Apply WEC-Sim#1235 and WEC-Sim#1241 to dev branch (WEC-Sim#1240)

* Update master to main (WEC-Sim#1235)
* Rename incorrect main_doc option to root_doc (WEC-Sim#1241)

---------

Co-authored-by: Adam Keester <[email protected]>

.github/ISSUE_TEMPLATE/theory-or-implementation-clarification.md

@@ -10,8 +10,8 @@ assignees: ''
 
 **The development team requests that before submitting a question on the theory and implementation behind WEC-Sim to first please:**
 1. Read through our [WEC-Sim Documentation](http://wec-sim.github.io/WEC-Sim/man/theory.html) with additional description found in our [Advanced Features Section](http://wec-sim.github.io/WEC-Sim/man/advanced_features.html)
-1. Review MATLAB source code ([functions](https://github.com/WEC-Sim/WEC-Sim/tree/master/source/functions), [objects](https://github.com/WEC-Sim/WEC-Sim/tree/master/source/objects)) and the Simulink blocks ([libraries](https://github.com/WEC-Sim/WEC-Sim/tree/master/source/lib))
-1. Review the curated [WEC-Sim Examples](https://github.com/WEC-Sim/WEC-Sim/tree/master/examples) and the [WEC-Sim applications](https://github.com/WEC-Sim/WEC-Sim_Applications)
+1. Review MATLAB source code ([functions](https://github.com/WEC-Sim/WEC-Sim/tree/main/source/functions), [objects](https://github.com/WEC-Sim/WEC-Sim/tree/main/source/objects)) and the Simulink blocks ([libraries](https://github.com/WEC-Sim/WEC-Sim/tree/main/source/lib))
+1. Review the curated [WEC-Sim Examples](https://github.com/WEC-Sim/WEC-Sim/tree/main/examples) and the [WEC-Sim applications](https://github.com/WEC-Sim/WEC-Sim_Applications)
 1. Review the [WEC-Sim issues page](https://github.com/WEC-Sim/WEC-Sim/issues) which allows you to search past resolved issues or questions that might help answer your own question.
 
 **Note: italicized text below is include as an example and should be updated before submission. If you feel any section is not applicable to your request, please replace with 'N/A' rather than delete a section.**

.github/workflows/dispatch.yml

@@ -2,7 +2,7 @@ name: Trigger repository dispatch event
 on:
   push:
     branches:
-      - master
+      - main
       - dev
 jobs:
   dispatch:

.github/workflows/docs.yml

@@ -2,11 +2,11 @@ name: Documentation
 on:
   push:
     branches:
-      - master
+      - main
       - dev
   pull_request:
     branches:
-      - master
+      - main
       - dev
   workflow_dispatch:
 concurrency: 
@@ -68,8 +68,10 @@ jobs:
           cp docs/_assets/gh-pages.gitignore ${{ env.BUILD_DIR }}/.gitignore
           cp docs/_assets/gh-pages-redirect.html ${{ env.BUILD_DIR }}/index.html
           cp docs/_assets/gh-pages-readme.md ${{ env.BUILD_DIR }}/README.md
+          mkdir ${{ env.BUILD_DIR }}/master
+          cp docs/_assets/gh-pages-redirect.html ${{ env.BUILD_DIR }}/master/index.html
       - name: Deploy
-        if: ${{ github.event_name == 'push' && (env.BRANCH == 'dev' || env.BRANCH == 'master') }}
+        if: ${{ github.event_name == 'push' && (env.BRANCH == 'dev' || env.BRANCH == 'main') }}
         uses: peaceiris/actions-gh-pages@v3
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/run-tests-master.yml → .github/workflows/run-tests-main.yml

@@ -1,14 +1,14 @@
-name: Run MATLAB tests on master branch
+name: Run MATLAB tests on main branch
 on:
   # Trigger the workflow on push or pull request,
-  # but only for the master branch
+  # but only for the main branch
   workflow_dispatch: {}
   push:
     branches:
-      - master
+      - main
   pull_request:
     branches:
-      - master
+      - main
 concurrency: 
   group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
   cancel-in-progress: true

NOTICE

@@ -16,4 +16,4 @@ See the License for the specific language governing permissions and
 limitations under the License.
 
 See full list of WEC-Sim Developers and Acknowledgements on the 
-WEC-Sim Website (http://wec-sim.github.io/WEC-Sim/master/index.html).
+WEC-Sim Website (http://wec-sim.github.io/WEC-Sim/main/index.html).

