Update GitHub Actions: Build Triggers, upload-artifact (#720)

fix(GHA): Updates GHA build triggers

* update to v4 of upload-artifact gha
* fix(clang-format): v18 of workflow; allows for the newest version of clang-format to always be used by removing the clang-format version specification. This might be causing the issues with clang-format reordering the libraries and things
crashing on the R side when the package is tested.
* refactor(build-doxygen): Uses one file with an if statement to know if the doxygen workflow should deploy after building now that it is built on changes to both dev and main.
* fix(call-calc-coverage): Ignores paths on push and PR; it was ignoring paths just on workflow dispatch. Now the ignore calls are there for both PR and pushes.
* Adds dependabot.yml file to update GitHub actions
* Removes tags as trigger in package down
* Formats the GitHub action yml files consistently; moves summary above name: and arrange on in alphabetical order, as well as branch names and files are now in order too. This standardizes the way that the files are written.

References:
* https://kevsoft.net/2020/06/10/running-github-action-steps-and-jobs-only-on-push-to-master.html
* https://stackoverflow.com/questions/58139406/only-run-job-on-specific-branch-with-github-actions

Co-authored-by: Bai-Li-NOAA <[email protected]>
Co-authored-by: kellijohnson-NOAA <[email protected]>

.github/workflows/build-doxygen.yml

@@ -1,16 +1,16 @@
-# Run doxygen to generate documentation from C++ code
-# build doxygen, error on warnings.
+# Run doxygen to generate documentation from C++ code, which is the equivalent
+# of roxygen documentation in the R code. After building the html files, if the
+# action is being ran on main, the files are moved to the appropriate location
+# and pushed to NOAA-FIMS/FIMS-docs@main.
 name: run-doxygen
-# The default build trigger is to run the action on every push for any branch
+
 on:
-  workflow_dispatch:
   pull_request:
   push:
     branches: 
+      - dev
       - main
-  # To run the default repository branch weekly on sunday, uncomment the following 2 lines
-  #schedule:
-    #- cron: '0 0 * * 0'
+  workflow_dispatch:
 
 jobs:
   build-doxygen:
@@ -29,8 +29,28 @@ jobs:
         sudo apt install cmake doxygen gcc git ninja-build
 
     - name: Building HTML documentation with Doxygen
-    # Do not run mkdir docs and mv build/html docs locally
     # Do not run -DDOXYGEN_WARN_AS_ERROR=YES locally
+    # FIX? run cmake --build build --parallel 16
       run: |
         cmake -S . -B build -G Ninja -DDOXYGEN_WARN_AS_ERROR=YES
         cmake --build build
+    
+    - name: Deploy html documentation with Doxygen
+    # Do not run mkdir docs and mv build/html docs locally
+      if: ${{ github.ref == 'refs/heads/main' }}
+      run: |
+        mv build/html ./
+        mv ./html ./docs
+
+    - name: Push docs to FIMS-docs repo
+      if: ${{ github.ref == 'refs/heads/main' }}
+      uses: dmnemec/copy_file_to_another_repo_action@main
+      env:
+        API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }}
+      with:
+        source_file: 'docs'
+        destination_repo: 'NOAA-FIMS/FIMS-docs'
+        destination_branch: 'main'
+        user_email: '[email protected]' # your email
+        user_name: 'Christine Stawitz'           # your login
+        commit_message: 'Docs: run Doxygen'    

.github/workflows/call-allcontributors.yml

@@ -1,9 +1,12 @@
+# Runs allcontributors::add_contributors() to add, or update, an alphabetized
+# list of contributors to the README.md file and open a new PR with those
+# changes.
 name: Collect contributors
 
 on:
-  workflow_dispatch:
   schedule:
     - cron: '0 8 * * 1'
+  workflow_dispatch:
 
 jobs:
     run-r-script:

