merge from upstream master

Author: conraddelgado

.cursor/rules/mfc-agent-rules.mdc

@@ -0,0 +1,30 @@
+#!/bin/bash
+
+# MFC pre-commit hook
+# Runs ./mfc.sh precheck before allowing commits
+# Bypass with: git commit --no-verify
+
+# Only run if we're in the MFC repo root (where mfc.sh exists)
+if [ ! -f "$(git rev-parse --show-toplevel)/mfc.sh" ]; then
+    exit 0
+fi
+
+cd "$(git rev-parse --show-toplevel)"
+
+# Auto-detect CPU count (capped at 12 to avoid hogging resources)
+JOBS=$(nproc 2>/dev/null || sysctl -n hw.ncpu 2>/dev/null || echo 4)
+[ "$JOBS" -gt 12 ] && JOBS=12
+
+echo ""
+echo "mfc: Running precheck before commit (-j $JOBS)..."
+echo ""
+
+if ./mfc.sh precheck -j "$JOBS"; then
+    echo ""
+    exit 0
+else
+    echo ""
+    echo "mfc: Commit blocked. Fix issues above or use 'git commit --no-verify' to bypass."
+    echo ""
+    exit 1
+fi

.githooks/pre-commit

@@ -15,17 +15,17 @@ RUN apt-get update -y && \
     if [ "$TARGET" != "gpu" ]; then \
         apt-get install -y \
             build-essential git make cmake gcc g++ gfortran bc \
-            python3.11 python3.11-venv python3-pip \
+            python3.12 python3.12-venv python3-pip \
             openmpi-bin libopenmpi-dev libfftw3-dev \
             mpich libmpich-dev; \
     else \
         apt-get install -y \
             build-essential git make cmake bc \
-            python3.11 python3.11-venv python3-pip \
+            python3.12 python3.12-venv python3-pip \
             libfftw3-dev \
             openmpi-bin libopenmpi-dev; \
     fi && \
-    update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.11 2 && \
+    update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.12 2 && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 ENV OMPI_ALLOW_RUN_AS_ROOT=1
@@ -40,6 +40,13 @@ ENV FC=${FC_COMPILER}
 ENV PATH="${COMPILER_PATH}:$PATH"
 ENV LD_LIBRARY_PATH="${COMPILER_LD_LIBRARY_PATH}:${LD_LIBRARY_PATH:-}"
 
+# Pre-install numpy into the venv before mfc.sh runs, as it's required at
+# build time by several dependencies (pandas, cantera, matplotlib, etc.) that
+# may need to compile from source on architectures without pre-built wheels
+RUN python3.12 -m venv /opt/MFC/build/venv && \
+    /opt/MFC/build/venv/bin/pip install --upgrade pip && \
+    /opt/MFC/build/venv/bin/pip install numpy
+
 RUN echo "TARGET=$TARGET CC=$CC_COMPILER FC=$FC_COMPILER" && \
     cd /opt/MFC && \
     if [ "$TARGET" = "gpu" ]; then \

.github/Dockerfile

@@ -1,31 +1,85 @@
 name: 'Benchmark'
 
 on:
-  pull_request:
-  pull_request_review:
-    types: [submitted]
+  # Trigger when Test Suite completes (no polling needed)
+  workflow_run:
+    workflows: ["Test Suite"]
+    types: [completed]
   workflow_dispatch:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.workflow_run.head_branch || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   file-changes:
     name: Detect File Changes
+    # Only run if Test Suite passed (or manual dispatch)
+    if: github.event_name == 'workflow_dispatch' || github.event.workflow_run.conclusion == 'success'
     runs-on: 'ubuntu-latest'
-    outputs: 
+    outputs:
       checkall: ${{ steps.changes.outputs.checkall }}
+      pr_number: ${{ steps.pr-info.outputs.pr_number }}
+      pr_approved: ${{ steps.pr-info.outputs.approved }}
+      pr_author: ${{ steps.pr-info.outputs.author }}
     steps:
       - name: Clone
         uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.workflow_run.head_sha || github.sha }}
 
