Merge pull request #715 from JGCRI/krd/gh697/change_default_branch

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JGCRI · Dec 20, 2023 · 0ea644b · 0ea644b
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -3,7 +3,7 @@ name: R-CMD-check
 on:
   push:
     branches:
-      - master
+      - main
   pull_request:
     branches:
       - '**' # matches every branch

diff --git a/.github/workflows/codecov.yaml b/.github/workflows/codecov.yaml
@@ -1,7 +1,7 @@
 on:
   push:
     branches:
-      - master
+      - main
   pull_request:
     branches:
       - '**' # matches every branch

diff --git a/.github/workflows/command-line.yaml b/.github/workflows/command-line.yaml
@@ -1,13 +1,13 @@
 # This is a basic workflow to help you get started with Actions
-# based on https://github.com/JGCRI/hector/new/master?filename=.github%2Fworkflows%2Fmain.yml&workflow_template=blank
+# based on https://github.com/JGCRI/hector/new/main?filename=.github%2Fworkflows%2Fmain.yml&workflow_template=blank
 
 name: Command Line Hector
 
 # Controls when the action will run.
 on:
   push:
     branches:
-      - master
+      - main
   pull_request:
     branches:
       - '**' # matches every branch

diff --git a/.github/workflows/leeyabot.yml b/.github/workflows/leeyabot.yml
@@ -22,7 +22,6 @@ jobs:
           GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
         run: |
           install.packages(c("ggplot2", "rmarkdown", "dplyr", "remotes", "here"))
-          remotes::install_github("hadley/emo")
           remotes::install_deps(dependencies = TRUE)
         shell: Rscript {0}
 

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [master]
+    branches: [main]
   pull_request:
     branches:
       - '**' # matches every branch

diff --git a/R/messages.R b/R/messages.R
@@ -17,7 +17,8 @@ default_fetchvars <- c(CONCENTRATIONS_CO2, RF_TOTAL, RF_CO2, GLOBAL_TAS)
 #' The list of variables to fetch if you don't specify \code{vars} is stored in
 #' the \code{hector.default.fetchvars} option.  If this option is also unset, then
 #' the default variable list is CO2 concentration, total radiative forcing, CO2
-#' forcing, and global mean temperature.
+#' forcing, and global mean temperature. To see a list of the potential \code{vars}
+#' see \code{data(inputstable)} and \code{data(fxntable)}.
 #'
 #' @seealso \link{concentrations}, \link{emissions}, \link{forcings},
 #' \link{carboncycle}, \link{haloemiss}, \link{haloforcings}, \link{methane},
@@ -34,6 +35,14 @@ default_fetchvars <- c(CONCENTRATIONS_CO2, RF_TOTAL, RF_CO2, GLOBAL_TAS)
 #' of the Hector core object will be used.
 #' @family main user interface functions
 #' @export
+#' @examples
+#' \dontrun{
+#' ini <- system.file(package = "hector", "input/hector_ssp245.ini")
+#' hc <- newcore(ini)
+#' run(hc)
+#' out <- fetchvars(core = hc, dates = 1900:2100, vars = c(GLOBAL_TAS(), NPP()))
+#' print(out)
+#' }
 fetchvars <- function(core, dates, vars = NULL, scenario = NULL) {
   if (is.null(vars)) {
     vars <- getOption("hector.default.fetchvars",

diff --git a/README.Rmd b/README.Rmd
@@ -17,7 +17,7 @@ library(ggplot2)
 
