Bump package versions for v1.8.0

CHANGELOG.md

@@ -5,7 +5,7 @@ section for the next release.
 
 For more information about this file see also [Keep a Changelog](http://keepachangelog.com/) .
 
-## [Unreleased]
+## [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

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
 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/NEWS.md

@@ -1,4 +1,4 @@
-# PEcAn.all 1.7.2.9000
+# PEcAn.all 1.8.0
 
 ## Added
 

base/all/data/pecan_releases.csv

@@ -31,3 +31,4 @@
 "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/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
 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 +1,4 @@
-# PEcAn.DB 1.7.2.9000
+# 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
 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 +1,4 @@
-# PEcAn.logger (development version)
+# 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
 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
 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

@@ -1,4 +1,4 @@
-# PEcAn.remote 1.7.2.9000
+# PEcAn.remote 1.8.0
 
 
 ## Added

base/settings/DESCRIPTION

@@ -5,8 +5,7 @@ Authors@R: c(person("David", "LeBauer", role = c("aut", "cre"),
              person("Rob", "Kooper", role = c("aut"),
                      email = "[email protected]"),
              person("University of Illinois, NCSA", role = c("cph")))
-Version: 1.7.2
-Date: 2021-10-04
+Version: 1.8.0
 License: BSD_3_clause + file LICENSE
 Copyright: Authors
 LazyLoad: yes
@@ -29,5 +28,5 @@ Suggests:
     testthat (>= 2.0.0),
     withr
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)

base/utils/DESCRIPTION

@@ -2,8 +2,7 @@ Package: PEcAn.utils
 Type: Package
 Title: PEcAn Functions Used for Ecological Forecasts and
     Reanalysis
-Version: 1.7.2
-Date: 2021-10-04
+Version: 1.8.0
 Authors@R: c(person("Mike", "Dietze", role = c("aut"),
                      email = "[email protected]"),
              person("Rob", "Kooper", role = c("aut", "cre"),
@@ -58,5 +57,5 @@ License: BSD_3_clause + file LICENSE
 Copyright: Authors
 LazyData: true
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)

base/utils/NEWS.md

@@ -1,9 +1,15 @@
-# PEcAn.DB 1.7.2.9000
+# PEcAn.utils 1.8.0
 
 ## Added
 
 * Shifted `convert.input` function from `PEcAn.utils` to `PEcAn.DB` with a new name `convert_input`to remove circular dependency.
   (#3026; @nanu1605)
 * Added a stub function `convert.input`. (#3026; @nanu1605)
 * Updated unit conversions throughout PEcAn to use the `units` R package instead of the unmaintained `udunits2`. Note that both `units` and `udunits2` interface with the same underlying compiled code, so the `udunits2` *system library* is still required. (#2989; @nanu1605)
-* Fixed a bug in `ud_convert()` where it failed with objects of class "difftime" introduced by refactoring to use the `units` package instead of `udunits` (#3012)
+* Fixed a bug in `ud_convert()` where it failed with objects of class "difftime" introduced by refactoring to use the `units` package instead of `udunits` (#3012)
+
+# PEcAn.utils 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.

base/visualization/DESCRIPTION

@@ -1,8 +1,7 @@
 Package: PEcAn.visualization
 Type: Package
 Title: PEcAn visualization functions
-Version: 1.7.2
-Date: 2021-10-04
+Version: 1.8.0
 Authors@R: c(person("Mike", "Dietze", role = c("aut"),
                      email = "[email protected]"),
              person("David", "LeBauer", role = c("aut", "cre"),
@@ -50,5 +49,5 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)

base/workflow/DESCRIPTION

@@ -2,8 +2,7 @@ Package: PEcAn.workflow
 Type: Package
 Title: PEcAn Functions Used for Ecological Forecasts and
     Reanalysis
-Version: 1.7.2
-Date: 2021-10-04
+Version: 1.8.0
 Authors@R: c(person("Mike", "Dietze", role = c("aut"),
                      email = "[email protected]"),
              person("David", "LeBauer", role = c("aut", "cre"),
@@ -48,4 +47,4 @@ Suggests:
     withr
 Copyright: Authors
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

base/workflow/NEWS.md

@@ -1,4 +1,4 @@
-# PEcAn.workflow 1.7.2.9000
+# PEcAn.workflow 1.8.0
 
 * New functions `start_model_runs` and `runModule_start_model_runs`, both moved
   from package `PEcAn.remote` (where they were `start.model.runs` and

book_source/02_demos_tutorials_workflows/05_developer_workflows/03_coding_practices/04-roxygen.Rmd

@@ -84,7 +84,7 @@ When it is time for everyone to update to a newer Roxygen, follow the same proce
 * Run `make clean && make document` to be sure Roxygen has been run on all packages.
 * Check the console output for warnings from Roxygen, and fix them as needed. New versions often get pickier about formatting issues that used to be considered minor.
 * Run `./scripts/generate_dependencies.R` to update the version of Roxygen recorded as a Docker dependency.
-* Grep the PEcAn folder for the string `7.3.1` to make sure no references were missed.
+* Grep the PEcAn folder for the string `7.2.3` to make sure no references were missed.
   - e.g. this time I found  a remaining `RoxygenNote: 7.2.3` in models/cable/DESCRIPTION -- Make currently skips cable, so I redocumented it manually.
 * Review all changes.
   - The changes should mostly just consist of updated `RoxygenNote:` lines in all the DESCRIPTION files.

