +- models/linkages/LICENSE | 37 ++-------------------- models/linkages/NEWS.md | 10 ++++++ models/linkages/R/met2model.LINKAGES.R | 10 ------ models/linkages/R/model2netcdf.LINKAGES.R | 10 ------ models/linkages/R/read_restart.LINKAGES.R | 9 ------ models/linkages/R/sample.IC.LINKAGES.R | 9 ------ models/linkages/R/spinup.LINKAGES.R | 9 ------ models/linkages/R/split_inputs.LINKAGES.R | 7 ---- models/linkages/R/write.config.LINKAGES.R | 10 ------ models/linkages/R/write_restart.LINKAGES.R | 9 ------ models/linkages/tests/testthat.R | 8 ----- 12 files changed, 14 insertions(+), 116 deletions(-) create mode 100644 models/linkages/NEWS.md diff --git a/CHANGELOG.md b/CHANGELOG.md index 890e18f005a..e255ae4533a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,7 +16,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha * `apps/api` * Shiny apps `dbsync`, `Data-Ingest`, `Elicitation`, `ForecastingDashboard`, `global-sensitivity`, `Pecan.depend`, and `SDAdashboard` * 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.MAAT`, `PEcAn.MAESPA`, `PEcAn.SIBCASA`, `PEcAn.STICS`, and the new model package template. + * Model packages `PEcAn.BASGRA`, `PEcAn.CLM45`, `PEcAn.DALEC`, `PEcAn.dvmdostem`, `PEcAn.FATES`, `PEcAn.GDAY`, `PEcAn.JULES`, `PEcAn.LDNDC`, `PEcAn.LINKAGES`, `PEcAn.MAAT`, `PEcAn.MAESPA`, `PEcAn.SIBCASA`, `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/models/linkages/LICENSE b/models/linkages/LICENSE index 5a9e44128f1..09ef35a60b4 100644 --- a/models/linkages/LICENSE +++ b/models/linkages/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/models/linkages/NEWS.md b/models/linkages/NEWS.md new file mode 100644 index 00000000000..0899764fc20 --- /dev/null +++ b/models/linkages/NEWS.md @@ -0,0 +1,10 @@ +# PEcAn.LINKAGES 1.7.3.9000 + +## License change +* PEcAn.LINKAGES is now distributed under the BSD three-clause license instead of the NCSA Open Source license. + + +# PEcAn.LINKAGES 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/models/linkages/R/met2model.LINKAGES.R b/models/linkages/R/met2model.LINKAGES.R index 9d7c28136b7..f1db9f3e2b5 100644 --- a/models/linkages/R/met2model.LINKAGES.R +++ b/models/linkages/R/met2model.LINKAGES.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 -#------------------------------------------------------------------------------- - -##-------------------------------------------------------------------------------------------------# ##' Converts a met CF file to a model specific met file. The input ##' files are calld /.YYYY.cf ##' diff --git a/models/linkages/R/model2netcdf.LINKAGES.R b/models/linkages/R/model2netcdf.LINKAGES.R index e2a059c3fec..a24b9f017f7 100644 --- a/models/linkages/R/model2netcdf.LINKAGES.R +++ b/models/linkages/R/model2netcdf.LINKAGES.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 -#------------------------------------------------------------------------------- - -##-------------------------------------------------------------------------------------------------# ##' Convert MODEL output into the NACP Intercomparison format (ALMA using netCDF) ##' ##' @name model2netcdf.LINKAGES diff --git a/models/linkages/R/read_restart.LINKAGES.R b/models/linkages/R/read_restart.LINKAGES.R index c4173f888f1..c5d59f2957d 100644 --- a/models/linkages/R/read_restart.LINKAGES.R +++ b/models/linkages/R/read_restart.LINKAGES.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 -#------------------------------------------------------------------------------- - ##' @title read_restart.LINKAGES ##' @name read_restart.LINKAGES ##' @author Ann Raiho \email{araiho@@nd.edu} diff --git a/models/linkages/R/sample.IC.LINKAGES.R b/models/linkages/R/sample.IC.LINKAGES.R index 3c77427a5f2..0b278c74e55 100644 --- a/models/linkages/R/sample.IC.LINKAGES.R +++ b/models/linkages/R/sample.IC.LINKAGES.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 -#------------------------------------------------------------------------------- - sample.IC.LINKAGES <- function(ne, state, year = NULL) { ## g C * m-2 ground area in wood (above-ground + roots) biomass_tsca = ifelse(rep("biomass_tsca" %in% names(state), ne), diff --git a/models/linkages/R/spinup.LINKAGES.R b/models/linkages/R/spinup.LINKAGES.R index 1b9df3592e3..cff880fcf5a 100644 --- a/models/linkages/R/spinup.LINKAGES.R +++ b/models/linkages/R/spinup.LINKAGES.