Merge branch 'develop' into allowing_other_dose_coefficients

openmc-dev · May 14, 2024 · bd9e380 · bd9e380
2 parents 78f5edd + a7d6939
commit bd9e380
Show file tree

Hide file tree

Showing 334 changed files with 11,464 additions and 2,268 deletions.
diff --git a/.github/pull_request_template.md b/.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) on any C++ source files (if applicable)
+- [ ] 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)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -35,9 +35,6 @@ jobs:
         vectfit: [n]
 
         include:
-          - python-version: "3.7"
-            omp: n
-            mpi: n
           - python-version: "3.8"
             omp: n
             mpi: n
@@ -47,6 +44,9 @@ jobs:
           - python-version: "3.11"
             omp: n
             mpi: n
+          - python-version: "3.12"
+            omp: n
+            mpi: n
           - dagmc: y
             python-version: "3.10"
             mpi: y
@@ -93,10 +93,10 @@ jobs:
       RDMAV_FORK_SAFE: 1
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -111,24 +111,34 @@ jobs:
         run: |
           sudo apt -y update
           sudo apt install -y libpng-dev \
-                              libmpich-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: 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: cache-xs
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: |
             ~/nndc_hdf5
@@ -156,7 +166,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Coveralls Finished
-        uses: coverallsapp/github-action@master
+        uses: coverallsapp/github-action@v2
         with:
           github-token: ${{ secrets.github_token }}
           parallel-finished: true
diff --git a/.github/workflows/dockerhub-publish-dagmc-libmesh.yml b/.github/workflows/dockerhub-publish-dagmc-libmesh.yml
@@ -10,20 +10,20 @@ jobs:
     steps:
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:latest-dagmc-libmesh

diff --git a/.github/workflows/dockerhub-publish-dagmc.yml b/.github/workflows/dockerhub-publish-dagmc.yml
@@ -10,20 +10,20 @@ jobs:
     steps:
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v2 
+        uses: docker/login-action@v3 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:latest-dagmc

diff --git a/.github/workflows/dockerhub-publish-dev.yml b/.github/workflows/dockerhub-publish-dev.yml
@@ -10,20 +10,20 @@ jobs:
     steps:
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v2 
+        uses: docker/login-action@v3 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:develop

diff --git a/.github/workflows/dockerhub-publish-develop-dagmc-libmesh.yml b/.github/workflows/dockerhub-publish-develop-dagmc-libmesh.yml
@@ -10,20 +10,20 @@ jobs:
     steps:
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v2 
+        uses: docker/login-action@v3 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:develop-dagmc-libmesh

diff --git a/.github/workflows/dockerhub-publish-develop-dagmc.yml b/.github/workflows/dockerhub-publish-develop-dagmc.yml
@@ -10,20 +10,20 @@ jobs:
     steps:
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v2 
+        uses: docker/login-action@v3 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:develop-dagmc

diff --git a/.github/workflows/dockerhub-publish-develop-libmesh.yml b/.github/workflows/dockerhub-publish-develop-libmesh.yml
@@ -10,20 +10,20 @@ jobs:
     steps:
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v2 
+        uses: docker/login-action@v3 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:develop-libmesh

diff --git a/.github/workflows/dockerhub-publish-libmesh.yml b/.github/workflows/dockerhub-publish-libmesh.yml
@@ -10,20 +10,20 @@ jobs:
     steps:
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v2 
+        uses: docker/login-action@v3 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:latest-libmesh

diff --git a/.github/workflows/dockerhub-publish-release-dagmc-libmesh.yml b/.github/workflows/dockerhub-publish-release-dagmc-libmesh.yml
@@ -8,25 +8,25 @@ jobs:
   main:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set env
         run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:${{ env.RELEASE_VERSION }}-dagmc-libmesh

diff --git a/.github/workflows/dockerhub-publish-release-dagmc.yml b/.github/workflows/dockerhub-publish-release-dagmc.yml
@@ -8,25 +8,25 @@ jobs:
   main:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set env
         run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v2 
+        uses: docker/login-action@v3 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:${{ env.RELEASE_VERSION }}-dagmc

diff --git a/.github/workflows/dockerhub-publish-release-libmesh.yml b/.github/workflows/dockerhub-publish-release-libmesh.yml
@@ -8,25 +8,25 @@ jobs:
   main:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set env
         run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:${{ env.RELEASE_VERSION }}-libmesh

diff --git a/.github/workflows/dockerhub-publish-release.yml b/.github/workflows/dockerhub-publish-release.yml
@@ -8,25 +8,25 @@ jobs:
   main:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set env
         run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v2 
+        uses: docker/login-action@v3 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:${{ env.RELEASE_VERSION }}