swtich to the main branch

Author: kdorheim

.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
@@ -15,7 +15,7 @@ on:
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
-  
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}

.github/workflows/codecov.yaml

@@ -1,7 +1,7 @@
 on:
   push:
     branches:
-      - master
+      - main
   pull_request:
     branches:
       - '**' # matches every branch

.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

.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

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

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

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

vignettes/articles/BuildHector.Rmd

@@ -13,7 +13,7 @@ To install R, follow the [official instructions](https://cloud.r-project.org/) f
 
 Follow this [YouTube video](https://www.youtube.com/watch?v=Pg3WY8wg1cY) or continue reading. 
 
-To install the version associated with the current `master` git branch on GitHub, 
+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.)

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.

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

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`)