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

Author: wilfonba

.claude/settings.json

@@ -0,0 +1,14 @@
+{
+  "allowedTools": [
+    "Bash(gh pr view:*)",
+    "Bash(gh pr diff:*)",
+    "Bash(gh pr comment:*)",
+    "Bash(gh api:*)",
+    "Bash(gh search code:*)",
+    "Bash(cat:*)",
+    "Bash(ls:*)",
+    "Bash(grep:*)",
+    "Bash(python3:*)",
+    "Bash(git:*)"
+  ]
+}

.codeant/configuration.json

@@ -0,0 +1,14 @@
+{
+  "review_configuration": {
+    "include": [
+      "src/**/*.fpp",
+      "src/**/*.f90",
+      "toolchain/**/*.py"
+    ],
+    "exclude": [
+      "tests/**",
+      "examples/**",
+      "docs/**"
+    ]
+  }
+}

.coderabbit.yaml

@@ -3,52 +3,15 @@ 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 and the coding standards in
+        docs/documentation/gpuParallelization.md.
+    - path: "src/**/*.f90"
+      instructions: |
+        Fortran source. Follow the coding standards in
         docs/documentation/contributing.md.
     - path: "toolchain/**/*.py"
       instructions: |

.github/pull_request_template.md

@@ -30,11 +30,3 @@ 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

.github/workflows/bench.yml

@@ -28,7 +28,7 @@ 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.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') }}
+    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') }}
     needs: file-changes
     strategy:
       fail-fast: false

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

@@ -10,63 +10,68 @@ jobs:
     permissions:
       contents: read
       pull-requests: write
-      issues: write
+      issues: read
       actions: read
       id-token: write
 
     steps:
-      - 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)
+      - name: Checkout PR head (fork)
         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: >
-            --dangerously-skip-permissions
-            --max-turns 90
+            --dangerouslyDisableSandbox
+            --max-turns 10
             --allowedTools
-            "Bash"
+            "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:*)"
 
           prompt: |
-            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.
+            /code-review:code-review ${{ github.repository }}/pull/${{ github.event.pull_request.number }}
 
-            You may read local guidance ONLY from:
-            - ./CLAUDE.md (root) if present
-            - ./.claude/rules/*.md if present (max 10 files)
+            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 }} ...
 
-            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.
+            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
 
-            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)
+            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.
 
-            If posting is blocked, write the full review to the GitHub Actions job summary instead, then STOP.
+            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.
 
           additional_permissions: |
             actions: read

.github/workflows/test.yml

@@ -4,7 +4,6 @@ on:
   push:
     branches: [master]
   pull_request:
-    types: [opened, synchronize, reopened, ready_for_review]
   workflow_dispatch:
 
 concurrency:
@@ -152,7 +151,7 @@ jobs:
 
   self:
     name: "${{ matrix.cluster_name }} (${{ matrix.device }}${{ matrix.interface != 'none' && format('-{0}', matrix.interface) || '' }})"
-    if: github.repository == 'MFlowCode/MFC' && needs.file-changes.outputs.checkall == 'true' && github.event.pull_request.draft != true
+    if: github.repository == 'MFlowCode/MFC' && needs.file-changes.outputs.checkall == 'true'
     needs: [lint-gate, file-changes]
     continue-on-error: false
     timeout-minutes: 480

.lychee.toml

@@ -16,11 +16,8 @@ accept = ["200", "429", "502", "504"]
 
 verbose = "error"
 
-# Exclude files from scanning
-exclude_path = [
-    "sitemap\\.xml",  # Contains pre-publish production URLs
-    "404\\.html",     # Root-relative links (/, /documentation/) can't resolve in local checks
-]
+# Exclude sitemap file from scanning (it contains pre-publish production URLs)
+exclude_path = ["sitemap\\.xml"]
 
 # Exclude URLs that fail due to external issues (broken SSL, pre-deploy only, etc.)
 exclude = [

.pr_agent.toml

@@ -5,6 +5,9 @@ pr_commands = [
   "/improve",
 ]
 
+handle_push_trigger = true
+push_commands = ["/improve"]
+
 [pr_reviewer]                # (all fields optional)
 num_max_findings        = 10  # how many items to surface
 require_tests_review    = true

CLAUDE.md

@@ -51,7 +51,7 @@ source ./mfc.sh load -c p -m c             # Load Phoenix CPU modules
 
 # Other
 ./mfc.sh validate case.py                  # Validate case file without running
-./mfc.sh params <query>                    # Search 3,400 case parameters
+./mfc.sh params <query>                    # Search ~3,400 case parameters
 ./mfc.sh clean                             # Remove build artifacts
 ./mfc.sh new <name>                        # Create new case from template
 ```