Merge remote-tracking branch 'openmc-dev/openmc/develop' into Sensitivity-Analysis

Author: Ebiwonjumi

.github/pull_request_template.md

@@ -13,7 +13,7 @@ Fixes # (issue)
 # Checklist
 
 - [ ] I have performed a self-review of my own code
-- [ ] I have run [clang-format](https://docs.openmc.org/en/latest/devguide/styleguide.html#automatic-formatting) (version 15) on any C++ source files (if applicable)
+- [ ] I have run [clang-format](https://docs.openmc.org/en/latest/devguide/styleguide.html#automatic-formatting) (version 18) on any C++ source files (if applicable)
 - [ ] I have followed the [style guidelines](https://docs.openmc.org/en/latest/devguide/styleguide.html#python) for Python source files (if applicable)
 - [ ] I have made corresponding changes to the documentation (if applicable)
 - [ ] I have added tests that prove my fix is effective or that my feature works (if applicable)

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: CI
+name: Tests and Coverage
 
 on:
   # allows us to run workflows manually
@@ -21,60 +21,75 @@ env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
+  filter-changes:
+    runs-on: ubuntu-latest
+    outputs:
+      source_changed: ${{ steps.filter.outputs.source_changed }}
+    steps:
+      - name: Check out the repository
+        uses: actions/checkout@v4
+      - name: Examine changed files
+        id: filter
+        uses: dorny/paths-filter@668c092af3649c4b664c54e4b704aa46782f6f7c # latest master commit, not released yet
+        with:
+          filters: |
+            source_changed:
+              - '!docs/**'
+              - '!**/*.md'
+          predicate-quantifier: 'every'
   main:
+    needs: filter-changes
+    if: ${{ needs.filter-changes.outputs.source_changed == 'true' }}
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: ["3.11"]
+        python-version: ["3.12"]
         mpi: [n, y]
         omp: [n, y]
         dagmc: [n]
         libmesh: [n]
         event: [n]
-        vectfit: [n]
 
         include:
-          - python-version: "3.12"
+          - python-version: "3.13"
             omp: n
             mpi: n
-          - python-version: "3.13"
+          - python-version: "3.14"
+            omp: n
+            mpi: n
+          - python-version: "3.14t"
             omp: n
             mpi: n
           - dagmc: y
-            python-version: "3.11"
+            python-version: "3.12"
             mpi: y
             omp: y
           - libmesh: y
-            python-version: "3.11"
+            python-version: "3.12"
             mpi: y
             omp: y
           - libmesh: y
-            python-version: "3.11"
+            python-version: "3.12"
             mpi: n
             omp: y
           - event: y
-            python-version: "3.11"
+            python-version: "3.12"
             omp: y
             mpi: n
-          - vectfit: y
-            python-version: "3.11"
-            omp: n
-            mpi: y
     name: "Python ${{ matrix.python-version }} (omp=${{ matrix.omp }},
       mpi=${{ matrix.mpi }}, dagmc=${{ matrix.dagmc }},
-      libmesh=${{ matrix.libmesh }}, event=${{ matrix.event }}
-      vectfit=${{ matrix.vectfit }})"
+      libmesh=${{ matrix.libmesh }}, event=${{ matrix.event }}"
 
     env:
       MPI: ${{ matrix.mpi }}
       PHDF5: ${{ matrix.mpi }}
       OMP: ${{ matrix.omp }}
       DAGMC: ${{ matrix.dagmc }}
       EVENT: ${{ matrix.event }}
-      VECTFIT: ${{ matrix.vectfit }}
       LIBMESH: ${{ matrix.libmesh }}
       NPY_DISABLE_CPU_FEATURES: "AVX512F AVX512_SKX"
       OPENBLAS_NUM_THREADS: 1
+      PYTEST_ADDOPTS: --cov=openmc --cov-report=lcov:coverage-python.lcov
       # libfabric complains about fork() as a result of using Python multiprocessing.
       # We can work around it with RDMAV_FORK_SAFE=1 in libfabric < 1.13 and with
       # FI_EFA_FORK_SAFE=1 in more recent versions.
@@ -131,11 +146,6 @@ jobs:
           sudo update-alternatives --set mpirun /usr/bin/mpirun.mpich
           sudo update-alternatives --set mpi-x86_64-linux-gnu /usr/include/x86_64-linux-gnu/mpich
 
-      - name: Optional apt dependencies for vectfit
-        shell: bash
-        if: ${{ matrix.vectfit == 'y' }}
-        run: sudo apt install -y libblas-dev liblapack-dev
-
       - name: install
         shell: bash
         run: |
@@ -153,7 +163,7 @@ jobs:
           path: |
             ~/nndc_hdf5
             ~/endf-b-vii.1
-          key: ${{ runner.os }}-build-xs-cache
+          key: ${{ runner.os }}-build-xs-cache-${{ hashFiles(format('{0}/tools/ci/download-xs.sh', github.workspace)) }}
 
       - name: before
         shell: bash
@@ -171,18 +181,68 @@ jobs:
         uses: mxschmitt/action-tmate@v3
         timeout-minutes: 10
 