docker/depends/pecan_package_dependencies.csv

@@ -485,48 +485,48 @@
 "rmarkdown",">= 2.19","modules/assim.batch","Suggests",FALSE
 "rmarkdown",">= 2.19","modules/meta.analysis","Suggests",FALSE
 "rmarkdown",">= 2.19","modules/photosynthesis","Suggests",FALSE
-"roxygen2","== 7.3.1","base/all","Roxygen",FALSE
-"roxygen2","== 7.3.1","base/db","Roxygen",FALSE
-"roxygen2","== 7.3.1","base/logger","Roxygen",FALSE
-"roxygen2","== 7.3.1","base/qaqc","Roxygen",FALSE
-"roxygen2","== 7.3.1","base/remote","Roxygen",FALSE
-"roxygen2","== 7.3.1","base/settings","Roxygen",FALSE
-"roxygen2","== 7.3.1","base/utils","Roxygen",FALSE
-"roxygen2","== 7.3.1","base/visualization","Roxygen",FALSE
-"roxygen2","== 7.3.1","base/workflow","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/basgra","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/biocro","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/cable","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/clm45","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/dalec","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/dvmdostem","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/ed","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/fates","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/gday","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/jules","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/ldndc","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/linkages","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/lpjguess","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/maat","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/maespa","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/preles","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/sibcasa","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/sipnet","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/stics","Roxygen",FALSE
-"roxygen2","== 7.3.1","models/template","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/allometry","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/assim.batch","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/assim.sequential","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/benchmark","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/data.atmosphere","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/data.land","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/data.remote","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/emulator","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/meta.analysis","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/photosynthesis","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/priors","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/rtm","Roxygen",FALSE
-"roxygen2","== 7.3.1","modules/uncertainty","Roxygen",FALSE
+"roxygen2","== 7.3.2","base/all","Roxygen",FALSE
+"roxygen2","== 7.3.2","base/db","Roxygen",FALSE
+"roxygen2","== 7.3.2","base/logger","Roxygen",FALSE
+"roxygen2","== 7.3.2","base/qaqc","Roxygen",FALSE
+"roxygen2","== 7.3.2","base/remote","Roxygen",FALSE
+"roxygen2","== 7.3.2","base/settings","Roxygen",FALSE
+"roxygen2","== 7.3.2","base/utils","Roxygen",FALSE
+"roxygen2","== 7.3.2","base/visualization","Roxygen",FALSE
+"roxygen2","== 7.3.2","base/workflow","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/basgra","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/biocro","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/cable","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/clm45","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/dalec","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/dvmdostem","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/ed","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/fates","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/gday","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/jules","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/ldndc","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/linkages","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/lpjguess","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/maat","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/maespa","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/preles","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/sibcasa","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/sipnet","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/stics","Roxygen",FALSE
+"roxygen2","== 7.3.2","models/template","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/allometry","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/assim.batch","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/assim.sequential","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/benchmark","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/data.atmosphere","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/data.land","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/data.remote","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/emulator","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/meta.analysis","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/photosynthesis","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/priors","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/rtm","Roxygen",FALSE
+"roxygen2","== 7.3.2","modules/uncertainty","Roxygen",FALSE
 "RPostgres","*","base/db","Suggests",FALSE
 "RPostgreSQL","*","base/db","Suggests",FALSE
 "RPostgreSQL","*","models/biocro","Suggests",FALSE

models/basgra/DESCRIPTION

@@ -1,8 +1,7 @@
 Package: PEcAn.BASGRA
 Type: Package
 Title: PEcAn Package for Integration of the BASGRA Model
-Version: 1.7.2
-Date: 2021-10-04
+Version: 1.8.0
 Authors@R: c(person("Istem", "Fer", role = c("aut", "cre"),
                      email = "[email protected]"),
              person("University of Illinois, NCSA", role = c("cph")))
@@ -24,4 +23,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

models/biocro/DESCRIPTION

@@ -1,8 +1,7 @@
 Package: PEcAn.BIOCRO
 Type: Package
 Title: PEcAn Package for Integration of the BioCro Model
-Version: 1.7.2
-Date: 2021-10-04
+Version: 1.7.3
 Authors@R: c(person("David", "LeBauer", role = c("aut", "cre"),
                      email = "[email protected]"),
              person("Chris", "Black", role = c("aut"),
@@ -39,4 +38,4 @@ Copyright: Energy Biosciences Institute, Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

models/cable/DESCRIPTION

@@ -1,8 +1,7 @@
 Package: PEcAn.CABLE
 Type: Package
 Title: PEcAn package for integration of the CABLE model
-Version: 1.7.2
-Date: 2021-10-04
+Version: 1.7.3
 Authors@R: c(person("Kaitlin", "Ragosta", role = c("aut")),
              person("Tony", "Gardella", role = c("aut", "cre"),
                      email = "[email protected]"),
@@ -22,4 +21,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2