README.md

@@ -1,25 +1,25 @@
 # Refer to [WEC-Sim documentation](http://wec-sim.github.io/WEC-Sim) for more information.
 [![DOI](https://zenodo.org/badge/20451353.svg)](https://zenodo.org/badge/latestdoi/20451353)
 [![Documentation](https://github.com/WEC-Sim/WEC-Sim/actions/workflows/docs.yml/badge.svg)](https://github.com/WEC-Sim/WEC-Sim/actions/workflows/docs.yml)
-[![Run MATLAB tests on master branch](https://github.com/WEC-Sim/WEC-Sim/actions/workflows/run-tests-master.yml/badge.svg?branch=master)](https://github.com/WEC-Sim/WEC-Sim/actions/workflows/run-tests-master.yml)
+[![Run MATLAB tests on main branch](https://github.com/WEC-Sim/WEC-Sim/actions/workflows/run-tests-main.yml/badge.svg?branch=main)](https://github.com/WEC-Sim/WEC-Sim/actions/workflows/run-tests-main.yml)
 [![Run MATLAB tests on dev branch](https://github.com/WEC-Sim/WEC-Sim/actions/workflows/run-tests-dev.yml/badge.svg?branch=dev)](https://github.com/WEC-Sim/WEC-Sim/actions/workflows/run-tests-dev.yml)
 
 ## WEC-Sim Repository
 
-* **Docs**: [WEC-Sim documentation](http://wec-sim.github.io/WEC-Sim), to refer to [doc compile instructions](https://github.com/WEC-Sim/WEC-Sim/tree/master/docs) 
+* **Docs**: [WEC-Sim documentation](http://wec-sim.github.io/WEC-Sim), to refer to [doc compile instructions](https://github.com/WEC-Sim/WEC-Sim/tree/main/docs) 
 * **Examples**: WEC-Sim  examples
 * **Source**: WEC-Sim source code
 * **Tests**: WEC-Sim tests for [MATLAB Continuous Integration](https://www.mathworks.com/solutions/continuous-integration.html)
-* **Tutorials**: [WEC-Sim tutorials](http://wec-sim.github.io/WEC-Sim/master/user/tutorials.html)
+* **Tutorials**: [WEC-Sim tutorials](http://wec-sim.github.io/WEC-Sim/main/user/tutorials.html)
 
 Refer to the [WEC-Sim Applications](https://github.com/WEC-Sim/WEC-Sim_Applications) repository for more applications of WEC-Sim.
 
 ## Source Code Management
 
-A stable version of WEC-Sim is maintained on WEC-Sim's [master branch](https://github.com/WEC-Sim/WEC-Sim), and WEC-Sim [releases](https://github.com/WEC-Sim/WEC-Sim/releases) are tagged on GitHub. 
+A stable version of WEC-Sim is maintained on WEC-Sim's [main branch](https://github.com/WEC-Sim/WEC-Sim), and WEC-Sim [releases](https://github.com/WEC-Sim/WEC-Sim/releases) are tagged on GitHub. 
 WEC-Sim development is performed on WEC-Sim's [dev branch](https://github.com/WEC-Sim/WEC-Sim/tree/dev) using a [forking workflow](https://www.atlassian.com/git/tutorials/comparing-workflows/forking-workflow). 
 New WEC-Sim features are developed on forks of the WEC-Sim repository, and [pull-requests](https://github.com/WEC-Sim/WEC-Sim/pulls) are submitted to merge new features from a development fork into the main WEC-Sim repository. 
 Pull requests for new WEC-Sim features should be submitted to the WEC-Sim dev branch. 
-The only exception to this workflow is for bug fixes; pull requests for bug fixes should be should submitted to the WEC-Sim master branch.
-When a new version of WEC-Sim is released, the dev branch becomes the master branch, and all updates are included in the tagged release.
+The only exception to this workflow is for bug fixes; pull requests for bug fixes should be should submitted to the WEC-Sim main branch.
+When a new version of WEC-Sim is released, the dev branch becomes the main branch, and all updates are included in the tagged release.
 

docs/README.md

@@ -39,7 +39,7 @@ The front page of the docs can be accessed at
 
 The final documentation can be built locally for inspection prior to 
 publishing. They are built in the `docs/_build` directory. Note, docs are 
-built from the remote so only pushed changes on the `master` and `dev` 
+built from the remote so only pushed changes on the `main` and `dev` 
 branches will be shown. To build the docs use the following command:
 
 ```
@@ -51,12 +51,12 @@ branches will be shown. To build the docs use the following command:
 ```
 
 The front page of the docs can be accessed at 
-`docs/_build/html/master/index.html`. 
+`docs/_build/html/main/index.html`. 
 
