Merge remote-tracking branch 'upstream/master' into MovingBubblesFresh

Author: wilfonba

.claude/settings.json

@@ -3,15 +3,52 @@ language: en-US
 
 reviews:
   profile: chill
+
+  # Hide the “Review skipped / Draft detected” status message
+  review_status: false
+
+  # Remove the “Prompt for all review comments with AI agents” block
+  enable_prompt_for_ai_agents: false
+
+  # Disable extra/non-default summary sections
+  high_level_summary: false
+  related_issues: false
+  sequence_diagrams: false
+  changed_files_summary: false
+
+  # Further reduce walkthrough noise (footer itself isn't currently configurable)
+  collapse_walkthrough: true
+  review_details: false
+  estimate_code_review_effort: false
+  assess_linked_issues: false
+  related_prs: false
+  suggested_labels: false
+  suggested_reviewers: false
+  in_progress_fortune: false
+  poem: false
+
+  # Remove "Finishing Touches" section content
+  finishing_touches:
+    docstrings:
+      enabled: false
+    unit_tests:
+      enabled: false
+
+  auto_review:
+    enabled: true                  # initial PR-open review
+    auto_incremental_review: false # no re-run on every push
+
   path_instructions:
+    - path: "**/*"
+      instructions: |
+        IMPORTANT: Only comment on code that is within this PR’s diff (changed lines / files).
+        Do not add feedback that requires commenting outside the diff range.
+
     - path: "src/**/*.fpp"
       instructions: |
         Fortran source (Fypp-preprocessed). Follow the coding standards in
         docs/documentation/contributing.md and the GPU macro API in
-        docs/documentation/gpuParallelization.md.
-    - path: "src/**/*.f90"
-      instructions: |
-        Fortran source. Follow the coding standards in
+        docs/documentation/gpuParallelization.md and the coding standards in
         docs/documentation/contributing.md.
     - path: "toolchain/**/*.py"
       instructions: |

.codeant/configuration.json

@@ -30,3 +30,11 @@ See the [developer guide](https://mflowcode.github.io/documentation/contributing
 - [ ] Tested on NVIDIA GPU or AMD GPU
 
 </details>
+
+## AI code reviews
+
+Reviews are not triggered automatically. To request a review, comment on the PR:
+- `@coderabbitai review` — incremental review (new changes only)
+- `@coderabbitai full review` — full review from scratch
+- `/review` — Qodo review
+- `/improve` — Qodo code suggestions

.coderabbit.yaml

@@ -14,50 +14,27 @@ device="$2"
 interface="$3"
 cluster="$4"
 
-# Get the directory where this script lives
-SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-
 echo "[$dir] Submitting benchmark for $device-$interface on $cluster..."
 cd "$dir"
 
-# Submit job
-submit_output=$(bash .github/workflows/$cluster/submit-bench.sh \
-  .github/workflows/$cluster/bench.sh "$device" "$interface" 2>&1)
-
-job_id=$(echo "$submit_output" | sed -n 's/.*Submitted batch job \([0-9][0-9]*\).*/\1/p')
-job_slug="bench-$device-$interface"
-output_file="${job_slug}.out"
-
-if [ -z "$job_id" ]; then
-  echo "[$dir] ERROR: Failed to submit job"
-  echo "$submit_output"
-  exit 1
-fi
-
-echo "[$dir] Job ID: $job_id, monitoring output file: $output_file"
-
-# Use the monitoring script from PR (where this script lives)
-monitor_exit=0
-bash "${SCRIPT_DIR}/monitor_slurm_job.sh" "$job_id" "$output_file" || monitor_exit=$?
-if [ "$monitor_exit" -ne 0 ]; then
-  echo "[$dir] WARNING: SLURM job exited with code $monitor_exit"
-else
-  echo "[$dir] Monitoring complete for job $job_id"
-fi
+# Submit and monitor job (submit.sh auto-detects bench mode from script name)
+bash .github/workflows/$cluster/submit.sh \
+    .github/workflows/$cluster/bench.sh "$device" "$interface"
 