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 -#------------------------------------------------------------------------------- - spinup.LINKAGES <- function(start.year, end.year, temp.mat, precip.mat, paleon = NULL) { if (is.null(paleon)) { paleon <- TRUE # Why not just have `paleon = TRUE` above? diff --git a/models/linkages/R/split_inputs.LINKAGES.R b/models/linkages/R/split_inputs.LINKAGES.R index 142b9d64423..9be21c69ddb 100644 --- a/models/linkages/R/split_inputs.LINKAGES.R +++ b/models/linkages/R/split_inputs.LINKAGES.R @@ -1,10 +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 -#------------------------------------------------------------------------------- - ##' @title split_inputs.LINKAGES ##' @name split_inputs.LINKAGES ##' @author Ann Raiho diff --git a/models/linkages/R/write.config.LINKAGES.R b/models/linkages/R/write.config.LINKAGES.R index b656d14f294..3cb2dec58fe 100644 --- a/models/linkages/R/write.config.LINKAGES.R +++ b/models/linkages/R/write.config.LINKAGES.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 -#------------------------------------------------------------------------------- - -##-------------------------------------------------------------------------------------------------# ##' Writes a LINKAGES config file. ##' ##' Requires a pft xml object, a list of trait values for a single model run, diff --git a/models/linkages/R/write_restart.LINKAGES.R b/models/linkages/R/write_restart.LINKAGES.R index 77b073590b5..39b0a24cec4 100644 --- a/models/linkages/R/write_restart.LINKAGES.R +++ b/models/linkages/R/write_restart.LINKAGES.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 -#------------------------------------------------------------------------------- - ##' @title write_restart.LINKAGES ##' @name write_restart.LINKAGES ##' @author Ann Raiho \email{araiho@@nd.edu} diff --git a/models/linkages/tests/testthat.R b/models/linkages/tests/testthat.R index 15a638d15e9..bf752b76016 100644 --- a/models/linkages/tests/testthat.R +++ b/models/linkages/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) From c429ae76af7c21b33e887b6bca19a28b800ca69a Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 4 Sep 2024 11:16:51 -0700 Subject: [PATCH 12/17] relicense PEcAn.LPJGUESS as BSD3 with agreement of all contributors --- CHANGELOG.md | 2 +- models/lpjguess/LICENSE | 37 ++------------------ models/lpjguess/NEWS.md | 10 ++++++ models/lpjguess/R/met2model.LPJGUESS.R | 9 ----- models/lpjguess/R/model2netcdf.LPJGUESS.R | 9 ----- models/lpjguess/R/readStateBinary.LPJGUESS.R | 9 ----- models/lpjguess/R/write.config.LPJGUESS.R | 10 ------ models/lpjguess/tests/testthat.R | 8 ----- 8 files changed, 14 insertions(+), 80 deletions(-) create mode 100644 models/lpjguess/NEWS.md diff --git a/CHANGELOG.md b/CHANGELOG.md index e255ae4533a..0c16f9f9c6e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,7 +16,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha * `apps/api` * Shiny apps `dbsync`, `Data-Ingest`, `Elicitation`, `ForecastingDashboard`, `global-sensitivity`, `Pecan.depend`, and `SDAdashboard` * 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.MAAT`, `PEcAn.MAESPA`, `PEcAn.SIBCASA`, `PEcAn.STICS`, and the new model package template. + * 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.SIBCASA`, `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/models/lpjguess/LICENSE b/models/lpjguess/LICENSE index 5a9e44128f1..09ef35a60b4 100644 --- a/models/lpjguess/LICENSE +++ b/models/lpjguess/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/models/lpjguess/NEWS.md b/models/lpjguess/NEWS.md new file mode 100644 index 00000000000..63b168f3e3f --- /dev/null +++ b/models/lpjguess/NEWS.md @@ -0,0 +1,10 @@ +# PEcAn.LPJGUESS 1.7.3.9000 + +## License change +* PEcAn.LPJGUESS is now distributed under the BSD three-clause license instead of the NCSA Open Source license. + + +# PEcAn.LPJGUESS 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/models/lpjguess/R/met2model.LPJGUESS.R b/models/lpjguess/R/met2model.LPJGUESS.R index 9b05a54db8f..3b719881d14 100644 --- a/models/lpjguess/R/met2model.LPJGUESS.R +++ b/models/lpjguess/R/met2model.LPJGUESS.