Adding notebook running ci on merge to main

.clang-format

@@ -84,6 +84,7 @@ PenaltyBreakTemplateDeclaration: 10
 PenaltyExcessCharacter: 1000000
 PenaltyReturnTypeOnItsOwnLine: 200
 PointerAlignment: Left
+QualifierAlignment: Left
 ReflowComments:  true
 SortIncludes:    true
 SortUsingDeclarations: true

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# Applied clang-format to all source files
+1bc2bd84600c8d2ca9253339c167401127f6a9f3

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,29 @@
+---
+name: Bug report
+about: Report a bug that is preventing proper operation
+title: ''
+labels: Bugs
+assignees: ''
+
+---
+
+<!--
+If you are a user of OpenMC and are running into trouble with the code or are
+seeking general user support, we highly recommend posting on the OpenMC
+discourse forum first. GitHub issues should be used specifically for bug reports
+and feature requests.
+
+https://openmc.discourse.group/
+
+-->
+
+## Bug Description
+<!--A clear and concise description of the problem (Note: A missing feature is not a bug).-->
+
+
+## Steps to Reproduce
+<!--Steps to reproduce the behavior (input file, or modifications to an existing input file, etc.)-->
+
+
+## Environment
+<!--Operating system, OpenMC version, how OpenMC was installed, nuclear data being used, etc.-->

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Troubleshooting and User Support
+    url: https://openmc.discourse.group/
+    about: For user support and troubleshooting, please use our Discourse forum

.github/ISSUE_TEMPLATE/documentation.md

@@ -0,0 +1,10 @@
+---
+name: Documentation improvement
+about: Found something incomplete or incorrect in our documentation?
+title: ''
+labels: Documentation
+assignees: ''
+
+---
+
+<!--Describe the issue with the documentation and include a URL to the corresponding page-->

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,19 @@
+---
+name: Feature request
+about: Suggest a new feature or enhancement to existing capabilities
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+## Description
+<!--What is the feature or enhancement?-->
+
+
+## Alternatives
+<!--If alternative solutions have been considered, describe them here and the reasoning for the chosen solution --->
+
+
+## Compatibility
+<!--Will the enhancement change existing APIs or add something new?-->

.github/pull_request_template.md

@@ -0,0 +1,24 @@
+<!--
+If you are a first-time contributor to OpenMC, please have a look at our
+contributing guidelines:
+https://github.com/openmc-dev/openmc/blob/develop/CONTRIBUTING.md
+-->
+
+# Description
+
+Please include a summary of the change and which issue is fixed if applicable. Please also include relevant motivation and context.
+
+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 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)
+<!--
+While tests will automatically be checked by CI, it is good practice to
+ensure that they pass locally first. See instructions here:
+https://docs.openmc.org/en/latest/devguide/tests.html
+-->

.github/workflows/ci.yml

@@ -20,119 +20,173 @@ env:
   COVERALLS_PARALLEL: true
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
-
 jobs:
   main:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: ["3.10"]
         mpi: [n, y]
         omp: [n, y]
         dagmc: [n]
+        ncrystal: [n]
         libmesh: [n]
         event: [n]
         vectfit: [n]
 
         include:
-          - python-version: 3.6
+          - python-version: "3.8"
+            omp: n
+            mpi: n
+          - python-version: "3.9"
             omp: n
             mpi: n
-          - python-version: 3.7
+          - python-version: "3.11"
+            omp: n
+            mpi: n
+          - python-version: "3.12"
             omp: n
             mpi: n
           - dagmc: y
-            python-version: 3.8
+            python-version: "3.10"
             mpi: y
             omp: y
+          - ncrystal: y
+            python-version: "3.10"
+            mpi: n
+            omp: n
           - libmesh: y
-            python-version: 3.8
+            python-version: "3.10"
             mpi: y
             omp: y
           - libmesh: y
-            python-version: 3.8
+            python-version: "3.10"
             mpi: n
             omp: y
           - event: y
-            python-version: 3.8
+            python-version: "3.10"
             omp: y
             mpi: n
           - vectfit: y
-            python-version: 3.8
+            python-version: "3.10"
             omp: n
             mpi: y
-    name: 'Python ${{ matrix.python-version }} (omp=${{ matrix.omp }},
-      mpi=${{ matrix.mpi }}, dagmc=${{ matrix.dagmc }},
+    name: "Python ${{ matrix.python-version }} (omp=${{ matrix.omp }},
+      mpi=${{ matrix.mpi }}, dagmc=${{ matrix.dagmc }}, ncrystal=${{ matrix.ncrystal }},
       libmesh=${{ matrix.libmesh }}, event=${{ matrix.event }}
-      vectfit=${{ matrix.vectfit }})'
+      vectfit=${{ matrix.vectfit }})"
 
     env:
       MPI: ${{ matrix.mpi }}
       PHDF5: ${{ matrix.mpi }}
       OMP: ${{ matrix.omp }}
       DAGMC: ${{ matrix.dagmc }}
+      NCRYSTAL: ${{ matrix.ncrystal }}
       EVENT: ${{ matrix.event }}
       VECTFIT: ${{ matrix.vectfit }}
       LIBMESH: ${{ matrix.libmesh }}
+      NPY_DISABLE_CPU_FEATURES: "AVX512F AVX512_SKX"
+      OPENBLAS_NUM_THREADS: 1
+      # 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.
+      RDMAV_FORK_SAFE: 1
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      -
-        name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      -
-        name: Environment Variables
+
+      - name: Environment Variables
         run: |
           echo "DAGMC_ROOT=$HOME/DAGMC"
           echo "OPENMC_CROSS_SECTIONS=$HOME/nndc_hdf5/cross_sections.xml" >> $GITHUB_ENV
           echo "OPENMC_ENDF_DATA=$HOME/endf-b-vii.1" >> $GITHUB_ENV
 