 # Verify the YAML output file was created
+job_slug="bench-$device-$interface"
 yaml_file="${job_slug}.yaml"
 if [ ! -f "$yaml_file" ]; then
-  echo "[$dir] ERROR: Expected output file not found: $yaml_file"
-  echo "[$dir] Directory contents:"
-  ls -la *.yaml 2>/dev/null || echo "  No YAML files found"
-  echo ""
-  echo "[$dir] Last 100 lines of job output ($output_file):"
-  echo "----------------------------------------"
-  tail -n 100 "$output_file" 2>/dev/null || echo "  Could not read output file"
-  echo "----------------------------------------"
-  exit 1
+    echo "[$dir] ERROR: Expected output file not found: $yaml_file"
+    echo "[$dir] Directory contents:"
+    ls -la *.yaml 2>/dev/null || echo "  No YAML files found"
+    echo ""
+    output_file="${job_slug}.out"
+    echo "[$dir] Last 100 lines of job output ($output_file):"
+    echo "----------------------------------------"
+    tail -n 100 "$output_file" 2>/dev/null || echo "  Could not read output file"
+    echo "----------------------------------------"
+    exit 1
 fi
 
 echo "[$dir] Verified output file exists: $yaml_file ($(stat -f%z "$yaml_file" 2>/dev/null || stat -c%s "$yaml_file" 2>/dev/null) bytes)"
-

.github/pull_request_template.md

@@ -13,6 +13,9 @@ concurrency:
 jobs:
   file-changes:
     name: Detect File Changes
+    if: >
+      github.event_name != 'pull_request_review' ||
+      github.event.review.user.type != 'Bot'
     runs-on: 'ubuntu-latest'
     outputs:
       checkall: ${{ steps.changes.outputs.checkall }}
@@ -28,7 +31,7 @@ jobs:
 
   self:
     name: "${{ matrix.name }} (${{ matrix.device }}${{ matrix.interface != 'none' && format('-{0}', matrix.interface) || '' }})"
-    if: ${{ github.repository=='MFlowCode/MFC' && needs.file-changes.outputs.checkall=='true' && ((github.event_name=='pull_request_review' && github.event.review.state=='approved') || (github.event_name=='pull_request' && (github.event.pull_request.user.login=='sbryngelson' || github.event.pull_request.user.login=='wilfonba')) || github.event_name=='workflow_dispatch') }}
+    if: ${{ github.repository=='MFlowCode/MFC' && needs.file-changes.outputs.checkall=='true' && github.event.pull_request.draft != true && ((github.event_name=='pull_request_review' && github.event.review.state=='approved') || (github.event_name=='pull_request' && (github.event.pull_request.user.login=='sbryngelson' || github.event.pull_request.user.login=='wilfonba')) || github.event_name=='workflow_dispatch') }}
     needs: file-changes
     strategy:
       fail-fast: false

.github/scripts/submit_and_monitor_bench.sh

@@ -10,68 +10,63 @@ jobs:
     permissions:
       contents: read
       pull-requests: write
-      issues: read
+      issues: write
       actions: read
       id-token: write
 
     steps:
-      - name: Checkout PR head (fork)
+      - name: Install unzip (required by bun setup)
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y unzip
+
+      # IMPORTANT: checkout BASE repo only (safe on forks)
+      - name: Checkout base repo (safe)
         uses: actions/checkout@v4
         with:
-          ref: ${{ github.event.pull_request.head.sha }}
           fetch-depth: 1
 
       - name: Run Claude Code Review
-        id: claude-review
         uses: anthropics/claude-code-action@v1
         with:
           claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
           github_token: ${{ github.token }}
 
-          plugin_marketplaces: 'https://github.com/anthropics/claude-code.git'
-          plugins: 'code-review@claude-code-plugins'
+          plugin_marketplaces: "https://github.com/anthropics/claude-code.git"
+          plugins: "code-review@claude-code-plugins"
 