 ### Publishing Final Version Remotely
 
 The WEC-Sim docs are rebuilt automatically following every merge commit made 
-to the master or dev branch of the [WEC-Sim/WEC-Sim](
+to the main or dev branch of the [WEC-Sim/WEC-Sim](
 https://github.com/WEC-Sim/WEC-Sim) repository.
 
 

docs/_assets/gh-pages-readme.md

@@ -1,5 +1,5 @@
 # WEC-Sim Documentation
 
-This branch is auto-generated by TravisCI upon pushes to the master or
-dev branches. See the README.md file in the master branch for instructions
+This branch is auto-generated by GitHub Actions upon pushes to the main or
+dev branches. See the README.md file in the main branch for instructions
 regarding building the docs locally.

docs/_assets/gh-pages-redirect.html

@@ -1,10 +1,10 @@
 <!DOCTYPE html>
 <html>
   <head>
-    <title>Redirecting to master branch</title>
+    <title>Redirecting to main branch</title>
     <meta charset="utf-8">
-    <meta http-equiv="refresh" content="0; url=./master/index.html">
+    <meta http-equiv="refresh" content="0; url=/WEC-Sim/main/index.html">
     <meta name="description" content="WEC-Sim is a versatile open-source simulation platform for wave energy converter devices. Simulate, design, and optimize your wave energy systems with WEC-Sim to harness clean and renewable energy from ocean waves."
-    <link rel="canonical" href="https://wec-sim.github.io/WEC-Sim/master/index.html">
+    <link rel="canonical" href="https://wec-sim.github.io/WEC-Sim/main/index.html">
   </head>
 </html>

docs/_include/mooring.rst

@@ -130,7 +130,7 @@ Applications <https://github.com/WEC-Sim/WEC-Sim_Applications>`_ repository.
 
 .. _WECSimInputMoorDyn:
 
-.. rli:: https://raw.githubusercontent.com/WEC-Sim/WEC-Sim_Applications/master/Mooring/MoorDyn/wecSimInputFile.m
+.. rli:: https://raw.githubusercontent.com/WEC-Sim/WEC-Sim_Applications/main/Mooring/MoorDyn/wecSimInputFile.m
    :language: matlab
 
 * **MoorDyn Input File**: A mooring folder that includes a moorDyn input file 

docs/_include/pto.rst

@@ -213,7 +213,7 @@ accumulator, low pressure accumulator, hydraulic motor, and generator.
   
 .. _WECSimInput:
 
-.. rli:: https://raw.githubusercontent.com/WEC-Sim/WEC-Sim_Applications/master/PTO-Sim/RM3/RM3_cHydraulic_PTO/wecSimInputFile.m
+.. rli:: https://raw.githubusercontent.com/WEC-Sim/WEC-Sim_Applications/main/PTO-Sim/RM3/RM3_cHydraulic_PTO/wecSimInputFile.m
    :language: matlab   
 
 **Simulation and Post-processing**

docs/_include/viz.rst

@@ -15,7 +15,7 @@ However, the SimMechanics explorer shows the following information not included
 Visualization with ParaView requires additional output files to be written to a ``vtk`` directory. 
 This makes the WEC-Sim simulation take more time and the case directory larger, so it should only be used when additional visualization is desired. 
 Users will also need to have some familiarity with using ParaView.
-For more information about using ParaView for visualization, refer to the :ref:`webinar4`, and the `Paraview_Visualization <https://github.com/WEC-Sim/WEC-Sim_Applications/tree/master/Paraview_Visualization>`_ examples on the `WEC-Sim Applications <https://github.com/WEC-Sim/WEC-Sim_Applications>`_ repository.
+For more information about using ParaView for visualization, refer to the :ref:`webinar4`, and the `Paraview_Visualization <https://github.com/WEC-Sim/WEC-Sim_Applications/tree/main/Paraview_Visualization>`_ examples on the `WEC-Sim Applications <https://github.com/WEC-Sim/WEC-Sim_Applications>`_ repository.
 
