Merge branch 'develop' into integ-testing

CHANGELOG.md

@@ -7,6 +7,21 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 
 ## [Unreleased]
 
+### Added
+
+### Fixed
+
+### Changed
+- The following components have changed their licensing. With approval of all their contributors, we now provide them under a BSD 3-clause license rather than the previously used NCSA Open Source license. As a reminder, we intend to relicense the entire system and this list will expand as we gather permission from the relevant copyright owners.
+    * Shiny apps `dbsync`, `Data-Ingest`, and `Elicitation`
+    * Base packages `PEcAn.all` and `PEcAn.QAQC`
+    * Model packages `PEcAn.LDNDC`, `PEcAn.SIBCASA`, and `PEcAn.STICS`
+
+### Removed
+
+
+## [1.8.0] - 2024-07-12
+
 ### Added
 - Created a new soilgrids function to extract the mean soil organic carbon profile with associated undertainty values at each depth for any lat/long location (#3040). Function was created for the CMS SDA workflow
 

CITATION.cff

@@ -2,7 +2,7 @@ cff-version: 1.2.0
 title: >-
   The Predictive Ecosystem Analyzer (PEcAn) is an
   integrated ecological bioinformatics toolbox.
-version: 1.7.2
+version: 1.8.0
 abstract: >-
   The Predictive Ecosystem Analyzer (PEcAn) (see
   pecanproject.org) is an integrated ecological
@@ -77,7 +77,7 @@ authors:
   - affiliation: University of Cambridge
     given-names: Anne Thomas
     orcid: 'https://orcid.org/0000-0002-2808-6462'
-  - affiliation: CK Black Science Consulting
+  - affiliation: Pools and Fluxes LLC
     given-names: Chris Black
     orcid: 'https://orcid.org/0000-0001-8382-298X'
   - affiliation: Rutgers University

LICENSE

@@ -32,3 +32,37 @@ 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.
 
+
+
+
+--------------------
+
+
+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.

Makefile

@@ -46,7 +46,7 @@ ALL_PKGS_D := $(BASE_D) $(MODULES_D) $(MODELS_D)
 
 SETROPTIONS := "options(Ncpus = ${NCPUS})"
 
-EXPECTED_ROXYGEN_VERSION := 7.3.1
+EXPECTED_ROXYGEN_VERSION := 7.3.2
 INSTALLED_ROXYGEN_VERSION := $(shell Rscript \
 	-e "if (requireNamespace('roxygen2', quietly = TRUE)) {" \
 	-e   "cat(as.character(packageVersion('roxygen2')))" \

base/all/DESCRIPTION

@@ -2,8 +2,7 @@ Package: PEcAn.all
 Type: Package
 Title: PEcAn functions used for ecological forecasts and
     reanalysis
-Version: 1.7.2.9000
-Date: 2021-10-04
+Version: 1.8.0.9000
 Authors@R: c(person("Mike", "Dietze", role = c("aut"),
                      email = "[email protected]"),
              person("David", "LeBauer", role = c("aut", "cre"),
@@ -79,4 +78,4 @@ Copyright: Authors
 LazyData: true
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

base/all/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

base/all/NEWS.md

@@ -1,4 +1,9 @@
-# PEcAn.all 1.7.2.9000
+# PEcAn.all 1.8.0.9000
+
+## License change
+* PEcAn.all is now distributed under the BSD three-clause license instead of the NCSA Open Source license.
+
+# PEcAn.all 1.8.0
 
 ## Added
 

base/all/data-raw/record_versions.R

@@ -1,5 +1,7 @@
 #!/usr/bin/env Rscript
 
+# SUPERSEDED, DO NOT USE -- instead just edit the CSVs in `data/`.
+
 # Adds the current versions of all PEcAn packages to `pecan_version_history`,
 # and adds the specified tag and version number to `pecan_releases`.
 

base/all/data/pecan_releases.R

@@ -0,0 +1,8 @@
+
+pecan_releases <- utils::read.csv(
+  "pecan_releases.csv",
+  colClasses = c(tag = "character", date = "Date", version = "character"))
+
+pecan_releases$version <- package_version(pecan_releases$version)
+
+rownames(pecan_releases) <- pecan_releases$tag