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 -#------------------------------------------------------------------------------- - # R Code to convert NetCDF CF met files into LPJ-GUESS met files ## If files already exist in 'Outfolder', the default function is NOT to overwrite them and only diff --git a/models/lpjguess/R/model2netcdf.LPJGUESS.R b/models/lpjguess/R/model2netcdf.LPJGUESS.R index a92c343fb77..c5202833104 100644 --- a/models/lpjguess/R/model2netcdf.LPJGUESS.R +++ b/models/lpjguess/R/model2netcdf.LPJGUESS.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 -#------------------------------------------------------------------------------- - ##' Convert LPJ-GUESS output to netCDF ##' ##' @name model2netcdf.LPJGUESS diff --git a/models/lpjguess/R/readStateBinary.LPJGUESS.R b/models/lpjguess/R/readStateBinary.LPJGUESS.R index 89ffb0f5969..ffba146ac52 100644 --- a/models/lpjguess/R/readStateBinary.LPJGUESS.R +++ b/models/lpjguess/R/readStateBinary.LPJGUESS.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 -#------------------------------------------------------------------------------- - # R Code to convert NetCDF CF met files into LPJ-GUESS met files ## If files already exist in 'Outfolder', the default function is NOT to overwrite them and only diff --git a/models/lpjguess/R/write.config.LPJGUESS.R b/models/lpjguess/R/write.config.LPJGUESS.R index 8c5f900704f..c326edab6ec 100644 --- a/models/lpjguess/R/write.config.LPJGUESS.R +++ b/models/lpjguess/R/write.config.LPJGUESS.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 -#------------------------------------------------------------------------------- - -##-------------------------------------------------------------------------------------------------# ##' Writes a LPJ-GUESS config file. ##' ##' Requires a pft xml object, a list of trait values for a single model run, diff --git a/models/lpjguess/tests/testthat.R b/models/lpjguess/tests/testthat.R index 59cf12a4475..481a3f96014 100644 --- a/models/lpjguess/tests/testthat.R +++ b/models/lpjguess/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) From 6bcda259b100ffe5369c6a9ec9d377c09d8dfa21 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 4 Sep 2024 11:20:14 -0700 Subject: [PATCH 13/17] relicense PEcAn.PRELES as BSD3 with agreement of all contributors --- CHANGELOG.md | 2 +- models/preles/LICENSE | 37 +++------------------------ models/preles/NEWS.md | 10 ++++++++ models/preles/R/runPRELES.jobsh.R | 10 -------- models/preles/R/write.config.PRELES.R | 10 -------- models/preles/tests/testthat.R | 8 ------ 6 files changed, 14 insertions(+), 63 deletions(-) create mode 100644 models/preles/NEWS.md diff --git a/CHANGELOG.md b/CHANGELOG.md index 0c16f9f9c6e..badfa5286cf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,7 +16,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha * `apps/api` * Shiny apps `dbsync`, `Data-Ingest`, `Elicitation`, `ForecastingDashboard`, `global-sensitivity`, `Pecan.depend`, and `SDAdashboard` * 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.SIBCASA`, `PEcAn.STICS`, and the new model package template. + * 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.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/models/preles/LICENSE b/models/preles/LICENSE index 5a9e44128f1..09ef35a60b4 100644 --- a/models/preles/LICENSE +++ b/models/preles/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/models/preles/NEWS.md b/models/preles/NEWS.md new file mode 100644 index 00000000000..460c0509e66 --- /dev/null +++ b/models/preles/NEWS.md @@ -0,0 +1,10 @@ +# PEcAn.PRELES 1.7.3.9000 + +## License change +* PEcAn.PRELES is now distributed under the BSD three-clause license instead of the NCSA Open Source license. + + +# PEcAn.PRELES 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/models/preles/R/runPRELES.jobsh.R b/models/preles/R/runPRELES.jobsh.R index deb925a4b3a..26237e003d5 100644 --- a/models/preles/R/runPRELES.jobsh.R +++ b/models/preles/R/runPRELES.jobsh.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 -#------------------------------------------------------------------------------- - -#--------------------------------------------------------------------------------------------------# ##' @title Function to process ncdf file, run PRELES model, and convert output .nc file in CF standard ##' @param in.path location on disk where inputs are stored ##' @param in.prefix prefix of input and output files diff --git a/models/preles/R/write.config.PRELES.R b/models/preles/R/write.config.PRELES.R index fb31d2e705d..9a7e6423247 100644 --- a/models/preles/R/write.config.PRELES.R +++ b/models/preles/R/write.config.PRELES.