-      - name: after_success
+      - name: Generate C++ coverage (gcovr)
+        shell: bash
+        run: |
+          # Produce LCOV directly from gcov data in the build tree
+          gcovr \
+            --root "$GITHUB_WORKSPACE" \
+            --object-directory "$GITHUB_WORKSPACE/build" \
+            --filter "$GITHUB_WORKSPACE/src" \
+            --filter "$GITHUB_WORKSPACE/include" \
+            --exclude "$GITHUB_WORKSPACE/src/external/.*" \
+            --exclude "$GITHUB_WORKSPACE/src/include/openmc/external/.*" \
+            --gcov-ignore-errors source_not_found \
+            --gcov-ignore-errors output_error \
+            --gcov-ignore-parse-errors suspicious_hits.warn \
+            --merge-mode-functions=separate \
+            --print-summary \
+            --lcov -o coverage-cpp.lcov || true
+
+      - name: Merge C++ and Python coverage
         shell: bash
         run: |
-          cpp-coveralls -i src -i include -e src/external --exclude-pattern "/usr/*" --dump cpp_cov.json
-          coveralls --merge=cpp_cov.json --service=github
+          # Merge C++ and Python LCOV into a single file for upload
+          cat coverage-cpp.lcov coverage-python.lcov > coverage.lcov
 
-  finish:
-    needs: main
+      - name: Upload coverage to Coveralls
+        if: ${{ hashFiles('coverage.lcov') != '' }}
+        uses: coverallsapp/github-action@v2
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          parallel: true
+          flag-name: C++ and Python
+          path-to-lcov: coverage.lcov
+          fail-on-error: false
+
+  coverage:
+    needs: [filter-changes, main]
+    if: ${{ always() }}
     runs-on: ubuntu-latest
     steps:
       - name: Coveralls Finished
+        if: ${{ needs.filter-changes.outputs.source_changed == 'true' }}
         uses: coverallsapp/github-action@v2
         with:
-          github-token: ${{ secrets.github_token }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
           parallel-finished: true
+          fail-on-error: false
+
+  ci-pass:
+    needs: [filter-changes, main, coverage]
+    name: Check CI status
+    if: ${{ always() }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check CI status
+        run: |
+          if [[ "${{ needs.filter-changes.outputs.source_changed }}" == "false" ]]; then
+            echo "Documentation-only change - CI skipped successfully"
+            exit 0
+          fi
+          if [[ "${{ needs.main.result }}" == "success" && "${{ needs.coverage.result }}" == "success" ]]; then
+            echo "CI passed"
+            exit 0
+          fi
+          echo "CI failed"
+          exit 1

.github/workflows/format-check.yml

@@ -5,13 +5,22 @@ on:
   workflow_dispatch:
 
   pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - labeled
+      - unlabeled
     branches:
       - develop
       - master
 
 jobs:
   cpp-linter:
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: write
     steps:
       - uses: actions/checkout@v4
       - uses: cpp-linter/cpp-linter-action@v2
@@ -22,11 +31,30 @@ jobs:
           style: file
           files-changed-only: true
           tidy-checks: '-*'
-          version: '15' # clang-format version
+          version: '18' # clang-format version
+          format-review: ${{ github.event_name == 'pull_request' && contains(github.event.pull_request.labels.*.name, 'cpp-format-suggest') }}
+          passive-reviews: ${{ github.event_name == 'pull_request' && contains(github.event.pull_request.labels.*.name, 'cpp-format-suggest') }}
           file-annotations: true
           step-summary: true
           extensions: 'cpp,h'
 
+      - name: Comment with suggestion instructions
+        if: steps.linter.outputs.checks-failed > 0 && !contains(github.event.pull_request.labels.*.name, 'cpp-format-suggest')
+        uses: actions/github-script@v7
+        with:
+          script: |
+            const {owner, repo} = context.repo;
+            const issue_number = context.payload.pull_request.number;
+            await github.rest.issues.createComment({
+              owner,
+              repo,
+              issue_number,
+              body: "C++ formatting checks failed. Add the `cpp-format-suggest` label to this PR for inline formatting suggestions on the next run."
+            });
+
       - name: Failure Check
         if: steps.linter.outputs.checks-failed > 0
-        run: echo "Some files failed the formatting check! See job summary and file annotations for more info" && exit 1
+        run: |
+          echo "Some files failed the formatting check."
+          echo "See job summary and file annotations for details."
+          exit 1

.gitignore

@@ -30,7 +30,7 @@ docs/source/_images/*.aux
 docs/source/pythonapi/generated/
 
 # Source build
-build
+build*/
 
 # build from src/utils/setup.py
 src/utils/build

.gitmodules

@@ -1,12 +1,6 @@
 [submodule "vendor/pugixml"]
 	path = vendor/pugixml
 	url = https://github.com/zeux/pugixml.git
-[submodule "vendor/xtensor"]
-	path = vendor/xtensor
-	url = https://github.com/xtensor-stack/xtensor.git
-[submodule "vendor/xtl"]
-	path = vendor/xtl
-	url = https://github.com/xtensor-stack/xtl.git
 [submodule "vendor/fmt"]
 	path = vendor/fmt
 	url = https://github.com/fmtlib/fmt.git