From 37ee1af9c5e618be4fdc0025eac083c90345b50c Mon Sep 17 00:00:00 2001 From: Harsh Agrawal Date: Tue, 29 Oct 2024 02:39:19 +0530 Subject: [PATCH 1/3] Updated VignetteBuilder field to include knitr and rmarkdown --- base/db/DESCRIPTION | 2 +- base/qaqc/DESCRIPTION | 2 +- base/visualization/DESCRIPTION | 2 +- models/biocro/DESCRIPTION | 2 +- models/ed/DESCRIPTION | 2 +- models/maat/DESCRIPTION | 2 +- modules/allometry/DESCRIPTION | 2 +- modules/assim.batch/DESCRIPTION | 2 +- modules/data.atmosphere/DESCRIPTION | 2 +- modules/meta.analysis/DESCRIPTION | 2 +- modules/photosynthesis/DESCRIPTION | 2 +- modules/priors/DESCRIPTION | 2 +- modules/rtm/DESCRIPTION | 2 +- 13 files changed, 13 insertions(+), 13 deletions(-) diff --git a/base/db/DESCRIPTION b/base/db/DESCRIPTION index 76b55aed16..f88a16982e 100644 --- a/base/db/DESCRIPTION +++ b/base/db/DESCRIPTION @@ -73,7 +73,7 @@ Suggests: tidyverse, withr License: BSD_3_clause + file LICENSE -VignetteBuilder: knitr +VignetteBuilder: knitr, rmarkdown Copyright: Authors LazyLoad: yes LazyData: FALSE diff --git a/base/qaqc/DESCRIPTION b/base/qaqc/DESCRIPTION index 5334347a90..041f957d25 100644 --- a/base/qaqc/DESCRIPTION +++ b/base/qaqc/DESCRIPTION @@ -35,6 +35,6 @@ Copyright: Authors LazyLoad: yes LazyData: FALSE Encoding: UTF-8 -VignetteBuilder: knitr +VignetteBuilder: knitr, rmarkdown Config/testthat/edition: 3 RoxygenNote: 7.3.2 diff --git a/base/visualization/DESCRIPTION b/base/visualization/DESCRIPTION index 136d5a9dbb..8b38be4c66 100644 --- a/base/visualization/DESCRIPTION +++ b/base/visualization/DESCRIPTION @@ -51,6 +51,6 @@ Copyright: Authors LazyLoad: yes LazyData: FALSE Encoding: UTF-8 -VignetteBuilder: knitr +VignetteBuilder: knitr, rmarkdown RoxygenNote: 7.3.2 Roxygen: list(markdown = TRUE) diff --git a/models/biocro/DESCRIPTION b/models/biocro/DESCRIPTION index 981621c212..51a2475e4d 100644 --- a/models/biocro/DESCRIPTION +++ b/models/biocro/DESCRIPTION @@ -38,5 +38,5 @@ Remotes: License: BSD_3_clause + file LICENSE Copyright: Energy Biosciences Institute, Authors Encoding: UTF-8 -VignetteBuilder: knitr +VignetteBuilder: knitr, rmarkdown RoxygenNote: 7.3.2 diff --git a/models/ed/DESCRIPTION b/models/ed/DESCRIPTION index 91181d1f47..308781f1a3 100644 --- a/models/ed/DESCRIPTION +++ b/models/ed/DESCRIPTION @@ -63,7 +63,7 @@ Suggests: Additional_repositories: https://pecanproject.r-universe.dev/ License: BSD_3_clause + file LICENSE Copyright: Authors -VignetteBuilder: knitr +VignetteBuilder: knitr, rmarkdown LazyData: true Encoding: UTF-8 RoxygenNote: 7.3.2 diff --git a/models/maat/DESCRIPTION b/models/maat/DESCRIPTION index 47d8001c37..ce1684852b 100644 --- a/models/maat/DESCRIPTION +++ b/models/maat/DESCRIPTION @@ -23,7 +23,7 @@ SystemRequirements: MAAT OS_type: unix License: BSD_3_clause + file LICENSE Copyright: Authors -VignetteBuilder: knitr +VignetteBuilder: knitr, rmarkdown LazyLoad: yes LazyData: FALSE Encoding: UTF-8 diff --git a/modules/allometry/DESCRIPTION b/modules/allometry/DESCRIPTION index f53cf4c06e..c031dc0276 100644 --- a/modules/allometry/DESCRIPTION +++ b/modules/allometry/DESCRIPTION @@ -30,4 +30,4 @@ LazyLoad: yes LazyData: FALSE Encoding: UTF-8 RoxygenNote: 7.3.2 -VignetteBuilder: knitr +VignetteBuilder: knitr, rmarkdown diff --git a/modules/assim.batch/DESCRIPTION b/modules/assim.batch/DESCRIPTION index e94c946485..6283791ace 100644 --- a/modules/assim.batch/DESCRIPTION +++ b/modules/assim.batch/DESCRIPTION @@ -14,7 +14,7 @@ Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation. -VignetteBuilder: knitr +VignetteBuilder: knitr, rmarkdown Imports: abind, BayesianTools, diff --git a/modules/data.atmosphere/DESCRIPTION b/modules/data.atmosphere/DESCRIPTION index fceb2f2d7f..8b8ae89246 100644 --- a/modules/data.atmosphere/DESCRIPTION +++ b/modules/data.atmosphere/DESCRIPTION @@ -80,6 +80,6 @@ License: BSD_3_clause + file LICENSE Copyright: Authors LazyLoad: yes LazyData: FALSE -VignetteBuilder: knitr +VignetteBuilder: knitr, rmarkdown Encoding: UTF-8 RoxygenNote: 7.3.2 diff --git a/modules/meta.analysis/DESCRIPTION b/modules/meta.analysis/DESCRIPTION index b231707a04..60ba579a6e 100644 --- a/modules/meta.analysis/DESCRIPTION +++ b/modules/meta.analysis/DESCRIPTION @@ -42,7 +42,7 @@ Suggests: testthat (>= 1.0.2) SystemRequirements: JAGS License: BSD_3_clause + file LICENSE -VignetteBuilder: knitr +VignetteBuilder: knitr, rmarkdown Copyright: Authors LazyData: FALSE Encoding: UTF-8 diff --git a/modules/photosynthesis/DESCRIPTION b/modules/photosynthesis/DESCRIPTION index 2605358e80..123d64c4f5 100644 --- a/modules/photosynthesis/DESCRIPTION +++ b/modules/photosynthesis/DESCRIPTION @@ -40,4 +40,4 @@ Collate: plots.R Encoding: UTF-8 RoxygenNote: 7.3.2 -VignetteBuilder: knitr +VignetteBuilder: knitr, rmarkdown diff --git a/modules/priors/DESCRIPTION b/modules/priors/DESCRIPTION index 39b066910e..abfc6f2bb5 100644 --- a/modules/priors/DESCRIPTION +++ b/modules/priors/DESCRIPTION @@ -24,5 +24,5 @@ Suggests: rmarkdown, testthat Encoding: UTF-8 -VignetteBuilder: knitr +VignetteBuilder: knitr, rmarkdown RoxygenNote: 7.3.2 diff --git a/modules/rtm/DESCRIPTION b/modules/rtm/DESCRIPTION index 2c86cb2ba8..2be3ff4f0a 100644 --- a/modules/rtm/DESCRIPTION +++ b/modules/rtm/DESCRIPTION @@ -37,6 +37,6 @@ Copyright: Authors LazyLoad: yes LazyData: FALSE Encoding: UTF-8 -VignetteBuilder: knitr +VignetteBuilder: knitr, rmarkdown Roxygen: list(markdown = TRUE) RoxygenNote: 7.3.2 From 6d55bb148af67c4c1a0c06808c38391fe9a3e810 Mon Sep 17 00:00:00 2001 From: Harsh Agrawal Date: Sat, 2 Nov 2024 13:46:43 +0530 Subject: [PATCH 2/3] Added rmarkdown to Suggests in DESCRIPTION --- modules/data.atmosphere/DESCRIPTION | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/data.atmosphere/DESCRIPTION b/modules/data.atmosphere/DESCRIPTION index 8b8ae89246..ebfc9bbc63 100644 --- a/modules/data.atmosphere/DESCRIPTION +++ b/modules/data.atmosphere/DESCRIPTION @@ -69,6 +69,7 @@ Suggests: PEcAn.settings, progress, reticulate, + rmarkdown, testthat (>= 3.1.7), withr Remotes: From a9b76ffe35ff0d3a4e76cde519bec8efc4503f33 Mon Sep 17 00:00:00 2001 From: Chris Black Date: Sun, 3 Nov 2024 10:57:14 -0800 Subject: [PATCH 3/3] update deps --- docker/depends/pecan_package_dependencies.csv | 1 + 1 file changed, 1 insertion(+) diff --git a/docker/depends/pecan_package_dependencies.csv b/docker/depends/pecan_package_dependencies.csv index c332b010bc..1e8d04c40a 100644 --- a/docker/depends/pecan_package_dependencies.csv +++ b/docker/depends/pecan_package_dependencies.csv @@ -495,6 +495,7 @@ "rmarkdown","*","models/biocro","Suggests",FALSE "rmarkdown","*","models/ed","Suggests",FALSE "rmarkdown","*","models/maat","Suggests",FALSE +"rmarkdown","*","modules/data.atmosphere","Suggests",FALSE "rmarkdown","*","modules/priors","Suggests",FALSE "rmarkdown","*","modules/rtm","Suggests",FALSE "rmarkdown",">= 2.19","base/db","Suggests",FALSE