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 -#------------------------------------------------------------------------------- - -##-------------------------------------------------------------------------------------------------# ##' Writes a PRELES config file. ##' ##' @name write.config.PRELES diff --git a/models/preles/tests/testthat.R b/models/preles/tests/testthat.R index 73f5a5f9fb8..4d3ef970446 100644 --- a/models/preles/tests/testthat.R +++ b/models/preles/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) From 05edb4915bdc73d7520efb511a6bb8a24c6668a3 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 4 Sep 2024 11:35:15 -0700 Subject: [PATCH 14/17] relicense PEcAn.SIPNET as BSD3 with agreement of all contributors --- CHANGELOG.md | 2 +- models/sipnet/LICENSE | 37 +++----------------------- models/sipnet/NEWS.md | 13 +++++++++ models/sipnet/R/met2model.SIPNET.R | 10 ------- models/sipnet/R/model2netcdf.SIPNET.R | 9 ------- models/sipnet/R/read_restart.SIPNET.R | 9 ------- models/sipnet/R/sample.IC.SIPNET.R | 9 ------- models/sipnet/R/split_inputs.SIPNET.R | 9 ------- models/sipnet/R/write.configs.SIPNET.R | 10 ------- models/sipnet/R/write_restart.SIPNET.R | 9 ------- models/sipnet/tests/testthat.R | 8 ------ 11 files changed, 17 insertions(+), 108 deletions(-) create mode 100644 models/sipnet/NEWS.md diff --git a/CHANGELOG.md b/CHANGELOG.md index badfa5286cf..d69a3014c82 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,7 +16,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha * `apps/api` * Shiny apps `dbsync`, `Data-Ingest`, `Elicitation`, `ForecastingDashboard`, `global-sensitivity`, `Pecan.depend`, and `SDAdashboard` * 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.STICS`, and the new model package template. + * 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/models/sipnet/LICENSE b/models/sipnet/LICENSE index 5a9e44128f1..09ef35a60b4 100644 --- a/models/sipnet/LICENSE +++ b/models/sipnet/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/models/sipnet/NEWS.md b/models/sipnet/NEWS.md new file mode 100644 index 00000000000..e79578461af --- /dev/null +++ b/models/sipnet/NEWS.md @@ -0,0 +1,13 @@ +# PEcAn.SIPNET 1.8.0.9000 + +## License change +* PEcAn.SIPNET is now distributed under the BSD three-clause license instead of the NCSA Open Source license. + +# PEcAn.SIPNET 1.8.0 + +* Support for all Sipnet variables in read_restart and write_restart, for integration with state data assimilation workflows + +# PEcAn.SIPNET 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/models/sipnet/R/met2model.SIPNET.R b/models/sipnet/R/met2model.SIPNET.R index 1334e284317..919137eadbf 100644 --- a/models/sipnet/R/met2model.SIPNET.R +++ b/models/sipnet/R/met2model.SIPNET.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 -#------------------------------------------------------------------------------- - # R Code to convert NetCDF CF met files into SIPNET met files ## If files already exist in 'Outfolder', the default function is NOT to overwrite them and only diff --git a/models/sipnet/R/model2netcdf.SIPNET.R b/models/sipnet/R/model2netcdf.SIPNET.R index ca01fff0814..96a2b016abc 100644 --- a/models/sipnet/R/model2netcdf.SIPNET.R +++ b/models/sipnet/R/model2netcdf.SIPNET.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 -#------------------------------------------------------------------------------- - #' Merge multiple NetCDF files into one #' #' @param files \code{character}. List of filepaths, which should lead to NetCDF files. diff --git a/models/sipnet/R/read_restart.SIPNET.R b/models/sipnet/R/read_restart.SIPNET.R index adda2f55716..2260c71a476 100755 --- a/models/sipnet/R/read_restart.SIPNET.R +++ b/models/sipnet/R/read_restart.SIPNET.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 -#------------------------------------------------------------------------------- - ##' @title Read restart function for SDA with SIPNET ##' ##' @author Ann Raiho \email{araiho@@nd.edu} diff --git a/models/sipnet/R/sample.IC.SIPNET.R b/models/sipnet/R/sample.IC.SIPNET.R index d1578c4df33..0a68647d4fc 100644 --- a/models/sipnet/R/sample.IC.SIPNET.R +++ b/models/sipnet/R/sample.IC.SIPNET.