 # hector
 
-[![DOI](https://zenodo.org/badge/22892935.svg)](https://zenodo.org/badge/latestdoi/22892935) [![C++ unit tests](https://github.com/JGCRI/hector/actions/workflows/unit-testing.yaml/badge.svg)](https://github.com/JGCRI/hector/actions/workflows/unit-testing.yaml) [![Command Line Hector](https://github.com/JGCRI/hector/actions/workflows/command-line.yaml/badge.svg)](https://github.com/JGCRI/hector/actions/workflows/command-line.yaml)  [![R-CMD-check](https://github.com/JGCRI/hector/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/JGCRI/hector/actions/workflows/R-CMD-check.yaml) [![codecov](https://codecov.io/gh/JGCRI/hector/branch/master/graph/badge.svg?token=EGM0lXDxRv)](https://codecov.io/gh/JGCRI/hector)
+[![DOI](https://zenodo.org/badge/22892935.svg)](https://zenodo.org/badge/latestdoi/22892935) [![C++ unit tests](https://github.com/JGCRI/hector/actions/workflows/unit-testing.yaml/badge.svg)](https://github.com/JGCRI/hector/actions/workflows/unit-testing.yaml) [![Command Line Hector](https://github.com/JGCRI/hector/actions/workflows/command-line.yaml/badge.svg)](https://github.com/JGCRI/hector/actions/workflows/command-line.yaml)  [![R-CMD-check](https://github.com/JGCRI/hector/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/JGCRI/hector/actions/workflows/R-CMD-check.yaml) [![codecov](https://codecov.io/gh/JGCRI/hector/branch/main/graph/badge.svg?token=EGM0lXDxRv)](https://codecov.io/gh/JGCRI/hector)
 
 This is the repository for **Hector**, an open source, object-oriented, simple 
 global climate carbon-cycle model that runs very quickly while still

diff --git a/README.md b/README.md
@@ -9,7 +9,7 @@ tests](https://github.com/JGCRI/hector/actions/workflows/unit-testing.yaml/badge
 [![Command Line
 Hector](https://github.com/JGCRI/hector/actions/workflows/command-line.yaml/badge.svg)](https://github.com/JGCRI/hector/actions/workflows/command-line.yaml)
 [![R-CMD-check](https://github.com/JGCRI/hector/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/JGCRI/hector/actions/workflows/R-CMD-check.yaml)
-[![codecov](https://codecov.io/gh/JGCRI/hector/branch/master/graph/badge.svg?token=EGM0lXDxRv)](https://codecov.io/gh/JGCRI/hector)
+[![codecov](https://codecov.io/gh/JGCRI/hector/branch/main/graph/badge.svg?token=EGM0lXDxRv)](https://codecov.io/gh/JGCRI/hector)
 
 This is the repository for **Hector**, an open source, object-oriented,
 simple global climate carbon-cycle model that runs very quickly while

diff --git a/inst/input/hector_ssp119.ini b/inst/input/hector_ssp119.ini
@@ -226,7 +226,8 @@ delta_HFC32=0.0 				; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6
 molarMass=52.0					; grams
 HFC32_emissions=csv:tables/ssp119_emiss-constraints_rf.csv
 
-[HFC4310_halocarbon]				; This is equivalent to HFC-43-10mee
+[HFC4310_halocarbon]				
+; This is equivalent to HFC-43-10mee
 tau=17.0					; lifetime in years (Table 7.SM.7 IPPC AR6)
 rho_HFC4310=0.000357				; radiative efficiencies W/m2/ppt (Table 7.SM.7 IPPC AR6)
 delta_HFC4310=0.0 				; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6)

diff --git a/inst/input/hector_ssp126.ini b/inst/input/hector_ssp126.ini
@@ -226,7 +226,8 @@ delta_HFC32=0.0 				; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6
 molarMass=52.0					; grams
 HFC32_emissions=csv:tables/ssp126_emiss-constraints_rf.csv
 
-[HFC4310_halocarbon]				; This is equivalent to HFC-43-10mee
+[HFC4310_halocarbon]				
+; This is equivalent to HFC-43-10mee
 tau=17.0					; lifetime in years (Table 7.SM.7 IPPC AR6)
 rho_HFC4310=0.000357				; radiative efficiencies W/m2/ppt (Table 7.SM.7 IPPC AR6)
 delta_HFC4310=0.0 				; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6)

diff --git a/inst/input/hector_ssp245.ini b/inst/input/hector_ssp245.ini
@@ -226,7 +226,8 @@ delta_HFC32=0.0 				; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6
 molarMass=52.0					; grams
 HFC32_emissions=csv:tables/ssp245_emiss-constraints_rf.csv
 
