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robkooper committed Jul 13, 2024
2 parents 5c112ab + 1f4c805 commit 5617ceb
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -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

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4 changes: 2 additions & 2 deletions CITATION.cff
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Expand Up @@ -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
Expand Down Expand Up @@ -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
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107 changes: 48 additions & 59 deletions DEV-INTRO.md

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2 changes: 1 addition & 1 deletion Makefile
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Expand Up @@ -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')))" \
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5 changes: 2 additions & 3 deletions base/all/DESCRIPTION
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Expand Up @@ -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"),
Expand Down Expand Up @@ -79,4 +78,4 @@ Copyright: Authors
LazyData: true
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
RoxygenNote: 7.3.2
2 changes: 2 additions & 0 deletions base/all/data-raw/record_versions.R
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@@ -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`.

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8 changes: 8 additions & 0 deletions base/all/data/pecan_releases.R
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@@ -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
34 changes: 34 additions & 0 deletions base/all/data/pecan_releases.csv
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"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
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25 changes: 25 additions & 0 deletions base/all/data/pecan_version_history.R
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@@ -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)
}
}
54 changes: 54 additions & 0 deletions base/all/data/pecan_version_history.csv
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@@ -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
Binary file removed base/all/data/pecan_version_history.rda
Binary file not shown.
5 changes: 2 additions & 3 deletions base/db/DESCRIPTION
Original file line number Diff line number Diff line change
@@ -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"),
Expand Down Expand Up @@ -81,4 +80,4 @@ Copyright: Authors
LazyLoad: yes
LazyData: FALSE
Encoding: UTF-8
RoxygenNote: 7.3.1
RoxygenNote: 7.3.2
2 changes: 1 addition & 1 deletion base/db/NEWS.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# PEcAn.DB 1.7.2.9000
# PEcAn.DB 1.8.0

## Added

Expand Down
5 changes: 2 additions & 3 deletions base/logger/DESCRIPTION
Original file line number Diff line number Diff line change
@@ -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"),
Expand Down Expand Up @@ -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)
2 changes: 1 addition & 1 deletion base/logger/NEWS.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# PEcAn.logger (development version)
# PEcAn.logger 1.8.2

- `PEcAn.logger::setLevel()` now invisibly returns the previously set logger level

Expand Down
5 changes: 2 additions & 3 deletions base/qaqc/DESCRIPTION
Original file line number Diff line number Diff line change
@@ -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"),
Expand Down Expand Up @@ -38,4 +37,4 @@ LazyData: FALSE
Encoding: UTF-8
VignetteBuilder: knitr
Config/testthat/edition: 3
RoxygenNote: 7.3.1
RoxygenNote: 7.3.2
5 changes: 2 additions & 3 deletions base/remote/DESCRIPTION
Original file line number Diff line number Diff line change
@@ -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"),
Expand Down Expand Up @@ -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
2 changes: 1 addition & 1 deletion base/remote/NEWS.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# PEcAn.remote 1.7.2.9000
# PEcAn.remote 1.8.0


## Added
Expand Down
5 changes: 2 additions & 3 deletions base/settings/DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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)
10 changes: 4 additions & 6 deletions base/settings/R/check.all.settings.R
Original file line number Diff line number Diff line change
Expand Up @@ -260,13 +260,11 @@ check.bety.version <- function(dbcon) {
}

# check if database is newer
last_migration_date <- lubridate::ymd_hms(utils::tail(versions, n = 1))
pecan_release_date <- lubridate::ymd(
utils::packageDescription("PEcAn.DB")$Date)
if (last_migration_date > pecan_release_date) {
unknown_migrations <- setdiff(versions, .known_bety_migrations)
if (any(unknown_migrations)) {
PEcAn.logger::logger.warn(
"Last database migration", utils::tail(versions, n = 1),
"is more recent than this", pecan_release_date, "release of PEcAn.",
"Found database migration(s) not known by this release of PEcAn.settings:",
unknown_migrations,
"This could result in PEcAn not working as expected.")
}
}
Expand Down
69 changes: 69 additions & 0 deletions base/settings/R/known_bety_migrations.R
Original file line number Diff line number Diff line change
@@ -0,0 +1,69 @@
# List of the entries in bety table `schema_migrations` that are known to this
# version of PEcAn.settings. If a live query returns entries not in this table,
# we may wish to warn about a potential mismatch between package and database.
#
# TODO: Would it make sense to move this, and the checks it supports, to PEcAn.DB?
.known_bety_migrations <- c(
"1",
"20130104205059",
"20130104211901",
"20130104211946",
"20130109205535",
"20130222222929",
"20130425152503",
"20130624001504",
"20130629205658",
"20130707190720",
"20130717162614",
"20130813212131",
"20130829162053",
"20150904184512",
"20130830184559",
"20140418005637",
"20140422155957",
"20140423220457",
"20140506210037",
"20140515205254",
"20140521180349",
"20140604192901",
"20140617163304",
"20140610210928",
"20140621060009",
"20140623004229",
"20140624185610",
"20140708232320",
"20140729045640",
"20151007174432",
"20151011190026",
"20140904220035",
"20140904221818",
"20140909212759",
"20140915153555",
"20141009160121",
"20141208165401",
"20141211220550",
"20150202215147",
"20150202220519",
"20150213162341",
"20150313165132",
"20150521211114",
"20150624220952",
"20150624222656",
"20150625184958",
"20151014182146",
"20160303221049",
"20160412030352",
"20160523165531",
"20160617133217",
"20160711231257",
"20160720182233",
"20160930213737",
"20161003180105",
"20161005181021",
"20161129192658",
"20170118205944",
"20170415183619",
"20170712171513",
"20180510184222",
"20181129000515",
"20200329233137")
5 changes: 2 additions & 3 deletions base/utils/DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -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"),
Expand Down Expand Up @@ -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)
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