.github/workflows/call-build-pkgdown.yml

@@ -1,12 +1,15 @@
-# Checks that the pkgdown site builds for a repository.
-# this assumes pkgdown is already set up.
+# Checks that the pkgdown site builds for a repository, assuming that one
+# already exists, but it does not actually deploy it. See
+# call-update-pkgdown.yml for that.
 name: call-build-pkgdown
-# on specifies the build triggers. See more info at https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
+
 on:
-  workflow_dispatch:
   pull_request:
     branches:
+      - dev
       - main
+  workflow_dispatch:
+
 jobs:
   call-workflow:
     uses: nmfs-fish-tools/ghactions4r/.github/workflows/build-pkgdown.yml@main

.github/workflows/call-calc-coverage.yml

@@ -1,25 +1,34 @@
-# call a workflow that runs covr::codecov() to calculate code coverage
+# Runs covr::codecov() to calculate code coverage.
 name: call-calc_coverage
-# on specifies the build triggers. See more info at https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
-# The default is to run the workflow on every push or pull request to every branch.
+
 on:
-  workflow_dispatch:
+  pull_request:
+    branches:
+      - dev
+      - main
     paths-ignore:
       - .devcontainer
       - .github
-      - 'LICENSE'
-      - 'README.md'
-      - 'CONTRIBUTING.md'
-      - 'Rbuildignore'
       - '.gitignore'
+      - '.Rbuildignore'
+      - 'CONTRIBUTING.md'
+      - 'LICENSE'
       - 'man'
+      - 'README.md'
   push:
     branches:
-      - dev  
-  pull_request:
-    branches:
-      - main
-      - dev  
+      - dev
+    paths-ignore:
+      - .devcontainer
+      - .github
+      - '.gitignore'
+      - '.Rbuildignore'
+      - 'CONTRIBUTING.md'
+      - 'LICENSE'
+      - 'man'
+      - 'README.md'
+  workflow_dispatch:
+
 jobs:
   call-workflow:
     uses: nmfs-fish-tools/ghactions4r/.github/workflows/calc-coverage.yml@main

.github/workflows/call-doc-and-style-r.yml

@@ -1,15 +1,15 @@
-# document and style using reusable workflow
-# This workflow runs devtools::document and styler::style_active_package(), then opens a pull request to the branch
-# That started the workflow with the changes
+# Runs devtools::document() and styler::style_active_package(), then opens a
+# pull request to the branch that had changes in the push that triggered the
+# workflow.
 name: call-doc-and-style-r
-# on specifies the build triggers. See more info at https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
+
 on:
-# workflow_dispatch requires pushing a button to run the workflow manually. uncomment the following line to add:
-  workflow_dispatch:
-  # Runs the workflow on each push to the main or master branch:
   push:
-    branches: 
+    branches:
+      - dev 
       - main
+  workflow_dispatch:
+
 jobs:
   call-workflow:
     uses: nmfs-fish-tools/ghactions4r/.github/workflows/doc-and-style-r.yml@main

.github/workflows/call-r-cmd-check.yml

@@ -1,13 +1,10 @@
-# Run r cmd check
+# Runs R CMD CHECK on the package.
 name: call-r-cmd-check
-# on specifies the build triggers. See more info at https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
+
 on:
-  workflow_dispatch:
-# The default build trigger is to run the action on every push and pull request, for any branch
   push:
-  # To run the default repository branch weekly on sunday, uncomment the following 2 lines
-  #schedule:
-    #- cron: '0 0 * * 0'
+  workflow_dispatch:
+
 jobs:
   call-workflow:
     uses: nmfs-fish-tools/ghactions4r/.github/workflows/r-cmd-check.yml@main

.github/workflows/call-spell-check.yml

@@ -1,17 +1,17 @@
-# run devtools::spell_check()
+# Runs devtools::spell_check().
 name: call-spell-check
-# on specifies the build triggers. See more info at https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
+
 on:
-# this workflow runs on pushing to main, pull requests to main, and manually.
-  push:
-    branches:
-      - main
-      - dev
   pull_request:
     branches:
+      - dev
       - main
+  push:
+    branches:
       - dev
+      - main
   workflow_dispatch:
+
 jobs:
   call-workflow:
     uses: nmfs-fish-tools/ghactions4r/.github/workflows/spell-check.yml@main