-[HFC4310_halocarbon]				; This is equivalent to HFC-43-10mee
+[HFC4310_halocarbon]				
+; This is equivalent to HFC-43-10mee
 tau=17.0					; lifetime in years (Table 7.SM.7 IPPC AR6)
 rho_HFC4310=0.000357				; radiative efficiencies W/m2/ppt (Table 7.SM.7 IPPC AR6)
 delta_HFC4310=0.0 				; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6)

diff --git a/inst/input/hector_ssp370.ini b/inst/input/hector_ssp370.ini
@@ -226,7 +226,8 @@ delta_HFC32=0.0 				; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6
 molarMass=52.0					; grams
 HFC32_emissions=csv:tables/ssp370_emiss-constraints_rf.csv
 
-[HFC4310_halocarbon]				; This is equivalent to HFC-43-10mee
+[HFC4310_halocarbon]				
+; This is equivalent to HFC-43-10mee
 tau=17.0					; lifetime in years (Table 7.SM.7 IPPC AR6)
 rho_HFC4310=0.000357				; radiative efficiencies W/m2/ppt (Table 7.SM.7 IPPC AR6)
 delta_HFC4310=0.0 				; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6)

diff --git a/inst/input/hector_ssp434.ini b/inst/input/hector_ssp434.ini
@@ -226,7 +226,8 @@ delta_HFC32=0.0 				; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6
 molarMass=52.0					; grams
 HFC32_emissions=csv:tables/ssp434_emiss-constraints_rf.csv
 
-[HFC4310_halocarbon]				; This is equivalent to HFC-43-10mee
+[HFC4310_halocarbon]				
+; This is equivalent to HFC-43-10mee
 tau=17.0					; lifetime in years (Table 7.SM.7 IPPC AR6)
 rho_HFC4310=0.000357				; radiative efficiencies W/m2/ppt (Table 7.SM.7 IPPC AR6)
 delta_HFC4310=0.0 				; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6)

diff --git a/inst/input/hector_ssp460.ini b/inst/input/hector_ssp460.ini
@@ -226,7 +226,8 @@ delta_HFC32=0.0 				; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6
 molarMass=52.0					; grams
 HFC32_emissions=csv:tables/ssp460_emiss-constraints_rf.csv
 
-[HFC4310_halocarbon]				; This is equivalent to HFC-43-10mee
+[HFC4310_halocarbon]				
+; This is equivalent to HFC-43-10mee
 tau=17.0					; lifetime in years (Table 7.SM.7 IPPC AR6)
 rho_HFC4310=0.000357				; radiative efficiencies W/m2/ppt (Table 7.SM.7 IPPC AR6)
 delta_HFC4310=0.0 				; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6)

diff --git a/inst/input/hector_ssp534-over.ini b/inst/input/hector_ssp534-over.ini
@@ -226,7 +226,8 @@ delta_HFC32=0.0 				; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6
 molarMass=52.0					; grams
 HFC32_emissions=csv:tables/ssp534-over_emiss-constraints_rf.csv
 
-[HFC4310_halocarbon]				; This is equivalent to HFC-43-10mee
+[HFC4310_halocarbon]				
+; This is equivalent to HFC-43-10mee
 tau=17.0					; lifetime in years (Table 7.SM.7 IPPC AR6)
 rho_HFC4310=0.000357				; radiative efficiencies W/m2/ppt (Table 7.SM.7 IPPC AR6)
 delta_HFC4310=0.0 				; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6)

diff --git a/inst/input/hector_ssp585.ini b/inst/input/hector_ssp585.ini
@@ -226,7 +226,8 @@ delta_HFC32=0.0 				; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6
 molarMass=52.0					; grams
 HFC32_emissions=csv:tables/ssp585_emiss-constraints_rf.csv
 
-[HFC4310_halocarbon]				; This is equivalent to HFC-43-10mee
+[HFC4310_halocarbon]				
+; This is equivalent to HFC-43-10mee
 tau=17.0					; lifetime in years (Table 7.SM.7 IPPC AR6)
 rho_HFC4310=0.000357				; radiative efficiencies W/m2/ppt (Table 7.SM.7 IPPC AR6)
 delta_HFC4310=0.0 				; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6)

diff --git a/man/fetchvars.Rd b/man/fetchvars.Rd
diff --git a/scripts/OutputDifferences.Rmd b/scripts/OutputDifferences.Rmd
@@ -8,14 +8,13 @@ knitr::opts_chunk$set(echo = TRUE)
 