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 -#------------------------------------------------------------------------------- - ## samples intial conditions for SIPNET ##' @title sample.IC.SIPNET ##' @name sample.IC.SIPNET diff --git a/models/sipnet/R/split_inputs.SIPNET.R b/models/sipnet/R/split_inputs.SIPNET.R index cd674647817..b47289d567a 100644 --- a/models/sipnet/R/split_inputs.SIPNET.R +++ b/models/sipnet/R/split_inputs.SIPNET.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 -#------------------------------------------------------------------------------- - ## split clim file into smaller time units to use in KF ##' @title split_inputs.SIPNET ##' @name split_inputs.SIPNET diff --git a/models/sipnet/R/write.configs.SIPNET.R b/models/sipnet/R/write.configs.SIPNET.R index ffa65a5ee62..c294808b7b5 100755 --- a/models/sipnet/R/write.configs.SIPNET.R +++ b/models/sipnet/R/write.configs.SIPNET.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 -#------------------------------------------------------------------------------- - -#--------------------------------------------------------------------------------------------------# ##' Writes a configuration files for your model ##' @name write.config.SIPNET ##' @title Writes a configuration files for SIPNET model diff --git a/models/sipnet/R/write_restart.SIPNET.R b/models/sipnet/R/write_restart.SIPNET.R index 455266f971e..6bd62c3b3a7 100755 --- a/models/sipnet/R/write_restart.SIPNET.R +++ b/models/sipnet/R/write_restart.SIPNET.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 -#------------------------------------------------------------------------------- - ##' @title write_restart.SIPNET ##' @name write_restart.SIPNET ##' @author Ann Raiho \email{araiho@@nd.edu} diff --git a/models/sipnet/tests/testthat.R b/models/sipnet/tests/testthat.R index 339f0c32a30..7a1fc04289f 100644 --- a/models/sipnet/tests/testthat.R +++ b/models/sipnet/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) From d4b982c8429dbfc95fac9da01ef53e86768adc94 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 4 Sep 2024 11:42:10 -0700 Subject: [PATCH 15/17] relicense BenchmarkReport as BSD3 with agreement of all contributors --- CHANGELOG.md | 2 +- shiny/BenchmarkReport/LICENSE | 37 +++-------------------------------- 2 files changed, 4 insertions(+), 35 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d69a3014c82..9505f617768 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,7 +14,7 @@ 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`, `Pecan.depend`, and `SDAdashboard` + * Shiny apps `dbsync`, `BenchmarkReport`, `Data-Ingest`, `Elicitation`, `ForecastingDashboard`, `global-sensitivity`, `Pecan.depend`, and `SDAdashboard` * 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`. diff --git a/shiny/BenchmarkReport/LICENSE b/shiny/BenchmarkReport/LICENSE index 26efbfea4dc..09ef35a60b4 100644 --- a/shiny/BenchmarkReport/LICENSE +++ b/shiny/BenchmarkReport/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 From f0b2c9ec052ae1b62b100692f28859ac3519994c Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 4 Sep 2024 11:44:21 -0700 Subject: [PATCH 16/17] relicense ViewMet as BSD3 with agreement of all contributors --- CHANGELOG.md | 2 +- shiny/ViewMet/LICENSE | 37 +++---------------------------------- 2 files changed, 4 insertions(+), 35 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9505f617768..34a88e69145 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,7 +14,7 @@ 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`, `BenchmarkReport`, `Data-Ingest`, `Elicitation`, `ForecastingDashboard`, `global-sensitivity`, `Pecan.depend`, and `SDAdashboard` + * 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`. diff --git a/shiny/ViewMet/LICENSE b/shiny/ViewMet/LICENSE index 5a9e44128f1..09ef35a60b4 100644 --- a/shiny/ViewMet/LICENSE +++ b/shiny/ViewMet/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 From e64eba218ffd0e3e7f3f0f5186b912a274c76541 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Wed, 4 Sep 2024 11:49:47 -0700 Subject: [PATCH 17/17] majority of packages are now BSD3, so move to top of root LICENSE --- LICENSE | 67 ++++++++++++++++++++++++++++++--------------------------- 1 file changed, 35 insertions(+), 32 deletions(-) diff --git a/LICENSE b/LICENSE index 69b3e155809..91ed7f17c2b 100644 --- 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.