base/all/data/pecan_releases.csv

@@ -0,0 +1,34 @@
+"tag","date","version"
+"v1.0",2011-11-03,1.0
+"v1.0.1",2011-11-14,1.0.1
+"v1.1",2012-05-24,1.1
+"v1.2.5",2012-07-22,1.2.5
+"v1.2.6",2012-08-20,1.2.6
+"v1.3",2013-04-21,1.3
+"v1.3.2",2013-07-17,1.3.2
+"v1.3.4",2014-03-25,1.3.4
+"v1.3.5",2014-05-16,1.3.5
+"v1.3.6",2014-06-28,1.3.6
+"1.3.7",2014-09-09,1.3.7
+"v1.3.6.1",2014-09-27,1.3.6.1
+"v1.4.0",2014-12-10,1.4.0
+"v1.4.1",2015-01-27,1.4.1
+"v1.4.2",2015-05-08,1.4.2
+"v.1.4.3",2015-07-22,1.4.3
+"v1.4.4",2015-11-11,1.4.4
+"v1.4.5",2016-03-03,1.4.5
+"1.4.6",2016-05-06,1.4.6
+"1.4.7",2016-07-14,1.4.7
+"v1.4.8",2016-08-12,1.4.8
+"v1.4.9",2016-12-10,1.4.9
+"v1.4.10",2017-03-28,1.4.10
+"v1.4.10.1",2017-04-21,1.4.10.1
+"v1.5.0",2017-07-13,1.5.0
+"v1.5.1",2017-10-06,1.5.1
+"v1.5.2",2017-12-08,1.5.2
+"v1.5.3",2018-05-17,1.5.3
+"v1.6.0",2018-10-02,1.6.0
+"v1.7.0",2018-12-10,1.7.0
+"v1.7.1",2019-09-20,1.7.1
+"v1.7.2",2021-10-08,1.7.2
+"v1.8.0",2024-07-12,1.8.0

base/all/data/pecan_version_history.R

@@ -0,0 +1,25 @@
+
+
+pecan_version_history <- utils::read.csv(
+  "pecan_version_history.csv",
+  colClasses = "character",
+  check.names = FALSE)
+
+# We'd like to parse strictly to catch invalid versions (probably typos).
+# But we _need_ to allow NAs... and in R < 4.4, package_version did not
+# accept NAs unless strict=FALSE.
+strict <- TRUE
+na_version <- try(
+  package_version(NA_character_, strict = strict),
+  silent = TRUE)
+if (inherits(na_version, "try-error")) {
+  strict <- FALSE
+}
+
+for (col in colnames(pecan_version_history)) {
+  if (col != "package") {
+    pecan_version_history[[col]] <- package_version(
+      pecan_version_history[[col]],
+      strict = strict)
+  }
+}

