Use EdgeMask to handle boundary edges

.clang-format

@@ -0,0 +1,10 @@
+# We'll use defaults from the LLVM style, with 3 columns indentation.
+BasedOnStyle: LLVM
+IndentWidth: 3
+
+Language: Cpp
+AlignConsecutiveAssignments: true
+AlignConsecutiveBitFields: true
+AlignConsecutiveMacros: true
+AlignEscapedNewlines: true
+AlignTrailingComments: true

.github/actions/show-workflow-trigger/README.md

@@ -0,0 +1,3 @@
+# Composite action to show the trigger of a workflow
+
+If possible, prints also the user that triggered it

.github/actions/show-workflow-trigger/action.yml

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+name: 'Show workflow trigger'
+description: 'Prints what triggered this workflow'
+
+runs:
+  using: "composite"
+  steps:
+    - name: Print trigger info
+      uses: actions/github-script@v7
+      with:
+        script: |
+          const eventName = context.eventName;
+          const actor = context.actor || 'unknown';  // Default to 'unknown' if actor is not defined
+          let eventAction = 'N/A';
+
+          // Determine the event action based on the event type
+          if (eventName === 'pull_request') {
+            eventAction = context.payload.action || 'N/A';
+          } else if (eventName === 'pull_request_review') {
+            eventAction = context.payload.review.state || 'N/A';
+          } else if (eventName === 'workflow_dispatch') {
+            eventAction = 'manual trigger';
+          } else if (eventName === 'schedule') {
+            eventAction = 'scheduled trigger';
+          }
+          console.log(`The job was triggered by a ${eventName} event.`);
+          console.log(`  - Event action: ${eventAction}`);
+          console.log(`  - Triggered by: ${actor}`);

.github/actions/test-all-eamxx/README.md

@@ -0,0 +1,33 @@
+# Composite action to call test-all-eamxx inside a workflow
+
+This action is meant to be used inside a workflow. E.g.,
+
+```yaml
+jobs:
+  my-testing:
+    steps:
+      ...
+      - name: run-test-all-eamxx
+        uses: ./.github/actions/test-all-eamxx
+        with:
+          build_type: <build-type>
+          machine: <machine>
+          run_type: <run-type>
+```
+
+The input run_type is the only input that this action has to explicitly handle.
+As such, this action checks that its value is one of the following.
+
+- nightly: runs tests and then submit to cdash
+- at-run: runs tests without submitting to cdash
+- bless: runs tests and copy output files to baselines folder
+
+As for build_type and machine, we do not prescribe a list of
+valid values, as that will be handled by components/eamxx/scripts/test-all-eamxx.
+If their values are not supported, it is up to test-all-scram to handle the error.
+As a guideline, however, you may have to ensure that the following exist:
+
+- the file components/eamxx/cmake/machine-files/${machine}.cmake
+- the entry ${machine} in the MACHINE_METADATA dict in components/eamxx/scripts/machine_specs.py
+
+ Questions? Contact Luca Bertagna [[email protected]](mailto:[email protected])