.github/workflows/call-update-pkgdown.yml

@@ -1,12 +1,11 @@
-# updates exiting pkgdown site for a repository
-# deploys to a branch gh-pages
+# Updates the exiting pkgdown site for a repository by deploying the changes
+# made to the pkgdown site to a branch called gh-pages.
 name: call-update-pkgdown
-# on specifies the build triggers. See more info at https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
+
 on:
-# this workflow runs on pushes to main or master or any time a new tag is pushed
   push:
-    branches: [main, master]
-    tags: ['*']
+    branches: [main]
+
 jobs:
   call-workflow:
     uses: nmfs-fish-tools/ghactions4r/.github/workflows/update-pkgdown.yml@main

.github/workflows/dependabot.yml

@@ -0,0 +1,9 @@
+# Uses dependabot to check things
+version: 2
+updates:
+  # Enable version updates for GitHub Actions
+  - package-ecosystem: "github-actions"
+    # The default location of the bot is `.github/workflows`
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/get-gtest-codecov.yml

@@ -1,23 +1,16 @@
-# Get GoogleTest code coverage
+# Gets the GoogleTest code coverage metrics.
 name: get-gtest-codecov
-# on specifies the build triggers. See more info at https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
+
 on:
-  workflow_dispatch:
-  push:
-    branches:    
-      - main
-    paths-ignore:
-      - .devcontainer
-      - .github
-      - 'LICENSE'
-      - 'README.md'
-      - 'CONTRIBUTING.md'
-      - 'Rbuildignore'
-      - '.gitignore'
-      - 'man'
   pull_request:
     branches:
+      - dev
       - main
+  push:
+    branches:    
+      - dev
+      - main
+  workflow_dispatch:
 
 jobs:
   build:
@@ -63,7 +56,7 @@ jobs:
         gcovr --exclude tests/ --cobertura coverage.xml
 
     - name: save coverage report
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: coverage.xml
         path: coverage.xml
@@ -73,6 +66,3 @@ jobs:
       with:
         files: coverage.xml
         token: ${{ secrets.CODECOV_TOKEN }}
-
-
-

.github/workflows/pr-checklist.yml

@@ -1,9 +1,12 @@
-# This workflow automatically adds a comment containing a reviewer checklist
-# when a new pull request is opened.
+# Adds a comment to a newly opened PR letting reviewers know what should be
+# included in their review.
+# TODO: change this to email the assigned reviewer
 name: Add a comment with reviewer checklist when PR opened
+
 on:
   pull_request:
     types: [opened]
+
 jobs:
   pr-checklist:
     runs-on: ubuntu-latest

.github/workflows/run-clang-format.yml

@@ -1,20 +1,17 @@
-# Run clang-format
-# This workflow runs clang-format to format C++ code and then creates
-# a pull request to commit the changed files to the main branch. 
-# More details about clang-format can be found here: 
-# https://clang.llvm.org/docs/ClangFormat.html. To style 
-# C++ code in VS Code locally, you could follow the instructions on this 
-# website https://code.visualstudio.com/docs/editor/codebasics#_formatting 
-# to format the entire file or selected text. 
-
+# Runs clang-format to format C++ code and then creates a PR to the branch
+# which had changes and triggered this action. More details about clang-format
+# can be found here: https://clang.llvm.org/docs/ClangFormat.html. To style C++
+# code in VS Code locally, you could follow the instructions on this website
+# https://code.visualstudio.com/docs/editor/codebasics#_formatting to format
+# the entire file or selected text.
 name: run-clang-format
 
 on:
-  workflow_dispatch:
-# Runs the workflow on each push to the main or master branch:
   push:
     branches:
+      - dev
       - main
+  workflow_dispatch:
 
 jobs:
   job:
@@ -24,11 +21,10 @@ jobs:
     # We use Google style to format code.
     steps:
     - uses: actions/checkout@v4
-    - uses: DoozyX/clang-format-lint-action@v0.14
+    - uses: DoozyX/clang-format-lint-action@v0.18.1
       with:
         source: './inst/include ./src ./tests/gtest'
         extensions: 'hpp, cpp'
-        clangFormatVersion: 13.0.0
         style: Google
         inplace: True