+          # NOTE: do NOT use --dangerouslyDisableSandbox (it can crash the CLI).
+          # This flag is for non-interactive CI runs (bypasses approval prompts).
           claude_args: >
-            --dangerouslyDisableSandbox
-            --max-turns 10
+            --dangerously-skip-permissions
+            --max-turns 90
             --allowedTools
-            "Bash(gh pr view:*)"
-            "Bash(gh pr diff:*)"
-            "Bash(gh pr comment:*)"
-            "Bash(gh api repos/*/pulls/*:*)"
-            "Bash(gh api repos/*/issues/*/comments:*)"
-            "Bash(cat:*)"
-            "Bash(ls:*)"
-            "Bash(grep:*)"
-            "Bash(find:*)"
+            "Bash"
 
           prompt: |
-            /code-review:code-review ${{ github.repository }}/pull/${{ github.event.pull_request.number }}
+            You are running in pull_request_target.
+            DO NOT read or inspect any checked-out PR/fork code. Review ONLY using GitHub API/gh commands.
 
-            Always use the numeric PR form with --repo, e.g.:
-            - gh pr view ${{ github.event.pull_request.number }} --repo ${{ github.repository }} ...
-            - gh pr diff ${{ github.event.pull_request.number }} --repo ${{ github.repository }} ...
-            - gh pr comment ${{ github.event.pull_request.number }} --repo ${{ github.repository }} ...
+            You may read local guidance ONLY from:
+            - ./CLAUDE.md (root) if present
+            - ./.claude/rules/*.md if present (max 10 files)
 
-            Output requirements (even if no issues):
-            - Start with: files changed count + list up to 15 changed file paths
-            - Then: a short summary of what the PR changes (3–6 bullets)
-            - Then: findings:
-              - If issues: list them with file path + line numbers when possible
-              - If no issues: list at least 3 concrete "improvement opportunities" with file paths
+            Keep tool calls minimal and in this order:
+            1) ls -1 .claude/rules 2>/dev/null || true
+            2) cat CLAUDE.md 2>/dev/null || true
+            3) find .claude/rules -maxdepth 1 -name "*.md" -print | head -n 10 | xargs -I{} cat "{}" 2>/dev/null || true
+            4) gh pr view ${{ github.event.pull_request.number }} --repo ${{ github.repository }} --json title,body,files,changedFiles,additions,deletions,headRefOid
+            5) gh pr diff ${{ github.event.pull_request.number }} --repo ${{ github.repository }}
+            6) Post ONE top-level PR comment titled "Claude Code Review", then STOP.
 
-            Post the results as ONE top-level PR comment titled "Claude Code Review".
-            If you cannot access the diff/files, say exactly what is blocked.
-            If posting a PR comment is blocked, write the full review to the GitHub Actions job summary instead.
+            Output format:
+            - Head SHA
+            - Files changed count + list up to 10 file paths
+            - Summary (3–6 bullets, minimal)
+            - Findings with file + line numbers when possible
+            - If no issues: 0–3 improvement opportunities (only if confident)
 
-            IMPORTANT:
-            - Do NOT stop just because a previous "Claude Code Review" comment exists.
-            - If a prior Claude review exists, post a NEW comment titled "Claude Code Review (updated)" that includes:
-              - current head SHA: ${{ github.event.pull_request.head.sha }}
-              - files changed count + up to 15 file paths
-              - 3–6 bullet summary of changes
-              - findings or at least 3 improvement opportunities with file paths
-            Post as ONE top-level PR comment.
+            If posting is blocked, write the full review to the GitHub Actions job summary instead, then STOP.
 
           additional_permissions: |
             actions: read

.github/workflows/bench.yml

@@ -4,6 +4,7 @@ on:
   push:
     branches: [master]
   pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
   workflow_dispatch:
 
 concurrency:
@@ -28,18 +29,29 @@ jobs:
 
   run:
     name: Coverage Test on CodeCov
-    if: needs.file-changes.outputs.checkall == 'true'
+    if: needs.file-changes.outputs.checkall == 'true' && github.event.pull_request.draft != true
     needs: file-changes
     runs-on: "ubuntu-latest"
     steps:
       - name: Checkouts
         uses: actions/checkout@v4
 