.github/actions/test-all-eamxx/action.yml

@@ -0,0 +1,115 @@
+name: EAMxx standalone testing
+description: |
+  Run EAMxx standalone testing with required configuration inputs.
+  More precisely, it launches test-all-eamxx with the proper flags.
+  See components/eamxx/scripts/test-all-eamxx for more details.
+  The configuration inputs are:
+    - build_type: the type of build to pass to test-all-eamxx.
+    - machine: the name of the machine to pass to test-all-eamxx
+    - generate: whether to generate baselines
+    - submit: whether to submit to cdash (unused if generate is 'true')
+
+inputs:
+  build_type:
+    description: 'Build type to run'
+    required: true
+  machine:
+    description: 'Machine name for test-all-eamxx'
+    required: true
+  generate:
+    description: 'Generate baselines instead of running tests'
+    required: true
+    default: 'false'
+    valid_values:
+      - 'true'
+      - 'false'
+  submit:
+    description: 'Submit results to cdash (unused if generate=true)'
+    required: true
+    default: 'false'
+    valid_values:
+      - 'true'
+      - 'false'
+  ekat:
+    description: 'Whether to enable tests for EKAT as well'
+    required: true
+    default: 'false'
+    valid_values:
+      - 'true'
+      - 'false'
+  cmake-configs:
+    description: 'Semicolon-separated list of key=value pairs for CMake to pass to test-all-eamxx'
+    required: false
+    default: ''
+
+runs:
+  using: "composite"
+  steps:
+    - name: Set CA certificates env var
+      run: |
+        # Ensure the operating system is Linux
+        if [ "$(uname)" != "Linux" ]; then
+          echo "This action only supports Linux."
+          exit 1
+        fi
+        # Set env var to be used in upload-artifacts phase
+        if [ -f /etc/debian_version ]; then
+          echo "NODE_EXTRA_CA_CERTS=/etc/ssl/certs/ca-certificates.crt" >> $GITHUB_ENV
+        elif [ -f /etc/redhat-release ] || [ -f /etc/centos-release ] || [ -f /etc/fedora-release ]; then
+          echo "NODE_EXTRA_CA_CERTS=/etc/pki/tls/certs/ca-bundle.crt" >> $GITHUB_ENV
+        else
+          echo "Unsupported Linux distribution"
+          exit 1
+        fi
+      shell: sh
+    - name: Check repo presence
+      run: |
+        if [ ! -d ".git" ]; then
+          echo "Repository is not checked out. Please ensure the repository is checked out before running this action."
+          exit 1
+        fi
+      shell: sh
+    - name: Print build specs
+      run: |
+        echo "Testing EAMxx standalone, for the following configuration:"
+        echo "  build type   : ${{ inputs.build_type }}"
+        echo "  machine      : ${{ inputs.machine }}"
+        echo "  generate     : ${{ inputs.generate }}"
+        echo "  submit       : ${{ inputs.submit }}"
+        echo "  cmake-configs: ${{ inputs.cmake-configs }}"
+      shell: sh
+    - name: Run test-all-eamxx
+      working-directory: components/eamxx
+      run: |
+        cmd="./scripts/test-all-eamxx -m ${{ inputs.machine }} -t ${{inputs.build_type}} --baseline-dir AUTO -c EKAT_DISABLE_TPL_WARNINGS=ON"
+        if [ "${{ inputs.generate }}" = "true" ]; then
+          cmd+=" -g"
+        elif [ "${{ inputs.submit }}" = "true" ]; then
+          cmd+=" -s"
+        fi
+
+        if [ "${{ inputs.ekat }}" = "true" ]; then
+         cmd+=" -c EKAT_ENABLE_TESTS=ON"
+        fi
+
+        # If cmake-configs is non-empty, add tokens to test-all-eamxx via "-c key=val"
+        IFS=';' read -ra configs <<< "${{ inputs.cmake-configs }}"
+        for config in "${configs[@]}"; do
+          cmd+=" -c $config"
+        done
+
+        # Print the full command, then run it
+        echo "test-all-eamxx call: $cmd"
+        $cmd
+      shell: sh
+    - name: Upload ctest logs
+      if: always()
+      uses: actions/upload-artifact@v4
+      with:
+        name: log-files-${{ inputs.build_type }}-${{ inputs.machine }}
+        path: |
+          components/eamxx/ctest-build/*/Testing/Temporary/Last*.log
+          components/eamxx/ctest-build/*/ctest_resource_file.json
+          components/eamxx/ctest-build/*/CMakeCache.txt
+      env:
+        NODE_EXTRA_CA_CERTS: ${{ env.NODE_EXTRA_CA_CERTS }}

.github/dependabot.yml

@@ -7,7 +7,6 @@ updates:
     schedule:
       interval: "weekly"
     assignees:
-      - "rljacob"
+      - "bartgol"
     reviewers:
       - "mahf708"
-      - "bartgol"

.github/pull_request_template.md

@@ -0,0 +1,29 @@
+<!--
+Please add a description of what is accomplished in the PR here at the top:
+-->
+
+<!--
+Below are a few things we ask you or your reviewers to kindly check. 
+***Remove checks that are not relevant by deleting the line(s) below.***
+-->
+Checklist
+* [ ] Documentation:
+  * [ ] Design document has been generated and added to the docs
+  * [ ] User's Guide has been updated
+  * [ ] Developer's Guide has been updated
+  * [ ] Documentation has been [built locally](https://e3sm-project.github.io/Omega/omega/develop/devGuide/BuildDocs.html) and changes look as expected
+* [ ] Testing
+  * [ ] A comment in the PR documents testing used to verify the changes including any tests that are added/modified/impacted.
+  * [ ] CTest unit tests for new features have been added per the approved design. 
+  * [ ] Polaris tests for new features have been added per the approved design (and included in a test suite)
+  * [ ] Unit tests have passed. Please provide a relevant CDash build entry for verification.
+  * [ ] Polaris test suite has passed
+  * [ ] Performance related PRs: Please include a relevant PACE experiment link documenting performance before and after.
+* [ ] Stealth Features
+  * [ ] If any stealth features are included in the PR, please confirm that they have been documented.
+
+<!--
+Please note any issues this fixes using closing keywords: https://help.github.com/articles/closing-issues-using-keywords
+-->
+
+