       - name: Detect Changes
         uses: dorny/paths-filter@v3
         id: changes
-        with: 
+        with:
           filters: ".github/file-filter.yml"
 
+      - name: Get PR Info
+        id: pr-info
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          if [ "${{ github.event_name }}" = "workflow_dispatch" ]; then
+            echo "pr_number=" >> $GITHUB_OUTPUT
+            echo "approved=true" >> $GITHUB_OUTPUT
+            echo "author=${{ github.actor }}" >> $GITHUB_OUTPUT
+          else
+            # Get PR number from workflow_run
+            PR_NUMBER="${{ github.event.workflow_run.pull_requests[0].number }}"
+            if [ -n "$PR_NUMBER" ]; then
+              echo "pr_number=$PR_NUMBER" >> $GITHUB_OUTPUT
+
+              # Fetch actual PR author from API (workflow_run.actor is the re-runner, not PR author)
+              PR_AUTHOR=$(gh api repos/${{ github.repository }}/pulls/$PR_NUMBER --jq '.user.login')
+              echo "author=$PR_AUTHOR" >> $GITHUB_OUTPUT
+
+              # Check if PR is approved
+              APPROVED=$(gh api repos/${{ github.repository }}/pulls/$PR_NUMBER/reviews \
+                --jq '[.[] | select(.state == "APPROVED")] | length')
+              if [ "$APPROVED" -gt 0 ]; then
+                echo "approved=true" >> $GITHUB_OUTPUT
+              else
+                echo "approved=false" >> $GITHUB_OUTPUT
+              fi
+            else
+              echo "pr_number=" >> $GITHUB_OUTPUT
+              echo "approved=false" >> $GITHUB_OUTPUT
+              echo "author=" >> $GITHUB_OUTPUT
+            fi
+          fi
+
   self:
     name: "${{ 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'))) }}
-    needs: file-changes
+    if: >
+      github.repository == 'MFlowCode/MFC' &&
+      needs.file-changes.outputs.checkall == 'true' &&
+      (
+        github.event_name == 'workflow_dispatch' ||
+        needs.file-changes.outputs.pr_approved == 'true' ||
+        needs.file-changes.outputs.pr_author == 'sbryngelson' ||
+        needs.file-changes.outputs.pr_author == 'wilfonba'
+      )
+    needs: [file-changes]
     strategy:
       fail-fast: false
       matrix:
@@ -89,6 +143,7 @@ jobs:
       - name: Clone - PR
         uses: actions/checkout@v4
         with:
+          ref: ${{ github.event.workflow_run.head_sha || github.sha }}
           path: pr
 
       - name: Clone - Master

.github/workflows/bench.yml

@@ -1,6 +1,14 @@
 name: Cleanliness
 
-on: [push, pull_request, workflow_dispatch]
+on:
+  push:
+    branches: [master]
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   file-changes:

.github/workflows/cleanliness.yml

@@ -1,6 +1,14 @@
 name: Coverage Check
 
-on: [push, pull_request, workflow_dispatch]
+on:
+  push:
+    branches: [master]
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   file-changes:
@@ -35,10 +43,10 @@ jobs:
                 libfftw3-dev libhdf5-dev libblas-dev liblapack-dev
 
       - name: Build
-        run: /bin/bash mfc.sh build -j $(nproc) --gcov
+        run: /bin/bash mfc.sh build -v -j $(nproc) --gcov
 
       - name: Test
-        run: /bin/bash mfc.sh test -a -j $(nproc)
+        run: /bin/bash mfc.sh test -v -a -j $(nproc)
 
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v4

.github/workflows/coverage.yml

@@ -54,7 +54,7 @@ jobs:
           TAG="${{ github.event.inputs.tag || github.ref_name }}"
           echo "tag=$TAG" >> $GITHUB_OUTPUT
           echo "TAG=$TAG" >> $GITHUB_ENV
-          git clone --branch "$TAG" --depth 1 https://github.com/MFlowCode/MFC.git mfc
+          git clone --branch "$TAG" --depth 1 ${{ github.server_url }}/${{ github.repository }}.git mfc
 
       - name: Stage
         run: |