+      - name: Get system info for cache key
+        id: sys-info
+        run: |
+          {
+            uname -m
+            cat /proc/cpuinfo 2>/dev/null | grep 'model name' | head -1 || sysctl -n machdep.cpu.brand_string 2>/dev/null || true
+            ${FC:-gfortran} --version 2>/dev/null | head -1 || true
+            ${CC:-gcc} --version 2>/dev/null | head -1 || true
+          } | (sha256sum 2>/dev/null || shasum -a 256) | cut -c1-16 > /tmp/sys-hash
+          echo "sys-hash=$(cat /tmp/sys-hash)" >> "$GITHUB_OUTPUT"
+
       - name: Restore Build Cache
         uses: actions/cache@v4
         with:
           path: build
-          key: mfc-coverage-${{ hashFiles('CMakeLists.txt', 'toolchain/dependencies/**', 'toolchain/cmake/**', 'src/**/*.fpp', 'src/**/*.f90') }}
+          key: mfc-coverage-${{ steps.sys-info.outputs.sys-hash }}-${{ hashFiles('CMakeLists.txt', 'toolchain/dependencies/**', 'toolchain/cmake/**', 'src/**/*.fpp', 'src/**/*.f90') }}
 
       - name: Setup Ubuntu
         run: |

.github/workflows/claude-code-review.yml

@@ -16,7 +16,7 @@ if [ "$job_device" = "gpu" ]; then
 fi
 
 if [ "$job_device" = "gpu" ]; then
-    ./mfc.sh bench --mem 12 -j $n_ranks -o "$job_slug.yaml" -- -c frontier $device_opts -n $n_ranks
+    ./mfc.sh bench --mem 4 -j $n_ranks -o "$job_slug.yaml" -- -c $job_cluster $device_opts -n $n_ranks
 else
-    ./mfc.sh bench --mem 1 -j $(nproc) -o "$job_slug.yaml" -- -c frontier $device_opts -n $n_ranks
+    ./mfc.sh bench --mem 1 -j $(nproc) -o "$job_slug.yaml" -- -c $job_cluster $device_opts -n $n_ranks
 fi

.github/workflows/coverage.yml

@@ -3,6 +3,15 @@
 # Ignore SIGHUP to survive login node session drops
 trap '' HUP
 
+# Determine compiler flag from directory name
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+cluster_name="$(basename "$SCRIPT_DIR")"
+case "$cluster_name" in
+    frontier)     compiler_flag="f" ;;
+    frontier_amd) compiler_flag="famd" ;;
+    *) echo "ERROR: Unknown cluster '$cluster_name'"; exit 1 ;;
+esac
+
 job_device=$1
 job_interface=$2
 run_bench=$3
@@ -16,28 +25,25 @@ if [ "$job_device" = "gpu" ]; then
   fi
 fi
 
-. ./mfc.sh load -c f -m g
+. ./mfc.sh load -c $compiler_flag -m $([ "$job_device" = "gpu" ] && echo "g" || echo "c")
 
 # Only set up build cache for test suite, not benchmarks
 if [ "$run_bench" != "bench" ]; then
-    source .github/scripts/setup-build-cache.sh frontier "$job_device" "$job_interface"
+    source .github/scripts/setup-build-cache.sh "$cluster_name" "$job_device" "$job_interface"
 fi
 
 max_attempts=3
 attempt=1
 while [ $attempt -le $max_attempts ]; do
     echo "Build attempt $attempt of $max_attempts..."
     if [ "$run_bench" == "bench" ]; then
-        build_cmd_ok=true
-        for dir in benchmarks/*/; do
-            dirname=$(basename "$dir")
-            if ! ./mfc.sh run -v "$dir/case.py" --case-optimization -j 8 --dry-run $build_opts; then
-                build_cmd_ok=false
-                break
-            fi
-        done
+        if ./mfc.sh build -j 8 $build_opts; then
+            build_cmd_ok=true
+        else
+            build_cmd_ok=false
+        fi
     else
-        if ./mfc.sh test -v -a --dry-run --rdma-mpi -j 8 $build_opts; then
+        if ./mfc.sh test -v -a --dry-run $([ "$cluster_name" = "frontier" ] && echo "--rdma-mpi") -j 8 $build_opts; then
             build_cmd_ok=true
         else
             build_cmd_ok=false