base/all/data/pecan_version_history.csv

@@ -0,0 +1,54 @@
+"package","v1.0","v1.0.1","v1.1","v1.2.5","v1.2.6","v1.3","v1.3.2","v1.3.4","v1.3.5","v1.3.6","v1.3.6.1","1.3.7","v1.4.0","v1.4.1","v1.4.2","v.1.4.3","v1.4.4","v1.4.5","1.4.6","1.4.7","v1.4.8","v1.4.9","v1.4.10","v1.4.10.1","v1.5.0","v1.5.1","v1.5.2","v1.5.3","v1.6.0","v1.7.0","v1.7.1","v1.7.2","v1.8.0"
+"PEcAn",NA,NA,NA,1.2.5,1.2.6,1.2.6,1.3.1,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"PECAn",1.0,1.0,1.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"PEcAn.all",NA,NA,NA,1.2.5,1.2.6,1.2.6,1.3.1,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.8.0
+"PEcAn.allometry",NA,NA,NA,NA,NA,NA,NA,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3
+"PEcAn.assim.batch",NA,NA,NA,NA,1.2.6,1.2.6,1.3.1,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.8.0
+"PEcAn.assim.sequential",NA,NA,NA,NA,1.2.6,1.2.6,1.3.1,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,NA
+"PEcAn.BASGRA",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.7.2,1.8.0
+"PEcAn.benchmark",NA,NA,NA,NA,NA,NA,NA,NA,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3
+"PEcAn.BIOCRO",NA,NA,NA,NA,NA,1.2,1.3.1,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3
+"PEcAn.CABLE",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3
+"PEcAn.CLM45",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3
+"PEcAn.common",NA,NA,NA,1.2.5,1.2.6,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"PEcAn.dalec",NA,NA,NA,NA,NA,NA,NA,1.3.1,1.3.1,1.3.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"PEcAn.DALEC",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.3.7,1.3.1,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3
+"PEcAn.data.atmosphere",NA,NA,NA,NA,NA,1.2.6,1.3.1,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.8.0
+"PEcAn.data.hydrology",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,NA
+"PEcAn.data.land",NA,NA,NA,1.2.5,1.2.6,1.2.6,1.3.1,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.8.0
+"PEcAn.data.mining",NA,NA,NA,NA,NA,NA,NA,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3
+"PEcAn.data.remote",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.8.0
+"PEcAn.DB",NA,NA,NA,1.2.5,1.2.6,1.2.6,1.3.1,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.8.0
+"PEcAn.dvmdostem",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3
+"PEcAn.ED",NA,NA,NA,1.2.5,1.2.6,1.2.6,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"PEcAn.ED2",NA,NA,NA,NA,NA,NA,1.3.1,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.8.0
+"PEcAn.emulator",NA,NA,NA,NA,NA,1.0,1.3.1,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.8.0
+"PEcAn.FATES",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3
+"PEcAn.GDAY",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3
+"PEcAn.IBIS",NA,NA,NA,1.2.5,1.2.6,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"PEcAn.JULES",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3
+"PEcAn.LDNDC",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.0.0
+"PEcAn.LINKAGES",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3
+"PEcAn.logger",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.8.0,1.8.2
+"PEcAn.LPJGUESS",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3
+"PEcAn.MA",NA,NA,NA,1.2.5,1.2.6,1.2.6,1.3.1,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3
+"PEcAn.MAAT",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3
+"PEcAn.MAESPA",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3
+"PEcAn.ModelName",NA,NA,NA,NA,NA,1.2,1.3.1,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.8.0
+"PEcAn.photosynthesis",NA,NA,NA,NA,NA,1.2.6,1.3.1,1.3.3,1.3.3,1.3.6,1.3.7,1.3.6,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3
+"PEcAn.PRELES",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3
+"PEcAn.priors",NA,NA,NA,NA,NA,1.2.6,1.3.1,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3
+"PEcAn.qaqc",NA,NA,NA,NA,NA,1.0,1.3.1,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3
+"PEcAn.remote",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.8.0
+"PEcAn.rtm",NA,NA,NA,1.2.5,1.2.6,1.2.6,1.3.1,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+"PEcAn.settings",NA,NA,NA,NA,NA,NA,1.3.1,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.8.0
+"PEcAn.SIBCASA",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,0.0.1
+"PEcAn.SIPNET",NA,NA,NA,1.2.5,1.2.6,1.2.6,1.3.1,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.8.0
+"PEcAn.STICS",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.7.2,1.8.0
+"PEcAn.uncertainty",NA,NA,NA,1.2.5,1.2.6,1.2.6,1.3.1,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.8.0
+"PEcAn.utils",NA,NA,NA,1.2.5,1.2.6,1.2.6,1.3.1,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.8.0
+"PEcAn.visualization",NA,NA,NA,1.2.5,1.2.6,1.2.6,1.3.1,1.3.3,1.3.3,1.3.3,1.3.7,1.3.3,1.4.0,1.4.1,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.8.0
+"PEcAn.workflow",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.8.0
+"pecanapi",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.7.0,1.7.1,NA,NA
+"PEcAnAssimSequential",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.8.0
+"PEcAnRTM",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.4.2,1.4.3,1.4.4,1.4.5,1.4.6,1.4.7,1.4.8,1.4.9,1.4.10,1.4.10.1,1.5.0,1.5.1,1.5.2,1.5.3,1.6.0,1.7.0,1.7.1,1.7.2,1.7.3

base/all/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)
 

base/all/tests/testthat/test.workflow.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
-#-------------------------------------------------------------------------------
-
 # TODO This is an integration test (#1125)
 
 #context("tests of overall workflow")

base/db/DESCRIPTION

@@ -1,8 +1,7 @@
 Package: PEcAn.DB
 Type: Package
 Title: PEcAn Functions Used for Ecological Forecasts and Reanalysis
-Version: 1.7.2.9000
-Date: 2021-10-04
+Version: 1.8.0.9000
 Authors@R: c(person("David", "LeBauer", role = c("aut", "cre"),
                      email = "[email protected]"),
              person("Mike", "Dietze", role = c("aut"),
@@ -81,4 +80,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

base/db/NEWS.md

@@ -1,4 +1,8 @@
-# PEcAn.DB 1.7.2.9000
+# PEcAn.DB 1.8.0.9000
+
+
+
+# PEcAn.DB 1.8.0
 
 ## Added
 

base/logger/DESCRIPTION

@@ -1,7 +1,6 @@
 Package: PEcAn.logger
 Title: Logger Functions for 'PEcAn'
-Version: 1.8.1.9000
-Date: 2021-07-27
+Version: 1.8.2.9000
 Authors@R: c(person("Rob", "Kooper", role = c("aut", "cre"),
                      email = "[email protected]"),
              person("Alexey", "Shiklomanov", role = c("aut"),
@@ -30,5 +29,5 @@ Suggests:
     withr
 License: BSD_3_clause + file LICENSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)

base/logger/NEWS.md

@@ -1,4 +1,8 @@
-# PEcAn.logger (development version)
+# PEcAn.logger 1.8.2.9000
+
+
+
+# PEcAn.logger 1.8.2
 
 - `PEcAn.logger::setLevel()` now invisibly returns the previously set logger level