 
 Install ParaView and WEC-Sim Macros
@@ -58,39 +58,39 @@ You can color waves and bodies by any of the available properties and apply any
    :figwidth: 400pt
    :align: center
 
-   `Reference Model 3 <https://github.com/WEC-Sim/WEC-Sim/tree/master/examples/RM3>`_
+   `Reference Model 3 <https://github.com/WEC-Sim/WEC-Sim/tree/main/examples/RM3>`_
 
 
 .. figure:: /_static/images/overview/oswec_iso_side.png
    :width: 400pt
    :figwidth: 400pt
    :align: center
 
-   `Bottom-fixed Oscillating Surge WEC (OSWEC) <https://github.com/WEC-Sim/WEC-Sim/tree/master/examples/OSWEC>`_
+   `Bottom-fixed Oscillating Surge WEC (OSWEC) <https://github.com/WEC-Sim/WEC-Sim/tree/main/examples/OSWEC>`_
 
 
 .. figure:: /_static/images/overview/sphere_freedecay_iso_side.png
    :width: 400pt
    :figwidth: 400pt
    :align: center
 
-   `Sphere <https://github.com/WEC-Sim/WEC-Sim_Applications/tree/master/Free_Decay>`_
+   `Sphere <https://github.com/WEC-Sim/WEC-Sim_Applications/tree/main/Free_Decay>`_
 
 
 .. figure:: /_static/images/overview/ellipsoid_iso_side.png
    :width: 400pt
    :figwidth: 400pt
    :align: center
 
-   `Ellipsoid <https://github.com/WEC-Sim/WEC-Sim_Applications/tree/master/Nonlinear_Hydro>`_
+   `Ellipsoid <https://github.com/WEC-Sim/WEC-Sim_Applications/tree/main/Nonlinear_Hydro>`_
 
 
 .. figure:: /_static/images/overview/gbm_iso_side.png
    :width: 400pt
    :figwidth: 400pt
    :align: center
 
-   `Barge with Four Flexible Body Modes <https://github.com/WEC-Sim/WEC-Sim_Applications/tree/master/Generalized_Body_Modes>`_
+   `Barge with Four Flexible Body Modes <https://github.com/WEC-Sim/WEC-Sim_Applications/tree/main/Generalized_Body_Modes>`_
 
 
 .. figure:: /_static/images/overview/wigley_iso_side.png
@@ -120,9 +120,9 @@ You can color waves and bodies by any of the available properties and apply any
 
 
 
-Two examples using Paraview for visualization of WEC-Sim data are provided in the `Paraview_Visualization <https://github.com/WEC-Sim/WEC-Sim_Applications/tree/master/Paraview_Visualization>`_ directory of the WEC-Sim Applications repository.
-The `RM3_MoorDyn_Viz <https://github.com/WEC-Sim/WEC-Sim_Applications/tree/master/Paraview_Visualization/RM3_MoorDyn_Viz>`_ example uses ParaView for WEC-Sim data visualization of a WEC-Sim model coupled with `MoorDyn <http://wec-sim.github.io/WEC-Sim/advanced_features.html#moordyn>`_ to simulate a mooring system for the `RM3 <http://wec-sim.github.io/WEC-Sim/tutorials.html#two-body-point-absorber-rm3>`_ geometry.
-The `OSWEC_NonLinear_Viz <https://github.com/WEC-Sim/WEC-Sim_Applications/tree/master/Paraview_Visualization/OSWEC_NonLinear_Viz>`_ example uses ParaView for WEC-Sim data visualization of a WEC-Sim model with `nonlinear Hydro <http://wec-sim.github.io/WEC-Sim/advanced_features.html#nonlinear-buoyancy-and-froude-krylov-excitation>`_ to simulate nonlinear wave excitation on the flap of the `OSWEC <http://wec-sim.github.io/WEC-Sim/tutorials.html#oscillating-surge-wec-oswec.>`_ geometry.
+Two examples using Paraview for visualization of WEC-Sim data are provided in the `Paraview_Visualization <https://github.com/WEC-Sim/WEC-Sim_Applications/tree/main/Paraview_Visualization>`_ directory of the WEC-Sim Applications repository.
+The `RM3_MoorDyn_Viz <https://github.com/WEC-Sim/WEC-Sim_Applications/tree/main/Paraview_Visualization/RM3_MoorDyn_Viz>`_ example uses ParaView for WEC-Sim data visualization of a WEC-Sim model coupled with `MoorDyn <http://wec-sim.github.io/WEC-Sim/advanced_features.html#moordyn>`_ to simulate a mooring system for the `RM3 <http://wec-sim.github.io/WEC-Sim/tutorials.html#two-body-point-absorber-rm3>`_ geometry.
+The `OSWEC_NonLinear_Viz <https://github.com/WEC-Sim/WEC-Sim_Applications/tree/main/Paraview_Visualization/OSWEC_NonLinear_Viz>`_ example uses ParaView for WEC-Sim data visualization of a WEC-Sim model with `nonlinear Hydro <http://wec-sim.github.io/WEC-Sim/advanced_features.html#nonlinear-buoyancy-and-froude-krylov-excitation>`_ to simulate nonlinear wave excitation on the flap of the `OSWEC <http://wec-sim.github.io/WEC-Sim/tutorials.html#oscillating-surge-wec-oswec.>`_ geometry.
 
