Merge branch 'downscale/hourly' of https://github.com/Snafkin547/pecan …

…into downscale/hourly

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 package `PEcAn.all`
+    * Model packages `PEcAn.LDNDC` and `PEcAn.SIBCASA`
+
+### 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

CONTRIBUTING.md

@@ -86,7 +86,16 @@ git checkout -b GH-issuenumber-title-of-issue
 
 ### Work and commit
 
-Do you work, and commit as you see fit.Make your commit messages helpful.
+Do you work, and commit as you see fit. Make your commit messages helpful.
+
+### Update other files (CITATION, NEWS, CHANGELOG)
+
+Your PR should include:
+
+- CITATION.cff: if you are making or have made a non-trivial contribution (please ask if unsure; our approach is inclusive), add your name to the author section.
+- NEWS.md: for each package
+- CHANGELOG.md: add changes to [Unreleased] section
+
 
 ### Push your changes up to GitHub
 
@@ -96,6 +105,7 @@ If this is the first time pushing to GitHub you will need to extended command, o
 git push -u origin GH-issuenumber-title-of-issue
 ```
 
+
 ### Pull Request
 
  When finished create a pull request from your branch to the main pecan repository.

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
 

base/qaqc/DESCRIPTION

@@ -1,8 +1,7 @@
 Package: PEcAn.qaqc
 Type: Package
 Title: QAQC
-Version: 1.7.2
-Date: 2021-10-04
+Version: 1.7.3.9000
 Authors@R: c(person("David", "LeBauer", role = c("aut", "cre"),
                      email = "[email protected]"),
              person("Tess", "McCabe", role = c("aut"),
@@ -38,4 +37,4 @@ LazyData: FALSE
 Encoding: UTF-8
 VignetteBuilder: knitr
 Config/testthat/edition: 3
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

base/remote/DESCRIPTION

@@ -1,8 +1,7 @@
 Package: PEcAn.remote
 Type: Package
 Title: PEcAn Model Execution Utilities
-Version: 1.7.2
-Date: 2021-10-04
+Version: 1.8.0.9000
 Authors@R: c(person("David", "LeBauer", role = c("aut"),
                      email = "[email protected]"),
              person("Rob", "Kooper", role = c("aut", "cre"),
@@ -35,4 +34,4 @@ License: BSD_3_clause + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

base/remote/NEWS.md

@@ -1,6 +1,8 @@
-# PEcAn.remote 1.7.2.9000
+# PEcAn.remote 1.8.0.9000
 
 
+# PEcAn.remote 1.8.0
+
 ## Added
 
 * `start_rabbitmq` is now exported.