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Relicense 16 more packages as BSD3 #3371

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Sep 8, 2024
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c76ba6f
relicense PEcAn.DB as BSD3 with agreement of all contributors
infotroph Sep 4, 2024
3f4928f
relicense PEcAn.visualization as BSD3 with agreement of all contributors
infotroph Sep 4, 2024
6d0428c
relicense PEcAn.allometry as BSD3 with agreement of all contributors
infotroph Sep 4, 2024
76d3039
relicense PEcAn.assim.batch as BSD3 with agreement of all contributors
infotroph Sep 4, 2024
df35aae
relicense PEcAn.MA as BSD3 with agreement of all contributors
infotroph Sep 4, 2024
85a254f
relicense PEcAn.photosynthesis as BSD3 with agreement of all contribu…
infotroph Sep 4, 2024
a5d0a16
relicense PEcAn.priors as BSD3 with agreement of all contributors
infotroph Sep 4, 2024
28fc4c8
relicense PEcAn.CLM45 as BSD3 with agreement of all contributors
infotroph Sep 4, 2024
7e6eae5
relicense PEcAn.DALEC as BSD3 with agreement of all contributors
infotroph Sep 4, 2024
837f963
relicense PEcAn.JULES as BSD3 with agreement of all contributors
infotroph Sep 4, 2024
a9a32b7
relicense PEcAn.LINKAGES as BSD3 with agreement of all contributors
infotroph Sep 4, 2024
c429ae7
relicense PEcAn.LPJGUESS as BSD3 with agreement of all contributors
infotroph Sep 4, 2024
6bcda25
relicense PEcAn.PRELES as BSD3 with agreement of all contributors
infotroph Sep 4, 2024
05edb49
relicense PEcAn.SIPNET as BSD3 with agreement of all contributors
infotroph Sep 4, 2024
d4b982c
relicense BenchmarkReport as BSD3 with agreement of all contributors
infotroph Sep 4, 2024
f0b2c9e
relicense ViewMet as BSD3 with agreement of all contributors
infotroph Sep 4, 2024
e64eba2
majority of packages are now BSD3, so move to top of root LICENSE
infotroph Sep 4, 2024
afbf043
Merge branch 'develop' into relicense-16-more
mdietze Sep 8, 2024
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8 changes: 4 additions & 4 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -15,10 +15,10 @@ For more information about this file see also [Keep a Changelog](http://keepacha

- The following components have changed their licensing. With approval of all their contributors, we now provide them under a BSD 3-clause license rather than the previously used NCSA Open Source license. As a reminder, we intend to relicense the entire system and this list will expand as we gather permission from the relevant copyright owners.
* `apps/api`
* Shiny apps `dbsync`, `Data-Ingest`, `Elicitation`, `ForecastingDashboard`, `global-sensitivity`, `Pecan.depend`, and `SDAdashboard`
* Base packages `PEcAn.all`, `PEcAn.QAQC`, `PEcAn.remote`, `PEcAn.settings`, and `PEcAn.workflow`
* Model packages `PEcAn.BASGRA`, `PEcAn.dvmdostem`, `PEcAn.FATES`, `PEcAn.GDAY`, `PEcAn.LDNDC`, `PEcAn.MAAT`, `PEcAn.MAESPA`, `PEcAn.SIBCASA`, `PEcAn.STICS`, and the new model package template.
* Modules `PEcAn.data.mining`, `PEcAn.emulator`, amd `PEcAn.RTM`.
* Shiny apps `dbsync`, `BenchmarkReport`, `Data-Ingest`, `Elicitation`, `ForecastingDashboard`, `global-sensitivity`, `Pecan.depend`, `SDAdashboard`, and `ViewMet`
* Base packages `PEcAn.all`, `PEcAn.DB`, `PEcAn.QAQC`, `PEcAn.remote`, `PEcAn.settings`, `PEcAn.visualization`, and `PEcAn.workflow`
* Model packages `PEcAn.BASGRA`, `PEcAn.CLM45`, `PEcAn.DALEC`, `PEcAn.dvmdostem`, `PEcAn.FATES`, `PEcAn.GDAY`, `PEcAn.JULES`, `PEcAn.LDNDC`, `PEcAn.LINKAGES`, `PEcAn.LPJGUESS`, `PEcAn.MAAT`, `PEcAn.MAESPA`, `PEcAn.PRELES`, `PEcAn.SIBCASA`, `PEcAn.SIPNET`, `PEcAn.STICS`, and the new model package template.
* Modules `PEcAn.allometry`, `PEcAn.assim.batch`, `PEcAn.data.mining`, `PEcAn.emulator`, `PEcAn.MA`, `PEcAn.photosynthesis`, `PEcAn.priors`, and `PEcAn.RTM`.

### Removed

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67 changes: 35 additions & 32 deletions LICENSE
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@@ -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.

Expand Down Expand Up @@ -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.
32 changes: 3 additions & 29 deletions base/db/LICENSE
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@@ -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
2 changes: 2 additions & 0 deletions base/db/NEWS.md
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@@ -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
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10 changes: 0 additions & 10 deletions base/db/R/assign.treatments.R
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@@ -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
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10 changes: 0 additions & 10 deletions base/db/R/check.lists.R
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@@ -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.
##'
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9 changes: 0 additions & 9 deletions base/db/R/covariate.functions.R
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@@ -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 #################################

##--------------------------------------------------------------------------------------------------#
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9 changes: 0 additions & 9 deletions base/db/R/dbfiles.R
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@@ -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
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10 changes: 0 additions & 10 deletions base/db/R/derive.trait.R
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@@ -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.
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10 changes: 0 additions & 10 deletions base/db/R/derive.traits.R
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@@ -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.
##'
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10 changes: 0 additions & 10 deletions base/db/R/fetch.stats2se.R
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@@ -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
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10 changes: 0 additions & 10 deletions base/db/R/get.trait.data.R
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@@ -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:
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10 changes: 0 additions & 10 deletions base/db/R/get.trait.data.pft.R
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@@ -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!
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8 changes: 0 additions & 8 deletions base/db/R/pft.add.spp.R
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@@ -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
##'
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10 changes: 0 additions & 10 deletions base/db/R/query.data.R
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@@ -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
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9 changes: 0 additions & 9 deletions base/db/R/query.pft.R
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@@ -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
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9 changes: 0 additions & 9 deletions base/db/R/query.prior.R
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@@ -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.
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10 changes: 0 additions & 10 deletions base/db/R/query.trait.data.R
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@@ -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,
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9 changes: 0 additions & 9 deletions base/db/R/query.traits.R
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@@ -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
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10 changes: 0 additions & 10 deletions base/db/R/query.yields.R
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@@ -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
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9 changes: 0 additions & 9 deletions base/db/R/symmetric_setdiff.R
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@@ -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
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10 changes: 0 additions & 10 deletions base/db/R/take.samples.R
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@@ -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
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