 ## Differences in Hector outputs
 
-Hello, this is `leeyabot`! `r emo::ji("robot")`
+Hello, this is `leeyabot`! 
 
 ``` {r differences, echo = FALSE, message = FALSE, include = FALSE}
 # Load packages
 library(dplyr)
 library(ggplot2)
 library(hector)
-library(emo)
 library(here)
 
 # Set root directory

diff --git a/tests/testthat/test_old-new.R b/tests/testthat/test_old-new.R
@@ -1,6 +1,6 @@
 context("Old new tests")
 # Verify that hector output for the canonical rcps matches the output from the
-# master branch. This "bit for bit" comparison of the output is intended to help
+# main branch. This "bit for bit" comparison of the output is intended to help
 # guarantee that Hector's outputs don't change during "minor" and "patch" development.
 # When "major" development is expected to impact Hector output, the comparison data will
 # need to be updated by running data-raw/generate-comp-data.R

diff --git a/vignettes/articles/BuildHector.Rmd b/vignettes/articles/BuildHector.Rmd
@@ -9,9 +9,11 @@ building instructions for the R Hector package and the executable.
 
 # R Hector 
 
-To install R, follow the [official instructions](https://cloud.r-project.org/) for your platform.
+To install R, follow the [official instructions](https://cloud.r-project.org/) for your platform. 
 
-To install the version associated with the current `master` git branch on GitHub, 
+Follow this [YouTube video](https://www.youtube.com/watch?v=Pg3WY8wg1cY) or continue reading. 
+
+To install the version associated with the current `main` git branch on GitHub, 
 use the `remotes`::install_github` function.
 This will automatically install all of Hector's dependencies as well.
 (Note that because this requires compiling from source, you will need to have a C compiler installed and configured.)

diff --git a/vignettes/articles/ContributionsGuide.Rmd b/vignettes/articles/ContributionsGuide.Rmd
@@ -4,7 +4,7 @@ title: Contribution Guide
 
 The Hector team welcomes and values community contributions to Hector, but there are a few important things to know. 
 
-All contributions must pass through a pull request (PR) process before being merged into the master branch of Hector. Please note that opening a PR does **not** guarantee your work will be merged; we assess potential model changes for fit with Hector’s long-term strategic plan, compatibility, conformance to the model’s code style, and other factors.
+All contributions must pass through a pull request (PR) process before being merged into the main branch of Hector. Please note that opening a PR does **not** guarantee your work will be merged; we assess potential model changes for fit with Hector’s long-term strategic plan, compatibility, conformance to the model’s code style, and other factors.
 
 We encourage all contributors to read and comply with the following guidelines:
 
@@ -19,7 +19,7 @@ Hector adheres to the [semantic versioning](https://semver.org/) ideology. This
 
 * "Patch changes" that make no impact on Hector functionality, such as documentation fixes or removing dead code, are the easiest to assess and merge.
 * "Minor changes" that don’t change the model’s behavior in any fundamental way and don’t change its inputs may require unit tests and some more review.
-* "Major changes"  that change the model’s input or output structure or induce major behavioral shifts, are considered _breaking changes_. These are subject to the most stringent reviews and will require scientific justification of the development and evidence that the changes have the intended consequences. PRs will almost always be merged into a development branch, not master until a new version of the Hector is ready for release. 
+* "Major changes"  that change the model’s input or output structure or induce major behavioral shifts, are considered _breaking changes_. These are subject to the most stringent reviews and will require scientific justification of the development and evidence that the changes have the intended consequences. PRs will almost always be merged into a development branch, not main until a new version of the Hector is ready for release. 
 
 
 Thank you for your interest in contributing to Hector and we look forward to working with you! However, we maintain the right to refuse to merge PRs that do not comply with these guidelines or that do not meet contribution standards.

diff --git a/vignettes/articles/Hector-Wider-World.Rmd b/vignettes/articles/Hector-Wider-World.Rmd
@@ -95,17 +95,6 @@ pyhector is a Python interface for Hector.
 [Here](https://joss.theoj.org/papers/10.21105/joss.00248) is a paper describing pyhector by Sven N Wilner, Corrine Hartin, and Robert Gieseke.  
 Github found [here](https://github.com/openclimatedata/pyhector).
 
-### YouTube Walkthrough
-[Here](https://www.youtube.com/watch?v=EFJS-buvGN8) is a video walk through by Kalyn Dorheim including information on using Hector v2.5: 
-
-* Installing Hector
-* Running a core
-* Running a scenario
-* Accessing and plotting results
-* Shutting down a core
-* Changing a parameter
-* A brief explanation of documentation
-
 ### HectorUI
 HectorUI is an R Shiny web interface designed to be user-friendly and to provide an alternative to the command line for running Hector. This allows users who may not be fluent in C++ or R to explore model scenarios and outputs. 
 

diff --git a/vignettes/articles/HectorResources.Rmd b/vignettes/articles/HectorResources.Rmd
@@ -0,0 +1,21 @@
+---
+title: "Hector Videos & Tutorials"
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+## Hector V3 
+
+* [Interactive Jupyter notebook](https://hector.msdlive.org/)
+* Hector V3 installation [YouTube Video](https://www.youtube.com/watch?v=Pg3WY8wg1cY)
+
+
+## Hector V2.5
+
+[YouTube Video](https://www.youtube.com/watch?v=EFJS-buvGN8) that covers the following: Hector v2.5 Package setup; changing a parameter value; how to visualize
+
diff --git a/vignettes/articles/InputFiles.Rmd b/vignettes/articles/InputFiles.Rmd
@@ -6,7 +6,7 @@ title: Hector input files
 
 When Hector is invoked from the command line, it takes a single parameter: the name of the primary input file to read. This file, typically stored in the `input/` directory, contains configuration and parameter data controlling the model's run, output, and behavior.
 
-The primary input file is a text file with *sections*, *properties*, and *values*. For example, the beginning of the [SSP245 file](/tree/master/inst/input/hector_ssp245.ini) included in the repository looks like this:
+The primary input file is a text file with *sections*, *properties*, and *values*. For example, the beginning of the [SSP245 file](/tree/main/inst/input/hector_ssp245.ini) included in the repository looks like this:
 