-      -
-        name: Apt dependencies
+      - name: Apt dependencies
         shell: bash
         run: |
           sudo apt -y update
-          sudo apt install -y libmpich-dev \
+          sudo apt install -y libpng-dev \
                               libnetcdf-dev \
                               libpnetcdf-dev \
                               libhdf5-serial-dev \
-                              libhdf5-mpich-dev \
                               libeigen3-dev
+
+      - name: Optional apt dependencies for MPI
+        shell: bash
+        if: ${{ matrix.mpi == 'y' }}
+        run: |
+          sudo apt install -y libhdf5-mpich-dev \
+                              libmpich-dev
           sudo update-alternatives --set mpi /usr/bin/mpicc.mpich
           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: install
+      - name: Optional apt dependencies for vectfit
+        shell: bash
+        if: ${{ matrix.vectfit == 'y' }}
+        run: sudo apt install -y libblas-dev liblapack-dev
+
+      - name: install
         shell: bash
         run: |
           echo "$HOME/NJOY2016/build" >> $GITHUB_PATH
           $GITHUB_WORKSPACE/tools/ci/gha-install.sh
-      -
-        name: before
+
+      - name: cache-xs
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/nndc_hdf5
+            ~/endf-b-vii.1
+          key: ${{ runner.os }}-build-xs-cache
+
+      - name: before
         shell: bash
         run: $GITHUB_WORKSPACE/tools/ci/gha-before-script.sh
-      -
-        name: test
+
+      - name: test
         shell: bash
-        run: $GITHUB_WORKSPACE/tools/ci/gha-script.sh
+        run: |
+          CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
+          $GITHUB_WORKSPACE/tools/ci/gha-script.sh
 
-      -
-        name: after_success
+      - name: Install OpenMOC for notebook testing
+        if: github.base_ref == 'master'
+        shell: bash -l {0}
+        run: |
+          cd ~
+          git clone https://github.com/mit-crpg/openmoc &&
+          cd openmoc
+          # OpenMOC has some custom commands that rely on setuptools/distutils
+          python setup.py install
+          # install twice to make sure openmoc.py is copied into the installation location
+          python setup.py install
+
+      - name: Execute all Notebooks
+        if: github.base_ref == 'master'
+        shell: bash -l {0}
+        run: |
+          git clone https://github.com/mit-crpg/openmoc
+          cd openmoc
+          pytest -v .test
+
+      - name: after_success
         shell: bash
         run: |
-          cpp-coveralls -i src -i include --exclude-pattern "/usr/*" --dump cpp_cov.json
+          cpp-coveralls -i src -i include -e src/external --exclude-pattern "/usr/*" --dump cpp_cov.json
           coveralls --merge=cpp_cov.json --service=github
 
   finish:
     needs: main
     runs-on: ubuntu-latest
     steps:
-    - name: Coveralls Finished
-      uses: coverallsapp/github-action@master
-      with:
-        github-token: ${{ secrets.github_token }}
-        parallel-finished: true
+      - name: Coveralls Finished
+        uses: coverallsapp/github-action@v2
+        with:
+          github-token: ${{ secrets.github_token }}
+          parallel-finished: true

.github/workflows/ci_openmc-notebooks.yaml

@@ -0,0 +1,76 @@
+name: Test Notebooks
+
+on:
+  # Allow this workflow to be run manually
+  workflow_dispatch:
+  # Run for pull requests to master branch
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  # Set the job key
+  test-notebooks:
+    # Name the job
+    name: Test Jupyter Notebooks
+    # Set the type of machine to run on
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+
+      - name: Install conda environment
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: jupyter-actions
+          environment-file: .github/environment.yml
+          python-version: 3.7
+
+      - name: Install OpenMC
+        shell: bash -l {0}
+        run: |
+          conda install -n base conda-libmamba-solver
+          conda config --set solver libmamba
+          conda activate jupyter-actions
+          conda install -c conda-forge openmc
+
+      - name: Cache Cross Sections
+        id: xs-cache
+        uses: actions/cache@v3
+        with:
+          # use this cache as long as the download script doesn't change
+          key: xs-cache-${{ hashfiles('.test/download-xs.sh') }}
+          path: ~/endfb-vii.1-hdf5/*
+
+      - name: Download OpenMC Cross Sections
+        shell: bash -l {0}
+        if: steps.xs-cache.outputs.cache-hit != 'true'
+        run: |
+          ./.test/download-xs.sh
+
+      - name: Set Environment Variables
+        shell: bash -l {0}
+        run: |
+          echo "OPENMC_CROSS_SECTIONS=$HOME/endfb-vii.1-hdf5/cross_sections.xml" >> $GITHUB_ENV
+
+      - name: Install OpenMOC
+        shell: bash -l {0}
+        run: |
+          conda init bash
+          source ~/.bashrc
+          conda activate jupyter-actions
+          cd ~
+          git clone https://github.com/mit-crpg/openmoc &&
+          cd openmoc
+          # OpenMOC has some custom commands that rely on setuptools/distutils
+          python setup.py install
+          # install twice to make sure openmoc.py is copied into the installation location
+          python setup.py install
+
+      - name: Execute all Notebooks
+        shell: bash -l {0}
+        run: |
+          conda activate jupyter-actions
+          pytest -v .test