Merge branch 'main' into release

.devcontainer/Dockerfile.codespace

@@ -0,0 +1,12 @@
+FROM fedora:37
+
+RUN dnf -y update \
+    && dnf -y install \
+        cmake \
+        gcc-c++ \
+        gdb \
+        git \
+        make \
+        zlib-devel \
+        llvm-devel \
+    && dnf clean all

.devcontainer/devcontainer.json

@@ -0,0 +1,10 @@
+{
+  "name": "MICM Development Environment",
+  "dockerFile": "Dockerfile.codespace",
+  "extensions": [
+    "ms-vscode.cpptools"
+  ],
+  "settings": {
+  },
+  "postCreateCommand": "cd /workspaces/micm && mkdir build && cd build && cmake -D CMAKE_BUILD_TYPE=release -D ENABLE_CLANG_TIDY:BOOL=FALSE -D ENABLE_LLVM:BOOL=TRUE -D ENABLE_MEMCHECK:BOOL=TRUE .. && make install -j 2"
+}

.dockerignore

@@ -8,6 +8,8 @@
 !libs/
 !test/
 !etc/
+!examples/
 !cmake/
 !packaging
 !include/
+!examples

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,38 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/clang_format.yml

@@ -24,19 +24,31 @@ jobs:
         run: |
           find include -type f \( -name '*.hpp' -o -name '*.h' \) -exec clang-format -i --style=file {} +
           find src -type f \( -name '*.cu' -o -name '*.hpp' -o -name '*.h' -o -name '*.cpp' \) -exec clang-format -i --style=file {} +
-          find test -type f \( -name '*.hpp' -o -name '*.h' -o -name '*.cpp' \) -exec clang-format -i --style=file {} +
+          find test -type f \( -name '*.hpp' -o -name '*.h' -o -name '*.cpp' \) ! -path 'test/tutorial/*' -exec clang-format -i --style=file {} +
+
+      - name: Check for changes
+        id: check-changes
+        run: |
+          git diff --exit-code
+        continue-on-error: true
 
       - name: Commit and push changes
+        # a failue of this step means changes were detected
+        if: steps.check-changes.outcome != 'success'
         run: |
           git config --global user.name "GitHub Actions"
           git config --global user.email "[email protected]"
           git commit -am "Auto-format code using Clang-Format" || echo "No changes to commit"
 
       - name: Push changes to main-formatting branch
+        # a failue of this step means changes were detected
+        if: steps.check-changes.outcome != 'success'
         run: |
           git push origin HEAD:main-formatting
 
       - name: Create Pull Request
+        # a failue of this step means changes were detected
+        if: steps.check-changes.outcome != 'success'
         uses: peter-evans/create-pull-request@v3
         with:
           token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/docker_and_coverage.yml

@@ -0,0 +1,54 @@
+name: Docker
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  docker-build-and-test:
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    name: Build and Test - ${{ matrix.dockerfile }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        dockerfile:
+          - Dockerfile
+          - Dockerfile.coverage
+          - Dockerfile.llvm
+          - Dockerfile.memcheck
+          - Dockerfile.no_json
+          - Dockerfile.nvhpc
+          - Dockerfile.openmp
+          # - Dockerfile.intel # intel image is too large for GH action
+          # - Dockerfile.mpi
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+        with:
+          submodules: recursive
+
+      - name: Build Docker image
+        run: docker build -t micm -f docker/${{ matrix.dockerfile }} .
+
+      - name: Run tests in container
+        if: matrix.dockerfile != 'Dockerfile.coverage'
+        run: docker run --name test-container -t micm bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
+
+      - name: Run coverage tests in container
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        run: docker run --name test-container -t micm bash -c 'make coverage ARGS="--rerun-failed --output-on-failure -j8"'
+
+      - name: Copy coverage from container
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        run: docker cp test-container:build/coverage.info .
+
+      - name: Upload coverage report
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: coverage.info

.github/workflows/gh_pages.yml

@@ -51,9 +51,9 @@ jobs:
           set -x
           mkdir -p _build/html/versions
 