 MoorDyn Visualization in ParaView
 """"""""""""""""""""""""""""""""""""
@@ -184,7 +184,7 @@ If a previous ``*.pvsm`` ParaView state file was saved, the state can be applied
 * Select the desired ``$CASE/<filename>.pvsm`` Paraview state file to apply
 * Select the "Search files under specified directory" option, specify the desired WECS-Sim ``$CASE/vtk/`` directory, and click ``OK``
 
-Paraview state files are provided for both `Paraview_Visualization <https://github.com/WEC-Sim/WEC-Sim_Applications/tree/master/Paraview_Visualization>`_ examples provided onthe WEC-Sim Applications repository, one for the RM3 using MoorDyn, and another for the OSWEC with nonlinear hydro.
+Paraview state files are provided for both `Paraview_Visualization <https://github.com/WEC-Sim/WEC-Sim_Applications/tree/main/Paraview_Visualization>`_ examples provided onthe WEC-Sim Applications repository, one for the RM3 using MoorDyn, and another for the OSWEC with nonlinear hydro.
 
 
 ParaView Visualization Parameters

docs/conf.py

@@ -73,7 +73,7 @@
 matlab_keep_package_prefix = False
 
 # sphinx_multiversion settings
-smv_branch_whitelist = r'(master|dev)$'
+smv_branch_whitelist = r'(main|dev)$'
 smv_tag_whitelist = 'a^'
 smv_remote_whitelist = r'^(origin)$'
 
@@ -87,8 +87,9 @@
 # The encoding of source files.
 #source_encoding = 'utf-8-sig'
 
-# The master toctree document.
-master_doc = 'index'
+# The document name of the “root” document, that is, the document that contains
+# the root toctree directive. Default is 'index'.
+root_doc = 'index'
 
 # -- Project information -----------------------------------------------------
 # General information about the project.
@@ -276,7 +277,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-  (master_doc, 'WEC-Sim.tex', 'WEC-Sim Documentation',
+  (root_doc, 'WEC-Sim.tex', 'WEC-Sim Documentation',
    'Yi-Hsiang Yu, Kelley Ruehl, Jennifer Van Rij, Nathan Tom, Dominic Forbush', 'manual'),
 ]
 
@@ -306,7 +307,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'WEC-Sim', 'WEC-Sim Documentation',
+    (root_doc, 'WEC-Sim', 'WEC-Sim Documentation',
      [author], 1)
 ]
 
@@ -320,7 +321,7 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  (master_doc, 'WEC-Sim', 'WEC-Sim Documentation',
+  (root_doc, 'WEC-Sim', 'WEC-Sim Documentation',
    author, 'WEC-Sim', 'WEC-Sim Documentation',
    'Miscellaneous'),
 ]

docs/developer/pull_requests.rst

@@ -3,12 +3,12 @@
 Pull Requests
 ===============
 
-A stable version of WEC-Sim is maintained on the `WEC-Sim master branch <https://github.com/WEC-Sim/WEC-Sim>`_, and `WEC-Sim releases <https://github.com/WEC-Sim/WEC-Sim/releases>`_ are tagged on GitHub. 
+A stable version of WEC-Sim is maintained on the `WEC-Sim main branch <https://github.com/WEC-Sim/WEC-Sim>`_, and `WEC-Sim releases <https://github.com/WEC-Sim/WEC-Sim/releases>`_ are tagged on GitHub. 
 WEC-Sim development is performed on `WEC-Sim dev branch <https://github.com/WEC-Sim/WEC-Sim/tree/dev>`_ using a `fork-based workflow <https://www.atlassian.com/git/tutorials/comparing-workflows/forking-workflow>`_. 
 New WEC-Sim features are developed on forks of the WEC-Sim repository, and `pull-requests <https://github.com/WEC-Sim/WEC-Sim/pulls>`_ are submitted to merge new features from a development fork into the main WEC-Sim repository. 
 Pull-requests for new WEC-Sim features should be submitted to the WEC-Sim dev branch. 
-The only exception to this workflow is for bug fixes; pull-request for bug fixes should be should submitted to the WEC-Sim master branch.
-When a new version of WEC-Sim is released, the dev branch is pulled into master where all changes are incorporated into the code.
+The only exception to this workflow is for bug fixes; pull-request for bug fixes should be should submitted to the WEC-Sim main branch.
+When a new version of WEC-Sim is released, the dev branch is pulled into main where all changes are incorporated into the code.
 
 
 A `pull request (PR) <https://help.github.com/articles/using-pull-requests/>`_  should focus on one update at a time.