 ```
 ; Config file for hector model: SSP245

diff --git a/vignettes/articles/SimpleNBox.Rmd b/vignettes/articles/SimpleNBox.Rmd
@@ -90,9 +90,9 @@ At each Hector time step, `c` is solved by the `CarbonCycleSolver::run()` functi
 These steps are described in more detail below.
 The complete code for the terrestrial C cycle lives in [`src/simpleNbox.cpp`][cpp] file (with associated headers in [`inst/include/simpleNbox.hpp`][hpp]).
 
-[solver]: https://github.com/JGCRI/hector/blob/master/src/carbon-cycle-solver.cpp
-[cpp]: https://github.com/jgcri/hector/blob/master/src/simpleNbox.cpp
-[hpp]: https://github.com/JGCRI/hector/blob/master/inst/include/simpleNbox.hpp
+[solver]: https://github.com/JGCRI/hector/blob/main/src/carbon-cycle-solver.cpp
+[cpp]: https://github.com/jgcri/hector/blob/main/src/simpleNbox.cpp
+[hpp]: https://github.com/JGCRI/hector/blob/main/inst/include/simpleNbox.hpp
 
 ## Setting the `c` vector (`getCValues`)
 

diff --git a/vignettes/articles/manual.Rmd b/vignettes/articles/manual.Rmd
@@ -26,6 +26,7 @@ Building and Running Hector
 * How to [do a basic run and sensitivity analysis](intro-to-hector.html)
 * How to [run Hector under constraints](Constraints.html)
 * How to [run Hector with multiple biomes](multiple-biomes.html)
+* [Videos & other resources](HectorResources.html)
 
 For Developers
 --------------------