-          # create two copies of the documentaiton
+          # create two copies of the documentation
           # 1. the frozen version, represented as vX.X in the version switcher
-          docker build -t micm -f Dockerfile.docs .
+          docker build -t micm -f docker/Dockerfile.docs .
           id=$(docker create micm)
           docker cp $id:/build/docs/sphinx tmpdocs
           docker rm -v $id
@@ -62,18 +62,20 @@ jobs:
 
           # 2. stable, represented as vX.X (stable) in the version switcher
           # edit conf.py to produce a version string that looks like vX.X (stable)
-          docker build -t micm -f Dockerfile.docs --build-arg SUFFIX=" (stable)" .
+          docker build -t micm -f docker/Dockerfile.docs --build-arg SUFFIX=" (stable)" .
           id=$(docker create micm)
           docker cp $id:/build/docs/sphinx tmpdocs
           docker rm -v $id
           mv tmpdocs _build/html/versions/stable
-          mv docs/switcher.json _build/html
           # Delete everything under _gh-pages/ that is from the
           # primary branch deployment.  Excludes the other branches
           # _gh-pages/branch-* paths, and not including
           # _gh-pages itself.
           find _gh-pages/ -mindepth 1 ! -path '_gh-pages/branch*' ! -path '_gh-pages/versions*' -delete
           rsync -a _build/html/versions/stable/* _gh-pages/
+          mkdir -p _gh-pages/versions
+          rsync -a _build/html/versions/* _gh-pages/versions
+          # mv docs/switcher.json _gh-pages
 
       # If a push and not on default branch, then copy the build to
       # _gh-pages/branch/$brname (transforming '/' into '--')
@@ -83,7 +85,7 @@ jobs:
           !contains(github.ref, env.DEFAULT_BRANCH)
         run: |
           set -x
-          docker build -t micm -f Dockerfile.docs .
+          docker build -t micm -f docker/Dockerfile.docs .
           id=$(docker create micm)
           docker cp $id:/build/docs/sphinx tmpdocs
           docker rm -v $id

.github/workflows/mac.yml

@@ -0,0 +1,86 @@
+name: Mac
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  xcode_macos_12:
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    runs-on: macos-12
+    strategy:
+      matrix:
+        # all available versions of xcode: https://github.com/actions/runner-images/blob/main/images/macos/macos-12-Readme.md#xcode
+        xcode: ['13.1', '14.1']
+        build_type: [Debug, Release]
+    env:
+      DEVELOPER_DIR: /Applications/Xcode_${{ matrix.xcode }}.app/Contents/Developer
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Run Cmake 
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
+
+      - name: Build
+        run: cmake --build build --parallel 10
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10
+
+  xcode_macos_13:
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    runs-on: macos-13
+    strategy:
+      matrix:
+        # all available versions of xcode: https://github.com/actions/runner-images/blob/main/images/macos/macos-13-Readme.md#xcode
+        xcode: ['14.1', '15.0']
+        build_type: [Debug, Release]
+    env:
+      DEVELOPER_DIR: /Applications/Xcode_${{ matrix.xcode }}.app/Contents/Developer
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Run Cmake 
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
+
+      - name: Build
+        run: cmake --build build --parallel 10
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10
+
+  macos_lateset:
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        compiler:
+          - { cpp: g++-11, c: gcc-11}
+          - { cpp: g++-12, c: gcc-12}
+          - { cpp: clang++, c: clang}
+        build_type: [Debug, Release]
+    env:
+      CC: ${{ matrix.compiler.c }}
+      CXX: ${{ matrix.compiler.cpp }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Run Cmake 
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
+
+      - name: Build
+        run: cmake --build build --parallel 10
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10

.github/workflows/publish-package.yml

@@ -0,0 +1,50 @@
+name: Create and publish a Docker image
+
+on:
+  push:
+    branches: ['release']
+    tags:
+      - '*'
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          submodules: recursive
+
+      - name: Login to Container Registry
+        uses: docker/login-action@v2
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          platforms: linux/amd64
+          file: docker/Dockerfile.publish
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}